@article {pmid41954789, year = {2026}, author = {Schultz, J and García-Martínez, PM and Altalhi, S and Kontis, N and Dos Santos, A and Rosado, AS}, title = {Extreme Arabian environments and their microbiomes: new frontiers for astrobiology and biosignature discovery.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {41954789}, issn = {1433-4909}, abstract = {Astrobiology assesses the habitability of planetary bodies and the potential for extraterrestrial life. Analog environments on Earth serve as sites for studying extreme environments that resemble extraterrestrial conditions, aiding in validating life-detection methods, mission instrumentation, and biosignature preservation. These environments function as a source of model microorganisms and communities that define the habitability and biochemistry of such extraterrestrial environments. Well-known analog environments include the Atacama Desert (Chile) for space mission validation, the McMurdo Dry Valleys (Antarctica) for Mars analog studies, and Rio Tinto (Spain) for extreme acidic environments. Although significant research has been conducted on these sites, various alternative environments may also offer valuable opportunities for astrobiological studies. Saudi Arabia encompasses a variety of pristine (or with minimal anthropic influence) extreme environments with conditions analogous to extraterrestrial settings (e.g., deserts and salt flats as analogs to Mars, and terrestrial and marine volcanic fields as analogs to icy moons), yet their potential remains largely unexplored. Recent studies have identified a volcanic crater with sodium phosphates and chlorates that mimics Enceladus’s ocean chemistry, and researchers have cultured Halalkalibacterium halodurans strains with adaptations to survive these conditions, offering valuable biological models. Additionally, complex metabolic landscapes with implications for icy moon habitability have been observed in Red Sea systems, which could be employed as valuable natural laboratories in astrobiological research. Furthermore, these findings underscore the potential of the Saudi Arabian extremophilic microbiome for space-related research. This review explores the microbial diversity of extreme environments in Saudi Arabia, emphasizing their potential as new terrestrial analogs to Mars and icy moons and the role of their microbiomes as terrestrial proxies for extraterrestrial life.}, }
@article {pmid41957864, year = {2026}, author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F}, title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00886-8}, pmid = {41957864}, issn = {2524-6372}, support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.<br><br>RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.<br><br>CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.}, }
@article {pmid41957947, year = {2025}, author = {Cashin, PH and Artursson, S and Sköldberg, F and Melhus, &#xc5;}, title = {Association of the gut microbiome to colorectal anastomotic leakage: systematic review.}, journal = {BJS open}, volume = {10}, number = {2}, pages = {}, doi = {10.1093/bjsopen/zrag005}, pmid = {41957947}, issn = {2474-9842}, support = {24-0824//Cancerfonden/ ; }, mesh = {*Anastomotic Leak/microbiology/etiology ; Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/surgery/microbiology ; Animals ; }, abstract = {BACKGROUND: Research into the gut microbiome and its possible association with anastomotic leakage after colorectal surgery has increased recently with the growing availability of sequencing techniques. There is a lack of systematic reviews addressing specifically microbiomic differences between patients with anastomotic leakage and patients with a successful anastomotic healing. The objective was to systematically review the current research on the microbiome and its effect on the risk of anastomotic leakage in colorectal cancer.<br><br>METHODS: Pubmed/Medline, Cochrane, and Google scholar were searched on 14th February 2025, to identify relevant publications with the following inclusion criteria: colorectal surgery, microbiome sequencing data, anastomotic leakage as endpoint, and comparative groups. Exclusion criteria were studies conducted exclusively on animals, non-peer-reviewed studies, review articles, and unavailable full text. Alpha/beta diversity and microbiomic functional analyses were the focus of the results.<br><br>RESULTS: From 112 studies, 11 studies including 551 patients were included: 143 patients with anastomotic leakage and 408 as controls. Alpha diversity differences were found in 7 of 11 studies-1 of 4 with preoperative sampling versus 6 of 7 studies with intra/postoperative sampling (P = 0.044). Beta diversity differences were found in 5 of 11 studies. Three studies reported on functional analyses, with one study demonstrating an association between methanogenesis and anastomotic leakage. Bacterial abundance was inconsistent across the studies. Three studies involving rodent models indicated a causal effect of the clinical microbiome.<br><br>CONCLUSION: Evidence implicates the gut microbiome as a factor associated with anastomotic leakage in colorectal cancer surgery, with three studies suggesting a causal relationship. There is a shortage of studies evaluating cross-species functional profiling. Optimal sampling should be performed during surgery.}, }
@article {pmid41678296, year = {2026}, author = {Tamrakar, K and Chavez, ES and Miller, PW and Hale, B and DuVall, J and Williams, N and Brown, E and Mangan, S and Wijeratne, AJ}, title = {Integrated Multi-Omics Analysis Provides Insights into the Rhizosphere Microbial Dynamics in Soybean-Fusarium virguliforme Interaction.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI09250121FI}, doi = {10.1094/MPMI-09-25-0121-FI}, pmid = {41678296}, issn = {0894-0282}, abstract = {Sudden death syndrome (SDS) is a major disease that affects soybean (Glycine max) production, primarily caused by the soilborne fungus Fusarium virguliforme in North America. Understanding the interactions among soybeans, F. virguliforme, and microorganisms in the soil near the vicinity of roots can provide microbial candidates for SDS management. The objective of this study was to elucidate the role of rhizosphere microbial composition and activity, both in the presence and absence of F. virguliforme, across two commercial soybean cultivars with differing susceptibility to SDS. Bacterial and fungal community dynamics were assessed using full-length 16S rRNA and internal transcribed spacer 1 (ITS1) sequencing, respectively. Microbial activity was further evaluated with an optimized metatranscriptome workflow. Our analysis revealed that SDS-tolerant soybeans recruit microbes with growth-promoting and biocontrol potential, such as members of the genera Bacillus, Pseudomonas, Trichoderma, Mortierella, and Talaromyces, when exposed to F. virguliforme. This distinct microbial recruitment strategy in response to F. virguliforme could provide the ability for soybeans to survive under pathogen stress. In contrast, pathogen inoculation reduced the abundance and activity of the nitrogen-fixing Bradyrhizobium spp. These findings suggest that selective recruitment of beneficial microbes likely contributes to SDS tolerance, whereas pathogen pressure compromises symbiotic nitrogen fixation. The results highlight candidate taxa and interactions for developing synthetic microbial communities to support SDS management. The information generated from this study will be useful for assembling a combined synthetic microbial community and testing. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid41776697, year = {2026}, author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X}, title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41776697}, issn = {2524-4671}, abstract = {BACKGROUND: The gut microbiota plays a crucial role in metabolism, immune regulation, and ecological adaptation of mammals. Although significant advancements have been made in shotgun metagenomic sequencing and the emergence of algorithms for generation of metagenome-assembled genomes (MAGs), a comprehensive investigation of the gut microbiota at the species level of wild mammals, among these the Asian elephant (Elephas maximus), is still lacking.<br><br>RESULTS: Here, based on a total of 82 fresh fecal samples collected from Asian elephants residing in distinct regions of the Yunnan Province, we established a comprehensive genome catalog containing 1421 species-level genome bins (SGBs) and a gene catalog comprising 44,596,628 non-redundant genes covering the gut microbiota composition of representative Asian elephant populations. At the species level, 1368 bacteria and 53 archaea were identified, and more than 93% of the SGBs remained unclassified, indicating that there are a large number of potential new species in the Asian elephant gut microbiota. At the functional level, carbohydrate hydrolases, biosynthetic gene clusters, and metabolic pathways dominated the gut microbiome of Asian elephants. Lifestyle and migration affected the composition and functional potential of the gut microbiota of Asian elephants. A northward migration was accompanied by an increase in gut microbiota diversity, an increase in the abundance of the phylum Bacteroidota, and a decrease in the presence of potentially pathogenic genera. In contrast, a southward migration of elephant herds was accompanied by exposure to unfavorable environments, with changes in gut microbiota including increased xenobiotic degradation and metabolic capacity.<br><br>CONCLUSIONS: We constructed comprehensive catalogs of gut microbial genes and genomes representative for Asian elephant populations, providing a valuable data resource for future research. Our study elucidates migration and lifestyle may modulate the composition and functionality of the gut microbiota in Asian elephants, offering critical insights for monitoring their health and enhancing conservation strategies for wild populations.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00533-0.}, }
@article {pmid41950813, year = {2026}, author = {Jacobson, R and Soundararajan, R and Maurin, M and Bulard, B and Mishra, S and Kain, V and Halade, G and Yadav, H and Yeatman, T}, title = {Intratumoral microbiome varies by site of metastatic spread in colorectal cancer.}, journal = {Surgery}, volume = {194}, number = {}, pages = {110167}, doi = {10.1016/j.surg.2026.110167}, pmid = {41950813}, issn = {1532-7361}, }
@article {pmid41950983, year = {2026}, author = {Šigutová, H and Geislerová, P and Šigut, M and Pyszko, P}, title = {Trace amounts of insecticide, herbicide, and their combination disrupt the bacterial and fungal microbiome of a nontarget aquatic invertebrate.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128065}, doi = {10.1016/j.envpol.2026.128065}, pmid = {41950983}, issn = {1873-6424}, abstract = {The ubiquitous contamination of freshwater by pesticides contributes substantially to the ongoing diversity crisis. The animal microbiome affects a range of important functions, including host immunity and resilience to pesticide stress. Therefore, understanding how pesticides impact the microbiome of nontarget organisms is critical; however, this topic remains understudied in freshwater invertebrates. We investigated the effect of sublethal concentrations of pesticides on the host-associated microbiomes of larval Sympetrum vulgatum (Odonata: Libellulidae). Fifth-instar larvae reared in the laboratory and collected in the field were experimentally exposed to the herbicide metazachlor, the insecticide etofenprox, and their combination, and their bacterial and fungal microbiomes were profiled using 16S and ITS2 rRNA gene metabarcoding. Exposure to pesticides, particularly the insecticide, reduced bacterial richness, altered microbial community composition, reduced the complexity of co-occurrence networks, and neutral model deviations were more consistent with increased deterministic structuring. Simultaneously, our results suggested a loss of potentially beneficial taxa and an increase in pathogens, but also xenobiotic-degrading bacteria. The herbicide-insecticide mixture did not cause more profound effects than the insecticide alone, although it modified community assembly patterns. We found a shared set of prevalent genera persisting across treatments, alongside smaller treatment-associated subsets. Using a prevalence-based definition (detected in ≥3 samples per treatment), 91 bacterial and 22 fungal genera were shared across all treatments. The potentially contrasting responses of bacteria and fungi and the lab-reared and field-collected larvae to pesticides highlight the need to integrate the fungal component into microbiome research and suggest the importance of the naturally assembled microbiomes for host resilience.}, }
@article {pmid41950992, year = {2026}, author = {Liu, K and Chen, Y and Zhao, M and Yang, D and Hu, Q and Cao, Y and Guo, X and Liu, Z}, title = {Integrative microbiome-transcriptome analysis reveals immune activation linked to gut dysbiosis in Vespa magnifica.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108618}, doi = {10.1016/j.jip.2026.108618}, pmid = {41950992}, issn = {1096-0805}, abstract = {The gut microbiota plays a central role in the health of social wasps, contributing to nutrition, immunity, and environmental adaptation. However, its role in disease occurrence and host responses in the hornet Vespa magnifica remains poorly understood. Here, we investigated the gut microbial composition and host transcriptomic responses in diseased and healthy V. magnifica from Yunnan, China. High-throughput 16S rRNA gene sequencing revealed that diseased individuals exhibited significantly reduced microbial richness and diversity, characterized by depletion of beneficial taxa such as Lactobacillus (Lb.), Leuconostoc (Leu.), and Bifidobacterium (B.), alongside increased abundance of potential pathobionts including Lactococcus (Lc.) and Yokenella (Y.). Transcriptomic analysis identified 32 differentially expressed genes (DEGs), some of which were enriched for immune signaling pathways. Key immune-related genes, including peptidoglycan recognition proteins (PGRPs) and defensins (DEF), were strongly upregulated, indicating activation of host immune recognition and effector responses. Mantel correlation analysis further revealed significant associations between the top 30 differentially abundant bacterial genera and host immune genes, highlighting microbiota-host interactions in disease development. Collectively, these findings demonstrate that gut dysbiosis is associated with microbial imbalance and immune activation in V. magnifica, providing new insights into its gut health and potential strategies for disease management in hornet farming.}, }
@article {pmid41951111, year = {2026}, author = {Fässler, D and Wittfeld, K and Frenzel, S and der Auwera, SV and Merhjerd, A and Gholizadeh, M and Simm, S and Kaderali, L and Franck, M and Rühlemann, M and Bang, C and Franke, A and Friedrich, N and Nauck, M and Lerch, MM and Weiss, FU and Völker, U and Bülow, R and Völzke, H and Peuker, K and Zeißig, S and Grabe, HJ and Frost, F and Hertel, J}, title = {Bilophila wadsworthia is linked to basal ganglia atrophy in the general population.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {106587}, doi = {10.1016/j.bbi.2026.106587}, pmid = {41951111}, issn = {1090-2139}, abstract = {Bilophila wadsworthia, a sulfite-reducing bacterium stimulated by bile acids and enriched under high-fat diets, has been linked to several neurological disorders involving disturbances of motor function and basal ganglia circuitry. However, its potential association with alterations of brain structure remains unclear. Here, we investigated relationships between Bilophila (wadsworthia) abundance and basal ganglia volumes in two independent population-based cohorts combining gut microbiome profiling and brain MRI. Genus-level Bilophila abundance was assessed using 16S rRNA gene sequencing and complemented by species-level analyses of B. wadsworthia using whole-genome shotgun sequencing. Higher abundance of Bilophila (wadsworthia) was consistently associated with reduced volumes of basal ganglia regions, particularly the globus pallidus and nucleus accumbens. These associations were largely specific to basal ganglia regions when compared across a broad set of cortical thickness and other volumetric brain measures. Additionally, Bilophila (wadsworthia) was linked to elevated liver enzymes, elevated triglycerides, and pro-inflammatory states, confirming prior evidence from animal models while revealing novel associations in the general population. Constraint-based community modeling revealed that B. wadsworthia-enriched microbiomes exhibit increased functional redundancy for bile acid and sulfur metabolism and may modulate trimethylamine (TMA/TMAO) pathways. Together, these findings link variation in B. wadsworthia abundance to structural differences within basal ganglia regions and to unfavorable metabolic and inflammatory profiles in the general population, suggesting a potential role of this microbial species in gut-brain axis alterations relevant to neurodegenerative disease progression.}, }
@article {pmid41951277, year = {2026}, author = {Bajer, L and Polakovicova, P and Heczkova, M and Holm, K and Hole, MJ and Hlavaty, M and Bohdanecka, A and Drastich, P and Tichanek, F and Meyer-Myklestad, MH and Medhus, AW and Reikvam, DH and Jørgensen, KK and Brezina, J and Macinga, P and Wohl, P and Fabian, O and Hov, JR and Cahova, M}, title = {Geography-independent mucosal microbiota alterations in primary sclerosing cholangitis persist after liver transplantation.}, journal = {JHEP reports : innovation in hepatology}, volume = {8}, number = {4}, pages = {101716}, pmid = {41951277}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Primary sclerosing cholangitis (PSC)-associated alterations of fecal gut microbiota have already been described, but data on the mucosal microbiota are still limited. We aimed to further define disease-specific mucosal microbial patterns independent of geography and assess the relationship to liver transplantation (LTx), gut inflammation (inflammatory bowel disease), and PSC recurrence (rPSC).<br><br>METHODS: We performed 16S ribosomal RNA gene (V3-V4) sequencing of ileocolonic biopsies from 115 patients with PSC (pre-LTx), 159 liver-transplanted patients (post_LTx, recurrence occurred in 38), and 96 healthy controls (HC) from Norway and the Czech Republic.<br><br>RESULTS: Alpha diversity was lower in all PSC groups compared with HC. Elastic net models discriminated pre_LTx (AUC ileum 0.97; colon 0.93; p <0.001) and post_LTx PSC patients (AUC ileum 0.97; colon 0.97; p <0.001) from HC, and distinguished pre_LTx from post_LTx (AUC ileum 0.83; colon 0.83; p <0.001). The shared, cohort-independent PSC microbiota was dominated by Enterococcus, Pseudomonas, Veillonella, Klebsiella, and Streptococcus, while several common commensals were underrepresented. A microbial dysbiosis index calculated from PSC-associated genera correlated negatively with alpha diversity and serum albumin, while a positive correlation was observed with markers of cholestatic disease (ALP, GGT) and liver fibrosis (APRI). There were no associations with the presence of inflammatory bowel disease or fecal calprotectin. Differences between post-LTx patients with and without recurrence were limited, but several genera deregulated in pre-LTx PSC (Klebsiella, Bilophila, Coprococcus, Odoribacter) showed similar trends in rPSC.<br><br>CONCLUSIONS: Our findings in two European countries revealed a distinct mucosal microbiota composition associated with PSC that persists after LTx. These microbial patterns correlate with the severity of liver injury in PSC but not with markers of intestinal inflammation.<br><br>IMPACT AND IMPLICATIONS: This study provides an extensive evaluation of mucosa-associated microbiota in primary sclerosing cholangitis (PSC) before and after liver transplantation across two European cohorts. The persistence of PSC-related dysbiosis after transplantation highlights the importance of the gut-liver axis in PSC and supports further investigation into microbiota-driven mechanisms. Together with the strong association between microbiota composition and markers of cholestasis and fibrosis, this suggests potential clinical utility as an indicator of disease activity or even as a target for prevention or therapy.}, }
@article {pmid41951350, year = {2026}, author = {Shokoohi, E and Masoko, P}, title = {Soil Biodiversity of Eucalyptus saligna: Insights Into Bacterial and Nematode Communities.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70341}, pmid = {41951350}, issn = {1758-2229}, support = {RNA-2022//University of Limpopo/ ; }, mesh = {*Eucalyptus/parasitology/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Biodiversity ; Animals ; *Nematoda/classification/genetics/isolation &amp; purification ; Soil/chemistry/parasitology ; RNA, Ribosomal, 16S/genetics ; South Africa ; Phylogeny ; Rhizosphere ; }, abstract = {Soil microorganisms and nematodes are key regulators of soil function, yet their co-occurrence in Eucalyptus rhizospheres remains poorly understood. In this exploratory study, we characterised bacterial and nematode communities associated with Eucalyptus saligna soils in Limpopo, South Africa, using high-throughput 16S rRNA gene sequencing and nematode surveys. Bacterial assemblages were dominated by Proteobacteria (42%), Acidobacteria (28%), Actinobacteria (12%) and Planctomycetes (9%). Eleven bacterial genera occurred across all sites, with Rhizobiales (prominence value, PV = 315,350) and Xanthobacteraceae (PV = 292,930) emerging as the most prominent taxa. Nematode surveys identified 19 genera, including plant-parasitic such as Meloidogyne (PV = 5759.1) and abundant free-living such as Tylolaimorphus (PV = 4150.0) and Acrobeloides (PV = 2900.0). Principal component analysis showed that bacterial communities were associated with soil pH, salinity and nitrogen forms, whereas nematode assemblages were associated with phosphate and sand content, together explaining 83%-90% of total variance. Network analysis indicated that all sampling sites functioned as central hubs (degree = 19-23; eigenvector centrality = 0.90-1.0), integrating nematode-bacteria associations. Key connector taxa included Acrobeloides, Wilsonema and Aphelenchoides, as well as bacteria such as Rhizobiales and Acidothermus. These findings provide a baseline framework for understanding belowground biodiversity and co-occurrence patterns in Eucalyptus plantation soils.}, }
@article {pmid41951359, year = {2026}, author = {Zhang, J and Hu, J and Tang, X and Ruan, Y and Hao, F and Zhang, W and Trakman, G and Hamilton, AL and Lin, W and Sun, Y and Ching, JYL and Teh, JJ and Kang, S and Wilson-O' Brien, A and Stanley, A and Zhang, L and Sung, JJY and Yu, J and Miao, Y and Chan, FKL and Morrison, M and Kamm, M and Ng, SC}, title = {Quantifying artificial sweeteners and emulsifiers in Crohn's disease and its relationship with disease activity: the ENIGMA study - a novel and targeted approach.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333999}, pmid = {41951359}, issn = {1468-3288}, abstract = {BACKGROUND: Food additives have been linked to increased Crohn's disease (CD) risk and activity, but their human quantification has not been explored.<br><br>OBJECTIVE: We aimed to measure artificial sweeteners and emulsifier polysorbate-80 (P-80) in patients with CD and assess their associations with disease activity.<br><br>DESIGN: 1461 biosamples from 487 subjects (245&#x2009;CD and 242 controls) across Australia, Hong Kong and Chinese Mainland were analysed for aspartame, sucralose, saccharin and P-80 levels in stool, urine and serum. CD activity was assessed using Crohn's Disease Activity Index and faecal calprotectin. A generalised linear model (GLM) with P-80 and sweeteners distinguished active CD from inactive CD.<br><br>RESULTS: Patients with CD had higher sweetener levels compared with controls across cohorts (all p<0.0001). P-80 underwent predominantly hydrolytic and oxidoreductive degradation in CD and controls, respectively, while its native form was undetectable. CD-associated P-80 metabolites positively correlated with urinary sweeteners in patients with CD. In vitro, CD-associated P-80 metabolites increased gut permeability, enabling translocation of sweeteners across the epithelium. Sweeteners and specific CD-associated P-80 metabolites were higher in active CD. The GLM built using sweeteners and P-80 metabolites distinguished active CD from inactive CD, achieving an area under the curve (AUC) of 0.86 in the discovery cohort and average AUC of 0.94 in two independent validation cohorts from Australia and Chinese Mainland.<br><br>CONCLUSION: This is the first human study to demonstrate distinct P-80 metabolism in patients with CD compared with controls. Dietary sweeteners and P-80 metabolites showed significant correlations with disease activity, suggesting their potential utility as non-invasive biomarkers for CD activity assessment.}, }
@article {pmid41951494, year = {2026}, author = {Li, C and Braaten, K and Moser, AB and Fallatah, W and Lorentson, M and Huguenin, S and Torrey, A and Terluk, MR and Durose, W and Nolan, E and Staley, C and Subramanian, S and Lund, TC and Kartha, RV}, title = {Nervonic acid supplementation mitigates disease severity biomarkers in adrenoleukodystrophy.}, journal = {Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics}, volume = {}, number = {}, pages = {e00890}, doi = {10.1016/j.neurot.2026.e00890}, pmid = {41951494}, issn = {1878-7479}, abstract = {X-linked adrenoleukodystrophy (ALD) is a severe neurometabolic disorder caused by mutations in the ABCD1 gene, leading to impaired peroxisomal β-oxidation of very long-chain fatty acids (VLCFAs). The accumulation of saturated VLCFAs, predominantly C26:0, in plasma and across all tissues, contributes to adrenal dysfunction and progressive neurodegeneration. No approved therapy addresses the diverse spectrum of ALD manifestations, underscoring the urgent need for safe, accessible, and preventive treatments. Nervonic acid (NA), a monounsaturated fatty acid, is potentially beneficial for ALD through its neuroprotective effects. Here, we report the safety and therapeutic efficacy of NA in a 4-week dietary intervention study using a mouse model of ALD. NA treatment significantly decreased plasma C26:0-lysophosphatidylcholine, a diagnostic and disease-severity biomarker of ALD, by about 60% as early as one week after intervention. After 4-week treatment, NA markedly reduced free C26:0 and total saturated VLCFA levels in plasma and tissues. Moreover, we observed approximately 56% reduction in brain C26:0-lysophosphatidylcholine levels in NA-fed mice, an effect not reported with other drug intervention. Through comparative microbiome analysis, we show for the first time distinct baseline differences between ALD and wild-type mice, with dietary fatty acid supplementation preventing further dysbiosis. No adverse effects on body weight or food intake were observed throughout the study. Overall, this is the first report demonstrating that an oral dietary fatty acid can ameliorate the hallmark biochemical abnormalities of ALD in plasma and brain, highlighting its potential as a safe and effective therapy, particularly for presymptomatic individuals carrying this genetic defect.}, }
@article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07154-x}, pmid = {41951635}, issn = {2052-4463}, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, }
@article {pmid41951653, year = {2026}, author = {He, L and Yuan, D and Li, Q and Zhang, X and Niu, K and Li, X and Ou, Y and Du, H and Yuan, J and Duan, Y and Niu, H}, title = {Fecal virome transplantation attenuates arthritis in mice by remodeling gut ecology, systemic tryptophan metabolism, and innate immune responses.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00980-2}, pmid = {41951653}, issn = {2055-5008}, support = {2024VPPC-S02//the Open Project of the Key Laboratory of Viral Pathogenesis and Infection Prevention and Control (Jinan University), Ministry of Education/ ; 2025A1515012786//the Natural Science Foundation of Guangdong Province/ ; 2022YFF0710702 and 2022YFF0710701//the National Key &amp;D Programs of China/ ; 202201020381//the Guangzhou Joint Fund for Key Laboratory/ ; YXJC2022004//the Medical Joint Fund of Jinan University/ ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disorder characterized by chronic joint inflammation and systemic immune dysregulation. Emerging evidence suggests that the gut microbiome plays an important role in immune modulation in RA, yet the role of the gut virome remains poorly understood. Here, using the K/BxN serum-transfer arthritis model, we systematically evaluated the potential role of fecal virome transplantation (FVT) in modulating gut ecology and innate inflammatory responses. Arthritic mice exhibited marked alterations in gut virome composition compared with healthy controls. Administration of purified virus-like particles (VLPs) from healthy donors correlated with reductions in paw swelling, histopathological inflammation, bone erosion, circulating proinflammatory cytokines, and myeloid cell infiltration in inflamed tissues. In parallel, 16S rRNA sequencing showed that FVT remodeled the gut bacterial community toward a composition more similar to that of healthy controls. Targeted serum metabolomics revealed increased levels of microbiota-derived tryptophan metabolites, including indole-3-lactic acid and related indole derivatives, suggesting a link between gut microbial remodeling and systemic immunometabolic regulation. Collectively, these findings indicate that FVT may attenuate inflammatory arthritis by remodeling gut microbial ecology, potentially involving virome-bacteriome interactions and immunometabolic pathways.}, }
@article {pmid41951862, year = {2026}, author = {Ocejo, A and Kotecha, RR and Voss, MH}, title = {From diversity to function: microbiome precision in RCC.}, journal = {Nature reviews. Urology}, volume = {}, number = {}, pages = {}, pmid = {41951862}, issn = {1759-4820}, }
@article {pmid41952069, year = {2026}, author = {Klimesova, B and Ruane, NM and Domingo-Bretón, R and Moroni, F and Naya-Català, F and Pérez-Sánchez, J and O'Dwyer, K and Lyashevska, O and Rodger, H and Talbot, A}, title = {Sea Lice (Lepeophtheirus salmonis) Harbour Putative Fish Pathogens: Insights From Illumina and Nanopore Sequencing.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70182}, doi = {10.1111/jfd.70182}, pmid = {41952069}, issn = {1365-2761}, support = {CS/21/005//Marine Institute, Marine Reseach Programme Irish Government/ ; 871108//European Union's Horizon 2020 Research and Innovation Programme/ ; CIAPOS/2024/092//Generalitat Valenciana/ ; FSE+//European Union, Eyropean Social Fun Plus/ ; MMT24-IATS-01-01//NextGeneration EU MOMENTUM-CSIC Postdoctoral Research Contract/ ; }, abstract = {Ectoparasites that penetrate host skin can act as biological or mechanical vectors for pathogens and, in some cases, serve as reservoirs. Crustacean ectoparasites of fish are potential vectors of pathogens, which is especially relevant for obligate pathogens (e.g., Aeromonas salmonicida) with limited seawater survival. Sea lice (Lepeophtheirus salmonis), affecting Atlantic salmon, cause dermal damage and can facilitate secondary infections, resulting in economic losses. While the physical impact of sea lice is well known, their role in pathogen transmission is less clear. The gut bacterial microbiome of lice collected over four months from a salmon farm in Ireland was analysed using Illumina MiSeq and Oxford Nanopore Technologies (ONT) PromethION sequencing for comparison. Illumina and Nanopore sequencing identified 15 and 24 genera of known fish pathogens, respectively. Moreover, Nanopore data revealed up to 15 putative pathogenic species, including Tenacibaculum maritimum, T. dicentrarchi and Vibrio anguillarum, causative agents of tenacibaculosis and vibriosis. The results of this study provide a gut bacterial microbiome characterisation of L. salmonis in a commercial aquaculture setting and demonstrate the potential of sea lice to act as pathogen vectors or reservoirs. These findings have important implications for pathogen surveillance, management, and prevention strategies in salmon aquaculture.}, }
@article {pmid41952172, year = {2026}, author = {Zhang, J and Jiang, C and Zhou, X and Gao, P and Wong, S and Snyder, M and Shen, X}, title = {Cross-body site microbial interactions influence the human plasma metabolome.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02405-w}, pmid = {41952172}, issn = {2049-2618}, support = {#025402-00001//Ministry of Education - Singapore/ ; }, abstract = {BACKGROUND: The human microbiome profoundly influences the host plasma metabolome and health, but most studies have focused on the gut microbiome in isolation. A comprehensive assessment of how microbiomes from multiple body sites jointly shape host metabolism has been lacking.<br><br>RESULTS: Using data from three independent human cohorts (n&#x2009;=&#x2009;435), we systematically analyzed the selective and joint influences of microbiomes from multiple body sites on the human plasma metabolome (814 annotated metabolites). Microbiomes from all body sites contributed to plasma metabolome variation, collectively explaining 30.13% of the inter-individual variation. The gut microbiome showed the largest contribution (18.44%), followed by oral (14.70%), skin (11.5%), and nasal (5.88%) microbiomes. Microbial composition did not necessarily predict metabolic function for example, despite distinct compositions, oral and gut microbiomes exhibited similar associations with circulating metabolites. Machine learning and mediation analyses revealed widespread cooperative and synergistic microbial interactions across body sites, particularly along the oral-gut axis. Over half of the metabolites were jointly influenced by multiple body-site microbiomes. This axis showed cross-site microbial crosstalk and sequential metabolic processing, regulating metabolites such as indole derivatives and carboxylic acids. The oral-gut microbiome-metabolome axis was further amplified in insulin resistance (IR), linking enhanced microbial cooperation to metabolic dysregulation.<br><br>CONCLUSION: Our findings reveal the systemic and interactive nature of microbiome-metabolome relationships and highlight the need to integrate spatially distributed microbial ecosystems to fully understand host metabolic regulation and disease mechanisms. Video Abstract.}, }
@article {pmid41952630, year = {2026}, author = {Wim, T and Mehraveh, S and Katalina, L and Cheah, CW and Pisha, P and Ana, C and Andy, T and Naiera, Z and Wannes, VH}, title = {Not a miracle, not a myth: The role of probiotics in periodontal health.}, journal = {Periodontology 2000}, volume = {}, number = {}, pages = {}, doi = {10.1111/prd.70039}, pmid = {41952630}, issn = {1600-0757}, support = {C3/24/081//KU Leuven/ ; }, abstract = {BACKGROUND: As the understanding of periodontal disease has evolved, therapeutic strategies have increasingly shifted from pathogen eradication toward ecological modulation of the oral microbiome. Within this paradigm, probiotics have emerged as potential adjuncts for maintaining periodontal health by promoting microbial balance and modulating host responses.<br><br>OBJECTIVE: To summarize the historical development, definitions, and mechanisms of probiotics and to critically evaluate the current clinical evidence supporting their use in periodontal therapy.<br><br>METHODS: This narrative review examines the conceptual framework of probiotics in oral health, distinguishing them from related approaches including prebiotics, postbiotics, and synbiotics. Literature from randomized controlled trials and meta-analyses was reviewed to assess the clinical effectiveness of probiotic interventions in periodontal therapy and to explore their proposed mechanisms of action.<br><br>RESULTS: Probiotic effects are highly strain-specific and involve multiple mechanisms, including production of antimicrobial compounds, competition for ecological niches, inhibition of biofilm formation and quorum sensing, strengthening of epithelial barrier integrity, and modulation of host immune and inflammatory responses. Evidence from randomized controlled trials and meta-analyses, particularly those evaluating Limosilactobacillus reuteri strains, suggests that probiotics used as adjuncts to nonsurgical periodontal therapy can significantly improve clinical parameters such as probing pocket depth, clinical attachment level, and bleeding on probing. However, substantial heterogeneity in study design, probiotic strains, delivery systems, and follow-up periods limits the comparability and generalizability of findings.<br><br>CONCLUSIONS: Probiotics represent a biologically plausible and ecologically oriented adjunct in periodontal therapy. While current evidence indicates beneficial clinical effects, further standardized and long-term clinical trials incorporating advanced microbiome analyses (e.g., next-generation sequencing) are needed to clarify mechanisms, optimize formulations, and support personalized probiotic strategies in periodontal care.}, }
@article {pmid41952964, year = {2026}, author = {Peñalba, F and Guisande, A and Lamberti, L and Rusiñol, C and Irastorza, M and Konik, F and Iglesias, C and Mendive, P and Garrido, G and Parada, A and Riera, N}, title = {Gut microbiota and its association with gastrointestinal symptoms and pharmacological treatments in a sibling-matched cohort with autism spectrum disorder.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1777385}, pmid = {41952964}, issn = {2813-4338}, abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder marked by difficulties in communication, social interaction, and restricted, repetitive behaviors. The gut microbiota has emerged as a key factor in the gut-brain axis relevant to ASD. We conducted a cross-sectional study comparing the gut bacterial composition of children with ASD (n=29) and their neurotypical siblings (NT, n=29). To minimize environmental and lifestyle confounders, all pairs were 4 to 10 years old and cohabiting in the same household in Uruguay. We used full-length 16S rRNA gene (V1-V9) sequencing with the latest R10.4.1 Oxford Nanopore Technologies chemistry, enabling high-resolution microbial characterization. While overall β-diversity did not differ significantly between the ASD and NT groups, we identified specific taxonomic shifts. The ASD group was enriched in taxa like Sellimonas, while the NT group showed enrichment of genera like Faecalibacterium and Coprococcus. Furthermore, we found GI symptoms to be significantly more prevalent in the ASD group and some bacterial genera associated with GI symptomatology. In addition, we explored the association of pharmacological treatments. Antipsychotic use was associated with reduced Akkermansia abundance, whereas melatonin and methylphenidate use were associated with the enrichment of Negativibacillus. This study provides novel insights into the gut microbiome of Uruguayan children with ASD, delineating the influence of GI symptoms and pharmacological load on microbial diversity and composition.}, }
@article {pmid41953022, year = {2026}, author = {Han, W and Li, Q and Yuan, G}, title = {The gut microbiome as an actionable drug-sensitivity modulator for immune checkpoint blockade: clinical evidence for FMT, live biotherapeutics, and defined consortia.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1802676}, pmid = {41953022}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology ; *Fecal Microbiota Transplantation/methods ; Animals ; }, abstract = {Immune checkpoint inhibitors (ICIs) deliver durable benefit to only a subset of patients and can be limited by immune-related adverse events (irAEs). The gut microbiome has emerged as an actionable, host-level modulator of ICI drug sensitivity and toxicity. This mini-review links microbial ecology to antigen presentation, T-cell priming and fitness, metabolite signaling, and barrier inflammation, and summarizes interventional evidence across three modalities. Responder-derived fecal microbiota transplantation (FMT) provides the strongest proof-of-concept for re-sensitization in anti-PD-1-refractory melanoma. Microbiome repair can also improve refractory ICI-associated colitis. Early trials of live biotherapeutics and defined consortia support scalability but highlight context dependence and design pitfalls, including antibiotic preconditioning. We discuss practical determinants of reproducibility, including co-medications, diet, engraftment and functional readouts, and conclude with safety, regulatory, and reporting priorities for clinically deployable microbiome engineering.}, }
@article {pmid41953110, year = {2026}, author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J}, title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101380}, pmid = {41953110}, issn = {2352-7714}, abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.}, }
@article {pmid41953220, year = {2025}, author = {El-Saadony, MT and Saad, AM and Sitohy, M and Alkafaas, SS and Dladla, M and Ghosh, S and Mohammed, DM and Ibrahim, EH and Fahmy, MA and Elkelish, A and AbuQamar, SF and El-Tarabily, KA}, title = {Probiotics and human health: biological activities, nutritional aspects, immunomodulatory properties, applications, and future perspectives - a comprehensive review.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1713426}, pmid = {41953220}, issn = {1664-3224}, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; }, abstract = {Probiotics, defined as living microorganisms, are widely recognized for their ability to positively influence the gut microbiota, an effect increasingly linked to a wide array of health benefits. They are claimed to treat or prevent conditions ranging from infant colic to cardiovascular disease, respiratory infections, and certain cancers. Since the beginning of the 21st century, consumer demand for probiotic-enriched foods has risen significantly, propelled by these health assertions. The consumption of such products has been associated with the alleviation of disorders, including irritable bowel syndrome, lactose intolerance, gastroenteritis, obesity, chronic diarrhea, allergies, atopic dermatitis, and infectious diseases. Recent advancements in microbiome and microbiota research are fundamentally transforming probiotic science. Cutting-edge studies on novel strains, their mechanisms, and potential applications are expected to revolutionize our understanding of their roles in human nutrition and medicine. Nevertheless, despite extensive research efforts, critical gaps remain regarding strain-specific mechanisms, optimal dosages, long-term safety, and interactions among probiotics, host genetics, and dietary factors. Addressing these gaps necessitates a comprehensive synthesis of current knowledge and emerging trends. This review aims to critically integrate historical foundations, dosage strategies, mechanisms of action, therapeutic applications, and potential risks associated with probiotics. Unlike previous reviews, this review emphasizes next-generation probiotics, live biotherapeutics, and genetically engineered microbes, and their synergistic interactions with dietary bioactives such as polyphenols and fibers. By providing a forward-looking perspective, this work contributes to the rational design of functional foods, targeted therapies, and microbiome-based interventions, thereby informing future advancements in human nutrition and medicine. It critically examines current and emerging trends in probiotic research, while acknowledging potential adverse effects and risks.}, }
@article {pmid41953221, year = {2025}, author = {Zhao, Z and Wang, X and Bao, Y and Meng, J and Gong, J and Zhang, L and Li, Z and Yao, W and Chuo, Y and Shi, W and Li, J}, title = {Dietary Bazhen San solid-state fermentation product improves laying performance, immunity and intestinal health in laying hens during the late laying period.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1673604}, pmid = {41953221}, issn = {1664-3224}, mesh = {Animals ; *Chickens/immunology ; Female ; *Animal Feed/analysis ; Fermentation ; *Intestines/immunology/microbiology ; Diet ; Dietary Supplements ; Gastrointestinal Microbiome ; *Oviposition ; Eggs ; Cytokines ; Immunoglobulin A/blood ; }, abstract = {The aim of this study was to investigate the effects of solid-state fermentation products of Bazhen San (FB) on the production performance, immunity, and intestinal health of laying hens during the late laying stage. A total of 150 70-week-old laying hens were randomly assigned to five treatment groups, with five replicates per group and six hens per replicate. The control group (CON) was fed a corn-soybean meal-based diet, whereas the other four treatment groups were supplemented with 0.3% FB (LFB), 0.6% FB (MFB), 0.9% FB (HFB), and 0.6% unfermented Bazhen San (BZ), respectively. The results showed that, compared with the CON group, all treatments significantly increased the egg production rate and reduced the feed-to-egg ratio (P < 0.05). Moreover, the effect in the MFB group was significantly greater than that in the BZ group (P < 0.05). In terms of egg quality, the MFB and HFB groups significantly improved yolk color and Haugh units (P < 0.05). Regarding immune function, serum immunoglobulin A (IgA) levels were significantly increased in all treatment groups (P < 0.05), whereas interleukin-1β (IL-1β) and interleukin-6 (IL-6) concentrations were significantly decreased (P < 0.05). The MFB and HFB groups also significantly increased serum immunoglobulin G (IgG) levels (P < 0.05), as well as jejunal and ileal secretory immunoglobulin A (sIgA) levels (P < 0.05). In addition, serum IgG levels in the MFB group were significantly higher than those in the BZ group (P < 0.05). In terms of intestinal health, FB treatment significantly enhanced antioxidant enzyme activity in the jejunum and ileum, reduced malondialdehyde (MDA) content, improved intestinal morphology. The microbiome analysis of the cecum showed that FB improved the abundance of beneficial bacteria in the intestine. Spearman correlation analysis revealed that the relative abundance of Odoribacter and Enterococcus was positively correlated with serum IgA levels and negatively correlated with IL-6 concentration. Therefore, dietary supplementation with FB can improve intestinal health, and systematically improve the immune status of the body, thereby promoting the health of laying hens during the late laying stage and improving production performance, dietary 0.6% to 0.9% FB inclusion is suggested.}, }
@article {pmid41953438, year = {2026}, author = {Li, H and Yu, Z and Wu, Z and Lin, Y and Liu, T and Liu, Y and Li, Z and Zhang, S and Su, Z and Wang, H}, title = {Quantifying human-environment interactions through Bayesian modeling of species-resolved microbial transfer signatures: an exploratory proof-of-concept study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781392}, pmid = {41953438}, issn = {1664-302X}, abstract = {BACKGROUND: Microbial trace evidence offers potential for forensic reconstruction of human-environment interactions, but current methods lack standardized quantitative frameworks. While 2bRAD-M (type IIB restriction site-associated DNA markers for microbiomes) sequencing provides species-level resolution from low-biomass samples, its integration with robust statistical models for forensic applications remains unexplored.<br><br>METHODS: We developed an integrated framework combining 2bRAD-M sequencing with a Bayesian hierarchical model to quantify microbial transfer patterns. The model incorporates geospatial parameters, substrate-specific persistence kinetics, and temporal decay functions. We generated 2bRAD-M data from host-associated (skin, saliva; n&#x202f;=&#x202f;12) and environmental samples (personal devices, high-touch surfaces; n&#x202f;=&#x202f;14), integrated with public 16S rRNA data (Qiita studies; n&#x202f;=&#x202f;2,263 samples) for model training.<br><br>KEY FINDINGS: The Bayesian model demonstrated preliminary accuracy in attributing microbial traces to their likely source environment categories (within ~100 meters in preliminary tests) and provided initial estimates for deposition time. Personal devices were found to retain taxa associated with host such as Staphylococcus hominis for extended periods (exceeding 72&#x202f;h in our observations), suggesting persistent microbial transfer.<br><br>CONCLUSION: This proof-of-concept study suggests that integrating 2bRAD-M sequencing with Bayesian modeling could provide a framework for quantitative reconstruction of microbial transfer histories. The approach indicates potential for forensic applications but is not yet validated for casework. Extensive validation with larger, independent datasets is imperative to assess its reliability and admissibility standards.}, }
@article {pmid41953447, year = {2026}, author = {Wang, X and Hu, W and Li, R and Sun, R and Liong, MT and Yu, Q and Chen, D}, title = {Gi-MAPS: a quantitative engineering framework for AI-guided pediatric gut microbiome ecological interpretation and digital-twin simulation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1739103}, pmid = {41953447}, issn = {1664-302X}, abstract = {BACKGROUND: Quantitative and reproducible microbiome analysis is limited by fragmented workflows lacking standardized anaerobic sampling, absolute quantification methods, and transparent AI inference. Patent-documented engineering integration is required for reliable microbiome analytics at population scale.<br><br>METHODS: Gi-MAPS was designed as an end-to-end analytical system integrating several core patented innovations, including (i) a press-activated anaerobic sample-preservation device that maintains ultra-low residual oxygen to protect obligate anaerobes during transport, (ii) a multiplex qPCR assay enabling simultaneous absolute quantification of key HMO-utilizing Bifidobacterium species in a single reaction, and (iii) a CIT-Net-based digital-twin engine that supports forward simulation of gut microbiota ecological trajectories. These modules are coupled with explainable ensemble artificial intelligence models to form a fully quantitative and simulation-enabled microbiome analysis framework. Each subsystem was validated under granted patents to define engineering performance boundaries and reproducibility specifications.<br><br>RESULTS: System validation demonstrated <0.1% residual oxygen stability for anaerobic preservation, detection sensitivity down to five genomic copies per microliter, AUC&#x202f;>&#x202f;0.97 for ecological maturity estimation, 89% accuracy for disease-risk classification, and 95% concordance for digital-twin forecasting. Execution-layer software copyright modules and filed patents extend automation, visualization, and future application domains.<br><br>CONCLUSION: Gi-MAPS provides a patent-anchored, standardized engineering framework whose key novelties lie in oxygen-controlled anaerobic sampling, absolute microbial quantification via multiplex qPCR, and digital-twin ecological simulation, enabling quantitative, function-aware, and prospective microbiome analysis. It establishes a reproducible foundation enabling large-scale cohort deployment, longitudinal ecological monitoring, digital-twin simulation, and future multi-omics integration.}, }
@article {pmid41953448, year = {2026}, author = {Bautista, J and López-Cortés, A}, title = {Biohacking the human gut microbiome for precision health and therapeutic innovation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1776983}, pmid = {41953448}, issn = {1664-302X}, abstract = {Biohacking, the self-directed application of biotechnology, digital tools, and lifestyle interventions, has rapidly converged with gut microbiome science to create adaptive, individualized, and minimally invasive precision-health paradigms. This narrative review integrates current evidence on diet-based modulation, microbial therapeutics (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation), and synthetic-biology approaches (engineered strains and phage or synthetic consortia) within a multi-omics and continuous-phenotyping framework. Mechanistically, short-chain fatty acids (SCFAs), bile-acid derivatives, and tryptophan catabolites operate as endocrine-like mediators linking gut microbial ecology with host immunity, metabolism, and neuroendocrine signaling. Pathways mediated by microbial metabolites underpin translational applications that span metabolic optimization, through improved insulin sensitivity, reduced adiposity, and attenuation of inflammation, and neurocognitive enhancement via the microbiome-gut-brain axis. Evidence from oncology further indicates that microbial metabolites and engineered taxa remodel stromal and immune niches, shaping therapeutic response and disease progression. Concurrently, emerging digital infrastructures, wearables, biosensors, metabolic avatars, and AI-driven "health twins," enable real-time, closed-loop modulation of host-microbe dynamics. Persistent challenges include methodological heterogeneity, safety concerns regarding live biotherapeutics and unsupervised fecal microbiota transplantation (FMT), fragmented regulation, and vulnerabilities in cyberbiosecurity and data equity. We propose a translational roadmap emphasizing standardized metadata (STORMS), validated reference frameworks, longitudinal multi-omics for causal inference, strain-level safety genomics, and governance integrating ethical and cybersecurity oversight. Under these conditions, microbiome-focused biohacking may evolve from anecdotal experimentation into a more reproducible and scientifically grounded component of preventive and personalized medicine. This manuscript is presented as a narrative and conceptual review, integrating validated microbiome research with emerging biohacking frameworks while explicitly distinguishing evidence-based findings from exploratory or speculative concepts.}, }
@article {pmid41953516, year = {2026}, author = {Qu, HQ and Kao, C and Hakonarson, H}, title = {Redefining the role of the thiol-based agent N-acetylcysteine in human health and disease and elucidating potential advantages of its amide derivative.}, journal = {RSC medicinal chemistry}, volume = {}, number = {}, pages = {}, pmid = {41953516}, issn = {2632-8682}, abstract = {N-Acetylcysteine (NAC) is the established antidote for acetaminophen toxicity and an approved mucolytic agent. Beyond these traditional uses, increasing evidence highlights its broader role as a modulator of thiol-redox biology. Rather than functioning as a nonspecific antioxidant, NAC modulates glutathione metabolism, redox-sensitive signaling, immune checkpoints, thiol-based post-translational modifications, ferroptosis susceptibility, and glutamatergic neurotransmission. This review synthesizes mechanistic, preclinical, and clinical evidence across pulmonary, hepatic, neuropsychiatric, metabolic, cardiovascular, and oncologic disorders, emphasizing how variability in baseline redox state, pharmacogenetics, and delivery contributes to heterogeneous outcomes. Strategies to improve pharmacokinetics and tissue targeting include structural derivatives such as N-acetylcysteine amide (NACA), and combination regimens such as NAC with probenecid or GlyNAC. Emerging applications span long COVID, neurodegeneration, psychiatric disorders, microbiome-redox interactions, environmental toxicology, and cancer immunotherapy. NAC and NACA exemplify the evolution of redox-targeted therapeutics. NAC is well established for safety and clinical utility, but its pharmacokinetic and tissue distribution properties constrain broader efficacy. NACA, a lipophilic amide derivative, enhances membrane permeability and cellular uptake, suggesting it may achieve higher tissue exposure at lower doses. Future progress will rely on biomarker-guided, precision approaches that optimize dosing, formulation, and delivery while exploring rational combinations across disease contexts defined by redox biology.}, }
@article {pmid41953552, year = {2026}, author = {Hwang, JH and Choi, YK}, title = {Herbal and Natural Product Interventions in Animal Models of Antibiotic-Associated Diarrhea and Their Effects on Gut Microbiota: a protocol for systematic review.}, journal = {Journal of pharmacopuncture}, volume = {29}, number = {1}, pages = {42-47}, pmid = {41953552}, issn = {2093-6966}, abstract = {OBJECTIVES: Antibiotic-associated diarrhea (AAD) is a frequent complication of antibiotic use and is commonly used to investigate gut microbiota dysbiosis and potential therapeutic interventions in animals. Herbal medicines and natural product-derived compounds have shown promising effects in restoring microbial balance; however, no systematic review has yet synthesized the preclinical evidence. Therefore, this review aimed to systematically identify, evaluate, and synthesize animal studies examining herbal and natural product interventions for AAD, with a particular focus on gut microbiota restoration and related functional outcomes.<br><br>METHODS: This protocol has been registered in PROSPERO (CRD420251136553). A systematic search was performed in PubMed, Embase, Web of Science, Scopus, CNKI, and other major Korean medical databases from inception to the search date. Controlled preclinical studies that evaluated herbal or natural product interventions for AAD in animal models and reported gut microbiota outcomes were also included. Two reviewers independently screened the studies, extracted the data, and assessed the risk of bias.<br><br>RESULTS: This systematic review was conducted in accordance with the PRISMA guidelines. The findings were synthesized narratively and, where appropriate, organized by intervention type, animal model, and microbiome analytic method.<br><br>CONCLUSION: This review systematically evaluates the effects of herbal and natural products on the gut microbiota in animal models of antibiotic-associated diarrhea. These findings provide foundational preclinical evidence to support microbiome-directed development of herbal, polysaccharide-based, and synbiotic interventions for antibiotic-associated dysbiosis.}, }
@article {pmid41953674, year = {2026}, author = {Zhou, H and Saha, S and Morrill, S and Kelly, T and Lewis, WG and Lewis, AL}, title = {Gardnerella biofilm formation in vitro is facilitated by braided sutures: implications for cervical cerclage.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1763531}, pmid = {41953674}, issn = {2235-2988}, mesh = {*Biofilms/growth &amp; development ; *Sutures/microbiology/adverse effects ; Female ; Humans ; *Cerclage, Cervical/adverse effects ; Pregnancy ; *Gardnerella/physiology/growth &amp; development ; *Gardnerella vaginalis/physiology/growth &amp; development ; }, abstract = {INTRODUCTION: In pregnant individuals with certain indications, sutures may be placed circumferentially around the uterine cervix to prevent dilation. Compared to monofilament sutures, the use of braided suture materials has been linked with the development of a dysbiotic vaginal microbiome, as well as higher rates of infection-associated pregnancy outcomes such as chorioamnionitis and preterm birth. In bacterial vaginosis (BV) anaerobic bacteria, including pathogens, overgrow, forming biofilms in direct proximity to the host epithelium. Gardnerella is highly represented among bacterial vaginosis-like microbiotas.<br><br>METHODS: To test our working hypothesis that braided sutures may better support the establishment of high biomass bacterial biofilms compared to monofilament sutures, we measured the extent of Gardnerella bacteria biofilm formation on braided and monofilament sutures in the laboratory. Multiple Gardnerella strains were grown in the presence of braided or monofilament suture materials (polyester or polybutylate-coated polyester versus polypropylene or nylon), and the (biofilm) biomass was measured using crystal violet staining.<br><br>RESULTS: Sutures incubated without Gardnerella were included as controls. To compare staining of biofilm biomass between groups, one-way ANOVA was performed and &#x160;id&#xe1;k was used for pairwise comparisons to control for multiple comparisons between groups. Gardnerella formed significantly more biofilm biomass (>10-fold) on braided polyethylene terephthalate (polyester) sutures compared to monofilament (polypropylene or nylon) sutures (p < 0.0001). This feature was applicable to multiple strains across different taxonomic subsets of Gardnerella.<br><br>DISCUSSION: Together with existing literature, these findings suggest that braided sutures might promote the development of dysbiotic BV-like microbiomes after cerclage placement by facilitating Gardnerella biofilm formation.}, }
@article {pmid41953764, year = {2026}, author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF}, title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41953764}, issn = {2312-0541}, abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.<br><br>METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.<br><br>RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in &#x3b1;- and &#x3b2;-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.<br><br>CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.}, }
@article {pmid41953919, year = {2026}, author = {Murmu, M and Singh, R and Barage, S and Kumar, AWS}, title = {Exploratory Study of Virulence Factors and Protein-Protein Interaction Networks in Major Oral Pathogens.}, journal = {Contemporary clinical dentistry}, volume = {17}, number = {1}, pages = {16-30}, pmid = {41953919}, issn = {0976-237X}, abstract = {INTRODUCTION: Periodontitis is a prevalent inflammatory disease driven by dysbiotic microbial consortia. Red-complex pathogens (Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia) and emerging taxa (Filifactor alocis and Aggregatibacter actinomycetemcomitans) are central contributors, yet their virulence mechanisms remain incompletely defined.<br><br>OBJECTIVE: To construct protein-protein interaction (PPI) networks of key periodontopathogens and identify conserved as well as pathogen-specific virulence hubs.<br><br>METHODOLOGY: High-confidence PPI networks were generated for 1136 proteins across the five pathogens. Network topology was analyzed to identify hubs, and enrichment analyses were performed to map functional clusters.<br><br>RESULTS: Hub proteins such as guaA, metG, pheT, lysS, thrA, rplA, purD, and rpsH demonstrated significant interactions with accessory proteins. Conserved hubs, including guaA and ileS, were shared across pathogens and were essential in purine biosynthesis and aminoacyl-tRNA ligation. Pathogen-specific hubs comprised gingipains (P. gingivalis), leukotoxin (A. actinomycetemcomitans), and dentilisin (T. denticola). Functional clustering revealed adhesion, peptidoglycan biosynthesis, and immune modulation pathways.<br><br>CONCLUSION: PPI networks provide system-level mechanistic insights into pathogen virulence, revealing conserved vulnerabilities and species-specific mechanisms.}, }
@article {pmid41954023, year = {2026}, author = {Anagnostopoulou, L and Ktenopoulos, N and Apostolos, A and Fragoulis, C and Vlachakis, P and Karakasis, P and Sagris, M and Milaras, N and Drakopoulou, M and Synetos, A and Kyriazis, I and Ioannidis, I and Tsioufis, C and Toutouzas, K}, title = {Intersecting Molecular Pathways in Cardiovascular Disease and Diabetes Mellitus: Emerging Roles of Inflammation and Therapeutics.}, journal = {Diabetes/metabolism research and reviews}, volume = {42}, number = {4}, pages = {e70167}, pmid = {41954023}, issn = {1520-7560}, mesh = {Humans ; *Cardiovascular Diseases/metabolism/pathology/etiology ; *Inflammation/metabolism/pathology ; *Hypoglycemic Agents/therapeutic use ; Gastrointestinal Microbiome ; Animals ; *Diabetes Mellitus/metabolism/drug therapy ; }, abstract = {Diabetes mellitus (DM) and cardiovascular diseases (CVD) remain leading contributors to global morbidity and mortality, imposing a substantial burden on healthcare systems worldwide. The pathophysiological mechanisms underlying these conditions are complex and closely interconnected, with chronic low-grade inflammation, oxidative stress, endothelial dysfunction, insulin resistance and dysregulated lipid metabolism serving as pivotal shared pathways. Persistent hyperglycaemia and metabolic imbalance in DM accelerate vascular injury and atherosclerotic progression, thereby significantly increasing cardiovascular risk. Consequently, therapeutic strategies that concurrently target both metabolic and cardiovascular dysfunction may offer meaningful clinical advantages and improved long-term outcomes. In recent years, novel antidiabetic agents such as sodium-glucose co-transporter 2 (SGLT-2) inhibitors and glucagon-like peptide-1 (GLP-1) receptor agonists have demonstrated not only glycaemic control but also substantial cardiovascular protection, including reductions in major adverse cardiovascular events, heart failure hospitalisations and renal disease progression. These pleiotropic effects extend beyond glucose lowering and involve modulation of inflammatory pathways, improvement of endothelial function, attenuation of oxidative stress and favourable haemodynamic changes. Additionally, emerging evidence highlights the role of the gut microbiota as a critical mediator in the bidirectional relationship between DM and CVD. Alterations in microbial composition and diversity, collectively termed dysbiosis, have been associated with systemic inflammation, impaired metabolic homoeostasis, increased intestinal permeability and the production of pro-atherogenic metabolites such as trimethylamine N-oxide. Understanding these microbiome-related mechanisms may open new avenues for preventive and therapeutic interventions targeting the gut-metabolic-cardiovascular axis. This narrative review provides an updated and comprehensive overview of the molecular and cellular mechanisms linking DM and CVD, with particular emphasis on inflammatory signalling, metabolic dysregulation and the emerging influence of the gut microbiome in their shared pathogenesis and therapeutic modulation.}, }
@article {pmid41954158, year = {2026}, author = {Glass, BH and Aichelman, HE and Grupstra, CGB and Valadez-Ingersoll, M and Swank, A and Guerra, V and Gondola, P and Nagree, A and Schipfer, J and Gilmore, TD and Davies, SW}, title = {Legacy Effects of an Extreme Marine Heatwave on a Stress-Tolerant Coral.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70853}, doi = {10.1111/gcb.70853}, pmid = {41954158}, issn = {1365-2486}, support = {//Boston University/ ; 1937650//National Science Foundation/ ; 2506815//National Science Foundation/ ; }, mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; Panama ; *Extreme Heat/adverse effects ; *Coral Bleaching ; Symbiosis ; *Hot Temperature ; Stress, Physiological ; }, abstract = {During the 4th Global Coral Bleaching Event (GCBE4; January 2023-September 2025), an extreme marine heatwave occurred on the Bocas del Toro Reef Complex (BTRC) in Panama. We characterized how this heatwave impacted the health and holobiont communities of the stress-tolerant coral Siderastrea siderea at four sites across the BTRC. Tagged colonies at each site (N = 30-53 colonies per site) were visited before, during, and after the heatwave (early May 2022, mid-August 2023, and late April 2024, respectively), and images and DNA samples were collected at each time point. In situ temperature logger data showed that sites reached maxima of 32.1°C-33.9°C in October 2023, resulting in the accumulation of ~12-20 maximum degree-heating weeks (DHWs). Consequently, S. siderea colonies displayed widespread bleaching (i.e., the loss of algal endosymbionts), with an increase from 8.6% to 33% of colonies bleached per site in May 2022 to 33%-70% in August 2023, followed by a decline to 15%-63% by April 2024. Colony-level partial mortality increased significantly between 2022 and 2024 at three of the four sites, and was observed even in colonies that were not bleached in August 2023. Further, many corals hosting Cladocopium spp. algal symbionts in 2022 shifted towards less diverse communities dominated by heat-tolerant Breviolum and Durusdinium spp., and most of these corals continued to host modified symbiont communities for months. The heatwave also reshaped corals' bacterial microbiomes, including increases in α-diversity and abundances of potentially pathogenic taxa (e.g., Vibrionaceae), and these shifts were persistent following the heatwave. Together, these findings demonstrate that GCBE4 had lasting impacts on S. siderea holobiont health across the BTRC, underscoring that extreme heat events can compromise even stress-tolerant coral species and induce legacy effects that will likely affect their future resilience. Rapid action to minimize further ocean warming is thus necessary to safeguard reef ecosystems.}, }
@article {pmid41954174, year = {2026}, author = {Torregrosa-Chinillach, A and Tsiara, I and Haberek, W and Lin, W and Globisch, D}, title = {Chemical Metabolomics: Chemical Biology Tools for Advanced Metabolism Investigations.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e26122}, doi = {10.1002/anie.202526122}, pmid = {41954174}, issn = {1521-3773}, support = {2020-04707//Swedish Research Council/ ; FO2024-0407//Swedish Brain Foundation/ ; 254898Pj//Swedish Cancer Society/ ; }, abstract = {Human metabolism has been investigated to understand disease onset for the discovery of new selective pharmaceuticals and the development of diagnostics for early disease detection. Metabolomics, as an interdisciplinary research field, has been implemented to investigate the entirety of the complex metabolite profiles predominantly using mass spectrometry. In the past two decades, the development of chemical biology tools for the detailed metabolism investigation has received a boost to advance metabolomics analyses. Especially, the identification of the microbiome and its importance for human physiology were the main motivation for these strategies. These new tools at the intersection of Chemistry and Biology have especially aided to uncover previously unknown metabolites in humans and have slowly elucidated metabolites produced by microbial communities. These Chemical Biology tools, integrated with metabolomics tools and technologies, build the foundation for Chemical Metabolomics investigations, which have led to the discovery of important metabolites that are modulators or readouts for disease development and human homeostasis. This overview article focuses on the recent developments and the diversity of Chemical Biology tools and technologies, particularly methods involving chemoselective probes, in vivo analysis, host-microbiome co-metabolism, and activity metabolomics, in the context of understanding human metabolism at the molecular level.}, }
@article {pmid41954380, year = {2026}, author = {Hu, J and Chung, R and Odeneal, R and Zhang, SJ}, title = {AANA Journal Course-The Gut-Brain Axis and Chronic Pain: The Emerging Role of Microbiota.}, journal = {AANA journal}, volume = {94}, number = {2}, pages = {141-151}, doi = {10.70278/AANAJ/.0000001078}, pmid = {41954380}, issn = {2162-5239}, mesh = {Humans ; *Chronic Pain/microbiology/physiopathology/nursing ; *Gastrointestinal Microbiome/physiology ; *Nurse Anesthetists/education ; Dysbiosis ; *Brain ; }, abstract = {Chronic pain is a complex and disabling condition that significantly impairs quality of life. It often arises from central sensitization, an amplified response to pain stimuli driven by neuroinflammatory changes in both the peripheral and central nervous systems. Emerging evidence highlights the gut microbiome's crucial role in the process because it modulates inflammation, immune function, and neurotransmitter production via the gut-brain axis. An imbalance in gut flora, known as dysbiosis, can exacerbate neuroinflammation by altering intestinal barrier integrity, facilitating the release of pro-inflammatory mediators, and activating microglia within the central nervous system. These changes contribute to increased pain sensitivity and the progression of chronic pain states. Consequently, strategies promoting a healthy gut microbiome, such as targeted dietary measures and microbiota-focused therapies, represent promising adjuncts to conventional chronic pain management. This journal course evaluates current research on the connection between the gut microbiome and chronic pain, offering a novel perspective on holistic, microbiome-centered interventions for alleviating pain disorders. As certified registered nurse anesthetists increasingly participate in pain management, understanding this emerging approach is vital for improving patient outcomes in chronic pain conditions.}, }
@article {pmid41954396, year = {2026}, author = {Drankhan, HR and Taylor, KR and Shah, DH and Park, CH and Grieser, AM and Wild, MA}, title = {An experimental infection model for rapid reproduction of treponeme-associated hoof disease in captive elk (Cervus canadensis).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0382225}, doi = {10.1128/spectrum.03822-25}, pmid = {41954396}, issn = {2165-0497}, abstract = {Treponeme-associated hoof disease (TAHD) is an emerging, polybacterial infection that causes painful foot lesions and lameness in free-ranging elk (Cervus canadensis) across the northwestern USA. Although TAHD is associated with multiple Treponema species and other anaerobic bacteria, current understanding of disease etiology is limited and based primarily on cross-sectional analyses of naturally infected elk, in which lesions were examined at single time points using histopathology and 16S rRNA gene sequencing. Our objective was to develop a rapid and reliable experimental infection model to study TAHD pathogenesis in captive elk under controlled conditions. Inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria derived from TAHD lesions was applied onto abraded interdigital skin on the hind feet of five treatment elk. Inoculated feet were wrapped to expedite lesion development. Over the 7 week study period, all inoculated feet (10/10) developed interdigital erosions consistent with mild to moderate TAHD lesions observed in free-ranging elk. Lesions were observed on the majority of inoculated feet (9/10) after 28 days, coinciding with concurrent 16S rRNA gene amplicon sequencing detection of three putative pathogens of TAHD: Treponema, Fusobacterium, and Mycoplasma. In contrast, mock-inoculated control elk feet did not exhibit pathological or microbiological changes indicative of TAHD. This experimental infection model provides a valuable platform to investigate the complex interactions between the host, pathogens, and environmental factors that influence TAHD susceptibility, lesion progression, and disease transmission.IMPORTANCEOur study details a new approach for consistent and rapid induction of treponeme-associated hoof disease (TAHD) lesions in captive elk. TAHD is an emerging polybacterial disease of conservation concern that causes chronic lameness and debilitation in free-ranging elk across the northwestern USA. We rapidly and reliably reproduced TAHD lesions following challenge with inoculum consisting of macerated lesion tissue and mixed cultures of Treponema spp. and other anaerobic bacteria. This experimental infection model provides a valuable platform for investigation of the complex interactions between the host, pathogens, and environmental factors influencing TAHD susceptibility, lesion progression, and disease transmission in elk.}, }
@article {pmid41954620, year = {2026}, author = {Gou, YR and Gu, H and Wang, L}, title = {Beyond tumor biology: nursing interventions for psychological and immune health in cancer patients.}, journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer}, volume = {34}, number = {5}, pages = {}, pmid = {41954620}, issn = {1433-7339}, mesh = {Humans ; *Neoplasms/psychology/immunology/nursing/therapy ; *Stress, Psychological/therapy/etiology/nursing ; *Oncology Nursing/methods/organization &amp; administration ; Depression ; Social Support ; Anxiety ; }, abstract = {Cancer care requires an integrative approach that addresses psychological distress, immune dysfunction, and health disparities across global populations. Psychoneuroimmunology research reveals bidirectional links between psychological well-being, neural signaling, immune activity, and clinical outcomes, underscoring the need for nursing‑led holistic interventions. This review synthesizes evidence on the prevalence and impact of anxiety, depression, fear of recurrence, and stress-mediated neuroendocrine pathways that suppress immune surveillance. It examines tumor-associated immune dysregulation, therapy-induced immune imbalance, and inflammation as a mechanistic bridge between emotional and physical health. Nursing-driven strategies including cognitive-behavioral therapy, mindfulness, narrative care, social support, lifestyle counseling, nutrition, microbiome support, physical rehabilitation, and integrative practices demonstrate measurable benefits for resilience, immune stability, and treatment adherence. Emerging technologies such as AI-enabled telehealth expand the reach and personalization of oncology nursing pathways. Persistent barriers workload, training gaps, cultural differences, and limited resources require policy reform, multidisciplinary integration, and capacity-building. Future directions highlight precision nursing models utilizing biomarkers, digital analytics, and survivorship planning to deliver equitable, patient-centered psychological-immune oncology care.}, }
@article {pmid41954752, year = {2026}, author = {Saha, S and Shah, AS and Wang, P and Burgess, TI and Bayliss, KL}, title = {Seed Potato Bacteria Transfer Across Generations Within the Tuber Flesh.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02758-7}, pmid = {41954752}, issn = {1432-184X}, abstract = {Potato crops are susceptible to pathogens and environmental extremes. Microbiomes support plant health and stress tolerance, and microbes can transfer across generations in vegetatively propagated potatoes. However, the extent and functional relevance of this transfer are poorly understood. This study investigated bacterial transfer across three tuber generations, from seed to granddaughter in two potato cultivars, Nadine and Royal Blue. Bacterial communities in the peel and flesh compartments were sequenced. The granddaughter generation was cultivated in two separate fields to determine the consistency of vertical transfer, and the tare soil bacterial community was a proxy for environmental acquisition. The overall community composition was influenced by generation, compartment, cultivar and field. Horizontal acquisition significantly increased across generations and was the primary source, accounting for more than 98% of the granddaughter tuber bacteria. Peel had a significantly higher number of horizontally acquired ASVs than flesh. Only a small set of seed tuber bacteria ASVs were vertically transferred to the granddaughter tubers. The overall vertical transfer probability was 1.8% across compartments, cultivars, and fields, and it was higher in flesh than in peel. Cultivar-specific probabilities were 1.8% for Nadine and 1.5% for Royal Blue. Field variance was minimal, indicating consistent vertical transfer regardless of where the tubers were grown. Taxa with stable vertical transfer included Streptomycetaceae, Xanthobacteraceae, Devosiaceae, Sphingomonadaceae, and Micrococcaceae. Vertically transferred ASVs were predicted to have functions associated with core metabolic and stress response pathways. This study confirmed consistent vertical transfer of bacteria across potato tuber generations, mainly in the flesh.}, }
@article {pmid41954871, year = {2026}, author = {Mac Aogáin, M and Gilmour, A and Chalmers, JD and Chotirmall, SH}, title = {Targeting Inflammation in Bronchiectasis.}, journal = {Drugs}, volume = {}, number = {}, pages = {}, pmid = {41954871}, issn = {1179-1950}, support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001636//National Medical Research Council/ ; MOH-001356//National Medical Research Council/ ; MOH-001855//National Medical Research Council/ ; }, abstract = {Bronchiectasis is defined by chronic infection, dysregulated inflammation and impaired mucociliary clearance underpinning progressive structural lung injury. While airway infection remains a clinical hallmark, numerous studies demonstrate that excessive neutrophil-dominated inflammation is a key determinant of disease severity, exacerbation risk and quality of life. Recent developments have transformed our understanding of inflammatory drivers uncovering distinct inflammatory endotypes defined by dominant microbial species, pattern-recognition receptor activation, inflammasome signalling, Th17-associated cytokine networks and failures of mucosal immunity. The emerging roles of viral-bacterial interactions, fungi, pathobionts and the broader microbiome challenge the conventional infection-only paradigm and highlight gaps in current therapeutic strategies. Such developments underpin the rationale behind anti-inflammatory strategies in bronchiectasis, ranging from suppression of neutrophil-driven injury through direct neutrophil elastase or upstream dipeptidyl peptidase-1 (DPP-1) inhibition, to immunomodulatory macrolides, toward therapies aimed at recalibrating epithelial and mucosal homeostasis. While several antibacterial and anti-infective trials have produced mixed results, this is likely to reflect unresolved heterogeneity in microbiome composition and host immune signalling. In contrast, emerging anti-inflammatory strategies show strong positive signals, reinforcing the need for better endotyping and biomarker-guided patient selection. Here we synthesize recent mechanistic and clinical insights to propose a more integrated framework for understanding and ultimately targeting airway inflammation in bronchiectasis.}, }
@article {pmid41954918, year = {2026}, author = {Specchia, ML and Beccia, F and Cacciuttolo, MG and Petrella, L and Mungo, T and Thiella, S and Lucarelli, A and Zace, D and Di Pietro, ML}, title = {Maternal and child nutrition insecurity, microbiome, and early neurodevelopment: an intricate interplay. Results from a systematic review.}, journal = {European journal of public health}, volume = {36}, number = {2}, pages = {}, pmid = {41954918}, issn = {1464-360X}, mesh = {Humans ; Female ; Infant ; *Child Development/physiology ; *Gastrointestinal Microbiome/physiology ; *Food Insecurity ; *Neurodevelopmental Disorders ; Child ; *Nutritional Status ; Pregnancy ; Child, Preschool ; Infant, Newborn ; }, abstract = {Emerging research suggests nutrition insecurity influences microbiome composition, which in turn affects early neurodevelopment through the gut-brain axis. This systematic review aimed to evaluate evidence on these relationships. A comprehensive search of the scientific literature was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Studies investigating the links between nutrition insecurity in mothers and children, microbiome, and early neurodevelopment were included. Data on maternal characteristics, microbiota composition, neurodevelopmental outcomes, and nutritional status were extracted from eligible studies. The review included 11 studies, primarily cohort studies, conducted in various countries. According to the study findings, gut maternal and infant microbiota composition in early life appear to be closely connected to early neurodevelopment both in terms of cognitive/motor skills and temperament. Nutrition insecurity has a significant influence in shaping these outcomes as it can alter microbiota balance and contribute to gut dysbiosis and delayed neurodevelopmental milestones. Breastfeeding emerges as a crucial factor in modulating the infant microbiome and supporting neurodevelopment. Also, other factors such as pre-pregnancy overweight/obesity and environment seem to influence offspring gut colonization and neurodevelopmental outcomes. This systematic review highlights the intricate interplay between maternal and child nutrition insecurity, microbiota, and early neurodevelopment. These findings underscore the critical need for targeted interventions addressing maternal and child nutrition to mitigate the adverse effects of nutrition insecurity and support optimal early-life neurodevelopment. Future research should focus on longitudinal studies to explore the causal pathways and to develop nutrition-based strategies to prioritize microbiome health in vulnerable and at-risk populations.}, }
@article {pmid41955160, year = {2026}, author = {Liu, J and Li, K and Zhang, Y and Huang, K and Guan, X}, title = {Predicting gut metabolites from gut microbiome and their interpretability analysis of IBD prediction based on LIME.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {18}, number = {}, pages = {}, doi = {10.1093/intbio/zyaf023}, pmid = {41955160}, issn = {1757-9708}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/diagnosis ; Dysbiosis/microbiology ; Oxides ; Calcium Compounds ; }, abstract = {The pathophysiology of inflammatory bowel disease (IBD) is influenced by the gut microbiome and gut metabolite, but understanding how IBD is affected remains challenging. It is crucial to understand which features affect IBD in order to effectively diagnose the disease. Traditional technology for measuring metabolite features is time-consuming and costly. The abundance of metabolite features in IBD patients is altered depending to changes in the abundance of gut microbiome. LSTM-VAE is proposed to predict gut metabolite features using gut microbiome of IBD patients. The pathogenesis of IBD is investigated by LSTM-VAE without gut metabolite data. In order to explore IBD is affected by the features, GBDT-LR is used to predict IBD disease using the gut microbiome and the generated gut metabolites. GBDT-LR achieved high-precision prediction, with an accuracy of 0.97 at the genus level and 0.95 at the species level. It is noteworthy that LIME is used to explain the prediction process of GBDT-LR, solving the prediction of the 'black box model'. The cost of measuring intestinal metabolites were reduced in this study and the researches were assisted in the diagnosis and drug research of IBD diseases. Insight Box Dysbiosis of the gut microbiota and the resulting abnormal metabolites were influenced in the IBD, promoting inflammatory responses and damaging intestinal barrier function. LSTM-VAE was proposed to predict changes in gut metabolite features in IBD patients without the need for direct measurement of costly and time-consuming metabolite data. Furthermore, high-precision prediction of IBD based on gut microbiome data was demonstrated and metabolite features were generated in the GBDT-LR, achieving accuracy rates of 0.97 at the genus level and 0.95 at the species level. Additionally, the LIME is employed to interpret the "black box" prediction process of GBDT-LR. The cost of measuring gut metabolites was reduced, but also strong support for the diagnosis and drug development of IBD was provided.}, }
@article {pmid41955174, year = {2026}, author = {Kowarsky, M and Dalman, M and Moufarrej, MN and Okamoto, J and Xie, Y and Neff, NF and Abdool Karim, SS and Garrett, N and Moore, PL and Camunas-Soler, J and Quake, SR}, title = {Cell-free RNA reveals host and microbial correlates of broadly neutralizing antibody development against HIV.}, journal = {PLoS pathogens}, volume = {22}, number = {4}, pages = {e1014066}, pmid = {41955174}, issn = {1553-7374}, mesh = {Humans ; *HIV Infections/immunology/virology ; *HIV-1/immunology/genetics ; *HIV Antibodies/immunology ; *Broadly Neutralizing Antibodies/immunology ; Male ; Female ; Adult ; *RNA, Viral/genetics/blood ; Middle Aged ; Longitudinal Studies ; Microbiota/immunology ; }, abstract = {A small number of people living with HIV (PLWH) develop broadly neutralizing antibodies (bNAbs) targeting multiple HIV strains. Although several viral and immune factors contribute to bNAb development, the genetic and environmental factors driving this response remain largely unknown. We performed combined cell-free DNA (cfDNA) and cell-free RNA (cfRNA) sequencing in 42 plasma samples from a longitudinal cohort of 14 PLWH (7 who develop bNAbs and 7 matched controls). This approach enabled us to non-invasively monitor the host transcriptome, viral genetic variation, and microbiome composition during HIV infection, and to identify molecular correlates of bNAb development. We find that development of bNAbs is associated with a transcriptomic signature of early immune activation characterized by elevated levels of MHC class I antigen presentation genes. This signature is independent of viral load or CD4 count and declines over time. In addition to host features, we recovered sufficient viral reads to reconstruct HIV consensus sequences, supporting the utility of cfRNA for viral genotyping. Finally, we also identified an enrichment of several microbial taxa in bNAb producers and increased levels of GB virus C (GBV-C), a non-pathogenic lymphotropic virus. Our findings suggest a distinct early immune activation profile in PLWH who develop bNAbs. More broadly, we show that combined cfDNA/cfRNA sequencing can reveal relationships between a protective immunogenic response to HIV infection, the host immune system, and microbiome, highlighting its potential for biomarker discovery in future vaccine and therapeutic studies.}, }
@article {pmid41955218, year = {2026}, author = {Yaakop, S and Senen, MA and Adila Rosli, NA and Mohammed, MA}, title = {Molecular identification and microbiome profiling of household casebearer, Phereoeca sp. (Lepidoptera: Tineidae) from Malaysia: Potential implications for human skin irritation.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0346590}, pmid = {41955218}, issn = {1932-6203}, mesh = {Animals ; Malaysia ; *Microbiota/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Phylogeny ; Skin/microbiology ; *Lepidoptera/microbiology/genetics ; DNA Barcoding, Taxonomic ; DNA, Bacterial/genetics ; *Moths/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Electron Transport Complex IV/genetics ; }, abstract = {In Malaysia, anecdotal accounts have linked the household casebearer (Lepidoptera: Tineidae) to skin lesions and localized inflammation; however, scientific evidence is lacking, and the species' taxonomic identity remains unclear. This study aimed to confirm the species identity and examine the bacteria associated with larvae that may be linked to skin irritation. Larvae were collected from three locations in Peninsular Malaysia and preserved. DNA was extracted from the larvae, and species identification was conducted by analyzing the cytochrome c oxidase subunit I (COI) gene through DNA barcoding. To study the bacteria present, the bacterial 16S rRNA gene was amplified and sequenced using Next-generation sequencing technology. The DNA sequences were analyzed to determine the species and profile the bacterial communities. The results identified the specimens as Phereoeca sp., suggesting they may represent an undescribed lineage. Microbiome analysis revealed that Proteobacteria (40.18%) and Actinobacteriota (32.13%) were the dominant bacterial phyla, with Cutibacterium acnes, Enterobacter, and Pseudomonas among the taxa previously associated with skin irritation or opportunistic infections. Several unclassified but potentially relevant taxa were also identified. These findings provide new insights into the microbial ecology and taxonomy of Phereoeca and underscore its potential role in medically significant interactions within human environments.}, }
@article {pmid41955304, year = {2026}, author = {Yang, JC and Situ, J and Troutman, R and Zhu, R and Black, M and Buri, H and Gutta, A and Tian, F and Kang, A and Aja, E and Zeng, A and Lai, RW and Tan, J and Liang, F and Brahim, C and Murphy, G and Ahdoot, A and Peng, C and Jacobs, JP}, title = {A microbiome quantitative trait locus in SLC39A8 modulates disease severity in synucleinopathy-induced models of Parkinson's disease.}, journal = {Human molecular genetics}, volume = {35}, number = {6}, pages = {}, doi = {10.1093/hmg/ddag024}, pmid = {41955304}, issn = {1460-2083}, mesh = {Animals ; Mice ; *Parkinson Disease/genetics/microbiology/pathology ; Humans ; alpha-Synuclein/genetics/metabolism ; Disease Models, Animal ; *Cation Transport Proteins/genetics ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci/genetics ; *Gastrointestinal Microbiome/genetics ; *Synucleinopathies/genetics/microbiology/pathology ; Male ; Dopaminergic Neurons/pathology/metabolism ; Female ; Genetic Predisposition to Disease ; Mice, Transgenic ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor deficits, dopaminergic neuron loss, and α-synuclein (α-syn) aggregation. While rare mutations underlie familial PD, around 85% of cases are idiopathic. Emerging evidence implicates common genetic variants and the gut microbiome in PD risk, but their interaction has not been studied. We previously demonstrated that the PD-protective SLC39A8 variant rs13107325 (human A391T, corresponding to A393T in mouse) is associated with microbial compositional shifts in humans and reshapes the microbiome in SLC39A8 A393T knock-in mice. Here, we test whether this SNP modifies PD phenotypes in two α-synucleinopathy mouse models. In the human α-synuclein overexpression model, A393T carrier mice show reduced motor deficits, consistent with a protective role. However, in the α-synuclein preformed fibril (PFF) injection model, A393T carriers exhibit worsened motor deficits, increased dopaminergic terminal loss, and enhanced α-synuclein pathology spread. SNP- and model-specific microbiome changes correlated with motor outcomes. These included enrichment of Lactobacillus and Lactobacillaceae HT002 genera in A393T carriers with α-synuclein overexpression, and enrichment of Erysipelatoclostridium in PFF-injected A393T carriers. These findings suggest that SLC39A8 A393T-induced microbiome alterations are associated with differential disease outcomes depending on context. Our results are consistent with a model in which susceptibility gene SNPs may influence PD progression via the gut microbiome, though direct causal effects remain to be tested.}, }
@article {pmid41955364, year = {2026}, author = {Jain, S}, title = {Pesticides may wreak havoc on the gut microbiome.}, journal = {Science (New York, N.Y.)}, volume = {392}, number = {6794}, pages = {134-135}, doi = {10.1126/science.aeh8589}, pmid = {41955364}, issn = {1095-9203}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Pesticides/toxicity/adverse effects ; Animals ; }, abstract = {Disruption of complex intestinal ecosystem could contribute to diabetes and other health issues, scientists say.}, }
@article {pmid41955483, year = {2026}, author = {Wang, M and Luo, N and Li, Y and Zhai, H and Xi, J and Li, HB and Zhou, D}, title = {Unlocking the Phyllosphere's Role: Selenium Nanoparticles Reprogram Sulfur Metabolism and Enrich Sphingomonas to Reduce Cadmium in Wheat.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12411}, pmid = {41955483}, issn = {1520-5851}, abstract = {Although selenium nanoparticles (SeNPs) can mitigate cadmium (Cd) accumulation in crops, comparative system-level mechanisms among different SeNPs remain unclear, particularly in wheat. Herein, we compare chemically and biologically synthesized SeNPs (CH/BI-SeNPs) to elucidate Cd detoxification via phyllosphere metabolism-microbiome interactions. Results showed that foliar application of both SeNPs significantly reduced Cd accumulation and mitigated cell membrane damage in wheat. CH-SeNPs exhibited the strongest Cd reduction effect, decreasing grain Cd content by 30.9%. Metabolomic profiling revealed a substantial reorganization of sulfur metabolic pathways under CH-SeNPs treatment, characterized by the accumulation of S-adenosylhomocysteine (SAH), decreased homomethionine, and reduced oxidized glutathione (GSSG), indicating a shift in sulfur flux toward enhanced synthesis of reduced thiol compounds. CH-SeNPs activated the glutathione biosynthesis pathway, significantly increasing the activity of γ-glutamylcysteine synthetase and the contents of cysteine and glutathione, thereby promoting Cd chelation, and reducing its translocation to grains. 16S rRNA sequencing further demonstrated that CH-SeNPs significantly enriched Sphingomonas, a genus involved in sulfur cycling, in the phyllosphere, rhizosphere, and rhizosphere soil, suggesting that microbial interactions facilitated sulfur metabolism and contributed to a systemic reduction in Cd bioavailability. Additionally, HPLC-ICP-MS analysis indicated an increased proportion of selenomethionine in grains under CH-SeNPs treatment, enhancing both nutritional value and food safety. This study reveals that SeNPs alleviate Cd stress in wheat via coordinated regulation involving phyllosphere sulfur metabolism and microbial interactions related to sulfur, providing a mechanistic basis for the application of SeNPs in the remediation of heavy metal contamination and nutritional fortification in agriculture.}, }
@article {pmid41955497, year = {2026}, author = {Zhang, W and Yang, Z and Zhang, Y and Wang, L and Zhang, X and Mao, J and Dai, Y and Yuan, Y and Wang, M and Yang, X and Yu, X and Liu, J and Chen, C}, title = {Multi-Enzyme Mimetic Molybdenum Nitride Nanozymes Reshape Subgingival Microenvironment for Synergistic Periodontitis Therapy via ROS Regulation and Microbiome Remodeling.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17770}, doi = {10.1002/advs.202517770}, pmid = {41955497}, issn = {2198-3844}, support = {2024YFA1210004//National Key Research and Development Program of China/ ; T2422006//National Natural Science Foundation of China/ ; T242200557//National Natural Science Foundation of China/ ; 82201017//National Natural Science Foundation of China/ ; 52422213//National Natural Science Foundation of China/ ; 52272212//National Natural Science Foundation of China/ ; F251001//Beijing Natural Science Foundation/ ; 22388101//Basic Science Center Project of the National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientist Sponsorship Program by CAST/ ; //Hundred-Talent Program of Chinese Academy of Sciences/ ; tsqn202211168//Taishan Scholar Project of Shandong Province/ ; ZR2022JQ20//Natural Science Foundation of Shandong Province/ ; }, abstract = {Periodontitis, a chronic inflammatory disease initiated and sustained by plaque microorganisms and host immune response, remains an intractable oral disease and a leading cause of tooth loss worldwide. Traditional mechanical debridement and adjunctive antibiotic or antiseptic therapy often shows limited efficacy due to the complex anatomical structure, concerns regarding antimicrobial resistance, and poor penetration and retention within the subgingival infection niche. To overcome this limitation, we designed a Mo-N coordinated nanozyme exhibiting synergistic mimetic activities of multiple enzymes, including peroxidase (POD)-like, oxidase (OXD)-like, and catalase (CAT)-like activity. Benefiting from Mo-N coordination and multi-enzyme mimetic behavior, Mo5N6 nanozymes dynamically modulate local oxidative reactions within the gingival sulcus, thereby effectively damaging pathogenic bacteria while avoiding excessive oxidative stress. The nanozymes efficiently suppress anaerobic Gram-negative periodontal pathogens sensitive to elevated reactive oxygen species (ROS), facilitating efficient attenuation of pathogenic stimuli. This strategy not only enhances the periodontal microenvironment but also facilitates the restoration of commensal microbiota and regeneration of periodontal tissues, highlighting the therapeutic potential of Mo5N6 nanozymes in periodontitis treatment.}, }
@article {pmid41955508, year = {2026}, author = {Chatrizeh, M and Tian, J and Rogers, M and Feturi, F and Wu, G and Firek, B and Nikonov, R and Cass, L and Sheppeck, A and Ojha, L and Carroll, A and Henkel, M and Azar, J and Aneja, RK and Campfield, B and Simon, D and Morowitz, MJ}, title = {Plant-based enteral nutrition outperforms ultra-processed formulas in mitigating consequences of antibiotic-induced dysbiosis.}, journal = {JCI insight}, volume = {}, number = {}, pages = {}, doi = {10.1172/jci.insight.199827}, pmid = {41955508}, issn = {2379-3708}, abstract = {Malnutrition, gut inflammation, and antibiotic-induced dysbiosis (AID) are well-recognized risk factors for poor clinical outcomes among critically ill patients. We previously showed that commercially available plant-based enteral nutrition (PBEN) preserves a commensal microbiome compared with commonly used artificial enteral nutrition (AEN). In this study, PBEN was superior to AEN in promoting recovery from antibiotic-induced dysbiosis in mice and humans. PBEN effectively mitigated anemia and leukopenia, restored naïve lymphocyte populations, and reduced bone marrow myeloid expansion. Animals randomized to PBEN also exhibited improved responses to infectious challenges following antibiotic exposure. A pilot clinical study validated these findings, demonstrating increased gut commensals, reduced pathogens, and improved leukocyte balance in critically ill children receiving PBEN compared with AEN. Together, these results suggest that PBEN offers a practical dietary approach to mitigate antibiotic-associated complications and potentially improve clinical outcomes among hospitalized patients requiring supplemental nutrition.}, }
@article {pmid41955569, year = {2026}, author = {Trunfio, M and Gianella, S and Gaitan, N and Porrachia, M and Gomez-Moreno, V and Lapke, B and Navarrete, A and Wells, A and Smith, D and Little, SJ and Chaillon, A}, title = {Minimal Disruption of the Rectal Microbiome in Acute and Early Untreated HIV Infection.}, journal = {Journal of acquired immune deficiency syndromes (1999)}, volume = {}, number = {}, pages = {}, doi = {10.1097/QAI.0000000000003883}, pmid = {41955569}, issn = {1944-7884}, abstract = {BACKGROUND: Alterations in the gut microbiome have been linked to chronic HIV infection, yet less is known about microbiome dynamics during the earliest phases of HIV acquisition. It remains unclear whether microbial changes precede or follow HIV infection, and whether specific taxa could serve as early biomarkers or modulators of disease progression.<br><br>SETTING: The San Diego Primary Infection Resource Consortium (PIRC), a large HIV resource infrastructure program that enrolled predominantly men who have sex with men in Southern California, USA.<br><br>METHODS: We analyzed rectal swabs from 316 participants, 86 without HIV, 100 with acute (&#x2264;30 days post-infection) and 130 with early (31-180 days) untreated HIV infection. 16S rRNA sequencing was used to characterize bacterial communities. Alpha and beta diversity metrics, and taxon-level relative abundance were compared across groups using generalized linear models and MaAsLin3, adjusting for confounders and correcting for false discovery rate (FDR).<br><br>RESULTS: No significant differences in Shannon and Pielou index or beta diversity were observed by HIV status or stage. However, HIV infection was independently associated with a modest reduction in microbial richness (observed species; p=0.039). Enterocloster clostridioformis was significantly depleted among people with HIV (a&#x3b2; -1.31, FDR p<0.001). Among participants with HIV, relative abundance of Akkermansia muciniphila was positively correlated with plasma HIV RNA levels (a&#x3b2; 0.48, FDR p=0.016).<br><br>CONCLUSION: The rectal bacteriome remains largely preserved during the first six months of untreated HIV infection. Subtle taxon-specific changes may reflect early viro-immunological perturbations but suggest limited diagnostic and prognostic utility of microbiome profiling.}, }
@article {pmid41955745, year = {2026}, author = {Etesami, H and Schaller, J}, title = {The soil silicon filter: A conceptual model of how mycorrhizal fungi and their microbiome may govern biosilicification and plant-silicon availability.}, journal = {Plant physiology and biochemistry : PPB}, volume = {233}, number = {}, pages = {111235}, doi = {10.1016/j.plaphy.2026.111235}, pmid = {41955745}, issn = {1873-2690}, abstract = {Silicon (Si) plays an important role in plant health and ecosystem function, yet the biological pathways controlling its cycling are often too simplified and underlying mechanisms are not clear. While the plant-centric model of Si uptake and phytolith formation is mostly used, it underestimates the complex role of the soil microbiome. This review synthesizes growing evidence on the importance of the mycorrhizosphere-the zone of interaction between roots, mycorrhizal fungi, and bacteria-as a central processing unit in the terrestrial Si cycle. We develop and evaluate the concept of a "microbial silicon filter" as a working hypothesis, where symbiotic partnerships, particularly between mycorrhizal fungi and their associated bacteria, may collectively influence the Si flux. We line out the mechanisms of mycorrhizal-mediated Si transport and review evidence for bacterial biosilicification alongside the more speculative evidence and open questions regarding fungal (particularly mycorrhizal) biosilicification. Furthermore, we examine potential synergistic microbial weathering of minerals that mobilizes Si and how biofilm matrices may enhance its retention within the hyphosphere. By integrating these processes, we present a more integrated, microbiome-inclusive model of the Si cycle that emphasizes the potential interdependencies between plants, mycorrhizal fungi, and bacteria. This perspective has profound implications, potentially influencing plant stress resilience modulated by Si supply and suggesting a possible, though not yet quantified, role in enhancing long-term carbon sequestration through phytolith formation. Finally, we outline future research directions to unravel the underlying mechanisms of this partnership of plants, mycorrhizal fungi, and bacteria and to harness it for sustainable agriculture and ecosystem restoration. A central focus of these recommendations is the critical need for advanced methodologies-particularly stable isotope tracing and nanoscale secondary ion mass spectrometry (NanoSIMS)-to move from correlative evidence to quantitative, mechanistic understanding of the microbial Si filter.}, }
@article {pmid41955806, year = {2026}, author = {Lee, EY and Lee, DG and Noh, G and Kwon, S and Shin, H and Shin, Y}, title = {Hierarchical alginate-bentonite beads enable instrument-free pre-analytic enrichment of liter-scale wastewater.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142013}, doi = {10.1016/j.jhazmat.2026.142013}, pmid = {41955806}, issn = {1873-3336}, abstract = {Wastewater-based surveillance (WBS) offers a test-independent window into public community health, but its fidelity depends critically on pre-analytic enrichment that must convert liter-scale, inhibitor-rich influent into microliter analytical inputs without compromising low-titer targets. Here we introduce hierarchical alginate-sulfuric acid-activated bentonite beads (Alg@SAB) that recast pre-analytic enrichment as an interfacial mass-transfer problem. A diffusion-optimized macro-mesoporous scaffold, amine-functionalized surfaces (-NH3[+]), and Ba[2+] crosslinks collectively enable dual-mode capture-electrostatic adsorption and Ba[2+]↔M[n+] cation-exchange-to retain free pathogens and pathogen-metal complexes under passive, pump-free operation, while batch-friendly fabrication from commodity precursors delivers reproducibility with per-test consumables of ∼US$0.06. Alg@SAB retains the two-fold-one-cycle linearity in input viral titer-Ct value while extending instrument-free concentration to the liter scale: 1 L inputs remain measurable where a vacuum-membrane kit fails at ≥ 500 mL; at 100 mL Alg@SAB achieves higher apparent recovery (56%, +27% versus kit). Validation used real municipal wastewater rather than synthetic surrogates, ensuring field realism in matrix complexity and inhibitor profiles. A single-tube, pH-dependent reversible crosslinking chemistry releases nucleic acids in situ while maintaining agreement and collapsing handoffs, enabling low-hardware deployment. Method-dependent microbiome profiling on these raw influent wastewater reveals mechanistically consistent selectivity without systematic inflation of alpha diversity, preserving ecological interpretability under real wastewater plant conditions. By integrating scalable materials engineering with practical deployment, Alg@SAB provides a simple and tunable route to decentralized, interpretable WBS, lowering technical barriers for real-time pathogen monitoring in diverse settings.}, }
@article {pmid41955863, year = {2026}, author = {Temiz, A and Tascilar, K}, title = {Why we need to maintain a critical view on big data and artificial intelligence predictions.}, journal = {Current opinion in immunology}, volume = {100}, number = {}, pages = {102776}, doi = {10.1016/j.coi.2026.102776}, pmid = {41955863}, issn = {1879-0372}, abstract = {Artificial intelligence (AI) and machine learning are widely promoted as transformative tools for medical practice, yet their impact in daily rheumatology remains limited. This review examines the gap between expectations and reality using historical parallels, conceptual considerations, and recent methodological evidence. Experiences with antioxidant supplementation, vitamin D, the microbiome, and the Human Genome Project illustrate a recurring pattern: early studies report large effects that diminish or disappear in larger, higher-quality studies. Meta-epidemiological work and the 'cursed auction' analogy explain why early and small studies systematically overestimate effects. Conceptually, individualized clinical risk remains a group-based construct, constrained by the reference class problem and irreducible uncertainty. Methodologically, many AI models in rheumatology suffer from small and heterogeneous datasets, overfitting, inadequate handling of missing data, poor calibration, and limited external or prospective validation. The failure of COVID-19 prediction models and the neutral trial of the Ada diagnostic assistant in rheumatology illustrate how strong retrospective performance often collapses in real-world use. In contrast, AI performs well in high signal-to-noise domains with abundant, structured data. Overall, AI can generate valuable insights and support narrowly defined tasks, but it cannot yet overcome the fundamental limits of noisy clinical data and group-based risk. Progress in rheumatology will require realistic expectations, large representative datasets, transparent methods, rigorous validation, and a focus on robust, interpretable tools that improve decisions for populations and well-defined patient subgroups rather than precise individual prediction.}, }
@article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.<br><br>METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.<br><br>RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.<br><br>CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, }
@article {pmid41955946, year = {2026}, author = {Jiang, S and Li, T and Lu, J and Cai, F and Pang, G and Liu, J and Liu, D and Shen, Q}, title = {From degradation to alleviation: Trichoderma facilitates plants resisting the PBAT stress through secreting a cutinase-like enzyme.}, journal = {Environment international}, volume = {210}, number = {}, pages = {110228}, doi = {10.1016/j.envint.2026.110228}, pmid = {41955946}, issn = {1873-6750}, abstract = {The ecological impacts of biodegradable plastics like poly (butylene adipate-co-terephthalate) (PBAT) demand urgent investigation due to their unresolved risks to soil-plant systems, including physical interference with root development, disruption of indigenous microbial ecology. While PBAT depolymerization is a prerequisite for its removal, the slow and inefficient breakdown of these polymers in soil often results in the persistent accumulation of phytotoxic monomers, creating a bottleneck for biological remediation. In this study, through transcriptomic and phylogenetic analyses, we identified a key secreted hydrolase CUT2, belonging to a distinct clade of cutinase-like polyester hydrolases. Overexpression of cut2 (OEThcut2) significantly enhanced PBAT depolymerization, resulting in 27.0% and 22.4% increases in the release of terephthalic acid (TPA) and butanediolic acid (BTA) compared to the wild-type strain, respectively. The direct catalytic activity of purified CUT2 was confirmed through vitro film weight-loss assays with a degradation rate of 4.3% observed. In pot experiments, integrated multi-omics analysis revealed that the OEThcut2 strain reconfigured the rhizosphere microbial community and activated the aromatic degradation pathways, coinciding with the attenuated accumulation of degradation monomers. Furthermore, the enrichment of carbohydrate-active enzymes (CAZys) and the reduction of monomer burdens which revitalized the tricarboxylic acid cycle (TCA) and normalized redox homeostasis thereby clearing the metabolic bottleneck for intermediate turnover. Complementary monomer-exposure assays established that the reduction of PBAT monomers is critical for alleviating plant oxidative stress and growth inhibition. These findings provide a depolymerization to detoxification framework that links fungal enzymatic activity to rhizosphere metabolic recovery, offering a robust strategy for mitigating biodegradable plastic toxicity in agroecosystem.}, }
@article {pmid41956062, year = {2026}, author = {Flury, JD and Schwartz, DJ}, title = {Don't keep this endopeptidase on the DL.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {4}, pages = {551-553}, doi = {10.1016/j.chom.2026.03.007}, pmid = {41956062}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant, Premature ; *Sepsis/microbiology/prevention &amp; control ; Infant, Newborn ; *Nod2 Signaling Adaptor Protein/metabolism/genetics ; *Endopeptidases/metabolism ; *Bacteria/enzymology ; }, abstract = {Gut-derived bacterial DL-endopeptidase may confer protection from late onset sepsis (LOS) in preterm infants. In this issue of Cell Host &amp; Microbe, Shen et al. identified delayed gut microbiome development in preterm infants as a risk factor for LOS and proposed a protective regulatory response by NOD2.}, }
@article {pmid41956066, year = {2026}, author = {Potiron, A and Francken, JC and El Aidy, S}, title = {Rethinking microbiome health through functional dynamics.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {4}, pages = {562-566}, doi = {10.1016/j.chom.2026.03.005}, pmid = {41956066}, issn = {1934-6069}, mesh = {Humans ; *Microbiota/physiology ; *Host Microbial Interactions/physiology ; *Gastrointestinal Microbiome ; Health ; }, abstract = {Translation in microbiome science is limited by static concepts of health that obscure dynamic host-microbe processes. We propose adaptive coherence: the capacity of host-microbiome systems to sustain integrated function through reorganization. This reframes health as emergent and relational, directing measurement toward system adaptability, functional integrity, and network interactions.}, }
@article {pmid41956067, year = {2026}, author = {Dillen, J and Dricot, CEMK and Croatti, V and Lebeer, S}, title = {The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {4}, pages = {567-587}, doi = {10.1016/j.chom.2026.03.015}, pmid = {41956067}, issn = {1934-6069}, mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology ; Probiotics/therapeutic use ; *Urogenital System/microbiology ; Host Microbial Interactions ; }, abstract = {Microbiome-based interventions for female urogenital health have gained attention, particularly in strategies aimed at restoring lactobacilli dominance to reduce infection and improve reproductive outcomes. These approaches include defined probiotic strains, engineered microbial consortia, and vaginal microbiota transfer. Observational studies have provided ecological insights into the composition and dynamics of the vaginal microbiome; its associations with infections, inflammation, and reproductive complications; and its interplay with urinary and mucosal niches. These data establish a correlative framework linking microbial community structure to health and disease. However, the efficacy of current interventions remains constrained by an incomplete mechanistic understanding of host-microbiome and microbe-microbe interactions. Recent discoveries highlight the role of vaginally derived microbial molecules in modulating host immune responses, stabilizing microbial communities, and influencing disease outcomes. These mechanistic insights provide a basis for the rational design of microbiome-based therapies. This review synthesizes clinical, observational, and mechanistic evidence and outlines research priorities for translation into clinical practice.}, }
@article {pmid41956093, year = {2026}, author = {Cao, Z and Zuo, W and Wang, L and Dai, L}, title = {Spatial mapping of microbial communities by an integrated automation platform of sequential FISH.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101381}, doi = {10.1016/j.crmeth.2026.101381}, pmid = {41956093}, issn = {2667-2375}, abstract = {Spatial mapping of microbial communities at single-cell resolution is opening up dimensions to understand microbiome organization and function. However, current fluorescence in situ hybridization (FISH) methods for microbiomes are limited by multiplexity and scalability. Here, we present the sequential error-robust FISH spatial mapping platform (SEER-Map) for fully automated imaging of complex microbial communities. We show that an integrated platform of fluidics control and fluorescence microscopy can perform 40 rounds of sequential FISH. We apply SEER-Map to profile complex microbial communities colonized on plant roots and identify distinct spatial patterns and species co-occurrence at the micron-scale. Our work establishes SEER-Map as a high-throughput and scalable platform for high-resolution spatial profiling of microbiomes.}, }
@article {pmid41956108, year = {2026}, author = {Kadandelu, M and Periya, S and Rekha, PD and Raghu, SV}, title = {Gut-brain axis mediated therapeutic intervention to mitigate the epileptogenesis: insights from Drosophila melanogaster.}, journal = {Reviews in the neurosciences}, volume = {}, number = {}, pages = {}, pmid = {41956108}, issn = {2191-0200}, abstract = {Drug-resistant epilepsy (DRE) is a prominent concern in the management of recurrent seizures. Anti-seizure medications (ASM), surgical intervention, and neurostimulation are a few classical remedial measures of epilepsy. Nevertheless, DRE requires immense investigation, a comprehensive understanding of holistic management, and additional therapeutic effects. Dysbiosis, an imbalance of the gut microbiome, is the foremost concern associated with various neurological disorders. In epilepsy, the gut microbiome plays a pivotal role in its pathophysiology, unveiling new avenues for microbiome-mediated strategies to treat epileptic patients. Furthermore, the differential gut microbial composition in epileptic patients serves as a cornerstone for advanced research to delineate the influence of each bacterial species on epilepsy. Drosophila melanogaster, a simple model organism with an evolutionarily conserved gut microbiome composition, can be efficiently deployed to scrutinize the role of discrete microbes and their influence on the gut-brain axis, impacting neurological disorders. In this review, the role of distinct bacterial species in influencing epileptic conditions and how model organisms like Drosophila can be employed to explore this realm are deliberated as a comprehensive overview.}, }
@article {pmid41956336, year = {2026}, author = {Huang, S and Ou, Y and Zhuang, W and Huang, J and Wang, B and Li, Z and Huang, H}, title = {Mapping the immune landscape of PCa: From tumor microenvironment to therapeutics.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {}, number = {}, pages = {189586}, doi = {10.1016/j.bbcan.2026.189586}, pmid = {41956336}, issn = {1879-2561}, abstract = {Prostate cancer (PCa) remains a leading cause of cancer-related mortality in men, yet its response to immunotherapy is notably limited compared to other solid tumors. This resistance stems primarily from a highly immunosuppressive tumor microenvironment (TME), characterized by "cold" tumor features such as low mutational burden, scarce cytotoxic T cell infiltration and extensive regulatory cell populations. Building upon the "tumor ecosystem" concept, we integrate emerging insights from single-cell and spatial transcriptomics to decode the spatiotemporal heterogeneity of the PCa ecosystem. We specifically highlight the underappreciated "neural-immune-microbiome" axis-a triangular regulatory network wherein sympathetic nerves suppress T cell motility, intratumoral microbiota drive chronic inflammation, and metabolic reprogramming creates lipid-mediated immune paralysis. We further dissect how cell-type specific remodeling mechanisms, particularly TREM2+ macrophage-mediated metabolic symbiosis, drive the transition from hormone-sensitive to castration-resistant disease. Furthermore, we critically assess how standard of care (ADT, chemotherapy, radiotherapy) and emerging agents (PARPi, HDACi) reprogram the immune landscape with time-dependent, often paradoxical effects. Finally, we propose a roadmap for precision oncology, emphasizing that future success lies in "ecological editing"-biomarker-driven patient stratification and rational combination strategies to overcome the physical and biological barriers of the TME.}, }
@article {pmid41956379, year = {2026}, author = {Wang, Y and Zhang, S and Cai, J and Shao, R and Zheng, F and Wang, Y and Xu, C and Yang, Y and Li, L}, title = {Reducing cadmium bioavailability in soil by micronutrient sulfates: Insights from duodenal transporter expression and intestinal microbiota in a mouse model.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124460}, doi = {10.1016/j.envres.2026.124460}, pmid = {41956379}, issn = {1096-0953}, abstract = {Micronutrient amendments have the potential to mitigate cadmium (Cd) accumulation in crops; however, their effects on soil Cd bioavailability remain unclear. To address this knowledge gap, mice were fed a diet containing 10% (w/w) amended Cd-contaminated calcareous soil (amendments: MnSO4, ZnSO4, FeSO4, or Na2SO4) for 15 days. Cd bioavailability was then assessed by measuring Cd accumulation in the kidney and liver (primary endpoints), duodenal transporter expression, fecal microbiota composition, and soil properties. The results demonstrated that all micronutrient sulfate treatments increased the acid-extractable fraction of Cd in soil. Concurrently, soil-available Mn and Zn increased by 94.79% and 89.31%, respectively, following their corresponding sulfate amendments, and available sulfur rose by 0.90- to 21.32-fold across all treatments. Compared with the control, Cd concentrations in the kidney and liver of mice treated with Mn, Zn, Fe, or Na sulfates significantly decreased by 25.95-35.36% and 20.75-35.30%, respectively, and Cd relative bioavailability (Cd-RBA) declined by 27.02-34.13% (p < 0.05). Significant negative correlations were observed between Cd-RBA and molar ratios of nMn/nCd, nFe/nCd, and nZn/nCd in the soil and mouse tissues. Further analyses identified a three-part protective mechanism: (1) Intestinal antagonism: downregulation of duodenal ZIP8 expression by Mn, Zn, and Fe treatments (by 66.49-88.30%), thereby limiting Cd uptake; (2) Microbiome restoration: significant reduction of the Firmicutes/Bacteroidota (F/B) ratio compared with the control group, with reductions of 6.02% (Mn), 15.53% (Zn), 51.11% (Fe), and 17.75% (Na); (3) Enterohepatic elimination: enhanced formation of Cd-S complexes and the resulting increase in fecal Cd excretion across all treatments (by 41.03-60.77%). In conclusion, micronutrient sulfate amendments mitigate Cd bioavailability through a concerted mechanism, involving soil chemical modification, luminal complexation, physiological antagonism, modulation of transporter gene expression, and microbiome-mediated enteric elimination.}, }
@article {pmid41956455, year = {2026}, author = {Ozduran, E and Gezmen-Karadag, M}, title = {Dietary Fiber in Sport: Implications for Performance and Body Composition Optimization.}, journal = {International journal of sport nutrition and exercise metabolism}, volume = {}, number = {}, pages = {1-13}, doi = {10.1123/ijsnem.2025-0170}, pmid = {41956455}, issn = {1543-2742}, abstract = {Although dietary fiber is widely recognized for its health benefits in the general population, including reduced risk of cardiovascular disease and improved metabolic regulation, its role in athletic performance and recovery remains comparatively underexplored. Current sports nutrition guidelines lack specific recommendations for fiber intake, despite evidence linking adequate consumption to gut microbiome stability, immune modulation, and body composition optimization. Athletes face unique physiological demands that influence gastrointestinal tolerance, nutrient absorption, and energy availability, particularly under high training loads. Although excessive fiber intake may lead to gastrointestinal discomfort or reduced caloric intake, moderate and periodized consumption has been associated with enhanced immune function, improved energy metabolism, and preservation of skeletal muscle mass. Recent findings suggest potential benefits in attenuating exercise-induced inflammation and regulating substrate utilization. Nevertheless, observational data indicate that many athletes fail to meet general population intake targets, often due to precompetition dietary restrictions or concerns about digestive comfort. This review critically synthesizes current evidence on the physiological impacts of dietary fiber in athletic populations, focusing on gastrointestinal health, immune function, body composition, and performance outcomes. It further outlines practical, evidence-based strategies to optimize intake according to individual needs and sport-specific demands, including fiber periodization, source selection, and gradual adaptation.}, }
@article {pmid41956649, year = {2026}, author = {Yan, Z and Song, F and Zhao, J and Zhang, M and Guan, J and Li, C and Li, D and Tian, H}, title = {Association between microbiome dynamics and aroma evolution in fermented Chinese white pears (Pyrus × bretschneideri): An integrated volatilomics and microbiome analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 2}, pages = {118959}, doi = {10.1016/j.foodres.2026.118959}, pmid = {41956649}, issn = {1873-7145}, mesh = {*Odorants/analysis ; *Fermentation ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Pyrus/microbiology/chemistry ; Saccharomyces cerevisiae/metabolism ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; Butylene Glycols/analysis ; *Fruit/microbiology/chemistry ; Bacteria/classification/metabolism ; }, abstract = {The flavor of pear cider exhibits regional features, with insufficient and unstable aroma constituting key quality issues. The role of its characteristic aroma and the contribution of native microorganisms to regional distinctiveness remain under explored. This study compared the brewing characteristics of representative white pears, conducted an in-depth analysis of aroma compound evolution and their relationship with microbial communities throughout fermentation, and successfully screened strains with aroma-enhancing function. Results indicated that "Xuehua" possessed the optimal processing quality. Six characteristic fermentation aroma were identified, including 2,3-butanediol, hexanal, ethyl caprylate, etc. The core microbes gradually converged, including Saccharomyces cerevisiae, Hanseniaspora, Leuconostoc, etc. Alcohol and total acid correlated strongly with fungi, while reducing sugars correlated strongly with bacteria. Except for hexanal, the characteristic aroma showed positive correlations with F:OTU235. Ethyl caproate and ethyl caprylate correlated positively with B:OTU118. Saccharomyces cerevisiae (F:OTU235) and Lactobacillus plantarum (B:OTU118) were screened selectively and contributed to aroma accumulation.}, }
@article {pmid41956809, year = {2026}, author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J}, title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336025}, pmid = {41956809}, issn = {1468-3288}, abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.<br><br>OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.<br><br>DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.<br><br>RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice&#x2009;and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice&#x2009;and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.<br><br>CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.}, }
@article {pmid41956875, year = {2026}, author = {Ye, M and Song, C}, title = {Microbiome eavesdropping: root-knot nematodes decode rhizosphere volatile dialogues.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2026.03.007}, pmid = {41956875}, issn = {1878-4372}, abstract = {Root-knot nematodes navigate the underground chemical landscape to find their hosts. Building on Wu et al.'s discovery that plant metabolites shape microbial cues guiding nematode behavior, this commentary explores how rhizosphere chemical communication integrates plant, microbial, and parasite interactions within a shared 'information network'.}, }
@article {pmid41957048, year = {2026}, author = {Wang, X and Song, Y and Zhao, W and Liu, Y and Fu, Y and Zhang, Y and Zhao, Q and Miao, M and Zhao, W and Wang, X and Li, Z}, title = {Cinnamaldehyde mitigates MASLD through SIRT1/FOXO1-induced autophagy and synergistic gut microbiota modulation.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00815-6}, pmid = {41957048}, issn = {2396-8370}, support = {ZYYZDXK-2023005//National Administration of Traditional Chinese Medicine Key Discipline Construction Project of High-Level TCM/ ; 82304831//National Natural Science Foundation of China/ ; 242300421090//Henan Science Fund for Excellent Young Scholars/ ; 2023TQ0109, GZB20230196//China Postdoctoral Science Foundation/ ; 232301420077//Associates Fund of Henan Province science and technology research and development program/ ; 2025HYTP092//Young Talent Support Program of Henan Association for Science and Technology/ ; NA (2024)//Central Plains Science and Technology Innovation Young Top Talent Project/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a global health burden with limited therapeutic options. Cinnamomum cassia, a medicinal-food homologous plant, contains principal bioactive cinnamaldehyde (CA), whose anti-MASLD mechanisms require clarification. ‌This study employed both a high-fat diet (HFD)-induced MASLD model and a free fatty acid (FFA)-stimulated cell model. CA administration attenuated intracellular lipid accumulation in vitro and ameliorated both hepatic steatosis and systemic hyperlipidemia in vivo, while inhibiting hepatic lipid peroxidation. Mechanistically, integrated RNA-seq, network pharmacology, siRNA, immunofluorescence, and transmission electron microscopy analyses identified the SIRT1/FOXO1-autophagy axis as CA's key regulatory pathway. Gut microbiome profiling revealed CA's capacity to ameliorate HFD-induced dysbiosis, particularly enriching Lachnospiraceae_NK4A136. Fecal microbiota transplantation (FMT) and Spearman correlations link serum lipids and hepatic injury factors to gut microbiota, indicating partially microbiota-mediated metabolic modulation by CA. Collectively, CA ameliorates MASLD through coordinated autophagy enhancement and microbial homeostasis restoration, holding promise as a functional food ingredient for ‌metabolic liver disease prevention.}, }
@article {pmid41957179, year = {2026}, author = {Li, X and Zhao, K and Chen, J and Ni, Z and Li, L and Chen, Y and Shi, W and Zhang, Y and Gao, X and Wang, C and Gu, L and Dong, Y and Shi, J and Liu, Y and Su, L and Xue, YX and Sun, H}, title = {The Cognitive benefits of nitrate in patients with alcohol use disorder: unraveling the oral microbiome ectopic colonization pathway.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {41957179}, issn = {1476-5578}, support = {81971235//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82071498//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82471514//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Our prior research revealed that dietary nitrate (NO3[-]) may mitigate alcohol-induced cognitive impairment through oral microbiota modulation and attenuation of inflammatory responses in mice. While alcohol use disorder (AUD) is known to associate with cognitive decline and gut dysbiosis, the therapeutic potential of nitrate supplementation in ameliorating these effects remains to be elucidated. In this randomized, double-blind, placebo-controlled pilot trial (NCT05963659), 70 AUD patients received either nitrate-rich beetroot juice or placebo for 14 days. Primary outcomes were spatial memory measured by Cambridge Neuropsychological Test Battery. Oral and gut microbiota were analyzed before and after intervention by 16S rRNA sequencing. To establish causality, germ-free (GF) mice were colonized with pre- and post-nitrate intervention saliva samples from AUD patients, followed by microbiota profiling across gastrointestinal regions. The mean difference in Delayed Matching to Sample (all delays) change between the nitrate consumption group and the placebo group after intervention was 9.784 (95%[CI], 1.85-17.72, P = 0.016), as analyzed using a generalized linear mixed model. Nitrate supplementation induced distinct shifts in oral microbiota, while gut microbiota exhibited less pronounced changes. GF mice receiving pre-intervention microbiota exhibited elevated Klebsiella abundance throughout the gut. Mechanistically, nitrate attenuated systemic inflammation, enhanced intestinal barrier integrity, and improved cognitive performance in mice. Dietary nitrate enhances cognitive function in AUD patients, partially mediated by ectopic colonization of oral microbiota. Our findings identify specific oral bacteria (e.g., Klebsiella) as key contributors to alcohol-induced cognitive impairment and suggest promising therapeutic potential for microbiota-targeted interventions in AUD.}, }
@article {pmid41957208, year = {2026}, author = {Metz, BN and Gallagher, P and Profet, P and Raymann, K and Tarpy, DR}, title = {Impact of Two Common Beekeeper-Applied Chemicals on Honey Bee Queen Fecundity and Gut Microbial Communities.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02755-w}, pmid = {41957208}, issn = {1432-184X}, support = {2022-67013-42296//National Institute of Food and Agriculture/ ; 2022-67013-42296//National Institute of Food and Agriculture/ ; }, }
@article {pmid41957267, year = {2026}, author = {Baruch, EN and Ajami, NJ and Wargo, JA}, title = {Cultivating the microbiome to enhance cancer immunotherapy.}, journal = {Nature reviews. Clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {41957267}, issn = {1759-4782}, }
@article {pmid41957274, year = {2026}, author = {Kotsiliti, E}, title = {Diet-microbiome associations.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {41957274}, issn = {1759-5053}, }
@article {pmid41957291, year = {2026}, author = {Yang, M and Fang, J and Liao, Q}, title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {41957291}, issn = {1434-9949}, }
@article {pmid41957416, year = {2026}, author = {Hunter, AK and Adair, K and Horgan, A and Jordan, J and Stadler, DD and Bohannan, BJM}, title = {Impact of dietary protein quantity on the non-dysbiotic human microbiome: a controlled feeding study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46663-y}, pmid = {41957416}, issn = {2045-2322}, }
@article {pmid41957526, year = {2026}, author = {Siow, TY and Wong, AM and Fang, JT and Chiu, CH and Yeh, YM and Cheng, ML and Lo, CJ and Lin, SN and Lin, CP and Toh, CH}, title = {Plasma acetic acid mediates the relationship between gut microbiome and various health measures in older adults.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01566-x}, pmid = {41957526}, issn = {2730-664X}, support = {CORPG3J0371//Chang Gung Memorial Hospital (CGMH)/ ; XMRPG3L102//Chang Gung Memorial Hospital (CGMH)/ ; }, abstract = {BACKGROUND: Short-chain fatty acids are believed to mediate microbiome-host interactions. Acetic acid is the most abundant systemic short-chain fatty acid, but knowledge about its physiological functions comes mainly from rodent experiments, with limited human research particularly in the aging population.<br><br>METHODS: In this cross-sectional observational study, we examined the association between the gut microbiota and plasma acetic acid, specifically investigating the mediating effect of plasma acetic acid on the relationship between the gut microbiota and blood lipid profile, body composition, brain gray matter volume, and cognitive performance in older adults. The gut microbiome was profiled using full-length 16S rRNA gene sequencing to enable taxonomic classification.<br><br>RESULTS: Here we show that specific gut microbial co-abundance group is associated with plasma acetic acid levels. Higher plasma levels of acetic acid are associated with lower plasma triglyceride levels, higher high-density lipoprotein cholesterol levels, lower body mass index, lower body fat mass, higher thalamic volume, and higher cognitive performance in certain domains. Additionally, we show that plasma acetic acid mediates the relationship between gut microbiome on these health measures.<br><br>CONCLUSIONS: This study identifies gut microbial group linked to plasma acetic acid and demonstrates its potential mediating role between the gut microbiome, blood lipid profile, brain volume and cognitive function in older adults. These insights pave the way for future research and highlight the potential of acetic acid as an intervention target for metabolic and neurological diseases, contributing to strategies that promote healthy aging.}, }
@article {pmid41957655, year = {2026}, author = {Sampath, V and Lee, K and Kim, M and Kim, YS and Min, DH and Han, K and Cho, S and Kang, DK and Kim, IH}, title = {Response of gut microbiome and metabolomic profiles to POLYCAN, a β-glucan derived from Aureobasidium pullulans SM-2001 in beagles.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41957655}, issn = {1674-9782}, abstract = {BACKGROUND: The importance of glucan additives has been widely recognized in farm animals. Yet the precise role of POLYCAN, a β-glucan derived from the black yeast Aureobasidium pullulans SM-2001, remains limited in companion animals. Therefore, this study aims to evaluate its effect on performance, nutrient digestibility, hematology, and the gut microbiome and serum metabolites in beagle dogs.<br><br>METHODS: Eight healthy male beagle dogs (8&#xa0;months old; 10.70&#x2009;&#xb1;&#x2009;1.79&#xa0;kg body weight; 3.00&#x2009;&#xb1;&#x2009;0.15 body condition score) were enrolled in a 10-week study comprising two phases: Phase 1 (weeks 0-4) and Phase 2 (weeks 6-10), separated by a 2-week washout period. The dogs were divided into two groups and fed a control (CON), basal diet and CON diet supplemented with 1,000&#xa0;mg/d of POLYCAN. Each of two diets were provided using a cross over design for eight weeks, with four beagles assigned to each treatment. During the washout period, all dogs were fed only the commercial basal diet.<br><br>RESULTS: Throughout the experimental period, POLYCAN supplementation did not affect growth performance, nutrient digestibility, or fecal pH in beagles. However, serum calcium, insulin-like growth factor-1 (IGF-1), growth hormone, and immunoglobulin G (IgG) concentrations were significantly higher (P&#x2009;<&#x2009;0.05) in the POLYCAN-supplemented group. Alpha-diversity indices of microbial richness and evenness, as well as beta-diversity based on Bray-Curtis dissimilarity and unweighted UniFrac distances, showed no significant differences between treatment group. At the phylum level, Actinobacteria and Proteobacteria were more abundant in the POLYCAN group, followed by Fusobacteria and Bacteroidota. At family level, Lachnospiraceae, Ruminococcaceae, Coriobacteriaceae, Lactobacillaceae, Peptostreptococcaceae, and Erysipelotrichaceae exhibited higher relative abundances. Furthermore, the core gut microbiota at genus level was dominated by Micrococcus and Fusobacterium. Untargeted metabolomic analysis also revealed distinct group separation, identifying key metabolites including lumichrome, D-mannitol, and 2'-deoxycytidine. Pathway enrichment analysis indicated alterations in pyrimidine, histidine, and bile acid metabolism with higher metabolite abundance observed in the POLYCAN-treated group.<br><br>CONCLUSION: Overall, our findings validate that adding 1,000&#xa0;mg/d POLYCAN to canines' diet could serve as a functional nutraceutical to enhance their immune and gut health without affecting growth and digestion.}, }
@article {pmid41765966, year = {2026}, author = {Kroon, MAGM and Wortelboer, K and Davids, M and Swart, EL and van Tellingen, O and Nieuwdorp, M and D'Haens, GRAM and van Laarhoven, HWM and de Boer, NKH and Kemper, EM}, title = {Effect of curcumin on the gut microbiota of patients with ulcerative colitis, Crohn's disease and healthy participants.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41765966}, issn = {2045-2322}, abstract = {UNLABELLED: Curcumin exhibits anti-inflammatory properties, but clinical evidence is limited, in part because of its low systemic bioavailability. Nevertheless, its limited absorption may favor local activity in the gut, where it could influence inflammatory bowel disease via microbiota modulation. This study assesses the impact of curcumin on gut microbiota diversity, as well as clinical and biochemical parameters in patients with ulcerative colitis, and Crohn’s disease in remission and healthy individuals. In a single-center, open-label, single-arm study, 29 male participants aged 18–65 were included. Participants received 3 g of curcumin twice daily for 8 weeks. Blood, urine, and fecal samples were collected at baseline, 4 weeks, and 8 weeks. Clinical and biochemical parameters, along with curcumin plasma, urine, and fecal concentrations, were assessed. Microbiome diversity was analysed using 16 S rRNA amplicon sequencing. The study was registered in the Dutch Clinical Trial Register with ID NL8770. Twenty-nine participants completed the study. Curcumin was well tolerated with stable clinical scores (SSCAI ≤ 2, HBI ≤ 5). Plasma levels were near the lower limit of quantification, while fecal levels were markedly higher. No significant changes in alpha-diversity were found. A temporary shift in beta-diversity appeared at 4 weeks but reversed by week 8. Curcumin caused only transient microbiota changes and slight alterations in taxa abundance, suggesting limited potential for sustained microbiota modulation in IBD management. Clinical trial registration: The study was registered in the Dutch Clinical Trial Register with ID NL8770.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42095-w.}, }
@article {pmid41943414, year = {2026}, author = {Yan, D and Zuo, P and Lin, M and Li, S}, title = {The Changes of Microbiome Attached on Clear Aligners after Drinking Coca-Cola.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {109-118}, pmid = {41943414}, issn = {2544-4646}, mesh = {Humans ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Male ; Adult ; *Carbonated Beverages/microbiology ; }, abstract = {This study aimed to investigate the changes in the microbiome on the inner surface of clear aligners following the consumption of Coca-Cola. The pH value and bacterial composition on the inner surface of clear aligners were assessed over five wearing cycles in three groups of subjects: those with a normal diet (Group A), those who drank Coca-Cola while wearing the aligners (Group C), and those who drank Coca-Cola after removing the aligners (Group B). Microbial analysis was performed using 16S rRNA gene sequencing and operational taxonomic unit (OTU) abundance profiling. The pH of the fluid inside the aligners significantly decreased immediately after Coca-Cola consumption (0 hour) in Groups B and C (p < 0.05). Group B exhibited the most pronounced decline in pH and alpha diversity at 12 hours, along with the highest beta diversity among the groups (p < 0.05). In Group A, the relative abundances of the phylum Actinobacteria was highest at 0 hour, Bacteroidetes at 12 hours, and class Actinobacteria, Gammaproteobacteria, and species Haemophilus influenzae peaked at 24 hours; conversely, Neisseria subflava showed the lowest abundance compared to Groups B and C (p < 0.05). Compared to Group C, Group B demonstrated higher levels of phylum Fusobacteria at 4 hours and 12 hours, and lower Actinobacteria abundance at 8 hours (p < 0.05). Consumption of Coca-Cola induces unfavorable changes in the microbiome on the inner surface of clear aligners. Notably, drinking Coca-Cola without wearing the aligners resulted in a lower pH and greater microbial imbalance, especially at 12 hours post-consumption.}, }
@article {pmid41943415, year = {2026}, author = {Zhou, B and Liu, J and Li, L and Yu, J and Sun, X and Wang, J and Shang, S}, title = {Comparative Analysis of Rhizosphere Bacteria of Phragmites australis and Suaeda salsa (L.) Pall. on Chenier Islands.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {55-74}, pmid = {41943415}, issn = {2544-4646}, mesh = {*Rhizosphere ; *Chenopodiaceae/microbiology ; *Poaceae/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; Microbiota ; Phylogeny ; Islands ; }, abstract = {The Chenier Islands are depositional areas within intertidal zones, characterized by unique soil textures and distinctive environmental conditions that shape specific vegetation distribution patterns. However, the adaptive mechanisms of Phragmites australis (common reed) and Suaeda salsa (L.) Pall. (common seepweed) two prevalent plant species in this region-in saline stress environments, as well as the composition and functional characteristics of their rhizosphere bacterial communities, remain largely unclear. In this study, rhizosphere soil samples were collected from common reed and common seepweed. DNA was extracted and subjected to high-throughput sequencing to analyze the composition and predictive functional profiles of the rhizosphere microbial communities. The results indicated that no significant differences were observed in the alpha diversity indices (Chao1, ACE, Simpson, and Shannon), indicating similar microbial species richness and evenness in the rhizospheres of common reed and common seepweed. Taxonomic analysis at the phylum level showed that the dominant bacterial phyla shared by both plants were Proteobacteria, Bacteroidota, Chloroflexota, and Actinomycetota. Notably, Acidobacteriota and Cyanobacteria were uniquely enriched in the common reed and common seepweed rhizospheres, respectively. At the genus level, the microbial communities of both plants were largely composed of unclassified taxa and minor groups, with Zeaxanthinibacter being the only cultivable dominant genus identified. Principal Coordinates Analysis (PCoA) explained 75.02% of the total β-diversity variance, and the clear separation of samples along the first coordinate axis revealed visually distinct community structures between the two plants. PERMANOVA further confirmed that plant species significantly influenced microbial community assembly, with a moderate explanatory strength (R[2] = 0.205, p = 0.008). Integrated results from LEfSe, PICRUSt2, and FAPROTAX analyses demonstrated that common seepweed rhizospheres were enriched with 19 photosynthesis-related biomarkers, suggesting a stronger photoautotrophic potential compared to common reed. In contrast, the common reed rhizosphere retained only two oligotrophic degraders Acidobacteriota and Chloroflexota. Although PICRUSt2 predictions indicated high overlap in core metabolic pathways between the two plants, FAPROTAX profiling revealed markedly divergent energy-acquisition strategies. Specifically, the common seepweed microbiome exhibited a "photoautotrophy nitrogen fixation" coupling strategy, whereas common reed relied predominantly on a "chemoheterotrophy nitrate reduction" pathway, reflecting niche partitioning in the saline environment. It should be noted that functional predictions derived from PICRUSt2 and FAPROTAX are computational inferences rather than empirical measurements, and thus mechanistic interpretations should be treated with caution. This study identifies a rhizosphere bacterial community assembly pattern characterized by "structural differentiation but functional convergence" offering valuable insights into microbial-mediated plant adaptation to saline stress.}, }
@article {pmid41943876, year = {2026}, author = {Šunić, I and Šarac, J and Havaš Auguštin, D and Pozdniakova, S and Ferguson, RMW and Jergović, M and Visentin, D and Borràs, S and Archer, E and Henderson, DK and Vitko, S and Ašić, A and Bošnjaković, A and Maglica, &#x17d; and Viegas, C and Novokmet, N and Karlović, N and Marjanović, D and Muszyński, A and Liu, Y and Karisola, P and Alenius, H and Krych, L and Lovrić, M}, title = {The Indoor Microbiome: Sampling, Analysis and Emerging Trends.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70272}, pmid = {41943876}, issn = {1758-2229}, support = {101057497//European Union's Horizon Europe research and innovation programme/ ; 101057779//European Union's Horizon Europe research and innovation programme/ ; 101056883//the European Union/ ; 22.00324//Swiss State Secretariat for Education, Research and Innovation/ ; 10040524//United Kingdom Research and Innovation/ ; APP2017786//Australian National Health and Medical Research Council/ ; APP2008813//Australian National Health and Medical Research Council/ ; 101057693//European Union's Call on Environment and Health (HORIZON-HLTH-2021-ENVHLTH-02)/ ; /AMS_/Academy of Medical Sciences/United Kingdom ; }, mesh = {*Microbiota ; *Fungi/isolation &amp; purification/genetics/classification ; *Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation &amp; purification ; *Air Microbiology ; Humans ; Dust/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as Staphylococcus, Streptococcus, and Corynebacterium, and fungal taxa including Cladosporium, Aspergillus, and Penicillium, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.}, }
@article {pmid41943884, year = {2026}, author = {Fonseca, LRS and Feijó, M and Vaz, CV and Pereira, BJ and Laurentino, S and Palmeira-de-Oliveira, A and Socorro, S}, title = {Urologic Bacteriome: The Hero or the Villain in Prostate Cancer Onset, Progression, and Treatment?.}, journal = {Medicinal research reviews}, volume = {}, number = {}, pages = {}, doi = {10.1002/med.70042}, pmid = {41943884}, issn = {1098-1128}, support = {MOD.PD.NAC.015.01//Liga Portuguesa Contra a Cancro (LPCC) Bolsa LPCC/Gillette-Cancro da Pr&#xf3;stata/ ; 2021.07634//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.07367//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Prostate cancer (PCa) is the second most frequently diagnosed cancer in men worldwide and the fifth leading cause of cancer-related mortality, presenting urgent unmet clinical needs in diagnosis and treatment. The recognition of the microbiome as a key factor in human health has prompted numerous studies, revealing an exciting new approach to cancer diagnosis and therapy. The bacteriome is the component of the microbiome that is most metabolically active and influenceable by internal and external factors, which is pivotal in the development of cancer. Initial studies exploring the link between the microbiome and PCa focused primarily on the gut bacteriome, which has been implicated in the onset and progression of the disease, as well as in resistance to therapy. Further research has demonstrated that the urologic bacteriome also plays a crucial role in the development of PCa, serving as an important factor for diagnosis and treatment. This review synthesizes current knowledge concerning the significance of the urologic bacteriome in PCa onset, progression, diagnosis/prognosis, and therapy. It also explores the impact of the bacterial metabolome in PCa, emphasizing the importance of this undervalued dimension of the bacteriome. Overall, the review provides a comprehensive analysis of how bacteria and their bioactive metabolites contribute to PCa, highlighting their clinical and therapeutic relevance. It also identifies the existing knowledge gaps, paving the way for the development of new approaches that could enhance PCa diagnosis and treatment.}, }
@article {pmid41944002, year = {2026}, author = {Liu, Y and Yang, Y and Zhu, L and Peng, W}, title = {Beyond Weight: Systems Biology and Precision Medicine Redefine Obesity as a Multidimensional Disease.}, journal = {Diabetes, obesity &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1111/dom.70724}, pmid = {41944002}, issn = {1463-1326}, support = {2025ZZTS0829//Central South University Graduate Student Independent Exploration and Innovation Project/ ; 82374552//the National Natural Science Foundation of China/ ; 20240304076//Support Plan for High-level Health and Medical Talents in Hunan Province/ ; 825B20009//National Natural Science Foundation of China for PhD Students/ ; 2024JJ2086//Hunan Provincial Natural Science Foundation for Distinguished Young Scholars/ ; }, abstract = {BACKGROUND: Traditional weight-centered models do not fully capture the biological complexity of obesity. Systems biology offers a new framework by integrating molecular, cellular, clinical, and environmental information to reframe obesity as a heterogeneous, multidimensional disease.<br><br>AIMS: This review aims to reframe obesity as a heterogeneous, multidimensional disease by integrating molecular, cellular, clinical, and environmental information through the lens of systems biology.<br><br>MATERIALS AND METHODS: This article summarizes findings from recent studies employing systems biology approaches, including single-cell transcriptomics, metabolomics, epigenomics, microbiome profiling, and computational modeling.<br><br>RESULTS: These approaches have revealed marked heterogeneity in adipose remodeling, inflammatory tone, mitochondrial stress, and inter-organ communication. Such insights help explain why individuals with similar body mass index (BMI) can differ substantially in insulin resistance, organ-specific vulnerability, and treatment response.<br><br>DISCUSSION: This review focuses on obesity-relevant mechanisms, including adipose tissue heterogeneity, immunometabolic dysfunction, immune aging, and obesity-related multi-system injury. We also discuss emerging precision obesity care strategies such as biomarker-guided subtyping, cell-specific targeting, microbiome-directed intervention, and artificial intelligence-assisted prediction.<br><br>CONCLUSION: Together, these advances support a shift from BMI-based classification alone toward mechanism-informed obesity prevention and treatment.}, }
@article {pmid41944101, year = {2026}, author = {Sohel, M and Aktar, S and Khatun, S and Hamidu, S and Nity, NU and Kumar, S and Hossain, MS and Sarker, MR and Das, SR and Dey, BR and Hasan, AMW and Islam, K and Islam, F and Al Mamun, A}, title = {A Narrative Review on Unravelling Bacterial-Mediated Carcinogenesis and Possible Alternative Treatment Strategies.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e6359088}, pmid = {41944101}, issn = {2314-6141}, mesh = {Humans ; *Carcinogenesis/pathology ; *Neoplasms/microbiology/pathology/therapy ; Animals ; *Bacteria/pathogenicity ; *Bacterial Infections/complications/microbiology ; Signal Transduction ; Cytokines/metabolism ; Apoptosis ; }, abstract = {The potential roles of chemical, physical, and viral factors in cancer development are well documented. Similarly, bacterial carcinogenesis has been reported previously, though not extensively. Therefore, we aimed to provide comprehensive, mechanistic evidence on the pathogenesis of bacteria-induced carcinogenesis and possible treatments to halt cancer progression. Infections by bacteria, including Salmonella typhi, Fusobacterium spp., Chlamydia pneumoniae, Staphylococcus aureus, Helicobacter pylori, and Mycobacterium tuberculosis, have been reported as the most common carcinogenic bacteria in humans. These bacteria can produce toxins and carcinogenic metabolites those promote the development of cancer in a variety of ways, including by changing the dynamics of the cell cycle, triggering signaling pathways in the cell, such as NF-κB, MAPK, PI3K-PKB/Akt, and JAK/STAT, and activating anti-apoptosis activities by increasing Bcl-2 and decreasing BAX, and caspases expression along with suppressing p53 and pRb tumor suppressor proteins. Moreover, inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interferon-gamma (INF-γ), interleukin-1β (IL-1β), IL-4, IL-6, IL-10, IL-1, IL-17, IL-23, and other inflammatory cytokines are a few of the factors that promote chronic inflammation and initiate carcinogenesis. In addition, bacterial infection can generate free radicals that induce DNA damage, thereby promoting carcinogenesis. Following these mechanisms, bacteria can cause a wide range of cancers, such as breast, colon, pancreas, stomach, lung, gallbladder, and oral carcinoma. Fortunately, supplementation with active natural phytochemicals and nano-based strategies may counteract bacterial infection-induced carcinogenesis by regulating several cellular proteins, including those that control the cell cycle, induce apoptosis, promote metastasis, interact with growth factor receptors and tyrosine kinases, and function as antioxidants. Therefore, this narrative review aims to provide a consolidated mechanistic overview of bacterial infection-induced carcinogenesis and to highlight emerging phytochemical and nanotechnology strategies as potential therapeutic approaches. Additionally, phytochemical-based interventions and nanotechnology strategies are discussed as potential alternative therapeutic approaches to counteract bacteria-induced carcinogenesis.}, }
@article {pmid41944109, year = {2026}, author = {Saini, O and Kaur, A and Haneef, M and Kosey, S}, title = {Pathophysiological Role of the Gut Brain Axis in Parkinson's Disease: From Microbial Metabolites and Intestinal Permeability to Central Neuroinflammation.}, journal = {Current neurovascular research}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115672026468149260326045511}, pmid = {41944109}, issn = {1875-5739}, abstract = {INTRODUCTION: Parkinson's Disease (PD) is the second most prevalent neurodegenerative disorder, affecting over 8.5 million individuals worldwide, with its incidence expected to rise. It is characterized by dopaminergic neuronal loss in the substantia nigra pars compacta and pathological aggregation of α-synuclein into Lewy bodies, leading to motor and non-motor symptoms. Increasing evidence implicates the Gut-Brain Axis (GBA) in PD pathophysiology.<br><br>METHODS: This review synthesizes findings from human and animal studies investigating the role of gut microbiota, gut permeability, microbial metabolites, and gastrointestinal dysfunction in the development and progression of PD.<br><br>RESULTS: Gut microbiota dysbiosis is associated with altered production of short-chain fatty acids, tryptophan metabolites, and neurotransmitter precursors, contributing to neuroinflammation, increased intestinal permeability, and &#x3b1;-synuclein misfolding. Gastrointestinal symptoms such as constipation, dysphagia, and gastroparesis often precede motor symptoms by decades, highlighting the gut as a potential origin of pathology. Therapeutic strategies targeting the microbiome, including Mediterranean and ketogenic diets, probiotics, prebiotics, postbiotics, and experimental phage therapy, have demonstrated promising preliminary outcomes.<br><br>DISCUSSION: Despite encouraging results, inconsistencies in methodology, mechanistic uncertainties, and the lack of longitudinal and individualized studies limit current understanding. Standardization and precision-based approaches are required to clarify causality and therapeutic efficacy.<br><br>CONCLUSION: Advancing knowledge of the gut-brain axis in PD presents valuable opportunities for early biomarkers and microbiota-targeted interventions, offering novel strategies to delay disease progression and improve patient quality of life.}, }
@article {pmid41944570, year = {2026}, author = {Ostner, J and Li, H and Müller, CL}, title = {Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data.}, journal = {Statistics in medicine}, volume = {45}, number = {8-9}, pages = {e70534}, pmid = {41944570}, issn = {1097-0258}, support = {ZT-I-PF-5-138//Helmholtz-Gemeinschaft/ ; R01GM123056/NH/NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods/statistics &amp; numerical data ; Computer Simulation ; *Models, Statistical ; Humans ; Single-Cell Analysis ; }, abstract = {The class of a-b power interaction models, proposed by [1], provides a general framework for modeling sparse compositional data with pairwise feature interactions. This class includes many distributions as special cases and enables modeling of zero entries through power transformations, making it particularly suitable for modern high-throughput sequencing data with excess zeros, including single-cell RNA-Seq and microbial amplicon data. Here, we present an extension of this class of models that allows inclusion of covariate information, thus enabling accurate characterization of covariate dependencies in heterogeneous populations. Combining this model with a tailored differential abundance (DA) test leads to a novel DA testing scheme, cosmoDA, that can reduce the false positive detection rate caused by correlated features. cosmoDA uses penalized generalized score matching for parsimonious model fitting. We show on simulated benchmarks that cosmoDA can accurately estimate feature interactions in the presence of population heterogeneity and significantly reduces the false discovery rate when testing for differential abundance of correlated features. Using single-cell and amplicon data, we illustrate cosmoDA's ability to estimate data-adaptive Box-Cox-type data transformations and assess the impact of zero replacement and power transformations on downstream differential abundance results. cosmoDA is available at https://github.com/bio-datascience/cosmoDA.}, }
@article {pmid41944618, year = {2026}, author = {Fróis-Martins, R and Mertens, S and Tran, VDT and Maufrais, C and d'Enfert, C and Sanglard, D and LeibundGut-Landmann, S}, title = {Manipulation of regulators of morphogenesis is not sufficient to render a Candida albicans colonizer strain pathogenic.}, journal = {mBio}, volume = {}, number = {}, pages = {e0041526}, doi = {10.1128/mbio.00415-26}, pmid = {41944618}, issn = {2150-7511}, abstract = {As a member of the microbiome, Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. While commensalism is tightly controlled by the host immune system, the fungal determinants enabling the fungus to colonize the host mucosa without causing tissue damage and inflammation remain less clear. In search of genetic determinants that may underlie the commensal lifestyle of the low-damage-inducing C. albicans isolate 101, we identified a small sequence duplication in one allele of the Brg1 hyphal morphogenesis regulator gene, resulting in a truncated loss-of-function allele (BRG1[TRUNC]). Replacing BRG1[TRUNC] by the full-length allele (BRG1[FL]) resulted in a modest increase in filamentation but did not alter the phenotype of the fungus in the oral mucosa of experimentally colonized mice. Analysis of a spontaneous hyperfilamentous variant of the BRG1[FL]/BRG1[FL] derivative of C. albicans strain 101 identified a Glu-to-Lys change at position 1541 in the Cyr1 adenylate cyclase (CYR1[E1541K]). While the CYR1[E1541K] mutation led to greatly increased filamentation, expression of hyphae-associated genes, and host cell damage when tested in vitro, it was insufficient to render C. albicans strain 101 more pathogenic in the oral mucosa in vivo, irrespective of the BRG1 status. Together, this highlights that the low-damage-inducing nature of strain 101 cannot be overcome by manipulating BRG1 and CYR1, two genes with known roles in C. albicans virulence.IMPORTANCEDuring homeostasis, the fungus Candida albicans establishes mutualistic interactions with its human host. It can, however, also adopt a pathogenic state and cause infections with diverse clinical manifestations that pose a significant challenge for diagnosis and therapy. Understanding the fungal determinants that underlie C. albicans colonization under steady-state conditions may thus provide new avenues for modulating the fungus-host interaction in candidiasis patients to restore homeostasis. Here, we report gene variants in key regulators of C. albicans morphogenesis and virulence that distinguish strains with distinct capacity to drive inflammation and cause disease. Gene-exchange mutants provided evidence for the impact of a BRG1 loss-of-function allele and a CYR1 gain-of-function mutation toward in vitro biomarkers of fungal pathogenicity. However, in vivo in an experimental model of C. albicans oral colonization, none of these gene variants individually or in combination was sufficient to change the pathogenic state of the fungus. These findings indicate that C. albicans mucosal colonization is regulated by a complex gene network rather than by single genetic determinants.}, }
@article {pmid41944629, year = {2026}, author = {Poopalarajah, R and Jha, AR}, title = {Human lifestyle-associated factors modulate the gut resistome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0145825}, doi = {10.1128/msystems.01458-25}, pmid = {41944629}, issn = {2379-5077}, abstract = {Antimicrobial resistance poses a serious threat to global public health in the 21st century. The human gut is a major reservoir of antimicrobial resistance genes and is strongly shaped by lifestyle factors linked to urbanization. Antibiotic use is widely known as a main driver of gut antimicrobial resistance; however, lifestyle encompasses other host and environmental determinants that also profoundly impact the gut resistome. These factors restructure gut microbiome composition and diversity, which, in turn, shape the abundance, persistence, and mobility of ARGs within the gut ecosystem. Lifestyle transitions along the urbanization gradient illustrate how antibiotic use, subsistence strategies, diet, agriculturally linked environmental exposures, host health, and global patterns of ARG distribution influence gut microbial diversity and ARG prevalence. Frequent antibiotic use in urban settings disrupts gut homeostasis and promotes resistome expansion. Transitions from traditional subsistence strategies to industrialized food systems are associated with dietary changes, such as reduced fiber intake, contributing to lower gut microbial diversity and increased ARG burden. Agrarian practices involving close human and livestock contact and antimicrobial use in animal husbandry facilitate ARG dissemination through the food chain. Host physiological factors and environmental exposures across diverse geographic regions additionally influence gut microbiome resilience and resistome composition. Integrating microbial community structure with ARG profiles provides insight into how lifestyle factors shape the gut resistome and influence ARG emergence and spread.}, }
@article {pmid41944651, year = {2026}, author = {Morrison, JM and Steuart, R and Russell, CJ}, title = {Pediatric tracheostomy-associated respiratory infections: an evolving paradigm.}, journal = {Current opinion in pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOP.0000000000001559}, pmid = {41944651}, issn = {1531-698X}, abstract = {PURPOSE OF REVIEW: Children with tracheostomy frequently experience tracheostomy-associated infections (TRAINs) such as pneumonia and tracheitis. This review will summarize current evidence regarding the diagnosis, treatment, and prevention of TRAINs.<br><br>RECENT FINDINGS: Recent evidence highlights limitations of respiratory culture testing in the face of a diverse, dynamic bacterial community within the airways of children with tracheostomy, challenging the notion that a positive bacterial culture is sufficient for diagnosing bacterial TRAIN. For this reason, recent consensus guidelines recommend against the routine obtainment of respiratory cultures for TRAIN diagnosis in the absence of specific clinical symptoms. Additional evidence for microbiome shifts and host inflammation as diagnostic tools may help identify those who will benefit from antibiotic treatment. Recent findings support selective anaerobic coverage when aspiration is suspected and suggest shorter antibiotic courses may be effective. Cycled inhaled tobramycin shows potential for reducing TRAIN frequency and related hospitalizations.<br><br>SUMMARY: With recent advances in TRAIN pathobiology, diagnosis, treatment, and prevention of TRAINs is undergoing a paradigm shift. Future translational research will define the airway microbiome during TRAINs and during wellness and its impact on host inflammation. Antibiotic clinical trials are needed to optimize treatment and prevention of TRAINs.}, }
@article {pmid41944793, year = {2026}, author = {Kumar, J and Hartzell, C and Abelson, E and Mano, KJ and Chidambaran, V}, title = {Prevalence, Expression, Assessment, Mechanisms, and Management of Pain in Autistic Children: A Scoping Review.}, journal = {A&amp;A practice}, volume = {20}, number = {4}, pages = {e02178}, doi = {10.1213/XAA.0000000000002178}, pmid = {41944793}, issn = {2575-3126}, mesh = {Humans ; Child ; *Pain Management/methods ; *Autism Spectrum Disorder/complications/epidemiology ; Prevalence ; Adolescent ; Child, Preschool ; Pain Measurement ; *Pain/epidemiology ; *Chronic Pain/epidemiology/therapy ; }, abstract = {Autism spectrum disorder is a neurodivergent condition affecting communication, social interaction, and behavior, and is characterized by sensory-processing abnormalities. There is a high incidence of chronic pain in autistic children, and pain can also be a presenting symptom of autism. With improved identification of autism in children, it is increasingly important to understand the implications for pain management. This scoping review describes and summarizes existing literature on pain prevalence, mechanisms, expression, and assessment challenges, as well as acute and chronic pain management in autistic children. A systematic search strategy of MEDLINE, PsycINFO, SCOPUS, and Web of Science was utilized to identify major findings of qualitative, quantitative, observational studies, and reviews reporting on pain in pediatric patients (3-18 years) with concomitant autistic symptomatology. We identified 260 eligible articles, of which 85 were included for review. Our findings challenge earlier assumptions that autistic children are not sensitive to pain. Rather, they react differently to pain than nonautistic peers, have comorbidities that increase pain risk, and are hypersensitive to painful stimuli. Altered sensory-processing, genetic mechanisms, and brain-gut microbiome interactions have been suggested as mechanisms for higher pain sensitivity. The combination of altered pain expression and lack of proper pain assessment tools in this population can lead to unnecessary testing or delays in diagnosis and management. Management of pain requires parental engagement, multidisciplinary coordination, and tailored interventions unique to the individual's responses.}, }
@article {pmid41944837, year = {2026}, author = {Weirauch, T and Vehreschild, MJGT}, title = {[Modulation of the gut microbiome for the eradication of multidrug-resistant pathogens: current approaches and perspectives].}, journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz}, volume = {}, number = {}, pages = {}, pmid = {41944837}, issn = {1437-1588}, abstract = {The global rise in antibiotic resistance represents one of the greatest threats facing modern medicine. Colonization of the gastrointestinal tract with multidrug-resistant organisms is considered a critical risk factor for nosocomial infections across various patient populations. In this context, targeted decolonization strategies are moving into the focus of clinical research. For a long time, non-absorbable antibiotics were considered a promising approach for local eradication; however, the evidence generated on this question does not suggest sufficient clinical efficacy of this approach. Alternative strategies, such as fecal microbiota transplantation, have shown encouraging results in case reports and small-scale studies for the decolonization of multidrug-resistant organisms. Live biotherapeutic products and certain probiotics are also being explored as potential options for microbiome modulation and reduction of antimicrobial resistance. However, the current evidence base remains heterogeneous, and robust randomized controlled trials are largely lacking. This article aims to provide an overview on the current understanding of gastrointestinal colonization with multidrug-resistant organisms and to discuss the clinical relevance of non-absorbable antibiotics as well as the potential role of microbiome-based therapies in the context of the global antibiotic resistance crisis.}, }
@article {pmid41944841, year = {2026}, author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME}, title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41944841}, issn = {1432-072X}, }
@article {pmid41945577, year = {2026}, author = {Faridoun, A and Carvalho, R and Smith, J and Gibb, A and Jain, L and Zhang, A and Sran, A and Redmond, J and Malik, MZ and Gibson, M and Haider, A and Rekhi, U and Bhagirath, A and Rock, LD and Altabtbaei, K}, title = {FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0331145}, pmid = {41945577}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Humans ; *Software ; Phylogeny ; *Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows-FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)-to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, integration of taxonomic knowledge when samples are sequenced with multiple primers using SMURF. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyl's integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.}, }
@article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, }
@article {pmid41946778, year = {2026}, author = {Nazir, I and Perez, D and Vargas, SJR and Ur Rehman, S and Arora, D and Chandra, M and Thimmapuram, J and Ebner, P}, title = {Assessing the impact of phage therapy on growth performance, microbiome and phage specific immune response in chickens.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45338-y}, pmid = {41946778}, issn = {2045-2322}, }
@article {pmid41946922, year = {2026}, author = {Ding, Y and Zhang, Z and Wang, K and Jiang, C}, title = {The microbiome regulates host metabolic health and diseases through microbial enzymes.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {41946922}, issn = {1759-5053}, abstract = {The microbiome is widely involved in host metabolism, with many omics studies suggesting that it is important for metabolic health. Although studies in this area have made great strides in furthering our understanding of the role of the microbiome in health and disease, key challenges still hinder the safe clinical application of gut microbiota-targeted therapies. These limitations include a lack of confirmation of causality between the gut microbiota and host health, insights into the molecular mechanisms by which the gut microbiota functions to affect host health, and the development of therapeutic strategies that accurately regulate the function of the gut microbiota towards specific microbial enzyme targets without affecting its overall composition and viability. Microbial enzymes with various functions and activities have attracted the attention of many researchers in the past few years, especially microbiota-host isozymes, which are enzymes in the microbiome and the host that share a similar function. Such isozymes, as well as microbial-specific enzymes involved in basic biological processes of the gut microbiota, metabolism of nutrients, and synthesis of active metabolites and interactions in microbial-host communities, are the key mediators of gut microbiota-host crosstalk and have received much attention. In this Review, we provide a holistic understanding of the multifaceted role of gut microbial enzymes, including providing guidance for their discovery, while highlighting the great potential of gut microbial enzyme-oriented therapies for precision medicine.}, }
@article {pmid41947036, year = {2026}, author = {Ali, S and Patel, AJ and Lehman, PC and Fitzjerrells, RL and Kasi, PM and Mangalam, AK}, title = {The distinct roles of Negativicoccus and Fusobacterium in proximal- and late-onset colorectal cancer.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655193}, doi = {10.1080/19490976.2026.2655193}, pmid = {41947036}, issn = {1949-0984}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; Feces/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Ribosomal/chemistry/genetics ; *Fusobacterium/isolation &amp; purification/genetics ; Anal Canal/microbiology ; DNA, Bacterial/genetics/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Adult ; }, abstract = {Despite the emerging role of the gut microbiome in colorectal cancer (CRC), its significance in early-onset CRC (EOCRC, < 50 y) versus late-onset CRC (LOCRC) and the molecular differences between proximal and distal CRC remain poorly understood. To circumvent the logistical and patient compliance challenges of stool collection, we explored the utility of anal swabs as a convenient alternative for characterizing gut microbiome signatures in CRC. We profiled the CRC microbiome using anal swabs (n = 76) and stool samples (n = 33) by 16S rRNA sequencing. Diversity indices were compared using Wilcoxon tests, compositional differences assessed by PERMANOVA, and correlations were performed in paired samples. Correlation analysis revealed strong associations between microbial phyla (Bacteroidetes, R = 0.86, p = 4.7 × 10[-6]; Firmicutes, R = 0.65, p = 3.4 × 10[-3]; Verrucomicrobiota, R = 0.81, p = 4.8 × 10[-5]; and Fusobacterium, R = 0.80, p = 7.3 × 10[-5]) and major genera (Bacteroides, R = 0.88, p = 1.7 × 10[-5]; Fusobacetrium, R = 0.75, p = 1.5 × 10[-3]; Blautia, R = 0.77, p = 8.5 × 10[-4]; and Bifidobacterium, R = 0.81, p = 3.3 × 10[-4]) across sample types, validating the use of anal swabs. However, Actinobacteriota and Prevotella were not correlated, likely reflecting the perianal skin-associated microbiota and underscoring the need for validation against stool or mucosal biopsies. Importantly, anal swabs revealed associations between Negativicoccus and proximal CRC (p = 0.047) and between the Fusobacteriota phylum and LOCRC (p = 0.042), suggesting subtype-specific CRC subtypes. In mechanistic studies, using the mucous-secreting HT-29 MTX cell line, we observed that Negativicoccus was associated with activation the RAS/MAPK pathway, upregulated c-MYC, KRAS, MAPK1, and Cyclin D1 (p < 0.05) and increased proinflammatory cytokines (IL-8) (p < 0.05), thereby increasing cell proliferation. In contrast, Fusobacterium modulates the WNT/β-catenin pathway, increasing β-catenin and AXIN1 (p < 0.05), promoting cell migration (p < 0.05), and extracellular matrix (ECM) remodeling. These findings highlight distinct microbial contributions to CRC pathogenesis, with Negativicoccus influencing proliferation and inflammation, whereas Fusobacterium promotes migration and invasion. Understanding these pathways offers potential for harnessing the gut microbiome's diagnostic and therapeutic power in CRC.}, }
@article {pmid41947046, year = {2026}, author = {Wieser, NV and Admiraal, I and Weiss, R and Ghiboub, M and Davids, M and Lefèvre, A and Emond, P and Powell, EA and Sim, K and Kroll, JS and de Jonge, WJ and Sovran, B and Kinross, JM}, title = {Fecal tryptophan metabolism predicts the development of infant eczema: a prospective longitudinal study.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655171}, doi = {10.1080/19490976.2026.2655171}, pmid = {41947046}, issn = {1949-0984}, mesh = {Humans ; *Tryptophan/metabolism ; Infant ; *Feces/microbiology/chemistry ; Prospective Studies ; Longitudinal Studies ; Male ; Female ; *Eczema/microbiology/diagnosis/metabolism ; Gastrointestinal Microbiome ; Infant, Newborn ; Metabolomics ; Biomarkers/analysis ; Bifidobacterium/metabolism/genetics ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Indoles/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolome ; United Kingdom ; }, abstract = {Early-life microbial metabolism of tryptophan plays a critical role in immune modulation and may influence susceptibility to inflammatory disorders such as eczema. However, longitudinal human data linking microbial tryptophan metabolism to eczema onset are limited. We conducted a prospective cohort study of 40 term-born UK infants, followed from birth to 24 months, stratified by early-onset (infants developing eczema <12 months, n = 12) or late-onset (infants developing eczema ≥12 months, n = 7) doctor-diagnosed eczema. Fecal samples underwent targeted tryptophan LC-MS metabolomics and 16S rRNA sequencing. Tryptophan metabolomics revealed dynamic changes in tryptophan metabolites that were associated with disease status compared to healthy infants. Infants with early-onset eczema (<12 months) exhibited elevated tryptophan and tryptamine levels at 6 months, while those with late-onset eczema (≥12 months) showed reduced indole-3-lactic acid (ILA) levels prior to diagnosis at 9 months. 16S and metabolomics correlations highlighted a metabolic shift in Bifidobacterium from ILA, a metabolite that predominated fecal metabolome during early infancy but decreases by 12 months, coinciding with increased indole-3-aldehyde (I3AD) metabolism by Bifidobacterium. Receiver operating characteristic (ROC) curve analysis identified a small panel of early predictive indole-pathway markers, including tryptophan and the indole/indole-3-sulfate (I3S), I3S/ILA, and tryptophan/ILA ratios, discriminating both early- and late-onset eczema development. Our findings reveal distinct, time-dependent disruptions in microbial tryptophan cometabolism associated with eczema onset. ILA may serve as a biomarker for the diagnosis of infantile eczema. Further validation studies to establish its clinical utility are now required.}, }
@article {pmid41947175, year = {2026}, author = {Xiao, Q and Wen, Z and Zhan, H and Zhao, H and Jiao, Y and Huang, D and Li, H and Chen, C}, title = {Si-Ni-San alleviates depression-like behavior via regulating the gut microbiota-tryptophan metabolism-AhR/NF-κB pathway axis.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {41947175}, issn = {1749-8546}, support = {82405203//the National Nature Science Foundation of China/ ; 20242BAB20451//Jiangxi Provincial Natural Science Foundation/ ; 202610094//The Science and Technology Program of Jiangxi Provincial Health Commission/ ; ZZ17-ND-12//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ17-YQ-054//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PY-2025004B//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; JSYL2025001//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {BACKGROUND: Si-Ni-San (SNS), a classic herbal formula from the Treatise on Cold Damage Diseases, is used to treat depression by relieving "liver qi stagnation". However, the underlying mechanism remains unclear.<br><br>PURPOSE OF THE RESEARCH: This study aimed to investigate the mechanism by which SNS alleviates depression-like behavior, specifically focusing on its role in modulating gut microbiota and host tryptophan metabolism.<br><br>METHODS: A depression model was induced in mice by chronic unpredictable mild stress (CUMS). The antidepressant effects of SNS were evaluated through behavioral tests. Integrated untargeted and targeted metabolomics, alongside 16S rRNA sequencing, were utilized to identify potential gut-brain signaling molecules. Molecular interactions between the gut-brain signaling molecule and its target were validated by surface plasmon resonance (SPR) and molecular docking. Key protein expression was measured via Western blot and ELISA. Finally, the function of gut microbiome-derived indole-3-acetic acid (IAA) as a key gut-brain signaling molecule was confirmed by oral supplementation experiments.<br><br>RESULTS: SNS significantly alleviated CUMS-induced depression-like behaviors. Multi-omics analysis revealed that SNS reversed tryptophan metabolic disorders and elevated gut microbiome-derived IAA levels in both the colon and prefrontal cortex, which was attributed to the enrichment of Lactobacillus. Further investigations confirmed that IAA directly binds to and activates the aryl hydrocarbon receptor (AhR), thereby inhibiting NF-&#x3ba;B pathway-mediated neuroinflammation. Moreover, oral supplementation with IAA replicated the antidepressant effects of SNS and suppressed CUMS-induced neuroinflammation via the AhR/NF-&#x3ba;B signaling pathway.<br><br>CONCLUSION: SNS alleviates depression-like behavior by modulating gut microbiota-mediated tryptophan metabolism to enhance IAA production, thereby activating central AhR signaling and suppressing NF-&#x3ba;B-mediated neuroinflammation.}, }
@article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02403-y}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.<br><br>RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.<br><br>CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, }
@article {pmid41947241, year = {2026}, author = {Wang, Z and Li, LK and Zhou, NN and Wang, T and Wang, YX and Qiao, F and Du, ZY and Zhang, ML}, title = {Microbiota-gut-muscle axis shapes fish muscle texture by regulating collagen synthesis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02400-1}, pmid = {41947241}, issn = {2049-2618}, support = {2022YFD2400800//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Increasing studies have emphasized the communication network between the gut microbiome and host organs, revealing that such interactions significantly influence host physiological performances. However, whether a gut-muscle axis exists to regulate muscle quality in animal production is unknown.<br><br>RESULTS: In two independent cohorts, the muscle hardness of tilapia subjected to a long-term faba bean diet exhibited significant inter-individual variation. RNA-Seq analyses of the high-hardness (H) and low-hardness (L) groups pointed to collagen-based extracellular matrix as a possible factor driving muscle hardness development. Transplantation of gut microbiota from the H donor resulted in enhanced collagen synthesis in gnotobiotic zebrafish. Muscular collagen deposition was featured with an increased abundance of gut Cetobacterium. Gnotobiotic models colonized with live C. somerae exhibited enhanced collagen synthesis. Integrated analyses of microbiome function, bacterial&#xa0;genome, and metabolic profiles identified acetate as a key effector of C. somerae. Acetate incubation upregulated collagen I expression in TGF-&#x3b2;-activated fibroblasts in an acetylation-dependent manner. Mechanistically, acetate promoted the acetylation of SMAD2/3, enhancing its nuclear transport and stability, which ultimately increased collagen expression. An acetate-supplemented feeding experiment corroborated these findings.<br><br>CONCLUSION: The comprehensive results provided evidences that gut microbes regulated&#xa0;tilapia muscle texture through SMAD2/3 acetylation-driven collagen synthesis. This study expands our understanding of the multifaceted role of the gut-muscle axis in muscle physiology. Furthermore, our findings highlight that targeting gut microbiota and the downstream collagen synthesis pathway could be promising for manipulating muscle quality in animal production. Video Abstract.}, }
@article {pmid41947254, year = {2026}, author = {Passmore, JS and Nieves Delgado, A and Happel, AU}, title = {Ethical design as a prerequisite for translational microbiome science.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41947254}, issn = {2049-2618}, support = {INV-037612/GATES/Gates Foundation/United States ; VI.Vidi.221F.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; K43TW012864/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical/ethics ; *Translational Science, Biomedical/ethics ; Research Design ; }, abstract = {Human microbiome research is expanding globally, yet remains dominated by samples, institutions, and leadership from the Global North. This imbalance undermines scientific validity, as microbiomes are shaped by socio-ecological context and temporal dynamics, and risks producing diagnostics and therapeutics that are not applicable across diverse populations. In this comment, we engage with van Daele et al.'s framework of co-laboration and argue for ethical, interdisciplinary, and locally led research models that center community participation, context-rich metadata, and equitable authorship. We outline structural requirements-governance tools, funding mechanisms, and accountability systems-needed to ensure these frameworks are implemented and advance both scientific integrity and global health equity. Video Abstract.}, }
@article {pmid41947255, year = {2026}, author = {Van Daele, W and Tito Tadeo, RY and Perera, J and Tshokey, T and Iversen, PO and Jayasinghe, S and Raffaetà, R and Wangmo, N and Fjeld, HE and R, SC and Thoradeniya, T and Raes, J}, title = {Toward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41947255}, issn = {2049-2618}, support = {Project no. 324158//Norwegian Research Council/ ; grant G0B7320N//Fonds Wetenschappelijk Onderzoek/ ; GA n. 949742 ERC-HealthXCross//European Union's Horizon 2020 Research and Innovation Programme/ ; }, mesh = {Humans ; *Microbiota ; *Biomedical Research/ethics ; Global Health ; Europe ; North America ; }, abstract = {As human microbiome research is globalizing, it raises ethical concerns regarding the European and North American dominance in the field, which may reproduce a colonial bias and perpetuate inequities in global health research and outcomes. We suggest disentangling this ethical quandary into three main concerns: 1) scientific bias toward European and North American populations; 2) limited meaningful community inclusion, participation, and ownership, and 3) scant significant inclusion of diverse global researchers. We then formulate three recommendations for their resolution, deploying co-laboration-joint labor of diverse partners in generating synergies between diverse disciplines, cultures, and knowledges around shared concerns-and co-laborative science-a form of citizen science based on such synergies between diverse partners-to guide meaningful inclusive, participatory, and ethical human microbiome research. To conclude, we promote a programmatic list for putting co-laborative ethical science into practice, benefiting global communities, individuals, and researchers alike and decolonizing and improving health worldwide.}, }
@article {pmid41947543, year = {2026}, author = {Samyn, M and Gasparetto, M}, title = {Is it time to consider oral vancomycin treatment for the management of pediatric inflammatory bowel disease irrespective of the presence of primary sclerosing cholangitis?.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70431}, pmid = {41947543}, issn = {1536-4801}, support = {//None/ ; }, }
@article {pmid41947788, year = {2026}, author = {Gorczyca, K and Kimber-Trojnar, &#x17b; and Kozioł, MM and Leszczyńska-Gorzelak, B}, title = {Association of culture-detected vaginal microbiota and body composition parameters with gestational diabetes outcomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1776505}, pmid = {41947788}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; Cross-Sectional Studies ; Adult ; *Diabetes, Gestational/microbiology/epidemiology ; *Vagina/microbiology ; *Body Composition ; *Microbiota ; Candida albicans/isolation &amp; purification ; Life Style ; Streptococcus agalactiae/isolation &amp; purification ; Poland/epidemiology ; Young Adult ; }, abstract = {OBJECTIVE: To evaluate associations between culture-detected vaginal microbial colonization, body composition parameters, and lifestyle factors in women with gestational diabetes (GD).<br><br>DESIGN: Cross-sectional observational study.<br><br>SETTING: Tertiary university hospital, Department of Obstetrics and Perinatology, Lublin, Poland.<br><br>POPULATION: One hundred pregnant women, including 47 with GD and 53 healthy controls.<br><br>METHODS: Anthropometric measurements, bioelectrical impedance analysis (BIA), and vaginal culture-based microbiological assessment were performed. Dietary habits, lifestyle behaviours, and supplement use were evaluated using a validated questionnaire. BIA assessed hydration status and body composition, including total body water, extracellular and intracellular water, lean tissue mass, and body cell mass.<br><br>MAIN OUTCOME MEASURES: Prevalence of selected vaginal microorganisms (Candida albicans, Streptococcus agalactiae), body composition indices, and lifestyle factors.<br><br>RESULTS: Women with GD had significantly higher BMI during pregnancy, greater lean tissue mass and body cell mass, and increased total and extracellular water compared with controls (all p < 0.05). Vaginal swabs showed a higher prevalence of Candida albicans (27.7% vs. 5.7%) and Streptococcus agalactiae (23.4% vs. 0%) in the GD group. Women with GD more frequently reported alcohol and coffee consumption before pregnancy and were less likely to use folic acid or probiotic supplements. Due to multiple comparisons, some findings may reflect type I error and should be interpreted cautiously.<br><br>CONCLUSIONS: GD was associated with a higher prevalence of selected culture-detected vaginal microorganisms, as well as differences in body composition and health-related behaviours. These findings highlight potential interactions between metabolic status, microbial colonization, and lifestyle factors in pregnancy. Given the cross-sectional design, causality cannot be inferred, and comprehensive microbiome studies are needed to confirm broader ecological changes.}, }
@article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation &amp; purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Chronic Disease ; Aged ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, }
@article {pmid41948035, year = {2026}, author = {Li, Y and Wang, B and Lan, C and Dai, P and Zhao, L and Zhang, M and Fang, Q}, title = {Differential responses of crop pollen microbial communities to insect visitation and host identity: fungi are more sensitive than bacteria.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1789970}, pmid = {41948035}, issn = {1664-302X}, abstract = {INTRODUCTION: In the pollination process, pollen serves not only as a key vehicle for plant reproductive success but also as an important ecological interface for microbial transmission and selection. However, how insect visitation and host plant identity jointly affect the assembly of pollen microbial communities in agroecosystems remains poorly understood.<br><br>METHODS: Here, we employed bagging and open-pollination treatments combined with high-throughput sequencing to investigate the effects of insect visitation and host plant identity on the structure, composition, diversity, interspecific interactions, and core taxa of pollen microbial communities in crops.<br><br>RESULTS: Results showed that insect visitation and host plant identity jointly and significantly influenced the structure of pollen bacterial asnd fungal communities and altered their taxonomic composition, diversity, and interaction patterns, with these effects being mainly evident in cross-pollinated plants and more pronounced in fungal than in bacterial communities. Further analyses revealed that insect visitation increased network connectivity while reducing modularity (0.046) in bacterial communities of cross-pollinated plants, whereas their fungal network exhibited reduced connectivity and increased modularity (0.787). In cross-pollinated plants, fungal core taxa dominated the fungal communities (>87%), while bacterial core taxa contributed relatively little to overall community.<br><br>DICUSSION/CONCLUSION: Overall, insect visitation and host plant identity jointly shape pollen microbial communities, but bacterial and fungal communities exhibit distinct response patterns, with bacterial communities being relatively stable and fungal communities being more sensitive. This study highlights the key roles of insect visitation and host plant identity in pollen microbiome assembly and provides a theoretical basis for understanding crop pollination ecology and plant-pollinator-microbe interactions.}, }
@article {pmid41948039, year = {2026}, author = {Wang, W and Liao, X and Liu, J and Liu, B and Zhou, C and Liang, P}, title = {Elevated postoperative IL-1β induces disorder of intestinal microenvironment and alteration of gut microbiota.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1744636}, pmid = {41948039}, issn = {1664-302X}, abstract = {INTRODUCTION: Previous research hinted at the importance of postoperative gut dysbiosis prevention, but the mechanisms remained unclear, posing a challenge for prevention and therapy. This study aims to investigate the characteristics of postoperative dysbiosis and the underlying mechanisms.<br><br>METHODS: The clinical cohort investigated the perioperative change of gut microbiota in patients undergoing thoracoscopy and its relationship with peripheral inflammatory indicators. Gut microbiome was characterized by 16S rRNA gene sequencing and Bugbase phenotype analysis. In the laboratory study, a mouse model of surgery/anesthesia stress was established to further investigate the potentially underlying mechanisms.<br><br>RESULTS: Microbiome analysis revealed a decrease in alpha diversity and a shift from obligate anaerobes to aerobes/facultative anaerobes after thoracoscopy. Postoperative IL-1&#x3b2; was negatively correlated with obligate anaerobe abundance and positively correlated with facultative anaerobe abundance. Higher facultative anaerobe abundance was associated with increased risk of postoperative complications and longer hospital stays. In the mouse model, surgery and rIL-1&#x3b2; intervention mirrored the oxygen phenotype changes in clinical cohort, and the colonic epithelium exhibited decreased ATP levels and hypoxic staining scores, with increased lactic acid. Downregulating postoperative IL-1&#x3b2; with IL-1&#x3b2; siRNA mitigated colonic hypoxic environment impairment and gut microbiota oxygen phenotype changes induced by surgery/anesthesia stress.<br><br>CONCLUSION: Postoperative gut dysbiosis involves a phenotypic shift of the gut microbiota from anaerobes toward aerobes and facultative anaerobes. This shift may be driven by an IL-1&#x3b2;-colonic epithelial oxygen metabolism-colonic oxygen environment-gut microbiota regulatory axis, offering potential insights for early risk stratification of severe postoperative complications and strategies to improve postoperative recovery.}, }
@article {pmid41948040, year = {2026}, author = {Mo, X and Liu, Y and Huang, Z and Yu, H and Huang, J and Wu, Z and Tan, M and Fan, H and Ma, F and Zeng, B}, title = {Soil N and P nutrient metabolism affected by fungal community in larch plantation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1658803}, pmid = {41948040}, issn = {1664-302X}, abstract = {INTRODUCTION: The time-response mechanism of soil nitrogen (N) and phosphorus (P) nutrients across different stand ages remains intricate and inadequately quantified, particularly unclear is the effects of rhizosphere soil microbial communities, which serve as crucial drivers on soil N and P nutrients. This study delved into the effects of soil fungal community on the shifts of soil physicochemical properties and their correlations between N-P distribution within rhizosphere of Larix kaempferi (Japanese larch) with different tree stands.<br><br>METHODS: This study investigated the responses of soil nitrogen (N) and phosphorus (P) along a stand age gradient (young: <20 years; mid-aged: 20-30 years; near-mature: 30-40 years; mature: >40 years) in Larix kaempferi forests, with a focus on the associations between rhizosphere microbial communities and soil nutrient dynamics. By covering key developmental stages of forest succession, we examined age-related changes in rhizosphere soil N and P concentrations, soil physicochemical properties, and fungal community structure.<br><br>RESULTS: The results showed that fungal community structure gradually diversified from young to near-mature forests and became more stable in the mature forest stage. Differences in forest age were associated with changes in the availability and distribution of soil N and P nutrients, accompanied by shifts in the relative abundance of microbial functional genes related to N and P cycling. In particular, the abundance of P cycling-related functional genes showed patterns consistent with soil N and P variations, while N fixation-related functional genes exhibited the highest abundance in the middle-aged forest stage.<br><br>DISCUSSION: Overall, variations in stand development along the forest age gradient were closely linked to changes in soil nutrient distribution and rhizosphere microbial biomass, highlighting the potential role of rhizosphere microbial communities in soil N and P cycling in larch plantation ecosystems.}, }
@article {pmid41948042, year = {2026}, author = {Dresel, FC and Gourlay, CW}, title = {Investigating the pH dependent antifungal effects of butyrate on Candida albicans.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1793162}, pmid = {41948042}, issn = {1664-302X}, abstract = {INTRODUCTION: Candida species are common members of the human gastrointestinal microbiome but are also associated with a range of diseases when microbial community balance is disrupted. Short-chain fatty acids produced by gut bacteria, particularly butyrate, play important roles in host-microbiome interactions and are increasingly explored as therapeutic modulators of microbial composition. Butyrate is present both as a microbial metabolite and dietary component and has been reported to influence Candida abundance within the gut. However, the antifungal activity of sodium butyrate (NaB) against Candida albicans under physiologically relevant gut pH conditions remains poorly understood.<br><br>METHODS: We examined the effects of NaB on C. albicans growth and physiology under pH conditions representative of the gastrointestinal environment. Growth, hyphal transition, respiration and biofilm formation were assessed in the presence of NaB at neutral pH. Parallel experiments at acidic pH (pH 4.0) evaluated fungicidal activity and associated cellular responses, including mitochondrial membrane potential, reactive oxygen species (ROS) accumulation, and intracellular calcium homeostasis. Histone deacetylase inhibitory activity of NaB was also assessed to determine its early cellular effects.<br><br>RESULTS: NaB displayed rapid histone deacetylase inhibitor activity in C. albicans and significantly inhibited growth, hyphal morphogenesis, respiration, and biofilm formation at neutral pH. In contrast, under acidic conditions (pH 4.0) NaB exhibited fungicidal activity. This lethal effect was associated with mitochondrial depolarisation, elevated ROS levels, and disruption of intracellular calcium regulation. Further analyses indicated that oxidative stress and loss of calcium homeostasis are key contributors to NaB-induced cell death under acidic conditions.<br><br>DISCUSSION: These findings reveal a strong pH dependence in the antifungal activity of butyrate against C. albicans. While NaB acts primarily as a physiological inhibitor of growth and virulence traits at neutral pH, acidic conditions convert its activity to a fungicidal mechanism driven by mitochondrial dysfunction, oxidative stress, and calcium dysregulation. This pH-dependent behaviour has implications for understanding microbiome-derived metabolites in fungal ecology within the gut and highlights the potential of butyrate-based strategies to modulate C. albicans overgrowth.}, }
@article {pmid41948045, year = {2026}, author = {Dong, Y and Du, B and Xie, C and Zhang, S and Pang, Q and Zhang, D}, title = {Potassium sorbate induces developmental and microbiome changes in Drosophila melanogaster with attenuated trans-generational toxicity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783630}, pmid = {41948045}, issn = {1664-302X}, abstract = {Potassium sorbate (PS) is a widely used antimicrobial additive employed as a preservative in food, cosmetics, and animal feed. Early childhood represents a critical developmental window characterized by rapid growth, immune system maturation, gut microbiota establishment, and physiological homeostasis development, which may be particularly vulnerable to chemical exposures (during which chemical exposures may exert heightened impacts). Nevertheless, the effects of PS on childhood development and gut microbiota remain poorly understood, and its potential trans-generational effects have yet to be elucidated. In this study, we employed Drosophila melanogaster, an established model for studying evolutionarily conserved aspects of development, metabolism, and host-microbiota interactions, to systematically evaluate PS toxicity across multiple parameters: developmental dynamics, gut microbiota composition, gene regulation in adulthood, and trans-generational effects. Our findings demonstrate a dose-dependent biphasic response: while low-dose PS exposure (25 mg/L) accelerated larval pupation and adult emergence, suggesting a potential growth-promoting effect, high-dose exposure (≥ 500 mg/L) significantly delayed development and reduced adult lifespan (observed in females at 1,000 and males at 500-1,000 mg/L). Notably, trans-generational analysis revealed persistent developmental delays in the F1 generation, with offspring of 1,000 mg/L-exposed parents showing prolonged larval pupation time despite normal adult emergence timelines, indicative of partial developmental recovery. Mechanistically, high-dose PS disrupted endocrine signaling and altered expression of key developmental pathway regulators (EcR, InR, TOR, and E74B). These transcriptional changes were largely reversible in offspring, further supporting a similar gradually wash out recovery. While gut microbiota remained stable in exposed parents, offspring of 1,000 mg/L-exposed flies had significant microbiome alterations, highlighting clear trans-generational dysbiosis. This study provides new evidence that PS exposure during a sensitive developmental period in D. melanogaster can perturb development and gut microbial homeostasis across generations, offering insights relevant to understanding how early-life chemical exposures might influence conserved biological processes in higher organisms.}, }
@article {pmid41948046, year = {2026}, author = {Liu, R and Liu, J and Li, Z and Wang, Z and Ding, J and Yuan, J and Yao, B and Dong, X and Dai, W and Huang, Z and Zhang, CS and Zhang, W and Zheng, Y}, title = {The composting microbiome and a multifunctional Bacillus tequilensis JZF3 with straw degradation and pathogen inhibition.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768200}, pmid = {41948046}, issn = {1664-302X}, abstract = {Aerobic composting is a sustainable approach for converting organic waste into bio-fertilizer, where microorganisms play a central role in the degradation of recalcitrant lignocellulose. This study employed high-throughput sequencing to analyze the dynamic changes in bacterial and fungal communities during composting using distillers' grains, oil cake and cattle manure as raw materials. The results revealed pronounced successional changes in both microbial community structure and predicted function over time. Specifically, Firmicutes and Ascomycota were the dominant bacterial and fungal phyla, respectively, with the genus Bacillus maintaining high abundance throughout the process. The predicted functional profile indicated a shift in bacterial functions from initial xenobiotic biodegradation to core metabolic processes (such as energy and carbohydrate metabolism) in later stages. A total of 97 bacterial strains belonging to 38 species were isolated from different composting samples, with four strains (Bacillus licheniformis JZF8, B. altitudinis JZF2, B. tequilensis JZF3, and B. siamensis FJ3-3) showing strong cellulase, ligninase and protease activities. Among them, strain JZF3 not only exhibited these enzymatic activities and significant antagonistic activity against plant pathogens, but also was a dominant culturable species within the compost community. Furthermore, strain JZF3 was able to directly degrade rice straw without chemical pretreatment, achieving a degradation rate of 22.5%. The resulting degradation products also significantly promoted the growth of tobacco seedlings. This study identifies B. tequilensis JZF3 as a multifunctional agent that combines straw degradation with pathogen suppression and plant growth promotion, offering a novel strategy for synergizing agricultural waste recycling with disease control.}, }
@article {pmid41948248, year = {2026}, author = {Padmavathy, K and Maakhni, E and Biswas, PS and Sheikh, F and Chhabra, T and Das, B}, title = {Oral-Systemic Interactions in Modern Healthcare: A Systematic Review of the Interrelationship Between Dental Pathologies and Systemic Diseases.}, journal = {Cureus}, volume = {18}, number = {3}, pages = {e104813}, pmid = {41948248}, issn = {2168-8184}, abstract = {Periodontitis is a prevalent chronic inflammatory disease characterised by destruction of the supporting structures of the teeth, and increasing evidence indicates that periodontal inflammation and oral microbial dysbiosis contribute to systemic diseases through inflammatory, immune, and vascular mechanisms. This systematic review examined associations between periodontitis and cardiovascular, metabolic, autoimmune, neurological, and inflammatory outcomes in adult populations. Studies published from 2015 onward were identified using a structured literature search, including cohort studies, randomised controlled trials, case-control studies, cross-sectional analyses, Mendelian randomisation studies, and microbiome-based investigations. Due to heterogeneity in study designs and outcomes, qualitative synthesis was performed. Eleven studies met the inclusion criteria, demonstrating consistent associations between periodontitis and increased risk of hypertension, atrial fibrillation, rheumatoid arthritis, dementia, and elevated systemic inflammatory markers. Quantitative findings showed higher blood pressure, increased C-reactive protein levels, greater autoantibody positivity, enhanced inflammasome activity, and reduced oral microbiome diversity in individuals with periodontal disease. Periodontal therapy improved periodontal health and systemic inflammation, although cardiometabolic improvements were modest or inconsistent. The evidence supports periodontitis as a chronic inflammatory condition with significant systemic consequences, mediated by inflammatory, immune, and endothelial pathways, underscoring the importance of integrating periodontal health into disease prevention and management strategies in modern healthcare.}, }
@article {pmid41948280, year = {2026}, author = {Algindan, Y and AboAlsamh, H and Ahmad, S}, title = {Professional perspectives on PN among registered dietitians in Saudi Arabia: a mixed-methods assessment.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1695919}, pmid = {41948280}, issn = {2296-861X}, abstract = {BACKGROUND: The clinical implementation of personalized nutrition (PN) remains limited, despite growing interest. Healthcare professionals' readiness for adoption must be better understood.<br><br>OBJECTIVE: The aim of this study is to explore registered dietitians' perceptions, attitudes, and readiness regarding PN and multi-omics approaches in Saudi Arabia.<br><br>METHOD: A mixed-methods survey of 88 registered dietitians in Saudi Arabia provided quantitative and qualitative data on personalized nutrition technology (PNT) adoption patterns and barriers, analysed using the Consolidated Framework for Implementation Research (CFIR) to identify implementation barriers and facilitators.<br><br>RESULTS: PNT adoption was low (16%). Work experience, but not education level, had a relatively greater correlation with perceived usefulness of PNT (r&#x202f;=&#x202f;0.280, p&#x202f;=&#x202f;0.007). Genomics, metabolomics, and microbiome testing demonstrated strong correlations with PNT usefulness (r&#x202f;=&#x202f;0.321-0.571, p&#x202f;&#x2264;&#x202f;0.004). Qualitative findings identified knowledge gaps as the primary challenge and emphasized education as the key facilitator.<br><br>CONCLUSION: While Saudi dietitians have positive attitudes toward PN, they face significant implementation barriers at both an organizational and educational levels. For PN integration to be achieved within the Kingdom's healthcare system, policy, academic, and institutional interventions are required to enhance organizational support, professional training gaps, and interprofessional collaboration frameworks.}, }
@article {pmid41948282, year = {2026}, author = {Verstegen, REM and de Bruijn, MJW and Garssen, J and Folkerts, G and Kostadinova, AI and Hendriks, RW and Willemsen, LEM}, title = {Dietary fructo-oligosaccharides dose-dependently modulate the microbiome and suppress type 2 lung inflammation in a murine model of house dust mite-induced allergic asthma.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1705988}, pmid = {41948282}, issn = {2296-861X}, abstract = {INTRODUCTION: A balanced microbiome is crucial for local and systemic immune regulation. Dietary fibers can support the intestinal microbiome, protecting the host from allergic diseases, including asthma. The effects of fibers depend on their type, dose, and disease context. Here, we investigated the preventative effects of four doses of fructooligosaccharides (FOS) in a murine model for house dust mite (HDM)-induced allergic asthma.<br><br>METHODS: BALB/c mice received a diet containing 1%, 2.5%, 5%, or 10% FOS (w/w) both prior to and during sensitization and challenges with HDM. Bronchoalveolar lavage fluid (BALF), lung tissue, serum, and cecum content were collected at the endpoint. Fecal microbiome composition was analyzed, and levels of short-chain fatty acids (SCFAs) were measured in cecum content, serum, and lung samples.<br><br>RESULTS: HDM-allergic mice showed eosinophilic airway inflammation and increased pulmonary type 2 inflammation, while cecal SCFA levels were lower compared to sham mice. Serum acetate concentrations showed a similar decline (p = 0.092). The 10% FOS diet did not prevent allergic sensitization or eosinophilic airway inflammation; however, it significantly reduced the proportions of T helper 2 (Th2) cells and the Th2/Th1 ratio in the lungs, decreased concentrations of chemokine (C-C motif) ligand 2 (CCL22) and interleukin (IL-13) in the BALF, and inhibited IL-13 production upon ex vivo HDM restimulation of lung cells. The 2.5% and 5% FOS diets also decreased Th2 cell frequency in the lungs. High doses of FOS increased the abundance of fecal Prevotellaceae, while reducing fecal Oscillospiraceae and Lactobacillaceae. These microbial shifts were correlated with protective effects against type 2 inflammation. In HDM-allergic mice, fecal Prevotellaceae abundance correlated positively with serum acetate concentrations, which were correlated with type protective effects. In allergic mice, the 2.5% and 5% FOS doses were associated with increased abundance of fecal Muribaculaceae and Bacteroidaceae, respectively, along with elevated cecal SCFA concentrations. In addition, the 5% FOS dose increased the relative abundance of fecal Lachnospiraceae, which correlated negatively with serum acetate levels and type prevention.<br><br>DISCUSSION: Dietary FOS modulated the gut microbiome and attenuated pulmonary type 2 immune responses in a dose-dependent manner. These findings underscore the importance of fiber dosing for precision nutrition strategies in allergy management.}, }
@article {pmid41948296, year = {2026}, author = {Asad, S and Gu, P and Jiang, F and Liu, J and Chen, M and Karunarathna, SC and Atiq, M and Younas, M and Yapa, PN and Kan, X and Zhang, J}, title = {Pseudomonas parafulva SAPEU-1 as a keystone modulator: reshaping citrus phyllosphere microbiome to suppress citrus canker.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1771742}, pmid = {41948296}, issn = {1664-462X}, abstract = {INTRODUCTION: Citrus canker disease, caused by the pathogen Xanthomonas citri subsp. citri (Xcc) poses a substantial challenge for citrus production due to the limited efficacy of chemical control and increasing pathogen resistance.<br><br>METHODS: In this study, we isolated an endophytic bacterial strain, Endophyte S2, from the phyllosphere of citrus plants in Yunnan Province, China. We evaluated its efficacy both as a biocontrol agent and as a modulator of the citrus leaf microbiome.<br><br>RESULTS AND DISCUSSION: In vitro antagonism assays revealed that Endophyte S2 achieved the highest inhibition rate (68.2%) against Xcc among all tested isolates. Molecular identification based on 16S rRNA gene sequencing classified S2 as Pseudomonas parafulva SAPEU-01. In greenhouse trials, citrus plants with Xcc infestation were treated with SAPEU-01, and phyllosphere samples were collected before treatment and one month after, and analyzed by Illumina MiSeq sequencing. Post-treatment, &#x3b1;-diversity (richness and evenness) increased significantly, and &#x3b2;-diversity (PCoA, Bray-Curtis) showed a clear separation of microbial community structure, with reduced intra-group variability. Taxonomic shifts included the enrichment of Proteobacteria (particularly Pseudomonadaceae and Sphingomonadaceae), as well as genera such as Pseudomonas, Sphingomonas, and Methylobacterium, concomitant with a marked decline in Xanthomonadaceae (including X. citri) and opportunistic taxa such as Escherichia coli O157:H7 and Klebsiella aerogenes. Beneficial taxa, including Leuconostoc tardus, Sphingomonas, and Curtobacterium luteum, also increased. These results suggest Pseudomonas parafulva SAPEU-01 not only suppresses the pathogen but also restructures the phyllosphere microbiome toward greater stability and potential resilience.}, }
@article {pmid41948323, year = {2026}, author = {Chao, K and Ding, Y and Ji, W and Wang, D and Liang, Q and Sun, S and Li, L and Yang, H and Zhao, J}, title = {Indole-3-acetic acid derived from Blautia protects against sepsis-induced acute lung injury.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1707493}, pmid = {41948323}, issn = {1664-3224}, mesh = {Animals ; *Sepsis/complications/microbiology/immunology ; Rats ; *Acute Lung Injury/etiology/prevention &amp; control/microbiology/immunology/metabolism ; Male ; Humans ; Gastrointestinal Microbiome/drug effects ; *Indoleacetic Acids/pharmacology/metabolism ; Disease Models, Animal ; Female ; CD8-Positive T-Lymphocytes/immunology ; Middle Aged ; Rats, Sprague-Dawley ; Aged ; }, abstract = {OBJECTIVES: Sepsis-induced acute lung injury (SI-ALI) significantly contributes to sepsis mortality, with CD8[+] T cell depletion being a critical pathogenic factor. While Blautia, a gut commensal bacterium with established probiotic benefits in diverse diseases, its role in SI-ALI pathogenesis remains undefined. Here, we investigated the therapeutic potential of Blautia in lethal SI-ALI.<br><br>METHODS: Gut microbiome profiling was performed in SI-ALI patients and healthy controls to identify disease-associated microbial alterations. A cecal ligation and puncture (CLP) rat model of sepsis was used to validate microbiota changes and evaluate the therapeutic effects of Blautia supplementation. Untargeted metabolomic analysis was conducted to identify key metabolites associated with Blautia. Functional studies were performed to assess lung injury, immune responses, CD8[+] T cell abundance, and survival following Blautia or metabolite administration.<br><br>RESULTS: Gut microbiome analysis identified significant Blautia depletion in SI-ALI patients compared to healthy controls. This pathogenic alteration was faithfully reproduced in cecal ligation and puncture (CLP) -modeled septic rats, in which Blautia supplementation attenuated lung injury, enhanced systemic immune responses,and improved survival. Untargeted metabolomic profiling identified indole-3-acetic acid (IAA) as a key Blautia-derived metabolite. Administration of IAA alone recapitulated the protective effects of Blautia, significantly ameliorating SI-ALI. Crucially, both interventions restored CD8[+] T cell populations and augmented their functional responses. Clinical analysis revealed that elevated Blautia abundance in sepsis patients inversely correlated with pulmonary injury severity and positively associated with augmented CD8[+] T cell effector functions.<br><br>DISCUSSION: Our findings establish that Blautia and Blautia-derived IAA mitigates SI-ALI by counteracting CD8[+] T cell depletion and dysfunction, highlighting a novel and promising mechanism-based therapeutic strategy for life-threatening sepsis.}, }
@article {pmid41948342, year = {2026}, author = {Gao, KP and Dou, JR and Ma, BB and Ma, TB and Li, N and Qian, AD and Shan, XF and Sun, WW and Zhang, L and Zhang, D and Wang, CF and Zhang, DX}, title = {Engineered Lactobacillus casei targets the IgT-pIgR axis to confer mucosal protection against Aeromonas veronii in snakehead (Channa argus).}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1759765}, pmid = {41948342}, issn = {1664-3224}, mesh = {Animals ; *Lacticaseibacillus casei/genetics/immunology ; *Aeromonas veronii/immunology ; *Fish Diseases/immunology/microbiology/prevention &amp; control ; *Gram-Negative Bacterial Infections/immunology/prevention &amp; control/veterinary/microbiology ; *Immunity, Mucosal ; Probiotics/administration &amp; dosage ; *Bacterial Outer Membrane Proteins/immunology/genetics ; Bacterial Vaccines/immunology ; *Fish Proteins/immunology/genetics ; *Fishes/immunology/microbiology ; }, abstract = {INTRODUCTION: Aeromonas veronii remains a pervasive aquatic pathogen precipitating catastrophic economic depletion and threats to global food security. Conventional therapeutic modalities are constrained by inadequate stability, prohibitive costs, and biosafety risks.<br><br>METHODS: To address such challenges, an engineered Lactobacillus casei strain was developed to constitutively express the A. veronii outer membrane protein OmpAI through a tandem promoter system to ensure optimized antigen delivery.<br><br>RESULTS: Anal intubation with engineered L. casei in Channa argus stimulated compartmentalized mucosal immunity, evidenced by a six-fold elevation in hindgut IgT transcripts, significant infiltration of IgT[+] B cells, and pIgR mediated transcytosis, synchronized with systemic IgM activation. The probiotic treament accelerated pathogen clearance, improved survival rates to 42.9% compared to 12.5% in control group, and reorganized the commensal microbiome through a specific enrichment of beneficial Firmicutes.<br><br>DISCUSSION: This study elucidated a novel engineered-probiotic mucosal vaccination strategy for teleosts, providing a noninvasive, mucosal targeted immunoprophylactic strategy to decrease antibiotic dependency in aquaculture.}, }
@article {pmid41948584, year = {2026}, author = {Yu, J and Liu, X}, title = {Gut microbiota and sepsis: mechanisms, clinical correlations, and therapeutic prospects.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1793041}, pmid = {41948584}, issn = {2296-858X}, abstract = {Sepsis is a life-threatening organ dysfunction triggered by a dysregulated host response to infection. According to the Global Burden of Disease Study, this condition affects over 50 million people annually and causes approximately 5.3 million deaths, with fatality rates varying significantly across populations and healthcare settings, ranging from about 20% to 50%, representing a major challenge in critical care medicine. In recent years, the gut microbiota, as the largest microbial ecosystem in the human body, has increasingly demonstrated a central role. It is not only essential for maintaining intestinal barrier integrity, immune homeostasis, and metabolic balance but also actively participates in the pathogenesis, progression, and outcomes of sepsis through modulating immune responses, influencing the production of key metabolites, and mediating gut-organ axes. This article systematically reviews the characteristics of sepsis-induced gut microbiota dysbiosis, delves into the molecular mechanisms by which dysbiosis drives immune disorders, metabolic disturbances, and multi-organ injury, evaluates the clinical potential and current limitations of microbiome-associated biomarkers, and summarizes recent advances and controversies in microbiota-targeted therapeutic strategies, including probiotics, fecal microbiota transplantation, precision nutrition, and antibiotic stewardship. This review aims to analyze the shortcomings and translational challenges in current research, providing a theoretical basis and forward-looking perspective for developing precise microbiome-based individualized management strategies for sepsis.}, }
@article {pmid41948629, year = {2026}, author = {Osei-Poku, P and Wilson, MB and Shardow, ALK and Abakah, A and Amewu, EKA and Kyerewaa, CA and Larbi, A and Kwarteng, A}, title = {Tetracycline Resistance Pattern Among Lymphatic Filariasis-Hyperendemic Communities in Southern Ghana: A Mixed-Method Approach.}, journal = {Health science reports}, volume = {9}, number = {4}, pages = {e72242}, pmid = {41948629}, issn = {2398-8835}, abstract = {BACKGROUND AND AIM: Tetracyclines continue to serve as a cost-effective and essential treatment for common infections, particularly in resource-limited regions such as lymphatic filariasis (LF)-hyperendemic communities. The growing use of tetracycline-based antibiotics by symptomatic filarial lymphedema patients, likely influenced by the demonstrated benefits of anti-Wolbachia therapy, especially following doxycycline trials, underlines the necessity for vigilant monitoring of tetracycline resistance patterns. This study evaluated patients' antibiotic knowledge, attitude and practice in LF-endemic communities, and the resistance profiles of tetracycline-class antibiotics to assess the clinical impact of resistance on current anti-Wolbachia treatments.<br><br>METHODS: This cross-sectional study in Ghana's Ahanta West District enrolled 71 filarial lymphedema patients from four LF-hyperendemic communities. Structured questionnaires evaluated KAP on antibiotic use and resistance, complemented by microbiological analysis of wound swabs from 28 patients to profile the wound microbiome and assess tetracycline resistance.<br><br>RESULTS: Mean antibiotic knowledge (1.8&#x2009;&#xb1;&#x2009;1.0), attitude (1.4&#x2009;&#xb1;&#x2009;1.1), and practice (1.9&#x2009;&#xb1;&#x2009;1.1) scores were low, yielding a combined KAP score of 5.0&#x2009;&#xb1;&#x2009;1.9 (31.2%&#x2009;&#xb1;&#x2009;11.9%) with no significant correlation to the educational level of patients. the facilities survey, the primary healthcare facilities in the area stocked at least one tetracycline-class antibiotic (specifically tetracycline and/or doxycycline). Microbiological testing identified 68 distinct bacterial isolates (20 genera, 36 species; dominated by S. sciuri, S. aureus). Varied tetracycline resistance observed: doxycycline (35.3%), tetracycline (26.5%), and minocycline (17.6%), with nine (13.2%) isolates resistant to all three. High-resolution melting analysis detected tet(M) gene in 34.1% (14) of isolates with Tm variation (69.27&#xb0;C-73.06&#xb0;C), suggesting variants.<br><br>CONCLUSION: Multifaceted strategies are essential to curb tetracycline resistance and overuse. These include culturally adapted education to enhance antibiotic stewardship among patients and providers, optimized wound care protocols addressing polymicrobial infections through improved hygiene and tailored regimens, and ongoing resistance surveillance to track trends while promoting therapeutic alternatives.}, }
@article {pmid41948819, year = {2026}, author = {Cheng, L and Cai, J and Auster, A and Cho, S and Keir, M and Rhee, H and Kapili, B and Shalon, D and Ning, M}, title = {Translational Modeling of Gut Microbiome-Mediated Drug Metabolism: A Case Example of Sulfasalazine.}, journal = {CPT: pharmacometrics &amp; systems pharmacology}, volume = {15}, number = {4}, pages = {e70246}, doi = {10.1002/psp4.70246}, pmid = {41948819}, issn = {2163-8306}, mesh = {Humans ; *Sulfasalazine/pharmacokinetics/administration &amp; dosage ; *Gastrointestinal Microbiome/physiology ; *Models, Biological ; Feces/microbiology ; Sulfapyridine/pharmacokinetics/metabolism ; Male ; Mesalamine/pharmacokinetics/metabolism ; Adult ; *Anti-Inflammatory Agents, Non-Steroidal/pharmacokinetics ; Female ; }, abstract = {The gut microbiome can contribute to drug metabolism and significantly influence pharmacokinetic (PK) behavior. Sulfasalazine is well-known to be metabolized by gut bacterial azoreductases into sulfapyridine and mesalamine. Despite in vitro and in vivo evidence of the gut microbiome's role in drug metabolism, quantitative predictions of its impact on drug PK are lacking. To address this gap, we used sulfasalazine and its metabolites as a case example to build a translational modeling framework to predict the extent of gut microbiome-mediated drug metabolism and subsequent PK of the metabolites. First, sulfasalazine conversion kinetics was measured in vitro using pooled human fecal homogenate incubation. In vitro Vmax was 650.5 and 200.9 pmol/min/mg feces, and Km was 3648 and 1605 μM for sulfapyridine and mesalamine formation, respectively. Based on colon and feces bacterial counts from nine healthy humans, a ratio of 0.47 was used to scale in vitro fecal Vmax to the colon level. Second, physiologically-based pharmacokinetic (PBPK) models for sulfasalazine, sulfapyridine, and mesalamine were built in Simcyp and verified to predict their oral PK when dosed directly. Lastly, sulfapyridine or mesalamine PK after dosing sulfasalazine was predicted by linking the parent and metabolite PBPK models with colon luminal metabolism kinetics. The observed sulfapyridine and mesalamine PK after dosing sulfasalazine were predicted with weighted average fold-errors of 1.21, 1.22, and 1.05 for Cmax, Tmax, and AUC, respectively. Overall, this in vitro to in vivo translation and modeling framework provides valuable insights for quantitatively predicting the in vivo impact of gut microbiome-mediated drug metabolism.}, }
@article {pmid41948926, year = {2026}, author = {Garg, I and Singh, N and Rawat, S and Negi, T and Chaurasia, U and Gupta, P}, title = {Decoding the Skin Micro-Immune Milieu, Homeostasis, and Keratinocyte Trafficking in Psoriatic Disease.}, journal = {Immunological investigations}, volume = {}, number = {}, pages = {1-31}, doi = {10.1080/08820139.2026.2651752}, pmid = {41948926}, issn = {1532-4311}, abstract = {INTRODUCTION: The skin, acting as a complex interface between the immune system and microbiome, maintains balance through coordinated interactions among the epidermal barrier, microbiome, and immune responses. Psoriasis, a chronic autoimmune and inflammatory disorder, disrupts this balance by altering keratinocyte growth, immune signaling, and microbial diversity.<br><br>RESULTS AND DISCUSSION: The psoriatic environment exhibits dysbiosis, with reduced &#x3b1;-diversity and increased &#x3b2;-diversity, thereby worsening lesions. Beneficial microbes like Staphylococcus epidermidis provide protection, while opportunistic pathogens such as Staphylococcus aureus, Streptococcus pyogenes, Malassezia, Candida albicans, and HPV can trigger psoriatic outbreaks. Keratinocytes, essential to disease development and progression, interact actively with immune cells, fibroblasts, and Langerhans cells through cytokines, chemokines, and extracellular vesicles, influencing cell movement and inflammation. Changes in pathways like GLUT-1-mediated glucose metabolism and PI3K/Akt/mTOR signaling promote epidermal overgrowth, new blood vessel formation, and immune imbalance. Oxidative stress and mitochondrial dysfunction also weaken skin homeostasis. The skin's lymphoid tissue (SALT) and inducible SALT are crucial for immune surveillance and autoimmunity but become hyperactive in psoriasis.<br><br>CONCLUSION: Understanding the complex network linking the skin microbiome, immune system, and keratinocyte behavior is essential for developing advanced treatments. Combining immunology, molecular biology, and drug delivery science, using molecular docking, in-silico modeling, and nanotherapy, offers promising options for targeted psoriasis therapy.}, }
@article {pmid41949018, year = {2026}, author = {Grabska, M and Gorecki, A and Pye, HV and Adriaenssens, EM and Grzesiuk, M}, title = {Phage Cocktail Designed for Wastewater Bioremediation Has Limited Effect on Crustacean Filtrator Microbiome Diversity and Health.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70329}, pmid = {41949018}, issn = {1758-2229}, support = {UMO-2021/03/Y/NZ9/00141 under the frame work of JPIAMR-ACTIONGA no. 963864//National Science Centre/ ; MR/W031205/1/MRC_/Medical Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13633/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13634/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13635/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13636/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Bacteriophages/physiology ; *Microbiota ; *Wastewater/microbiology/virology ; *Daphnia/microbiology/virology/growth &amp; development ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Bacteria/genetics/classification/virology ; Klebsiella pneumoniae/virology ; Pseudomonas aeruginosa/virology ; Enterobacter/virology ; Female ; Biodiversity ; }, abstract = {In this study we investigated the impact of a phage cocktail on Daphnia magna microbiome and the life-history parameters. A mixture of four phages able to infect strains of Klebsiella pneumoniae, Enterobacter sp. and Pseudomonas aeruginosa was tested on three D. magna clones. The host-associated microbiome composition in both the examined variants and the control was analysed using 16S rRNA amplicon sequencing. Additionally, the survival, growth rate, age, size at the first reproduction, and neonate per female were assessed. The analysis revealed minor shifts in microbial composition following phage exposure. Nevertheless, results showed that the phage cocktail increased microbiome diversity. None of the life-history parameters studied were affected by the presence of the phage cocktail, and no adverse effects were observed. The results indicated that under laboratory conditions the phage cocktail is safe for D. magna and its microbiome.}, }
@article {pmid41949064, year = {2026}, author = {Chongtham, C and Biswas, T and Kumari, N and Kar, R and Jyotsna,  and S, J and Pant, A and S Patil, V and Arimbasseri, GA}, title = {The JNK2-microbiome axis modulates gut barrier integrity through microbial acetate.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2651962}, doi = {10.1080/19490976.2026.2651962}, pmid = {41949064}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Acetates/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Milk ; *Mitogen-Activated Protein Kinase 9/metabolism/genetics ; Female ; Weaning ; Dextran Sulfate ; Male ; Diet, High-Fat ; }, abstract = {BACKGROUND: Weaning involves a nutritional shift from fat-rich milk to carbohydrate-based solid food, reshaping metabolism, microbiota, and gut immune tolerance. While dairy remains a component of the human diet beyond weaning, the impact of continued milk supplementation on gut epithelial homeostasis remains poorly understood.<br><br>RESULT: Here, using a mouse model, we show that continued milk-based feeding post-weaning promotes intestinal barrier function by enriching the commensal bacterium Dubosiella newyorkensis, which produces acetate to activate epithelial JNK2 signaling. This pathway enhances barrier integrity and suppresses inflammation induced by mild dextran sodium sulfate (DSS) treatment. In contrast, feeding a lard-based high-fat diet or transient pharmacologic inhibition of JNK2 induces epithelial P38 activation, resulting in barrier disruption and inflammation. Importantly, the beneficial effects of milk were observed only if they were initiated during the weaning period, when the microbiome is in a metastable transitional state. Initiation of the same intervention two weeks after weaning led to P38 activation and inflammatory responses.<br><br>CONCLUSION: Our findings show that immediate post-weaning milk supplementation preserves a beneficial gut microbiome, marked by the persistence of D. newyorkensis and enhanced gut barrier integrity. Even a one-week delay eliminates this protective effect, emphasizing the critical timing of post-weaning nutritional intervention for maintaining intestinal health.}, }
@article {pmid41949254, year = {2026}, author = {Du, J and Sun, Y and Yu, D and Lu, S and Yu, S and Wang, M and Zhou, G and Xu, S and Zhang, L and Zhu, Y and Zhou, L}, title = {Oral liposomal co-delivery of ultrasmall ceria and 5-aminosalicylic acid alleviates DSS colitis via ROS scavenging and microbiome remodeling.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6tb00173d}, pmid = {41949254}, issn = {2050-7518}, abstract = {Inflammatory bowel disease (IBD) is a refractory gastrointestinal disorder characterized by sustained intestinal inflammation, mucosal barrier dysfunction, and gut dysbiosis. Excess reactive oxygen species (ROS) is a key driver of these pathological processes. Although CeO2-based nanozymes can scavenge ROS, their clinical application is limited by poor aqueous stability. Here, we developed an oral nanozyme by co-encapsulating ultrasmall CeO2 nanoparticles and the clinical drug 5-aminosalicylic acid (5-ASA) within liposomes. The resulting formulation (CeLA) exhibited excellent colloidal stability and robust ROS-scavenging activity and provided marked cytoprotection against oxidative stress in vitro. In a dextran sulfate sodium (DSS)-induced colitis model, CeLA alleviated clinical symptoms, restored intestinal barrier integrity, and suppressed pro-inflammatory cytokine expression. Notably, CeLA also reshaped the dysbiotic gut microbiome by reducing pro-inflammatory bacterial taxa. This multifunctional nanozyme integrates antioxidant, anti-inflammatory, and microbiome-modulating effects, offering a promising therapeutic strategy for IBD.}, }
@article {pmid41949255, year = {2026}, author = {Wang, W and Guan, R and Wang, Q and Xiong, L and He, A and Bai, L and Li, Z and Lu, C and Zhang, S and Zhao, C and Yin, Y and Li, J and Wang, Y and Jiang, G}, title = {Traditional Fermentation Amplifies PFAS Bioaccessibility: Defining Fermented Fish Products as an Unrecognized Source of Dietary Exposure.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15723}, pmid = {41949255}, issn = {1520-5851}, abstract = {Per- and polyfluoroalkyl substances (PFAS), as a class of persistent organic pollutants, are well-characterized environmental and human health threats; however, their behavior in food systems, particularly during fermentation, remains poorly understood. Here, we show that traditional fermentation significantly enhances the PFAS bioaccessibility. Through a 300 day model fermentation system, we observed near-complete release of several major PFAS congeners. While microbial transformation of the PFAS precursor of N-ethyl perfluorooctane sulfonamide (N-EtFOSA) was observed, persistent congeners of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) remained unaffected during microbiome restructuring. We demonstrate that matrix degradation and microbial activity synergistically modify the PFAS binding states. In silico modeling reveals a shift in bioaccessibility determinants from specific binding to partitioning behavior, establishing that fermentation liberates PFAS via two key pathways: microbial degradation of structural components, releasing bound contaminants and altered PFAS partitioning during digestion. Our findings establish fermentation as a previously unrecognized amplifier of dietary PFAS exposure, with substantial implications for food safety and public health, especially in populations with high consumption of traditionally fermented products.}, }
@article {pmid41949309, year = {2026}, author = {Yang, P and Wu, Z and Zhang, S and Yan, L and Yan, Y and Zhou, F and Ren, X and Li, Y and Gu, S and Gao, S and Zhang, Z and Zhang, Y and Zhu, H and Li, H and Zhang, Z}, title = {Predicting dairy cattle PL via longitudinal rumen microbiome dynamics using machine learning approaches.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0296925}, doi = {10.1128/spectrum.02969-25}, pmid = {41949309}, issn = {2165-0497}, abstract = {Aging is a spontaneous biological process involving intricate regulatory mechanisms over time. Studies in mice and humans indicate that the gut microbiota is closely linked to the aging process and plays an important role in it. However, the relationship between the rumen microbiota and aging in dairy cows remains unclear. In this study, we characterized rumen microbial differences across different parities in 341 dairy cows using 16S rRNA amplicon sequencing and identified microbial markers associated with productive lifespan (PL) and farm profitability through machine learning analysis. Our findings reveal that as parity increases, the rumen microbiota undergoes systematic succession: alpha diversity indices significantly decrease, microbial interactions weaken, the abundance of Proteobacteria increases, while the abundance of Bacteroidetes decreases in higher-parity cows. By integrating machine learning with 16S sequencing, we identified characteristic microbial markers predictive of PL and farm profitability. Specifically, the support vector regression model achieved a predictive performance with an area under the curve (AUC) of 0.788 and identified eight key genera associated with the PL of dairy cows. Meanwhile, the random forest (RFTEST) model attained an AUC of 0.763 and selected eight key microorganisms linked to the economic benefits of the farm, with fivefold cross-validation confirming the reliability of RFTEST. Combined with SHapley Additive exPlanations (SHAP) analysis, the genus-level taxa Eubacterium_hallii_group and Prevotella_7 can serve as indicator strains for PL and farm profitability in dairy cows. Therefore, alterations in the rumen microbiota may serve as a key driver of aging in dairy cows. This study aims to provide insights for improving PL and farm profitability through the modulation of rumen microbiota.IMPORTANCEIn the dairy industry, longevity is a critical economic trait that directly impacts overall farm profitability. Although dairy cows have a natural lifespan of approximately 20 years-with optimal productivity often extending beyond the fifth parity-their average PL is only about 2.7 parities. Identifying factors influencing PL is therefore crucial. Given the vital role of the rumen microbiota in regulating dairy performance, milk fat/protein synthesis, and other key physiological processes, elucidating its correlation with PL is essential for developing probiotic interventions to enhance longevity. Furthermore, early detection of aging-associated microbial signatures could facilitate proactive adjustments to feeding strategies. Notably, this is the first study to link parity-driven microbiome succession with PL prediction in dairy cattle. Consequently, by identifying microbial molecular markers linked to PL and potential probiotic targets, this study highlights promising opportunities to improve dairy cow health and advance sustainable dairy farming practices.}, }
@article {pmid41949699, year = {2026}, author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B}, title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {41949699}, issn = {1869-1889}, abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.}, }
@article {pmid41950008, year = {2026}, author = {Mifflin, KA and Kigerl, KA and Hudson, LC and Guan, Z and Popovich, PG}, title = {Protocol for performing traumatic spinal cord injury surgery on mice in germ-free isolators and assessing injury recovery and pathophysiology.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104488}, doi = {10.1016/j.xpro.2026.104488}, pmid = {41950008}, issn = {2666-1667}, abstract = {An altered gut microbiome affects recovery from traumatic spinal cord injury (SCI). Here, we present a protocol for performing SCI survival surgery on mice in germ-free isolators. Specifically, we describe steps for colonization, preparing surgical tools, performing surgery, and post-surgical care. We then outline procedures for behavioral assessment, followed by collecting and processing tissue to assess injury recovery and pathophysiology. This protocol can be easily adapted to study the gut microbiome's influence on other forms of central nervous system injury.}, }
@article {pmid41950061, year = {2026}, author = {Dayman, NA and Patel, D and Wisniewska, A and Fletcher, E and Ahmed, MI and Modha, D and Barer, MR and Gaillard, EA}, title = {Face mask sampling for the detection of microbes in expelled aerosols and the impact of airway clearance on microbial yield in children with cystic fibrosis: a feasibility trial.}, journal = {Journal of medical microbiology}, volume = {75}, number = {4}, pages = {}, doi = {10.1099/jmm.0.002150}, pmid = {41950061}, issn = {1473-5644}, mesh = {Humans ; *Cystic Fibrosis/microbiology ; Child ; Male ; Female ; Adolescent ; Child, Preschool ; *Masks/microbiology ; Prospective Studies ; Cross-Sectional Studies ; Feasibility Studies ; Infant ; Sputum/microbiology ; *Bacteria/isolation &amp; purification/classification ; Specimen Handling/methods ; Pseudomonas aeruginosa/isolation &amp; purification ; Aerosols ; *Respiratory Tract Infections/microbiology/diagnosis ; }, abstract = {Background. Early identification of pulmonary exacerbations is vital for the management of cystic fibrosis (CF). Non-invasive airway sampling in preschool children can be inaccurate. Face mask sampling (FMS) is a novel non-invasive approach that can be used to assess microbial airway pathogens in patients with CF.Methods. Prospective cross-sectional study in children with CF. Children wore a suitably sized face mask fitted with two strips of a polyvinyl alcohol sampling matrix for a period of 15 min. Routine microbiology sampling using cough swab, sputum and/or bronchoalveolar lavage was completed following FMS. Children then completed their routine airway clearance with their physiotherapist. Following this, a separate face mask was worn for a further 15 min, after which further routine microbiology sampling (cough swab or sputum) was completed. The face masks were stored at room temperature before transfer and processing in the laboratory to quantify bacterial burden and identify key pathogens such as Mycobacterium abscessus and Pseudomonas aeruginosa.Results. Eleven children (six male, median age 12 years, range 1-16 years), from the Leicester CF cohort were included. All patients tolerated the FMS. Nine face mask samples from 11 participants isolated respiratory pathogens, including M. abscessus (n=3). P. aeruginosa was not detected on face mask samples. There was a trend towards an increase in microbial yield (prGen16s) following airway clearance (n=5), but this did not reach statistical significance.Conclusions. FMS systems are feasible for children and young people with CF. They may provide an effective method to detect exhaled lower airway pathogens including non-tuberculous mycobacteria. The effect of physiotherapy on the exhaled microbiome needs to be explored further.}, }
@article {pmid41950213, year = {2026}, author = {Babbo, CC and van Rensburg, J and Mellet, J and Velaphi, SC and Nakwa, FL and Masemola, MYK and Kali, GTJ and Foden, CJ and Oosthuizen-Vosloo, S and Chellan, V and Mosuwe, O and Mistry, P and Buyens, ARM and Barmania, F and Pillay, S and Ballot, DE and Coetzee, M and Horn, AR and Wright, C and Schubertand, PT and Pepper, MS}, title = {Protocol: A multi-factorial, multi-centre study, for biomarker identification in healthy controls for comparison to babies with moderate-severe NESHIE.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0346798}, pmid = {41950213}, issn = {1932-6203}, mesh = {Humans ; Infant, Newborn ; *Biomarkers/blood/analysis/metabolism ; *Hypoxia-Ischemia, Brain/genetics/metabolism/diagnosis ; Female ; Male ; DNA Methylation ; Case-Control Studies ; }, abstract = {Neonatal encephalopathy suspected to be hypoxic-ischaemic encephalopathy (NESHIE) remains a leading cause of neonatal mortality and long-term neurodevelopmental impairment, particularly in low- and middle-income countries. While therapeutic hypothermia reduces mortality in moderate to severe cases, a significant proportion of affected infants continue to experience adverse neurological outcomes. This multi-centre observational study aims to elucidate the clinical and biological mechanisms underlying NESHIE by conducting a comprehensive comparative analysis of neonates with moderate to severe NESHIE and healthy term controls. Participants with NESHIE were previously recruited under an existing approved protocol (University of Pretoria ethics reference: 481/2017), and healthy neonates will be newly enrolled. The study will integrate clinical and molecular data to: (1) identify clinical risk factors associated with NESHIE; (2) perform whole genome sequencing to detect relevant genetic variants; (3) analyse DNA methylation patterns via bisulfite sequencing; (4) assess gene expression using bulk and single-cell RNA sequencing (RNA-seq); (5) characterise proteomic and metabolomic profiles through liquid chromatography-mass spectrometry of dried blood spot samples; (6) examine the placental microbiome; and (7) evaluate placental histopathological differences between groups. By offering a multi-dimensional view of the molecular and microbial landscape of NESHIE in a South African cohort, this study aims to enhance understanding of the disease pathogenesis. Ultimately, the findings may support the development of biomarkers for early diagnosis, improve risk stratification, and guide novel therapeutic strategies for affected neonates. The study has received National Health Research Database (NHRD) registration under GP_202411_053 (Gauteng) and WC_202411_026 (Western Cape), with ethics approvals granted by the University of Pretoria (184/2024), University of the Witwatersrand (250406B), and Stellenbosch University (N24/12/154_RECIP_UP184/2024) as well as their respective tertiary academic hospitals.}, }
@article {pmid41950528, year = {2026}, author = {Federico, VA and Cliffel, DE and Gaddy, JA and Townsend, SD}, title = {Shaping of the Infant Gut Microbiome by Milk Oligosaccharides.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051024-062915}, pmid = {41950528}, issn = {1545-4509}, abstract = {The gut microbiome governs aspects of human growth and development. While human milk's primary purpose is metabolism, it also provides nonnutritious biologics and macromolecules. This mixture includes the human milk oligosaccharides (HMOs), which are indigestible and survive the low pH of the stomach and small intestine, reaching the large intestine intact. Here, HMOs serve as prebiotics for beneficial bacteria, providing a competitive growth advantage over potential pathogens. Upon metabolizing HMOs, commensals generate short-chain fatty acids and metabolites that enhance the gut community. Therefore, HMOs work to develop and sustain the gut microbial community as a living therapeutic that prevents illness from potential microbial pathogens and modulates development of the infant gut. The goal of this targeted review is to characterize the roles HMOs play in governing bacterial and viral members of the infant gut microbiome, describing how HMOs both define a healthy microbiota and prevent microbial dysbiosis.}, }
@article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, }
@article {pmid41950535, year = {2026}, author = {Adeniji, A and Liu, Q and Huang, X and Lu, X and Li, S and Guo, R}, title = {Correlation between root exudate composition and beneficial bacteria underlies Fusarium wilt resistance in cucumber.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128512}, doi = {10.1016/j.micres.2026.128512}, pmid = {41950535}, issn = {1618-0623}, abstract = {Rhizosphere microbes regulated by root exudates play important roles in promoting plant growth and suppressing soil-borne diseases. However, their functions in monoculture systems are not well studied. Here, we integrated metabolomic and microbiome analyses to compare root exudate profiles and rhizosphere communities of Fusarium oxysporum f. sp. cucumerinum (Foc) resistant (CL11) and susceptible (ZN6) cultivars grown in naturally infested, continuous-cropping soil. The asymptomatic, resistant cultivar CL11 (CL11H) exhibited a metabolic signature enriched in defensive compounds (ganoderic acid I and L-isoleucine) and harbored a beneficial bacterial community dominated by Streptomyces, Cellvibrio, and Ensifer. While the asymptomatic susceptible cultivar ZN6 (ZN6H) showed elevated levels of primary metabolites (methylmalonic and succinic acids) and an enrichment in the relative abundance of Amycolatopsis and Flavobacterium. Upon symptom development, susceptible symptomatic ZN6 (ZN6D) mounted a "cry-for-help" response, accumulating L-tryptophan and citric acid, which correlated with recruitment of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Conversely, resistant symptomatic CL11 (CL11D) deployed a metabolic profile (L-3-cyanoalanine, 4-hydroxybenzoyl glucose, D-fructose), which enriched Bacillus and Cellvibrio. Exogenous application of citric acid, L-isoleucine, L-tryptophan, hexadecanedioic acid, and succinic acid to susceptible ZN6 plants significantly suppressed wilt disease. These metabolites restructured the rhizosphere bacterial communities, demonstrated by enrichments of Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, and Comamonadaceae by L-tryptophan, as well as Pseudomonas and Bacillus promoted by L-isoleucine and citric acid, respectively. Moreover, succinic acid suppressed disease through microbiome-mediated mechanisms despite its in vitro positive effect on Foc growth. These findings demonstrate that root exudates are linked to cultivar-specific disease outcomes, and that target metabolite application can suppress Fusarium wilt through microbiome-mediated mechanisms or a combined antifungal mode.}, }
@article {pmid41950737, year = {2026}, author = {Jung, Y and Yeo, S and Kim, RH and Seo, CH and Joo, SY and Shin, JH and Cho, YS}, title = {Response to antihistamines in post-burn pruritus is associated with gut microbiota composition and function: A prospective cohort study with a nested case-control analysis.}, journal = {Burns : journal of the International Society for Burn Injuries}, volume = {52}, number = {5}, pages = {108005}, doi = {10.1016/j.burns.2026.108005}, pmid = {41950737}, issn = {1879-1409}, abstract = {Post-burn pruritus (PBP) is a common complication following burn injuries, with substantial interindividual variability in response to antihistamine treatment. While altered gut microbial communities have been observed in patients with histamine intolerance, no studies have examined the relationship between gut microbiota and antihistamine responsiveness in burn patients. Therefore, we hypothesized that the gut microbiome composition differs according to antihistamine responsiveness in patients with PBP. A total of 56 male burn patients categorized into no-pruritus, antihistamine-responsive (HR), and antihistamine-nonresponsive (HNR) groups. Fecal samples were collected at baseline and after 8 weeks of antihistamine treatment. Microbial composition was analyzed using 16S rRNA gene sequencing, and functional prediction was conducted with PICRUSt2. Overall microbial diversity did not differ significantly between groups; however, distinct taxonomic and functional features were identified. The HR group was characterized by enrichment of Sutterella and showed a temporal increase in microbial diversity and Bifidobacterium abundance after 8 weeks of treatment, accompanied by enrichment of redox-related microbial functions. In contrast, the HNR group showed increased Akkermansia and Acidaminococcus with reduced antioxidant defenses and activation of non-histaminergic pruritic pathways. This study is the first to suggest that gut microbiota composition and function are associated with antihistamine responsiveness in patients with PBP. Distinct microbial signatures and functional pathways were identified among non-pruritic individuals, antihistamine responders, and non-responders. Our findings indicate a potential involvement of gut microbes in the pathophysiology of PBP and highlight the possibility of microbiota-targeted therapeutic strategies.}, }
@article {pmid41938779, year = {2026}, author = {Luttenschlager, H and Noel, G and Alabi, T and Carpentier, J and Francis, F and Megido, RC}, title = {Microbial drivers of Black Soldier Fly biowaste valorization: from microbiome functions to scalable insect-microbe systems.}, journal = {AIMS microbiology}, volume = {12}, number = {1}, pages = {126-149}, pmid = {41938779}, issn = {2471-1888}, abstract = {Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.}, }
@article {pmid41938782, year = {2026}, author = {Mataragka, A and Ringø, E and Papastathis, AK}, title = {Climate-driven restructuring of sediment microbiomes and ecosystem functions in aquaculture systems.}, journal = {AIMS microbiology}, volume = {12}, number = {1}, pages = {150-172}, pmid = {41938782}, issn = {2471-1888}, abstract = {Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.}, }
@article {pmid41938867, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R}, title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779554}, pmid = {41938867}, issn = {2235-2988}, mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.<br><br>METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.<br><br>RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.<br><br>DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.}, }
@article {pmid41939093, year = {2026}, author = {}, title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers: Retraction.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {4}, pages = {2724}, pmid = {41939093}, issn = {2049-0801}, abstract = {[This retracts the article DOI: 10.1097/MS9.0000000000004567.].}, }
@article {pmid41939102, year = {2026}, author = {Mohan, A and Sultany, A and Fatima, SB and Hasan, ZW and Butt, MD and Alkhazender, AHJ and Lal, PM and Aminpoor, H and Karimi, H and Kumar, V and Tejwaney, U and Kumar, S}, title = {Association between atrial fibrillation and gastrointestinal bleeding: pathophysiology, risk stratification, and management - a narrative review.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {4}, pages = {2566-2573}, pmid = {41939102}, issn = {2049-0801}, abstract = {Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of thromboembolic events, necessitating anticoagulation therapy. However, anticoagulation, particularly with novel oral anticoagulants, elevates the risk of gastrointestinal bleeding (GIB), creating a clinical dilemma in managing AF patients. This narrative review explores the pathophysiology linking AF and GIB, emphasizing the hypercoagulable state in AF and the mucosal damage caused by anticoagulants. Epidemiological data reveal that GIB incidence in AF patients ranges from 1.32% to 5.4% annually, with risk factors including older age, prior GIB, and concomitant antiplatelet use. Risk stratification tools such as CHA2DS2-VASc and HAS-BLED aid in balancing thromboembolic and bleeding risks, though their predictive performance remains modest. Comparative studies highlight that rivaroxaban carries a higher GIB risk, while apixaban offers a safer profile. Management strategies include proton pump inhibitors for prophylaxis, endoscopic interventions for acute bleeding, and individualized decisions on resuming anticoagulation post-GIB, typically within 7-30 days. Emerging research on the gut microbiome's role in AF pathogenesis suggests potential novel therapeutic avenues. A multidisciplinary approach involving cardiologists, gastroenterologists, and hematologists is essential to optimize outcomes. Future directions include developing safer anticoagulants, refining risk prediction models, and exploring microbiome-targeted therapies.}, }
@article {pmid41939187, year = {2026}, author = {Zhang, H and Wu, ZH and Sun, XM and Sun, C and Chang, J and Yuan, L}, title = {Gender-specific and dose-dependent responses to L-se-methylselenocysteine are mediated by the gut microbiota-metabolite axis: implications for intestinal homeostasis and safe clinical application.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1803630}, pmid = {41939187}, issn = {2296-861X}, abstract = {INTRODUCTION: L-Se-methylselenocysteine is a prominent naturally occurring organic selenium compound with notable health benefits and validated efficacy in managing various diseases. However, its impacts on intestinal microecology and the role of the gut microbiota-metabolite axis in mediating host health outcomes remain unclear.<br><br>METHODS: Sprague-Dawley rats were subjected to a 90-day chronic toxicity study, combined with integrated intestinal microbiome and metabolome analysis, to explore L-Se-methylselenocysteine's effects and underlying mechanisms.<br><br>RESULTS: L-Se-methylselenocysteine at doses of 0.25-0.75 mg/kg bw/ day enhanced gut microbiota biodiversity, enriched probiotic abundance, ameliorated hematological and serum biochemical indices, and promoted synthesis of beneficial metabolites via modulating the gut microbiota-metabolite axis. Notably, high-dose L-Se-methylselenocysteine (2.25 mg/kg bw/day) induced irreversible hepatosplenic injury in female rats but not males, with gender-specific responses mediated by the axis.<br><br>DISCUSSION: L-Se-methylselenocysteine confers intestinal health benefits through the gut microbiota-metabolite axis, while defining a safe dosage range. This study provides a solid scientific basis for the rational application of L-Se-methylselenocysteine as a selenium supplement.}, }
@article {pmid41939240, year = {2026}, author = {Barrera-Suarez, MA and Zhao, CY and Karnatovskaia, LV and Sung, J}, title = {Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2650247}, pmid = {41939240}, issn = {2993-3935}, abstract = {Diet-gut microbiome interactions drive substantial inter-individual variability in metabolic responses to food, a fact that challenges the efficacy of uniform dietary recommendations. To address this complexity, advances in multi-omics profiling, dietary assessment technologies, and host clinical phenotyping now generate high-resolution multimodal datasets. However, managing these vast amounts of data necessitates the integration of artificial intelligence (AI) and machine learning (ML) approaches. In this review, we first delineate the multimodal data landscape and its associated computational workflows. These range from the initial preprocessing of heterogeneous inputs (filtering, normalization, dimensionality reduction) to ML modeling strategies designed to address high dimensionality, sparsity, and compositionality through feature engineering and regularization. We then summarize core ML applications, including the classification of habitual dietary patterns from microbiome signatures, prediction of postprandial metabolic responses, responder stratification, and in silico simulation of dietary perturbations. Furthermore, recent randomized controlled trials demonstrate the tangible clinical potential of AI-guided personalization. Next, we highlight composite microbiome health metrics and diet-specific indices, such as GMWI2 and DI-GM. These tools are essential because they condense high-dimensional taxonomic profiles into interpretable wellness scores for monitoring diet-induced shifts. We subsequently examine genome-scale metabolic models and microbiome "digital twins" that mechanistically link dietary substrates to community metabolism and host-relevant metabolites. We also discuss emerging hybrid AI-mechanistic frameworks that enhance interpretability, biological plausibility, and scalability. Finally, we outline translational priorities-including the development of diverse longitudinal cohorts, standardized benchmarking, and clinically trustworthy AI-that are required to realize equitable, microbiome-informed precision nutrition.}, }
@article {pmid41939241, year = {2026}, author = {Pereira, FC and El Aidy, S}, title = {Drug-microbiome interactions: What we know and why predictive translation remains elusive.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2649166}, pmid = {41939241}, issn = {2993-3935}, abstract = {Medication-induced alterations of the gut microbiome influence drug efficacy, toxicity, and long-term outcomes. Despite extensive evidence for drug-microbe interactions, predictive translation into clinical practice remains limited. Generalization from shifts in taxonomic profiles, mechanistic studies or isolated enzymatic assays is challenging because microbial activity is highly context-dependent. Drug-microbiome interactions are shaped by host factors including pH, transit time, nutrient and cofactor availability, and spatial organization along the gastrointestinal tract. Here, we argue that predictive translation requires measuring functional outputs, site-specific activity, ecological interactions, and host-contextual modulation, rather than static microbial properties.}, }
@article {pmid41939697, year = {2026}, author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M}, title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786817}, pmid = {41939697}, issn = {1664-302X}, abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.}, }
@article {pmid41939699, year = {2026}, author = {Zeng, H and Gao, Z and Wang, Z and Li, K and Xu, B and Yan, Z and Gu, Y and Du, W and Ding, H and Wang, J}, title = {Temporal succession and assembly of marine bacterial communities in Maxwell Bay, Antarctica during summer.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1748960}, pmid = {41939699}, issn = {1664-302X}, abstract = {INTRODUCTION: In recent years, ecological feedbacks driven by climate change have become increasingly prominent. The polar amplification effect has made Antarctic ecosystems pivotal indicators for reflecting global climatic impacts. As core drivers of biogeochemical cycling, marine microbes play a central role. Therefore, deciphering their temporal dynamics and assembly mechanisms is crucial for projecting the trajectories of polar ecosystems. However, the intrinsic ecological processes regulating microbial summer succession, particularly the relative contribution of deterministic processes, remain insufficiently quantified.<br><br>METHODS: In the present study, Maxwell Bay, Antarctica-a coastal marine region heavily influenced by glacial melt-was selected as the model system. Surface seawater samples were collected sequentially during the 2022 austral summer, followed by 16S rRNA gene amplicon sequencing and phylogenetic null model analysis.<br><br>RESULTS: Our results revealed a distinct shift in the assembly mechanisms of bacterial communities. In January, community structure was shaped jointly by stochastic and deterministic processes, with stochastic processes contributing a greater proportion to assembly. This state transitioned to the predominance of deterministic homogeneous selection (84.68%) in February. Mantel tests, followed by linear regression analyses, confirmed that this phylogenetic transition was driven by shifting environmental factors. Specifically, water temperature served as the primary influencing factor in January, whereas silicate and nitrate concentrations emerged as the key factors in February. Subsequent partial least squares path modeling (PLS-PM) and redundancy analysis (RDA) further validated these findings, demonstrating that the identified environmental variables collectively explained more than 50% of the observed variation in community structure. Notably, nitrate drawdown was significantly correlated with the increased relative abundances of dominant bacterial genera in February.<br><br>DISCUSSION: By quantifying the relative roles of deterministic and stochastic processes in microbial community assembly, this study demonstrates that environmental selection is the dominant factor mediating microbial responses to polar warming. These findings provide a mechanistic foundation for the development of predictive models for future marine biogeochemical cycles in polar regions.}, }
@article {pmid41939702, year = {2026}, author = {Shi, Y and Chu, H and He, R and Ma, W and Liang, Q and Li, Z and Gao, Y and Luo, C}, title = {Harnessing rhizosphere microbes: the synergistic roles of PGPR and AMF in sustainable tomato production under stress.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1746930}, pmid = {41939702}, issn = {1664-302X}, abstract = {Tomato (Lycopersicon esculentum L.) is among the most economically important vegetable crops worldwide, yet its production is severely constrained by multiple biotic and abiotic stresses, including pathogens, pests, drought, salinity, and heavy metal toxicity. Amid intensifying climate change and increasing demands for sustainable agriculture, plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) have emerged as key beneficial rhizospheric microorganisms with significant potential for enhancing plant stress tolerance and promoting growth. PGPR directly promote the growth of tomato plants through biological nitrogen fixation, solubilization of phosphate and potassium, siderophore-mediated iron uptake, and the production of phytohormones. Indirectly, PGPR suppress pathogens, activate induced systemic resistance (ISR), reinforce cell walls, enhance the activities of antioxidant enzymes, and regulate the accumulation of osmolytes. AMF form symbiotic associations with the roots of tomato plants, enhancing nutrient and water absorption via extraradical mycelial networks, improving phosphorus and nitrogen uptake, modulating abscisic acid (ABA), jasmonic acid (JA), and strigolactone signaling pathways, activating mycorrhiza-induced resistance (MIR), and enhancing photosynthetic efficiency and water-use efficiency under stress. The co-inoculation of PGPR and AMF yields synergistic effects by facilitating mutual colonization, optimizing nutrient bioavailability, coordinately strengthening antioxidant and osmotic regulation systems, and reinforcing systemic defense responses, thereby conferring more robust and efficient stress tolerance than single inoculations. Despite significant advances, key challenges persist in elucidating tripartite molecular crosstalk, maintaining stability during field applications, and developing tailored microbial consortia. This review synthesizes the individual and synergistic mechanisms through which PGPR and AMF enhance the resilience of tomato plants to biotic and abiotic stresses, offering valuable insights for engineering microbial communities to enhance stress resistance in crops.}, }
@article {pmid41939703, year = {2026}, author = {Liao, HY and Ren, YS and Li, J and Huang, HT and Li, ZL and Zeng, Y and Zhu, DH}, title = {Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1752887}, pmid = {41939703}, issn = {1664-302X}, abstract = {The yellow-spined bamboo locust (Ceracris kiangsu) is one of the most destructive forest pests in China, causing severe damage to bamboo forests across multiple provinces. Understanding the relationship between its gut microbiota and environmental factors is crucial for revealing its ecological adaptability and migration potential. This study used 16S rRNA high-throughput sequencing to analyze gut bacterial communities of C. kiangsu from six geographically distinct populations in China. The results showed that Firmicutes and Proteobacteria were the dominant phyla, while bacterial diversity and composition varied significantly among populations. Precipitation and sunshine duration were identified as the main environmental factors most strongly associated with microbial community structure. These findings suggest that environmental conditions are strongly associated with variation in the gut microbiota of C. kiangsu, potentially affecting its adaptability and outbreak dynamics. This research provides new insights into the ecological mechanisms underlying pest distribution and offers a microbiome-based foundation for developing sustainable control strategies to reduce the agricultural and forestry losses caused by this species.}, }
@article {pmid41939705, year = {2026}, author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP}, title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768977}, pmid = {41939705}, issn = {1664-302X}, abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.}, }
@article {pmid41939710, year = {2026}, author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J}, title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741638}, pmid = {41939710}, issn = {1664-302X}, abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.}, }
@article {pmid41939716, year = {2026}, author = {Zhang, B and Zhao, J and Zhuang, L and Liu, Y and Meng, P and Wang, S and Liu, Y and Zhang, T and Xu, J and Qin, W}, title = {Peat promotes production of the edible mushroom Oudemansiella raphanipes by regulating casing soil microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1774800}, pmid = {41939716}, issn = {1664-302X}, abstract = {INTRODUCTION: As an exotic edible mushroom, Oudemansiella raphanipes has attracted extensive attention for efficient cultivation. Peat-amended casing soil is known to increase its productivity, while the underlying mechanisms remain unclear.<br><br>METHODS: In this study, high-throughput 16S rRNA gene sequencing was performed to characterize bacterial communities in casing soils with five peat proportions.<br><br>RESULTS: Results showed that peat proportion had a significant effect on O. raphanipes yield, with the 70% peat treatment achieving the maximum yield of 279.21&#x202f;g per cultivation bag, 38.12% higher than the control without peat. Casing soil with 70% peat harbored higher bacterial richness, enriched beneficial taxa such as Paenisporosarcina, enhanced chemoheterotrophy and nitrogen fixation functions, and more deterministic community assembly compared with other treatments. The bacterial ecological network in casing soil with 70% peat also showed the highest average connectivity, shortest average path length, and strongest robustness. Further, soil physical properties had a greater influence on bacterial community structure in the casing soil than chemical properties. Soil density, available phosphorus and potassium significantly influenced the bacterial community in the 70% peat group.<br><br>CONCLUSION: Together, this study suggested that peat promoted O. raphanipes production by regulating the casing soil microbiome, providing a theoretical basis for optimizing practical cultivation strategies.}, }
@article {pmid41939722, year = {2026}, author = {Ryan, SM and Brayden, DJ}, title = {Food-derived molecules as regulators of intestinal tight junctions and barrier function: mechanisms and implications.}, journal = {Frontiers in drug delivery}, volume = {6}, number = {}, pages = {1692219}, pmid = {41939722}, issn = {2674-0850}, abstract = {Controlling TJ permeability in the small intestine facilitates nutrient absorption, maintains luminal osmotic balance, and prevents the paracellular entry of pathogens. The pharmaceutical industry has leveraged the capacity of medium-chain fatty acids and their derivatives to transiently and reversibly open epithelial TJs in formulations to enable oral administration of therapeutic peptides, some of which have received regulatory approval or are progressing in advanced clinical trials. Other food-derived agent including chitosan and its analogues enhance mucoadhesion and also modulate TJ permeability in the intestine. Recently, pelargonidin, a polyphenolic pigment isolated from strawberries, has emerged as a promising food-derived TJ opener, facilitating oral insulin delivery in rat models. Conversely, other food or food-derived molecules reinforce TJ integrity while exerting antioxidant effects, thereby offering potential therapeutic benefits for conditions characterized by increased intestinal permeability including inflammatory bowel disease, sepsis, and coeliac disease. Examples of such agents include the short-chain fatty acid (SCFA), sodium butyrate, various essential and non-essential amino acids, fermented food, the trace element, zinc, and anthocyanins. The exploration of food-derived substances as modulators of intestinal epithelial TJ dynamics is still in its early stages but holds significant promise for future health applications.}, }
@article {pmid41939734, year = {2026}, author = {Puppo, F and Carbone, RG}, title = {Microbiome in connective tissue diseases associated interstitial lung disease.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1738689}, pmid = {41939734}, issn = {2296-858X}, abstract = {Microbiome consists of a large community of bacteria, yeast, protozoa, and viruses that co-exist in symbiosis with human hosts. Changes in microbiome, named "dysbiosis," alter the interplay between microbiome and immune system triggering inflammation and contributing to the pathogenesis of connective tissue diseases (CTD). Interstitial lung diseases (ILD) are a group of pulmonary disorders characterized by lung tissue fibrosis and impaired lung function. The existence of a gut-lung axis is well demonstrated; however, it is not established whether gastrointestinal dysbiosis contributes to ILD development. ILD represent a major cause of morbidity and mortality in CTD patients. Lung microbiome changes and high microbial load are associated with worse prognosis and acute exacerbations in patients with CTD-ILD and especially in those affected by rheumatoid arthritis, systemic sclerosis and dermatomyositis. Probiotics are active microorganisms that normalize the intestinal flora and their use has been proposed as potential supportive treatment of CTD-ILD. Present knowledge of the relationships between dysbiosis and CTD-ILD development is largely incomplete and further studies are needed to validate this issue. Aim of this concise review is to report current knowledge on microbiome in CTD-ILD focusing on clinical lung aspects and therapeutic options.}, }
@article {pmid41939772, year = {2026}, author = {Zheng, B and Shen, X and Han, N and Guo, X and Wan, S}, title = {The microbiota-gut-brain-epigenome axis as a novel therapeutic target for decoding postpartum depression.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1778348}, pmid = {41939772}, issn = {2296-858X}, abstract = {BACKGROUND: Postpartum depression (PPD) is a psychological disorder affecting approximately 10-15% of women following childbirth, with significant implications for maternal and infant well-being. While hormonal fluctuations and psychosocial factors have long been considered primary contributors, recent reports demonstrated that gut microbiome is implicated in modulating maternal mood and behavior. The bidirectional communication between the gut and brain, mediated by microbiota-gut-brain axis, along with genetic and epigenetic modifications, has gained increasing attention as a potential mechanistic pathway in PPD. However, the precise genetic and epigenetic underpinnings of this interaction remain to be elucidated.<br><br>OBJECTIVE: This review aims to explore the genetic and epigenetic landscape of postpartum depression, with a significant focus pertinent to gut microbiota role in shaping neurobiological outcomes. By integrating recent findings from genomic, epigenomic, and microbiome research, we seek to elucidate novel mechanistic insights and potential therapeutic avenues.<br><br>METHODS: A comprehensive literature search was conducted using public databases, including PubMed, Google Scholar, and NCBI, to identify relevant studies on PPD, gut microbiota, genetics, and epigenetics.<br><br>RESULTS: Gut microbiota and neuroimmune modulation: peripartum changes in gut microbiota composition have been linked to immune dysregulation, inflammation, and neurotransmitter imbalances, all of which are implicated in PPD pathophysiology. Genetics and epigenetics of PPD: Genome-wide association studies (GWAS) revealed a profound genetic risk loci associated with PPD. Additionally, DNA methylation, histone modifications, and non-coding RNAs have profound functional implications in gene expression regulation, influencing PPD susceptibility. Epigenetic influence of the gut microbiome: The gut microbiome affects epigenetic modifications, such as DNA methylation and histone acetylation, which may lead to fetal programming and maternal mental health disorders. Choline metabolism and maternal mental health: Choline, an essential nutrient involved in epigenetic regulation, influences gut microbiota composition and brain function. Dysregulation in choline metabolism is associated with higher risk of PPD. Clinical and therapeutic implications: Understanding the genetic and epigenetic mechanisms underlying PPD offers new avenues for personalized therapeutic interventions, including probiotic and prebiotic strategies, microbiome-based treatments, and targeted epigenetic therapies.<br><br>CONCLUSION: The interplay between genetics, epigenetics, and gut microbiota represents a novel and promising area of research in understanding postpartum depression. The microbiota-gut-brain axis serves as a crucial mediator in this relationship, influencing neuroimmune regulation, neurotransmitter synthesis, and epigenetic modifications. Future studies should focus on integrating multi-omics approaches to unravel the molecular complexity of PPD and develop targeted interventions aimed at restoring microbiome and epigenetic homeostasis.}, }
@article {pmid41939831, year = {2026}, author = {Omolo, CA and Yata, VK and Janapati, YK and Dachani, SR}, title = {Editorial: Innovative therapeutic strategies for managing diabetic foot ulcers and mitigating associated complications.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1788742}, pmid = {41939831}, issn = {1663-9812}, }
@article {pmid41939871, year = {2026}, author = {Tonk-Rügen, M and Schilling, T and Cabezas-Cruz, A and Hoelzle, LE}, title = {Microbiota-immune crosstalk in livestock: implications for tick-borne disease control.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1731518}, pmid = {41939871}, issn = {1664-3224}, mesh = {Animals ; *Livestock/immunology/microbiology ; *Tick-Borne Diseases/immunology/prevention &amp; control/veterinary/microbiology ; *Microbiota/immunology ; Ticks/microbiology/immunology ; }, abstract = {Globally, livestock health, which impacts animal welfare and agricultural productivity, is continuously threatened by tick-borne diseases (TBDs). The growing issues of acaricide overuse in livestock, emerging resistance, and vector adaptation to climate change require novel and sustainable intervention strategies. Recent advances in microbiome research reveal how host and vector microbiota influence immune responses, particularly through natural antibodies (nAbs) that modulate vector competence and pathogen transmission. In livestock, nAbs targeting microbial glycans are heritable, measurable, and linked to health outcomes. In cattle, nAb titers to bacterial antigens are associated with mastitis risk and longevity, while in pigs, early-life nAb levels are proposed as resilience markers. Studies in poultry further demonstrate the importance of high nAb phenotypes for health and production. These findings highlight nAbs as both immunological markers and potential targets for genetic selection to improve disease resistance. Emerging interventions, such as anti-microbiota vaccines and immunobiotics, aim to modulate nAb repertoires, disrupt pathogen colonization, and enhance disease resilience. Additionally, microbial glycans serve as key targets for inducing cross-reactive immunity against TBDs. Manipulation of the livestock microbiota through diet, probiotics, and prebiotics shows promise in diversifying nAb profiles and improving robustness against infection. Despite these advances, research gaps remain, particularly in establishing causality and practical feasibility in livestock systems. This review emphasizes the need for integrative research across immunology, microbiology, and veterinary sciences to leverage microbiota-immune interactions in enhancing livestock resilience against TBDs, exploring how nAbs shaped by the gut microbiota can modulate tick microbiomes and impact pathogen transmission.}, }
@article {pmid41939876, year = {2026}, author = {Li, L and Zhu, G and Chen, M and Qiu, B and Li, Y and Liu, S and Gu, W and Liu, L}, title = {ARG1-polyamine axis: cell-type-specific functions in disease pathogenesis and therapeutic targeting.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1744890}, pmid = {41939876}, issn = {1664-3224}, mesh = {Humans ; *Polyamines/metabolism ; *Arginase/metabolism/antagonists &amp; inhibitors ; Animals ; Neoplasms/metabolism ; }, abstract = {ARG1 catalyzes the conversion of L-arginine to L-ornithine, urea, polyamines, and L-proline, thereby balancing nitrogen detoxification with tissue-specific roles in proliferation and immunity. This review delineates the context-dependent functions of ARG1 across diverse cell types-including tumor cells, immune cells, endothelial cells, keratinocytes, and stem cells. In tumors, ARG1 drives immunosuppression and metabolic reprogramming but can paradoxically suppress tumorigenesis. Immune modulation via ARG1-polyamine crosstalk regulates T cell differentiation, macrophage polarization, and microbiota interactions, influencing infection and autoimmunity. Endothelial ARG1 exacerbates obesity-related vascular dysfunction, while keratinocyte ARG1 impacts wound healing and psoriasis. Emerging therapies-such as ARG1 inhibitors, engineered extracellular vesicles, and microbiome interventions-show preclinical promise in cancer, cardiovascular, and neurodegenerative diseases. By mapping ARG1's spatiotemporal metabolic networks, this work highlights its dual roles and positions ARG1 as a central player for precision medicine in complex pathologies.}, }
@article {pmid41939907, year = {2026}, author = {Jayaraman, S and Mahalingam, SS and Zhu, Z and Faddoul, F and Paes da Silva, A and Asaad, R and Bhaskaran, N and Schneider, E and Taylor, T and Horne, S and Yoo, A and Zhang, L and Burgener, A and Pandiyan, P}, title = {Enrichment of Candida associated with dysbiosis contributes to mucosal CD4[+]FOXP3[+] regulatory T cell accrual and their dysfunction in aging.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1714595}, pmid = {41939907}, issn = {1664-3224}, mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Dysbiosis/immunology/microbiology ; Middle Aged ; *Aging/immunology ; *Mouth Mucosa/immunology/microbiology ; Male ; Female ; Aged ; *Candida/immunology ; Adult ; Forkhead Transcription Factors/metabolism/immunology ; }, abstract = {Age-associated T cell dysfunction is a defining feature of inflammaging and immunosenescence, the progressive decline in immune competence observed with advancing age. Here we identified the association between aging (defined as age >60) and fungal dysbiosis, notably characterized by increased colonization of Candida species in the oral mucosa. There is also a notable enrichment of other taxa related to the order Saccharomycetales in older individuals. In contrast, younger individuals exhibit a greater abundance of Cryptococcus, Yarrowia, Kluyveromyces, and various Incertae sedis lineages. Further analysis, stratified by HIV status, shows that older individuals in both healthy and HIV+ groups display significantly higher levels of Candida. Gingival tissues reveal that both healthy older group and HIV-positive group exhibit elevated levels of CD4[+]FOXP3[+] regulatory T cells (Tregs) along with increased salivary concentrations of soluble TLR-2 and IL-6 compared to younger healthy group. Importantly, the abundance of Candida is positively correlated with elevated levels of mucosal Tregs, dysfunctional Tregs (TregDys), and hyperactivated CD4[+] T cells. In vitro experiments provided mechanistic insights by further demonstrating that Candida can induce both proliferation and dysfunction of Tregs in an IL-6 dependent manner, supporting the notion that Candida plays a role in oral T cell senescence and inflammaging. Collectively, these findings underscore a direct relationship between the commensal mycobiome and Treg population, which normally promotes mucosal homeostasis but becomes susceptible to dysfunction with aging.}, }
@article {pmid41939911, year = {2026}, author = {Zhao, WY and Zhao, JW}, title = {Pancreatic cancer immunotherapy biomarkers: from traditional markers to multimodal integration and dynamic monitoring.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1686658}, pmid = {41939911}, issn = {1664-3224}, mesh = {Humans ; *Pancreatic Neoplasms/therapy/diagnosis/immunology ; *Biomarkers, Tumor ; *Immunotherapy/methods ; *Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis ; Animals ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains an intractable cancer marked by delayed diagnosis, rapid progression, and significant resistance to current treatments. Conventional biomarkers, such as CA19-9, have insufficient sensitivity and specificity. Meanwhile, the practical use of newer markers such as the tumor mutational burden and microsatellite instability is limited by the absence of standardized testing protocols and definitive threshold values. Circulating tumor DNA and exosomal miRNA hold promise for continuously tracking tumor dynamics and effectiveness of immunotherapy, but additional validation is necessary before their routine clinical application. Recent advancements in multiomics, nanotechnology, and artificial intelligence have opened new possibilities for more accurate and comprehensive biomarkers. For instance, Shah et al. developed shortwave-infrared-emitting nanoprobes to specifically target CD8[+] cytotoxic T cells, permitting high-sensitivity in vivo imaging in breast cancer models. Batool et al. utilized nanoplasmonic sensors to detect changes in serum programmed death-ligand 1 and cytokine levels within 1-2 weeks post-treatment, achieving picomolar sensitivity. Chang et al. combined fluorescence and photoacoustic imaging in the NanoTrackThera platform, facilitating the real-time monitoring of immunotherapy efficacy. This review highlights the evolution of PDAC biomarkers from traditional markers to multimodal integration and dynamic monitoring. The limitations of current markers and potential of emerging technologies, including metabolic reprogramming markers, epigenetic regulators, and AI-driven predictive models, are discussed. Future directions include multicenter prospective trials to validate multimodal models, standardize detection methods, and increase interdisciplinary collaboration. By integrating genomic, epigenetic, metabolic, and microbiome data, these models can better capture the complexity of PDAC, thereby improving patient outcomes through precision immunotherapy.}, }
@article {pmid41939913, year = {2026}, author = {Van Doorn, J and Brooks, SR and LiCausi, F and Zhou, K and Betrapally, NS and Gubitz-Hess, E and Cougnoux, A and Dell'Orso, S and Islam, S and Colbert, RA and Navid, F}, title = {Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1755132}, pmid = {41939913}, issn = {1664-3224}, mesh = {Animals ; *HLA-B27 Antigen/genetics/immunology ; *Sirolimus/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Transgenic ; Disease Models, Animal ; Cytokines/metabolism/genetics ; *Spondylarthritis/drug therapy/immunology/microbiology ; Humans ; Male ; Inflammation/drug therapy ; Colon/drug effects/immunology/microbiology/pathology ; }, abstract = {OBJECTIVE: To determine whether rapamycin affects HLA-B27-mediated gut inflammation in experimental spondyloarthritis (SpA).<br><br>METHODS: HLA-B27/human &#x3b2;2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal luminal contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.<br><br>RESULTS: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.<br><br>CONCLUSION: Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.}, }
@article {pmid41940020, year = {2026}, author = {Usman, S and Yan, Q and Gao, L and Deng, S and Lu, L and Pang, T and Lai, D and Jones, CS and Yi, X and Zhang, J}, title = {Inclusion of different levels of fermented elephant grass in broiler chicken diet: effects on growth, physiology, carcass traits and gut microbial community.}, journal = {Frontiers in physiology}, volume = {17}, number = {}, pages = {1767570}, pmid = {41940020}, issn = {1664-042X}, abstract = {The physiological and microbiome-modulating benefits of dietary forage in monogastrics are impeded by recalcitrant fiber and anti-nutritional factors. However, fermentation and appropriate inclusion levels may overcome these limitations. This study evaluated the effects of two fermented cultivars of elephant grass (Cenchrus purpureus cv. Guiminyin and cv. Purple) incorporated into broiler diets at different inclusion levels, with emphasis on cultivar-specific responses, growth performance, physiological status, and gut microbial composition. A total of 240 male (30-days old) Jinling earth-neck chickens were housed in four replicate pens of 12 birds each, and randomly assigned to five dietary treatments (48 birds per treatment): a control diet with no inclusion (0%), CpGui5 (5% Guiminyin inclusion), CpGui10 (10% Guiminyin inclusion), CpPur5 (5% Purple inclusion), and CpPur10 (10% Purple inclusion). CpGui5 and Control diets had statistically similar and higher final weight, total weight gain, average daily gain and feed efficiency which were higher than the other treatments (P < 0.05). On the other hand, Control, CpGui5 and CpPur5 had higher daily feed intake compared to CpGui10 and CpPur10 which had the lower daily feed intake (P < 0.05). Slaughter performance revealed significant differences (P < 0.05), with the control, CpGui5, CpPur5 and CpPur10 groups maintaining higher live weight, dressed weight, half-bore, and breast muscle rate while CpGui10 recorded the lowest values. Blood biochemical indices, including total protein, albumin, liver enzymes, and renal function markers, were unaffected by dietary treatments (P > 0.05), indicating no adverse physiological effects. Gut microbiome analysis showed stable richness (Chao1, ACE) across treatments, while diversity (Shannon, Simpson) was reduced in CpPur5 relative to other groups (P < 0.05). A shared core microbiome of 202 OTUs was detected across all treatments, alongside treatment-specific enrichment of taxa. LEfSe (Linear Discriminant Analysis Effect Size) analysis identified treatment-specific enrichment of functionally relevant bacterial genera, including Megamonas in CpGui5 and Ruminococcaceae_UCG-014 and unclassified Lachnospiraceae at higher inclusion levels (CpGui10). Overall, moderate inclusion of fermented elephant grass, especially CpGui5 supports broiler performance while maintaining physiological health and gut microbial stability, highlighting its potential as a sustainable functional feed resource for poultry production.}, }
@article {pmid41940149, year = {2026}, author = {Etesami, H and Yadegari, AH and Otabek, U and Zahro, B and Shavakatullo, N and Tolqinjon, A}, title = {The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100015}, pmid = {41940149}, issn = {2662-1738}, abstract = {Drought stress poses a significant threat to global agriculture, necessitating innovative strategies to enhance plant resilience. This review highlights the rhizosheath-the soil layer tightly bound to roots by mucilage and microbial biofilms-as a critical but underexplored microbial niche for sustainable drought mitigation. Unlike the vulnerable rhizosphere, the rhizosheath has a cohesive structure that acts as a protective "mini-oasis," preserving moisture and sustaining microbial activity when water is scarce. We synthesize evidence showing that resident rhizosheath bacteria, including genera such as Bacillus, Pseudomonas, and Azospirillum, enhance plant drought tolerance through multiple mechanisms: improving soil structure and water retention, modulating phytohormone levels, facilitating nutrient acquisition, and activating antioxidant and genetic defense pathways in the plant. Despite promising laboratory findings, there has been little field-scale validation of these effects. Here, we critically assess translational challenges and outline future research priorities, such as understanding plant-microbe specificity and optimizing synthetic microbial consortia. Addressing these questions will enable manipulation of the rhizosheath microbiome for development of climate-resilient crops and securing food production in water-limited environments.}, }
@article {pmid41940156, year = {2026}, author = {Ma, J and Qiao, J and Cao, Y and Cheng, Z}, title = {Harnessing artificial intelligence to decode the rhizosphere microbiome.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100005}, pmid = {41940156}, issn = {2662-1738}, abstract = {The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.}, }
@article {pmid41940273, year = {2026}, author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X}, title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.}, journal = {Current zoology}, volume = {72}, number = {1}, pages = {14-29}, pmid = {41940273}, issn = {1674-5507}, abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.}, }
@article {pmid41940285, year = {2025}, author = {Jeong, GH and Lim, KS}, title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.}, journal = {Journal of animal science and technology}, volume = {67}, number = {6}, pages = {1207-1214}, pmid = {41940285}, issn = {2055-0391}, abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.}, }
@article {pmid41940567, year = {2026}, author = {De Zutter, N and Audenaert, K}, title = {Can We Breed Microbiomes to Sustain Plant Productivity?.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70351}, pmid = {41940567}, issn = {1751-7915}, mesh = {*Microbiota ; *Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth &amp; development ; Quantitative Trait Loci ; *Plants/microbiology/genetics ; }, abstract = {Global food systems face challenges from population growth, shifting diets and climate change. While decades of plant-centric breeding and high-input agriculture have generated high yielding crops, this strategy has unintentionally reshaped the plant associated microbiomes, often coinciding with a depletion of their functional diversity. We revisit these breeding strategies and propose extending breeding targets beyond the plant genome to include the plant microbiome. In this regard, resistance breeding shows, albeit unintended, that plant genetics shape the microbiome: by narrowing the genetic base, we have selected for highly specialised pathogenic microbiomes. This raises a key question: can we intentionally apply the same principle to select for beneficial microbiomes? To answer this question, a thorough insight into microbial community architecture, hubs and functional redundancy is key. We outline two complementary avenues: (i) rewilding to restore ancestral microbial partners and (ii) microbiome breeding guided by QTL/GWAS mapped host loci that gate microbial recruitment, immune filtering and exudate composition. This approach comprises the integration of trait-based phenotyping, multi-omics, network-informed SynCom design and field testing across environments to capture G × E × M (genotype × environment × microbiome) interactions. Treating the microbiome as a selectable, designable and heritable trait can convert small gains into durable long-lasting crop resilience.}, }
@article {pmid41940646, year = {2026}, author = {Yin, X and Niu, Y and Chen, B and Zhang, H and Guo, R and Niu, C and Kang, J and Shi, H and Kong, X and Ma, W and Ma, Z and Wei, Y and Hua, Y}, title = {Screening and dynamic change study of microbial and metabolite markers for calf diarrhea based on multi-omics and machine learning.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0000526}, doi = {10.1128/msystems.00005-26}, pmid = {41940646}, issn = {2379-5077}, abstract = {UNLABELLED: Neonatal calf diarrhea is a leading cause of calf mortality and substantial economic loss in the livestock industry, yet the dynamic microbial and metabolic signatures accompanying disease onset remain poorly defined. Here, we integrated 16S rRNA high-throughput sequencing, untargeted metabolomics, and machine learning approaches to longitudinally profile fecal samples from neonatal calves at 0, 5, 10, 15, and 20 days of age. Diarrheic calves exhibited significantly reduced gut microbial α-diversity, as indicated by lower Chao1 richness and Shannon index compared with healthy counterparts. At the genus level, Tyzzerella and Fusobacterium emerged as core differential taxa associated with diarrhea and were further validated as robust biomarkers using an XGBoost predictive model. Metabolomic analysis showed that differential metabolites were mainly enriched in pathways including the phosphotransferase system. Notably, dulcitol, N-acetylmuramate, and D-fructose were highlighted as potential contributors to diarrhea, possibly through modulating intestinal osmolality and inflammatory responses. Pearson correlation analysis revealed significant associations between Tyzzerella/Fusobacterium and key metabolites, suggesting coordinated microbe-metabolite interactions during disease progression. Temporal pattern analysis identified an early-life signal: a high abundance of Escherichia-Shigella at birth may act as an important trigger for subsequent diarrhea. In addition, several metabolites displayed distinct age-dependent trajectories, indicating their potential as time-resolved metabolic biomarkers. Collectively, this study delineates dynamic shifts in the gut microbiome and metabolome during neonatal calf diarrhea, identifies Tyzzerella and Fusobacterium, together with characteristic metabolites such as dulcitol and N-acetylmuramate, as candidate biomarkers, and provides a high-performance predictive framework to support early diagnosis and targeted microbiota-based interventions.<br><br>IMPORTANCE: Neonatal calf diarrhea causes substantial early-life mortality and economic losses, yet the dynamic microbiota-metabolite alterations and early-warning biomarkers during disease onset remain poorly defined. Here, we longitudinally profiled fecal microbiota and metabolites in calves from birth to day 20 and integrated machine learning approaches to systematically characterize diarrhea-associated signatures. Diarrheic calves showed reduced &#x3b1;-diversity, and Tyzzerella and Fusobacterium emerged as core differential genera with predictive value validated using an XGBoost model. Differential metabolites were mainly enriched in pathways such as the phosphotransferase system (PTS), and dulcitol and N-acetylmuramate may contribute to diarrhea by modulating intestinal osmolality or inflammatory responses. Notably, a higher abundance of Escherichia-Shigella at birth was potentially associated with subsequent diarrhea risk, while L-glutamic acid, choline, and LysoPC exhibited distinct temporal trajectories. Collectively, these findings provide translational candidate biomarkers to support early warning and microbiota-targeted precision interventions for neonatal calf diarrhea.}, }
@article {pmid41940665, year = {2026}, author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X}, title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0191125}, doi = {10.1128/spectrum.01911-25}, pmid = {41940665}, issn = {2165-0497}, abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.<br><br>IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.}, }
@article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0190325}, doi = {10.1128/aem.01903-25}, pmid = {41940696}, issn = {1098-5336}, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, }
@article {pmid41940869, year = {2026}, author = {Sharif-Askari, Z and Atoui, K and El Zein, W and Rizk, M and Sharif Askari, E}, title = {From periodontitis to neurodegeneration: Can probiotics modulate the P. gingivalis-amyloid pathway in Alzheimer's disease?.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261432686}, doi = {10.1177/13872877261432686}, pmid = {41940869}, issn = {1875-8908}, abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the gradual destruction of cognitive and behavioral functions. Despite the continuous research efforts, there is still no cure for this disease. In recent years, researchers have investigated Porphyromonas gingivalis (P. gingivalis) as a potential cause of AD. P. gingivalis-lipopolysaccharides (LPS) and gingipains have been implicated in neuroinflammatory cascades relevant to AD. The gut-brain axis provides a pathway for microbial migration, immune activation, and regulation of the central nervous system function. Emerging evidence suggests that selected probiotics may modulate these pathways by restoring microbial balance, reinforcing epithelial barrier function, and regulating innate and adaptive immunity. Importantly, much of the evidence and mechanistic support for these effects derives from preclinical and animal studies, whereas human data remain limited to associative findings and early-stage clinical trials. Early clinical trials report modest improvements in cognitive scores and systemic inflammatory markers. Strain selection, dose, and treatment duration make direct comparisons challenging. This review integrates the literature on the links between P. gingivalis and AD, suggesting that probiotics may be used as neuroprotective agents. Taken together, current preclinical signals are consistent with the potential of probiotics as feasible adjuncts, pending confirmatory trials with standardized formulations.}, }
@article {pmid41941327, year = {2026}, author = {Strope, TA and Easson, CG and Fiore, CL}, title = {Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70331}, pmid = {41941327}, issn = {1758-2229}, support = {//Appalachian State University/ ; 1924540//National Science Foundation/ ; }, mesh = {*Symbiosis ; *Porifera/microbiology/growth &amp; development/physiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; Fresh Water/microbiology ; *Microbiota ; Flavobacterium/genetics ; Phylogeny ; }, abstract = {Freshwater sponges, most of which have a dormant stage with gemmules, are well poised for microbiome focused experiments. Here, we leveraged field collections of freshwater sponges pre-gemmule (Pre) and post-gemmule (Post) formation to compare the microbial symbiont metatranscriptome at the two developmental stages. There were no broad changes to the microbiome in composition between the two stages; however, there were significant differences in the abundance of several bacterial taxa and functional genes between Pre and Post sponge samples. For example, many Polynucleobacter spp. increased from Pre to Post samples, but no putative symbiosis factors were associated with Polynucleobacter and these may be loosely associated with the sponges. In contrast, we hypothesise that Flavobacterium spp. are facultative symbionts of freshwater sponges that begin to leave when the sponge tissue degrades, or they may decrease their metabolic activity. Functions attributed to Flavobacterium spp. such as type IX secretion system (T9SS) component and ankyrin repeat domains, all decreased in the Post samples and suggests that this group can interact with the sponge host or be free-living. These results provide a foundation for future hypothesis testing and experimental work with the microbiomes of freshwater sponges.}, }
@article {pmid41941330, year = {2026}, author = {Dunn, ES and Spalding, HL and Hill-Spanik, KM and Fullerton, H}, title = {Examining Short Temporal Changes in Intertidal Macroalgal Microbiomes at 'Ewa Beach, O'Ahu, Hawai'i: Some Hosts Varied While Others Remained Stable.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70333}, pmid = {41941330}, issn = {1758-2229}, mesh = {Hawaii ; *Microbiota ; *Seaweed/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Climate Change ; Rhodophyta/microbiology ; Seawater/microbiology ; Phaeophyceae/microbiology ; }, abstract = {Understanding the temporal variability of microbiomes is crucial for predicting dynamics within macroalgal communities under future climate change scenarios, rising temperatures, and increased marine heatwave events. Short-term variation has been observed in human- and coral-associated microbes, but these dynamics are less understood in macroalgae. Intertidal macroalgal communities are ideal systems for investigating microbiome temporal variation due to their exposure to daily fluctuations in abiotic conditions. We characterised and examined the variability in the microbiota of seven macroalgal species, with representatives from three different phyla, across five sequential low tides in May 2021 at a single intertidal bench at 'Ewa Beach, O'ahu, Hawai'i, USA. Bacterial community compositions found in two red algae, Acanthophora spicifera and Laurencia dendroidea, and one brown alga, Dictyota sandvicensis, had variable abundances of several amplicon sequence variants contributing to significant dissimilarity through time. Two green macroalgae (Avrainvillea lacerata and Halimeda discoidea) were stable over time. Temporal stability of the macroalgal microbiotas, therefore, was variable amongst macroalgal species, but may be dependent on its horizontal or vertical positioning within the intertidal zone, which can vary the level of environmental stress (e.g., temperature, light, desiccation). Additional work exploring the drivers of the temporal variability observed herein is needed.}, }
@article {pmid41941490, year = {2026}, author = {Ventero, MP and Herrero, R and Tyshkovska, I and Valverde-Fredet, MD and Rodríguez, JC and Rodríguez-Fernández, M and González-De-La-Aleja, P and Trigo, M and Parra, M and Aller, AI and Otero, S and Espindola-Gomez, R and Ramos, JM and León, EM and García, M and Navarrete-Lorite, MN and Llenas-García, J and Portillo, I and Jover, F and Tasias, M and Caston, JJ and Gil, C and Vinuesa-Garcia, D and Gomez-Ayerbe, C and Martínez Marcos, FJ and Merchante, N and De Lucas, EM}, title = {Dynamics of the microbiota in patients with Clostridioides difficile: Recurrence, treatment, sex, and immunosuppression.}, journal = {PLoS pathogens}, volume = {22}, number = {4}, pages = {e1014063}, doi = {10.1371/journal.ppat.1014063}, pmid = {41941490}, issn = {1553-7374}, abstract = {BACKGROUND: Alterations in the gut microbiome are central to the pathogenesis and recurrence of Clostridioides difficile infection (CDI).<br><br>OBJECTIVE: To evaluate intestinal microbiome changes during CDI and their association with recurrence, sex, age, and immunosuppression.<br><br>METHODS: Patients from the CDI-ANCRAID-SEICV cohort were consecutively enrolled. Stool samples were obtained at diagnosis (Dx), end of treatment (ET), and eight weeks post-treatment (8W) or upon recurrence. Microbiota composition was analyzed by 16S rRNA sequencing using QIIME2 and R. Outcomes were compared by demographics, immunosuppression, and treatment (vancomycin [VNC], vancomycin-bezlotuzumab [VNC-BZL], fidaxomicin [FDX]).<br><br>RESULTS: Among 143 patients, non-recurrent cases showed higher biodiversity at 8W versus diagnosis (H p&#x2009;=&#x2009;0.002, ASVs p&#x2009;<&#x2009;0.001), unlike recurrent cases. Diversity decreased with VNC (H p&#x2009;>&#x2009;0.001, ASVs p&#x2009;<&#x2009;0.001) but was preserved with FDX (H p&#x2009;=&#x2009;0.15). Recovery of Shannon diversity was limited in women (p&#x2009;=&#x2009;0.50) and immunocompromised patients (p&#x2009;=&#x2009;0.31). At ET, Fusobacteria and Verrucomicrobiota were less abundant in recurrent than non-recurrent cases (0.77%, 0.53% vs 3.43%, 3.50%). FDX-treated samples showed higher Bacteroidetes (31.33%) compared to VNC (5.23%) or VNC-BZL (3.12%). Women exhibited increased Firmicutes abundance (p&#x2009;=&#x2009;0.034).<br><br>CONCLUSIONS: Restoration of microbial diversity correlates with CDI resolution. FDX preserves gut microbiota better than VNC or VNC-BZL. Women and immunocompromised patients demonstrate impaired microbiota recovery.}, }
@article {pmid41941984, year = {2026}, author = {Margaux, E and Elise, T and Muriel, D and Matthijs, M and Jellina, P and Arnau, VV and Jean, S and Nicky, D and Bart, B and Jeroen, R and Kaat, A}, title = {A pilot study on the role of the oxytocinergic system in gut microbiome composition in children with autism: baseline associations and effects of intranasal oxytocin.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {106579}, doi = {10.1016/j.bbi.2026.106579}, pmid = {41941984}, issn = {1090-2139}, abstract = {Autistic children often experience behavioral difficulties alongside nutritional and gastro-intestinal (GI) problems, including gut dysbiosis. Recent research has highlighted important interactions between the oxytocinergic system and gut microbiome compositions, however, insights into how exogenous administration of oxytocin may influence GI health remain largely unexplored. Here, we first examined whether nutrition, GI symptoms and microbiome compositions vary in autistic versus non-autistic children, and how alterations link to clinical-behavioral difficulties and oxytocinergic signaling. Next, we examined the effect of a four-week intranasal oxytocin administration regimen on GI health/dysbiosis in autistic children enrolled in a randomized placebo-controlled trial. Compared to non-autistic children, autistic children consumed more soft drinks, and fewer vegetables and experienced abdominal pain more frequently over the past three months. Notably, epigenetic variations in the oxytocin receptor gene (OXTR) were associated with stool consistency, indicating that children with looser stools exhibited lower OXTR methylation levels, indicative of increased receptor expression. Additionally, a higher abundance of Romboutsia was associated with OXTR hypo-methylation and more anxiety-like behavior. In autistic children, the four-week oxytocin regimen had no effect on bacterial diversity but did modify stool consistency, leading to less dense stools with an overall more normal stool consistency, and an increased abundance of the potentially anti-inflammatory genus Fusicatenibacter. To conclude, this study provides novel insights into the role of the oxytocinergic system in GI symptoms and gut microbiome compositions in autistic children, and preliminary evidence suggesting a modulatory effect of exogenously administered oxytocin on these parameters.}, }
@article {pmid41941985, year = {2026}, author = {Bettio, MK and Vidal, T and Rose, JJ and Jois, M and Flavel, M and Petrovski, S}, title = {Polyphenol-Rich Feed Material increases Anaerostipes and reduces methanogenic archaea in the horse hindgut microbiome.}, journal = {Journal of equine veterinary science}, volume = {}, number = {}, pages = {105885}, doi = {10.1016/j.jevs.2026.105885}, pmid = {41941985}, issn = {0737-0806}, abstract = {BACKGROUND: The gastrointestinal microbiota plays a critical role in horse health and performance. While sugarcane-derived polyphenols have shown microbiota-modulating properties in other species, their effects in horses remain unexplored.<br><br>AIMS/OBJECTIVES: This study investigated whether supplementation with a sugarcane-derived polyphenol feed material modulates the hindgut microbiota of healthy adult horses.<br><br>METHODS: An observational longitudinal study was conducted on six horses over 12 weeks. Faecal samples were collected at three time points: baseline (P1), during supplementation (P2), and post-supplementation (P3). Microbial composition was assessed by 16S rRNA gene sequencing targeting the V3-V4 region. Alpha and beta diversity, as well as differential abundance analyses, were performed.<br><br>RESULTS: Alpha diversity metrics (Chao1, Shannon, Simpson) showed no significant differences across time points. However, Anaerostipes increased by 105.3% during supplementation and 23.6% post-supplementation. Prevotella abundance also rose post-supplementation. Methanogenic Archaea, including Methanomassiliicoccus, decreased by 79.1% during supplementation, while members of Methanobacteriales were reduced by 61.8%. These changes partially reversed in the post-supplementation phase. Core microbiota genera remained stable throughout.<br><br>CONCLUSION: Supplementation with a sugarcane-derived polyphenol feed material modulated specific microbial taxa without disrupting overall microbial diversity. The intervention enhanced fermentative SCFA-producing bacteria and suppressed methanogenic Archaea, supporting the potential use of this feed material as a microbiome enhancer for improving hindgut health and reducing methanogenesis in horses.}, }
@article {pmid41942049, year = {2026}, author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J}, title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.004}, pmid = {41942049}, issn = {2090-1224}, abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.<br><br>OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.<br><br>METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.<br><br>RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.<br><br>CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.}, }
@article {pmid41942109, year = {2026}, author = {Alsarahead, RA and El-Shehabi, FS and Hijjawi, NS}, title = {Prevalence and subtype diversity of Blastocystis hominis among gastroenteritis patients in northern and central Jordan.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {}, number = {}, pages = {}, doi = {10.1093/trstmh/trag033}, pmid = {41942109}, issn = {1878-3503}, support = {49//Deanship of Scientific Research at Hashemite University/ ; //Department of Graduate Studies/ ; }, abstract = {BACKGROUND: Blastocystis hominis is a common intestinal eukaryotic organism that infects both humans and animals. Although its pathogenicity remains debated, it has been associated with diarrhoea and gastroenteritis. This study aimed to determine its prevalence and characterize its genetic subtypes (STs) in symptomatic patients presenting with gastrointestinal complaints.<br><br>METHODS: DNA was extracted from 279 stool samples collected from patients in northern and central regions of Jordan. Nested polymerase chain reaction targeting the 18S rRNA gene locus and Sanger sequencing of positive samples were used for B. hominis detection and subtype identification. Phylogenetic relationships were analysed using Unipro UGENE and MEGA software. Statistical analyses, prevalence, Pearson's &#x3c7;2 test (p<0.05) were conducted using SPSS.<br><br>RESULTS: The present study found a B. hominis prevalence of 7.2% (20/279). Three subtypes were identified: ST1 35% (7/20), ST2 10% (2/20) and ST3 55% (11/20). No mixed-subtype infections were detected. A statistically significant association was observed between B. hominis infection and patient age (p<0.05), with infection rates influenced by age and not by gender. The highest prevalence, based on sequencing, was observed in the 6- to <12-y age group. The association between B. hominis infection and gender was not statistically significant.<br><br>CONCLUSIONS: The relatively low prevalence of B. hominis among patients suggests it may function more as an indicator of gut health rather than as a primary pathogen. However, confirmation of this hypothesis requires additional microbiome and longitudinal studies. The frequent detection of ST1 and ST3 aligns with previous findings that link these subtypes to clinical symptoms. Broader epidemiological studies are needed to clarify the distribution patterns and clinical significance of B. hominis in human populations.}, }
@article {pmid41942178, year = {2026}, author = {Opperman, C and Lloyd, C and Ratanpaul, V and Van, TTH and Brennan, C and Eri, R}, title = {Engineering SCFAs with dietary fibre combinations: insights from a kinetic-microbiome single-subject longitudinal study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118846}, doi = {10.1016/j.foodres.2026.118846}, pmid = {41942178}, issn = {1873-7145}, mesh = {*Dietary Fiber/metabolism/analysis ; Humans ; Fermentation ; Longitudinal Studies ; *Gastrointestinal Microbiome/physiology ; Male ; Manihot/chemistry ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Adult ; Saccharum ; Inulin/metabolism ; Female ; Starch/metabolism ; Kinetics ; Young Adult ; Musa ; Bifidobacterium/metabolism ; Psyllium ; }, abstract = {The human diet plays a pivotal role in health, yet many studies seeking to identify health-promoting foods rely on experimental designs that poorly reflect natural circumstances. The effects of dietary fibres on the microbiota are typically examined using pooled faecal material and isolated fibres, creating unrealistic environments. Additionally, little progress has been made in distinctly characterising the fermentation rates of dietary fibres. To evaluate the temporal dynamics of gut microbial composition and metabolite production, as well as to characterise the fermentation rates of dietary fibres at an individual level, we conducted an n-of-1 longitudinal study examining responses to eight distinct dietary fibres, fermented both individually and in combination. A blend of sugarcane fibre and cassava resistant starch produced significantly higher butyrate levels (p < 0.0001) than either fibre alone. Microbial profiling showed that inulin and pectin selectively enriched Bifidobacterium spp. Anaerobutyricum hallii was increased with psyllium husk, wheat dextrin, and banana resistant starch, but decreased with a mixture of sugarcane fibre and cassava resistant starch (p < 0.0001). Fermentation kinetics were distinctly categorised into "fast", "medium", "slow" and "poorly-fermentable". These findings indicate that combinations of dietary fibres can be used as a strategy to engineer synergistic health-promoting metabolite responses in an individual, while establishing a standardised framework for describing fermentation rates across studies.}, }
@article {pmid41942241, year = {2026}, author = {Cheng, W and Jiang, C and Pan, T and Zhu, Q and Liu, G and Li, N and Wu, Z and Li, X}, title = {Corrigendum to "Effects of quinoa addition on physicochemical properties, microbiome profiles, and volatile organic compounds in medium-temperature Daqu" [Food Res. Int. 223 (2026) 117868].}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {119013}, doi = {10.1016/j.foodres.2026.119013}, pmid = {41942241}, issn = {1873-7145}, }
@article {pmid41942569, year = {2026}, author = {Connolly, JA and Del Carratore, F and Schmidt, K and Bisesi, AT and Martinson, JNV and Chua, J and Kuhs, M and Boneza, MM and Heinsch, SC and Kinkel, LL and Smanski, MJ and Harcombe, WR and Breitling, R and Takano, E}, title = {Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41942569}, issn = {2045-2322}, support = {NE/T010959/1//UK Research and Innovation/ ; 1935458//National Science Foundation/ ; }, mesh = {*Streptomyces/metabolism/genetics ; *Siderophores/metabolism ; *Soil Microbiology ; Metabolomics/methods ; Iron/metabolism ; *Microbiota ; Deferoxamine/metabolism ; Transcriptome ; Multigene Family ; Multiomics ; }, abstract = {Streptomyces are key contributors to soil microbiome function, known for their biosynthetic diversity. While advances in -omics technologies have improved our understanding of microbiome composition and metabolic potential, the mechanisms underpinning interspecies interactions remain poorly resolved. Here, we investigate the molecular basis of interactions among four sympatric Streptomyces soil microbiome isolates, focusing on phenotypic, metabolomic and transcriptomic responses. Co-culture experiments revealed that one isolate, strain A, exhibited pronounced phenotypic changes when grown alongside each of the other three strains. Untargeted metabolomics and RNA-seq analyses showed that strain A undergoes distinct metabolic and transcriptional shifts depending on its partner, with the strongest response elicited by strain C. Despite all four strains possessing a conserved desferrioxamine biosynthetic gene cluster, only strain C constitutively produced desferrioxamine B (DFO-B), a hydroxamate siderophore, indicating a role for iron bioavailability in the interaction. Supplementation with DFO-B or iron mimicked the growth stimulation of strain A observed in co-culture with strain C, and CRISPR base editing of desD in strain C abolished both DFO production and the phenotypic induction of strain A. However, transcriptomic profiles of strain A varied significantly depending on the partner strain, with distinct sets of biosynthetic gene clusters and metabolic pathways activated in response to strains B and C, suggesting additional cues beyond DFO-B. In contrast, strain D did not elicit growth stimulation in its partners, and itself showed downregulation of amino acid and carbon metabolism when co-cultured with strain C. These findings indicate that Streptomyces interactions are not only mediated by siderophore piracy but also involve complex, strain-specific molecular responses. Our findings demonstrate that Streptomyces interactions are highly strain-specific and only partly mediated by siderophore piracy, with DFO-B acting as a potent interspecies cue. The divergent molecular responses to different partners suggest nuanced mechanisms of microbial sensing and competition. These insights advance our understanding of microbial crosstalk and highlight the ecological and evolutionary complexity of siderophore-mediated interactions. By integrating transcriptomics, metabolomics, and biochemical assays, we present a robust framework for dissecting microbial interactions, with implications for microbiome engineering and synthetic community design.}, }
@article {pmid41942702, year = {2026}, author = {Zhang, YK and Iskandar, MM and Kubow, S and Komarova, SV and Tauer, JT}, title = {Exploring the impact of collagen-I genetic variants on intestinal structure and gut microbiota in mouse models of osteogenesis imperfecta.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47221-2}, pmid = {41942702}, issn = {2045-2322}, support = {87500//Shriners of North America/ ; }, }
@article {pmid41942777, year = {2026}, author = {Verdegaal, AA and Oh, J and Javdan, B and Wang, R and Wu, Q and Wang, TRW and González-Hernández, JA and Donia, MS and Crawford, JM and Goodman, AL}, title = {A drug-microbiome-drug interaction impacts co-prescribed medications for Parkinson's disease.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41942777}, issn = {2058-5276}, support = {R35GM118159//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AT010014//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; F31DK132941//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01AI172144//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RM1GM141649//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Simultaneous prescription of multiple drugs is widespread in medicine. Although the gut microbiome is implicated in drug responses, its role in mediating drug-drug interactions is unexplored. Catechol-O-methyltransferase inhibitors (COMT-I), a class of drugs used alongside levodopa (L-DOPA) to treat Parkinson's disease symptoms, can alter microbiome composition in patients. Here we characterize the antibiotic properties of COMT-I drugs in vitro, ex vivo and in vivo and dissect how these interactions alter microbiome-mediated L-DOPA metabolism in vitro and ex vivo. Notably, in vitro iron availability determines COMT-I antibiotic activity at multiple levels: extracellular iron can drive non-enzymatic inactivation of COMT-I, rescuing COMT-I-mediated bacterial iron starvation responses. However, limitation of intracellular iron can protect sensitive bacteria from COMT-I antibiotic activity. Co-administration of COMT-I and L-DOPA to human faecal microbial communities ex vivo results in COMT-I-dependent alterations to L-DOPA metabolism in an individual-specific manner. These studies highlight a role for the gut microbiome in mediating drug-drug interactions and identify microbial features that could predict individual responses to co-prescribed drugs.}, }
@article {pmid41943076, year = {2026}, author = {Ghathian, KSA and Halkjær, SI and Krogfelt, KA and Frimodt-Møller, N and Hansen, KH and Frederiksen, AKS and Holm, A and Petersen, AM}, title = {The effect of the probiotic supplement-ASTARTE™-on the reduction of recurrent urinary tract infection in women aged 18-40 years: protocol for a randomized, double-blind, placebo-controlled study.}, journal = {Trials}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13063-026-09679-3}, pmid = {41943076}, issn = {1745-6215}, abstract = {BACKGROUND: Urinary tract infection (UTI) is one of the most common bacterial infections, contributing to increased antibiotic consumption and high healthcare costs. Clinical studies suggest that probiotics can be effective dietary supplements reducing the risk factors for the development of infections in the intestine and vagina. In this study, we investigate the effect of the orally ingested probiotic combination ASTARTE™ on the composition of bacteria in vaginal and fecal samples, as well as on the occurrence of bacteriologically confirmed UTIs in women of reproductive age.<br><br>METHODS: A randomized, placebo-controlled, double-blind study evaluating the effect of the probiotic combination ASTARTE&#x2122; (Chr. Hansen A/S, Part of Novonesis Group, Denmark) on reducing the number of recurrent urinary tract infections (rUTIs) in women aged 18-40&#xa0;years. Participants are randomized (1:1) to receive one daily probiotic capsule (5 &#xd7; 10[9] CFU) containing Lactobacillus crispatus LBV 88&#x2122; (DSM22566), Lacticaseibacillus rhamnosus LBV 96&#x2122; (DSM22560), Lactobacillus jensenii LBV 116&#x2122; (DSM22567), and Lactobacillus gasseri LBV 150N&#x2122; (DSM22583), or placebo, for 6 months. Assessments, including symptom questionnaires, urine culturing and microbiome analysis of vaginal and rectal samples by shotgun sequencing, are conducted at baseline, 2, 4, and 6&#xa0;months. Compliance is tracked by unused capsule counts. Follow-up visits occur at 8, 10, and 12&#xa0;months. The primary outcome is the incidence of symptomatic bacteriologically confirmed UTIs during the 6&#xa0;months intervention period. The secondary objective is the effect of ASTARTE&#x2122; on changes in vaginal and gut microbiome.<br><br>DISCUSSION: This randomized, placebo-controlled, double-blind study investigates the effectiveness of ASTARTE&#x2122; in restoring beneficial microbiomes and reducing UTI recurrence. The findings will provide valuable evidence on the effectiveness of a non-antibiotic strategy for the prevention of rUTI as well as insights into the complex interactions between the vaginal and gut microbiome and the risk of rUTI.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05553652. Registered 21 September 2022.}, }
@article {pmid41943109, year = {2026}, author = {Crouzet, L and Kelly, W and Andrews, C and Soni, P and Tong, B and Tavendale, R and Rajasekaran, K and Wieliczko, K and Pilkington, K and Kaminsky, R and Matiya, F and Molano, G and Sandoval, E and Dobson-Hill, B and Reid, P and Muetzel, S and Khan, A and Maclean, P and Doohan, H and Burgess-Smith, T and Atkins, N and Bassett, S and Dekker, J and Hill, J and Bermingham, E and Attwood, G}, title = {Early life treatment with Lacticaseibacillus rhamnosus strains drives reduced enteric methane emissions in dairy heifers.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41943109}, issn = {1674-9782}, support = {PGGRC-Fonterra project contract 20-FONT- LAB AGR MET 5.4, Contract AgR: A27147.//This study was funded by the Pastoral Greenhouse Gas Research Consortium (PGgRc) and Fonterra Ltd./ ; }, abstract = {BACKGROUND: Methane emissions from enteric fermentation in ruminant livestock make up 27% of anthropogenic methane emissions.<br><br>RESULTS: Screening&#x2009;>&#x2009;1,700 lactic acid bacteria identified Lacticaseibacillus rhamnosus FNZ118 (Kowbucha&#x2122; FNZ118) and L. rhamnosus FNZ142, (Kowbucha&#x2122; FNZ142) as capable of inhibiting rumen methanogens and methane production in vitro. FNZ118 or FNZ142 fed daily to Friesian heifer calves from birth to 14&#xa0;weeks substantially lowered methane production through the first year of life compared to control animals. These strains also decreased feed intake and reduced ruminal metabolite concentrations without affecting animal live weight, suggesting an improvement in feed conversion efficiency. The observed effects did not cause major changes in the structure of the rumen microbiome.<br><br>CONCLUSIONS: These findings demonstrate that early life provision of specific L. rhamnosus strains lower CH4 production and have potential for the mitigation of enteric greenhouse gas emissions from growing dairy cattle.}, }
@article {pmid41943321, year = {2026}, author = {Pu, D and Liang, T and Li, X and Xing, W and Luo, L and Ding, Y and Wan, C and Wu, M}, title = {Physicochemical properties and molecular weight-dependent gut microbiota modulation of inulin-type fructans from Codonopsis bulleynana.}, journal = {Carbohydrate polymers}, volume = {381}, number = {}, pages = {125217}, doi = {10.1016/j.carbpol.2026.125217}, pmid = {41943321}, issn = {1879-1344}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Fructans/chemistry/pharmacology/isolation &amp; purification ; *Codonopsis/chemistry ; *Inulin/chemistry/pharmacology ; Molecular Weight ; Mice ; Fermentation ; Molecular Dynamics Simulation ; }, abstract = {The therapeutic efficacy of dietary fibers is closely related to structural heterogeneity, yet the impact of chain length on physicochemical behavior and gut microbiota modulation remains unclear. Herein, three homologous linear β-(2 → 1)-linked inulin-type fructans with distinct molecular weights, hereafter referred to as CBP1-3, were isolated from Codonopsis bulleynana. All fractions spontaneously assembled into stable supramolecular nanoparticles/disks in water, a process thermodynamically driven by intermolecular hydrogen bonding according to molecular dynamics simulations. Biological evaluation revealed a striking divergence: while low-molecular-weight fractions showed superior efficacy in in vitro fermentation, the relatively high-molecular-weight CBP1 exhibited superior in vivo potency. Multi-omics analysis supports the hypothesis that this supramolecular structure, in synergy with extended chain length, may function as a structural barrier and confer sustained-release characteristics. This likely limits mucin-degrading Akkermansia proliferation via a nutrient-sparing effect, thereby maintaining metabolic homeostasis. These findings demonstrate that relatively high-molecular-weight polysaccharides possess unique ecological advantages in physiological contexts, challenging traditional in vitro screening paradigms and positioning CBP1 as a promising candidate for precision microbiome restoration.}, }
@article {pmid41936486, year = {2026}, author = {Pasta, A and Formisano, E and Calabrese, F and Navazzotti, G and Giannini, EG and Savarino, V and Savarino, EV and Marabotto, E}, title = {Dietary and nutraceutical interventions for functional dyspepsia: A narrative review.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dld.2026.03.010}, pmid = {41936486}, issn = {1878-3562}, abstract = {Functional dyspepsia (FD) is a prevalent disorder of gut-brain interaction. Commonly, meals may exacerbate FD symptoms like postprandial fullness, early satiation, epigastric pain, and nausea. We narratively synthesize meta-analyses, randomized trials, and observational evidence to outline mechanism-based dietary and nutraceutical options. Evidence favors small, regular, lower-fat meals and adjusting texture/osmolarity to minimize gastric distension. In selected phenotypes-particularly postprandial distress with bloating-a brief, dietitian-supervised low-FODMAP trial with staged reintroduction can define personal thresholds. Among nutraceuticals, peppermint-caraway, ginger, STW-5, curcumin, and selected probiotics show benefit, with melatonin and barrier-forming agents promising in subsets, while safety remains product-specific.}, }
@article {pmid41936491, year = {2026}, author = {Burns, KF and Blair, RH and Mares, JA and LaMonte, MJ and Wactawski-Wende, J and McSkimming, D and Liu, Z and Millen, AE}, title = {Gut bacteria associated with an atherogenic TMAO-dietary pattern and choline-rich foods among aging women.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {104635}, doi = {10.1016/j.numecd.2026.104635}, pmid = {41936491}, issn = {1590-3729}, abstract = {BACKGROUND AND AIMS: Choline can be metabolized by gut bacteria with a choline utilization gene, CutC, as identified through genome sequencing studies. This metabolism produces trimethylamine, the precursor to the atherosclerotic metabolite trimethylamine N-oxide (TMAO). Bacterial species involved in trimethylamine production in free-living humans have been under-investigated. We previously developed the TMAO dietary pattern (TMAO-DP), which is predictive of plasma TMAO and choline. We evaluated associations between the TMAO-DP, dietary choline, and choline-rich foods (fish, red meat, eggs) with the abundance of species with CutC. We also explored associations between the TMAO-DP and microbiome diversity.<br><br>METHODS AND RESULTS: This cross-sectional analysis included 287 women (mean age&#xa0;=&#xa0;79.6 years) from the Women's Health Initiative. Diet was assessed using a food frequency questionnaire. Stool samples were collected and the V3-V4 regions of the 16S ribosomal RNA were sequenced. Adjusted linear regression models evaluated associations between the TMAO-DP with the CLR-transformed abundance of species with CutC and with alpha-diversity indices. For beta-diversity, PERMANOVA examined measures of Aitchison distance within and between quartiles of the TMAO-DP. Associations between dietary choline and choline-rich foods with the abundance of species were evaluated using linear regression. The TMAO-DP was associated with Acidaminococcus intestini [Beta (SE): 0.23 (0.09), p-value&#xa0;=&#xa0;0.035] and Desulfovibrio desulfuricans [Beta (SE): 0.16 (0.6), p&#xa0;=&#xa0;0.035]. The TMAO-DP was not associated with alpha- or beta-diversity.<br><br>CONCLUSION: This study provides evidence that Desulfovibrio desulfuricans and Acidaminococcus intestini, two species identified as having CutC by gene sequencing, may produce trimethylamine from diet in free-living women.}, }
@article {pmid41936687, year = {2026}, author = {Viswan, A and Augustine, N}, title = {Insect Gut Microbiota as a Reservoir of Industrially Relevant Enzymes: A Comprehensive Review.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02726-1}, pmid = {41936687}, issn = {1432-184X}, }
@article {pmid41936794, year = {2026}, author = {Evans, C and Petry, A and Johnson, T and Kogut, MH and Walk, CL and York, T}, title = {A NEW FOCUS ON FIBER.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106863}, doi = {10.1016/j.psj.2026.106863}, pmid = {41936794}, issn = {1525-3171}, abstract = {Dietary fiber (DF) in poultry nutrition was once viewed mainly as an anti-nutritional factor that reduced energy density and nutrient digestibility. Current research shows DF can play important functional roles in gut health, nutrient utilization, and overall performance when its type and inclusion level are carefully managed. Fiber fractions differ widely in chemical composition and physical properties such as solubility, water-holding capacity, and water-binding capacity. These factors influence digesta viscosity, passage rate, microbial fermentation, and satiety, making precise fiber characterization critical for effective diet formulation. Traditional methods like crude fiber analysis underestimate total fiber and miss key soluble fractions. Modern approaches, including total dietary fiber analysis and near-infrared spectroscopy allow for better quantification of both insoluble and soluble components and support incorporation into real-time feed formulation. By understanding and targeting specific non-starch polysaccharides or oligosaccharides, nutritionists can promote beneficial fermentation, encourage short-chain fatty acid (SCFA) production, and minimize undesirable protein fermentation or pathogen growth. Dietary fiber also supports intestinal barrier function by stimulating gut development, increasing villus height, and fueling epithelial cells through SCFAs. However, poorly balanced fiber can impair nutrient absorption, increase maintenance energy needs, or elevate digesta viscosity, particularly in young birds. Monitoring gut health is now possible by using biomarkers as tools to evaluate intestinal integrity, inflammation, and microbial balance as we investigate the impact of dietary fiber, but further work is needed to standardize these measures and account for flock variability When properly applied, DF can enhance feed efficiency, improve welfare by reducing hunger-driven behaviors, support reproductive performance, and strengthen disease resilience. A data-driven, precision approach combining accurate fiber analysis, enzyme supplementation, microbiome profiling, and non-invasive gut health biomarkers offers the greatest potential to optimize both productivity and sustainability in poultry systems. The purpose of this symposium was to stimulate discussion and enhance understanding of dietary fiber and its potential benefits in improving poultry production. This paper provides an overview of each contributing author's role in the symposium. Dr. Caitlin Evans addressed the challenges associated with current fiber nomenclature and emphasized the need to improve analytical methods and overall understanding of fiber. She brings strong credibility to this topic as a Technical Manager for Near-Infrared Spectroscopy and Feed Milling Engineer at AB Vista, and as a Ph.D. graduate of Kansas State University. Dr. Amy Petry shared her expertise on the impact of fiber in swine nutrition and how these findings can be applied to poultry. She is an Assistant Professor in the Division of Animal Sciences at the University of Missouri, where her research focuses on improving fiber utilization and its effects on energy efficiency and animal health. Dr. Tim Johnson, Professor in the Department of Veterinary and Biomedical Sciences at the University of Minnesota, highlighted the importance of understanding the poultry microbiome and its role in developing strategies to enhance bird performance. Dr. Mike Kogut contributed his expertise as a Research Microbiologist and Lead Scientist with the Food and Feed Safety Research Unit at the Southern Plains Agricultural Research Center. Finally, Dr. Carrie Walk, Head of Research at AB Vista, along with Dr. Tara York, AB Vista's Technical Director for North America, integrated the key themes of the symposium, connecting the presented research and practical applications.}, }
@article {pmid41936807, year = {2026}, author = {Nualart C, D and Schwob, G and Orlando, J and Pashcke, K and Guerreiro, PM and McCormick, SD and Cheng, CC and Vargas-Chacoff, L}, title = {Microplastic pollution and thermal increase alter cellular stress responses and microbiomes in Antarctic and Sub-Antarctic fish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128039}, doi = {10.1016/j.envpol.2026.128039}, pmid = {41936807}, issn = {1873-6424}, abstract = {Antarctic and sub-Antarctic fishes of the genus Harpagifer inhabit extreme environments and face emerging anthropogenic stressors, including plastic pollution and warming. While each factor is known to affect fish physiology, their acute combined impacts on molecular responses and host-microbe interactions remain poorly understood. In this study, we investigated the immediate (24 h) transcriptional response of stress-related genes heat shock protein 70 (hsp70), S100 calcium binding protein (s100), High Mobility Group 1 box (hmg1b), E3 Ubiquitin Ligases (E3), and BCL2 Associated X (Bax) and gut microbiome diversity in H. antarcticus (King George Island, Antarctica) and H. bispinis (Punta Arenas, Chile) exposed to elevated temperature (TI), PVC microplastics (MP), or their combination (TI+MP). Both stressors altered gene transcription in a tissue- and species-specific manner, suggesting a synergistic stress response under combined treatment. Temperature rise consistently modulated stress markers, while acute PVC exposure intensified apoptotic signaling. Notably, species-specific patterns emerged: H. bispinis showed a more pronounced induction of pro-apoptotic pathways, whereas H. antarcticus maintained a higher induction of protective chaperones within this short temporal window. At the microbial level, while community-wide diversity metrics remained statistically stable, an exploratory analysis revealed increased inter-individual variability and the enrichment of specific stress-tolerant bacterial taxa. These results reveal that acute warming and microplastic exposure interactively disturb host, cellular homeostasis, with distinct transcriptional plasticity across closely related species. Our study provides mechanistic insights into the early physiological challenges faced by Notothenioids, highlighting the importance of coupling molecular biomarkers with microbiome analyses to assess the initial stages of response in cold-adapted fishes to environmental change.}, }
@article {pmid41936881, year = {2026}, author = {Liang, L and Fu, Y and Guan, D and Zeng, H and Wang, H and Peng, J and Shao, Y and Zhang, S and Liu, L}, title = {Effects of 16S rRNA hypervariable region selection on respiratory Microbiome profiling in healthy adults.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107493}, doi = {10.1016/j.mimet.2026.107493}, pmid = {41936881}, issn = {1872-8359}, abstract = {Selection of the 16S rRNA gene target region can substantially influence inferred respiratory microbiome profiles, particularly in low-biomass samples. In this study, we compared full-length V1-V9 (Pacific Biosciences) and V3-V4 (Illumina) amplicon sequencing using exhaled breath condensate collected from 50 healthy adults. Samples that yielded successful amplification for both approaches were included in paired, within-subject comparisons of sequencing depth, alpha diversity, and taxonomic composition. Sequencing of the V3-V4 region yielded significantly higher read counts and greater alpha diversity (richness and Shannon index) than full-length V1-V9 sequencing (all p < 0.001). Both approaches consistently identified a shared set of dominant respiratory-associated genera, including Acinetobacter, Streptococcus, Psychrobacter, Gemella, Neisseria, and Granulicatella. However, relative abundance estimates differed by target region, with Acinetobacter enriched in V1-V9 profiles, whereas Streptococcus and Neisseria were more abundant in V3-V4 data. In contrast, several genera showed comparable abundances across regions. These findings indicate that while overall community membership is broadly conserved, quantitative diversity metrics and genus-level abundance estimates are strongly influenced by primer and target-region selection. Overall, these results provide methodological guidance for interpreting respiratory microbiome data derived from exhaled breath condensate and highlight the importance of aligning sequencing strategies with specific study objectives.}, }
@article {pmid41936917, year = {2026}, author = {Zhang, S and Yue, T and Jin, P and Zhang, X and Huo, Q and Li, W and Tian, C and Dong, H and Dong, Y and Zhao, Y and Li, D}, title = {4-Octyl itaconate attenuates radiation-induced intestinal injury associated with ferroptosis inhibition and microbiota rebalance.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2026.04.006}, pmid = {41936917}, issn = {1873-4596}, abstract = {Radiation-induced intestinal injury (RIII) is a serious and common complication of radiotherapy, and there are currently no effective therapeutic strategies. This study investigates the protective role of 4-octyl itaconate (4-OI), a cell-permeable itaconate derivative, against RIII. In vitro, 4-OI pretreatment enhanced the viability of irradiated intestinal epithelial cells, reduced reactive oxygen species (ROS) accumulation, and alleviated DNA damage. In a murine model of total body irradiation, 4-OI administration mitigated intestinal structural disruption, promoted crypt stem cell regeneration, and suppressed epithelial apoptosis. Mechanistically, 4-OI exerted its cytoprotective effects by modulating the SLC7A11/GPX4 axis to inhibit ferroptosis and enhancing glutathione biosynthesis. Furthermore, 16S rRNA sequencing revealed that 4-OI treatment recalibrated radiation-induced gut microbiota dysbiosis, suggesting an additional microbiome-mediated protective pathway. To our knowledge, the results represent the first demonstration of 4-OI's protective effects in RIII pathogenesis, positioning it as a novel therapeutic candidate for clinical radioprotection through dual mechanism targeting.}, }
@article {pmid41936935, year = {2026}, author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F}, title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134553}, doi = {10.1016/j.biortech.2026.134553}, pmid = {41936935}, issn = {1873-2976}, abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.}, }
@article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.<br><br>METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.<br><br>RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).<br><br>CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, }
@article {pmid41937169, year = {2026}, author = {Mullin, CE and Louca, S}, title = {Effects of heat-assisted sample desiccation on microbiome surveys.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00889-5}, pmid = {41937169}, issn = {2524-6372}, abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.}, }
@article {pmid41937467, year = {2026}, author = {Lee, HJ and Lee, JH and Kwak, YS}, title = {A Keystone-Taxa SynCom Reveals Chlorella-Microbiome-Plant Communication and Enhances Suppression of Fusarium oxysporum.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2601023}, doi = {10.4014/jmb.2601.01023}, pmid = {41937467}, issn = {1738-8872}, mesh = {*Chlorella/physiology ; *Fusarium/drug effects/growth &amp; development ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; Solanum lycopersicum/microbiology/growth &amp; development ; Antifungal Agents/pharmacology ; Mannitol/pharmacology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Chlorella, a microalga renowned for its high protein and lipid content, is extensively used as a biofertilizer due to its plant growth promotion and disease suppression capabilities. To reveal, Chlorella-microbiome-plant communication, in-depth microbiota structure and network analyses were conducted. As a result, keystone taxa, which are microbial element in interaction with Chlorella, keystone taxa (Psedomonas, Duganella, Brevibacterium) interaction with C. fusca CHK0059 within plant hosts were identified. Here, however, the mechanistic insights into these interactions remain limited. Therefore, we aimed to investigate the characteristics of keystone taxa to elucidate Chlorella effects on plants. By applying various substances, including Chlorella, Chlorella methanol extract (methanol extract), and D-mannitol, we observed changes in microbial distribution and diversity, with a notable increase in Pseudomonas abundance following 2% D-mannitol treatment. Additionally, we assessed the impact of Chlorella on plant growth and disease suppression, finding that a synthetic community (SynCom) of keystone taxa exhibited enhanced antifungal effects against Fusarium oxysporum in both strawberry and tomato, compared to individual strains. The findings in this study suggested the fundamental data that the SynCom can contribute to the mechanism of action of C. fusca CHK0059 and expect to maximize the effect of Chlorella when combined.}, }
@article {pmid41937585, year = {2026}, author = {Chen, X and Dong, T and Wu, D and Pan, Q and Wei, J and Liang, G and Lin, Z}, title = {Shifts in the Lung Microbiota and Antibiotic Resistance Genes Occur With Aging in Patients With Lower Respiratory Tract Infections.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e9038281}, pmid = {41937585}, issn = {2314-6141}, mesh = {Humans ; Adult ; Aged ; *Microbiota/genetics ; Middle Aged ; Adolescent ; Child ; *Aging/genetics ; Female ; *Respiratory Tract Infections/microbiology/drug therapy/genetics ; Male ; Aged, 80 and over ; *Lung/microbiology ; Child, Preschool ; Young Adult ; *Drug Resistance, Microbial/genetics ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Lower respiratory tract infections (LRTIs) are a leading cause of critical illness and mortality. The lung microbiome represents an important reservoir for the exchange of antibiotic resistance genes (ARGs). The pathogenic microbes remain poorly understood among different age groups, including children (0-17 years), youth (18-39 years), middle-aged adults (40-64 years), and older adults (65-99 years). We conducted a retrospective study of 699 bronchoalveolar lavage fluid (BALF) samples from LRTI patients aged 30 days to 99 years. The differences in the lung microbiome and ARG expression shift with age were evaluated based on targeted next-generation sequencing (tNGS) results. Correlation analysis revealed that age had a strongly positive correlation effect on the relative abundances of Candida albicans, Candida glabrata, Corynebacterium striatum, and Stenotrophomonas maltophilia. Meanwhile, age had a largely negative correlation effect on Enterococcus faecium and Mycoplasma pneumoniae. We found that ARG expression was significantly higher in adults compared with children. The beta-lactam ARG TEM was the most abundant, and the primary carrier of ARGs was Streptococcus in the LRTI microbiota. The proportion of adults expressing beta-lactams, aminoglycosides, and phenicol antibiotic types was higher compared to children. Our results indicated that ARGs in the human LRTI microbiota accumulate and become more complex with age, as older groups tend to harbor the highest abundance of these genes. Collectively, these results presented the respiratory tract core microbiota and ARGs in different age groups, supplying a foundation for microbiome-targeted interventions and emphasizing the potential of tNGS to improve clinical diagnosis.}, }
@article {pmid41937700, year = {2026}, author = {Van Vu, S and Kundu, S and Woo, KH and Uttarotai, T and Van Doan, H}, title = {Impact of Body Weight on the Intestinal Microbiome of Cage-Cultured Oyster Pompano (Trachinotus anak).}, journal = {Animal genetics}, volume = {57}, number = {2}, pages = {e70092}, doi = {10.1002/age.70092}, pmid = {41937700}, issn = {1365-2052}, support = {106.05-2023.64//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; //Chey Institute for Advanced Studies' International Scholar Exchange Fellowship/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; *Body Weight ; Bacteria/classification/genetics ; *Ostreidae/microbiology ; }, abstract = {Oyster pompano (Trachinotus anak) is a commercially valuable marine species widely farmed in Southeast Asia, yet growth heterogeneity remains a persistent challenge in cage aquaculture. To investigate whether body weight influences the intestinal microbiota of this species, we compared the gut microbial communities of small and large T. anak using high-throughput 16S rRNA gene sequencing. The intestinal microbiota was dominated by Pseudomonadota (Proteobacteria) and Mycoplasmatota, together accounting for nearly 80% of total sequences, with additional contributions from minor phyla such as Spirochaetota, Thermodesulfo bacteriota, and Bacteroidota. While alpha- and beta-diversity analyses revealed no significant differences between groups, community composition and structure varied. Smaller fish harbored a more heterogeneous assemblage at the class level and a broader suite of core taxa, including Acinetobacter, Aeromonas, Bdellovibrio, and Comamonas. In contrast, larger fish were dominated by fewer classes, with Photobacterium and Brevinema emerging as distinctive core members. LEfSe analysis identified discriminant taxa between groups, although these trends were not statistically significant after multiple-testing correction. Network analysis highlighted striking differences in microbial interactions: smaller fish exhibited highly modular, densely connected networks with potential keystone taxa such as Paracidovorax and Ensifer, whereas larger fish displayed simpler, less structured networks indicative of reduced ecological stability. Together, these findings demonstrate that body weight is associated with subtle but ecologically meaningful shifts in microbiota composition, core membership, and interaction networks in cage-cultured T. anak. This work underscores the potential of microbiome-informed management strategies to mitigate growth variability and enhance the sustainability of marine aquaculture.}, }
@article {pmid41937731, year = {2026}, author = {Kong, JF and Phang, HC and Wan Kamal, WHB and Ng, Y and Mohamad, S and Kee, PE and Liew, KB}, title = {Role of Probiotics in Oral Health: A Review From Microbial Balance to Clinical Applications.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010421039251206192855}, pmid = {41937731}, issn = {1873-4316}, abstract = {A diverse microbial community exists within the human oral cavity that plays an essential role in maintaining health or inducing diseases such as dental caries, periodontal disease, and halitosis. Probiotics, live microorganisms that provide health benefits when consumed in adequate amounts, have been found to be promising as a means of modulating the oral microbiome and combating these diseases. This review incorporates present knowledge about the mechanism of probiotic action, including competitive exclusion of pathogens, antimicrobial metabolite production, biofilm disruption, and immune modulation. Efficacy against pathogenic bacteria like Streptococcus mutans and Porphyromonas gingivalis has been proven by prominent probiotic groups Lactobacillus, Bifidobacterium, and Streptococcus, resulting in oral microbial homeostasis. Clinical applications of probiotics include prevention of caries, plaque reduction, and management of gingivitis and periodontitis, with research focusing on strain-specific effects. Emerging trends include precision probiotics tailored to each oral condition, postbiotics as strong alternatives (formerly "strong contenders"), and innovative delivery systems to enhance viability and colonization. The hurdles of strain specificity, regulatory gaps, and inconsistencies of clinical outcome continue. Safety concerns, while rare, represent possible risks of horizontal gene transfer and opportunistic infections in immunocompromised hosts. Future directions lie in genetic modification, new delivery methods, and standard clinical protocols to enhance probiotic function. This review emphasizes the clinical potential of probiotics as adjunctive treatments in oral medicine, with the caveat that further work is needed to overcome current challenges and enhance their therapeutic efficacy.}, }
@article {pmid41937967, year = {2026}, author = {Hiratsuka, D and Matsuo, M and Hirota, Y}, title = {Endometrial Microbiome and Implantation: From Basic Knowledge to Clinical Medicine.}, journal = {Reproductive medicine and biology}, volume = {25}, number = {1}, pages = {e70040}, pmid = {41937967}, issn = {1445-5781}, abstract = {BACKGROUND: Recurrent implantation failure (RIF) is an infertility condition in which uterine factors remain difficult to diagnose and treat. Recent studies implicate the endometrial microbiome in implantation.<br><br>METHODS: This clinically oriented narrative review summarizes female reproductive tract microbiota and evidence on endometrial microbiome testing and management in infertility.<br><br>MAIN FINDINGS RESULTS: Vaginal dysbiosis is linked to adverse reproductive outcomes and provides a reference for interpreting upper-tract findings. Endometrial microbial signals are detectable by sequencing, but interpretation is challenged by the low-biomass environment and vulnerability to carry-over, kitome effects, and contamination. Across ART studies, a Lactobacillus-enriched endometrial profile is more often associated with favorable pregnancy-related outcomes, whereas non-Lactobacillus-dominant patterns are more frequently reported in implantation failure, although effect sizes and statistical significance vary across cohorts and depend on sampling validity and cutoff definitions. Limited nonrandomized intervention studies suggest that testing-guided targeted management (typically antibiotics with or without vaginal Lactobacillus-containing probiotics) may benefit selected patients, but protocols are heterogeneous and results remain inconsistent.<br><br>CONCLUSION: Evidence is rapidly evolving, yet observational designs and methodological variability limit causal inference. Future progress will require standardized sampling and contamination controls, outcome-anchored threshold validation, and pragmatic real-world evaluations of protocolized test-and-treat pathways using clinically meaningful endpoints.}, }
@article {pmid41938040, year = {2026}, author = {Khalil, A and Thayer, ZM and Rivera, LM}, title = {Preterm birth, airway microbiome, and the evolutionary origins of asthma.}, journal = {Evolution, medicine, and public health}, volume = {14}, number = {1}, pages = {1-2}, pmid = {41938040}, issn = {2050-6201}, }
@article {pmid41938156, year = {2026}, author = {Liu, YH and Huang, JR and Tao, Y and Wang, CC and Gu, CQ and Zhang, YM and Li, WJ and Jiang, HC}, title = {Aridity gradient overrides degradation in shaping the topsoil microbiome of the Tianshan wild fruit forest.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100586}, pmid = {41938156}, issn = {2666-5174}, abstract = {The Tianshan wild fruit forest, a critical relict ecosystem and biodiversity hotspot, is experiencing severe degradation, a process widely assumed to be the primary driver of negative shifts in soil microbial communities. However, in arid regions, the overarching influence of climatic aridity may supersede localized degradation effects, creating a pivotal scientific question: which factor-aridity or degradation-dominantly regulates the soil microbiome in this unique habitat? To address this, we analyzed 360 topsoil samples across degradation and aridity gradients using high-throughput sequencing. The results demonstrate that the aridity index, not degradation level, is the paramount factor shaping microbial community structure, explaining the largest proportion of variation in both bacterial (∼43%) and fungal (∼30%) communities. The ecosystem harbors an exceptionally stable core microbiome, with community assembly predominantly governed by stochastic processes. Notably, alternating wet-dry (dry sub-humid) conditions significantly enhanced the complexity and stability of microbial co-occurrence networks compared to semi-arid or humid regions. Additionally, soil microbes mediated multiple core ecological processes, with nitrogen cycling as the most abundant-dominated by Rhodoplanes, Alcaligenes, and rhizobial taxa (Bradyrhizobium, Allorhizob), among others-wherein nitrate reduction was exceptionally active in the Tianshan wild fruit forest, particularly in humid and semi-arid habitats. These findings challenge the prevailing degradation-driven paradigm, highlighting aridity as the master regulator of microbial communities. This insight is crucial for guiding conservation strategies, emphasizing that managing water availability and protecting dry sub-humid habitats are essential for maintaining the microbial stability and functional resilience of this invaluable ecosystem under climate change.}, }
@article {pmid41938217, year = {2026}, author = {Mphande-Nyasulu, FA and Meksang, S and Noranate, N and Kongpanyakul, S and Kulalert, P and Nilchan, P and Trivijitsilp, P}, title = {Investigating Candida species and associated bacteria from vaginal swabs and smears of symptomatic and asymptomatic adult women: A cross-sectional study.}, journal = {IJID regions}, volume = {19}, number = {}, pages = {100868}, pmid = {41938217}, issn = {2772-7076}, abstract = {OBJECTIVES: Vaginal Candida infections are common among women, affecting between 75% and 80% of women in their lifetime, with a higher prevalence in women of childbearing age. This study assessed vaginal carriage of Candida species and associated bacteria in adult women.<br><br>METHODS: A total of 101 vaginal swabs and smears from symptomatic and asymptomatic adult women were analyzed for the presence of Candida sp. using culture, Gram stain, and next-generation sequencing (NGS). Morphology of selected Candida sp. was examined using scanning electron microscopy.<br><br>RESULTS: Candida colonization was observed in 39.6% (40 of 101) of the women. Candida albicans was identified in 75.0% (30 of 40) of the women, whereas the non-albicans species Nakaseomyces glabrata was observed in 7.5% (three of 40), P. kudriavzevii in 5% (two of 40), and C. tropicalis in 2.5% (one of 40). Women aged 18-25 years had the highest prevalence of colonization among all age groups, 47.5% (19 of 40). A significant difference in vaginal bacterial composition was observed among age groups 18-25 and 26-35 years (&#x3b1; 0.05 <0.038*, 95% confidence interval [CI] -0.16 to 0.99); between women positive for Candida aged 26-35 years and those aged 46-55 years (&#x3b1; 0.05 <0.016*, 95% CI -0.28 to -0.03); and between women who were Candida-positive and those who were Candida-negative (&#x3b1; 0.05 <0.016*, 95% CI 0.17 to -0.40). Among the women positive for Candida, symptomatic individuals had predominantly Gram-positive bacterial species 92.6% (23 of 25) compared with 46% (19 of 42) in asymptomatic individuals. Five bacterial species were shared between the symptomatic and asymptomatic samples. Unique budding patterns, surface modifications, and phylogenetic clusters are reported.<br><br>CONCLUSION: Vaginal Candida colonization including differences in microbiome composition according to age, disease status, and colonizing Candida species are reported. This study opens new areas of study in vaginal Candida colonization, pathogen-pathogen interaction, and microbiome analysis in more specific age brackets, away from the traditional pre-menopausal and menopausal women.}, }
@article {pmid41938356, year = {2026}, author = {Chen, Y and Zhao, S and Ma, X and Ling, L and Du, P and Liu, X and Yao, Y and Ma, Q and Cheng, Y and Wang, Y and Wei, J and Nian, H and Lian, T}, title = {Selenium nanoparticles and glutathione synergistically enhance salt tolerance in soybean via the jasmonic acid pathway and arbutin-regulated rhizosphere microbiota.}, journal = {aBIOTECH}, volume = {7}, number = {2}, pages = {100022}, pmid = {41938356}, issn = {2662-1738}, abstract = {Soil salinity threatens agriculture worldwide. Nano-fertilizers offer a promising strategy to enhance tolerance to salinity and other stresses in crops, but their field performance is sometimes unpredictable, potentially due to complex interactions within the plant-microbe holobiont. Here, we designed chitosan-stabilized selenium nanoparticles (SeNPs@CS) as a novel nano-fertilizer. SeNPs@CS exhibited a uniform size (∼109.8 nm) and a positively charged surface (+14.7 mV), which confers good adhesion to plant tissues. Due to their good biocompatibility and small size, SeNPs@CS can be readily absorbed and utilized by plant leaves. When SeNPs@CS were combined with glutathione (GSH) to form a nanocomposite (SeG), they significantly promoted plant growth and enhanced salt tolerance in soybean (Glycine max). Multi-omics analyses revealed that SeG activates jasmonic acid (JA) pathways in the plant and remodels the root metabolic profile, leading to the enrichment of arbutin, a key signaling molecule, in the rhizosphere. This metabolic shift recruits and enriches beneficial salt-tolerant microbes, including Bacillus and Streptomyces, thereby establishing a protective microbiome. Treatment of plants with a synthetic microbial community (SynCom) composed of these elite strains, in combination with arbutin, reproduced the salt tolerance phenotype conferred by SeG treatment. Therefore, SeG improves salt tolerance in soybean via activation of the JA defense pathway and arbutin-driven recruitment of salt-tolerant rhizosphere microorganisms. Together, these two mechanisms enhance plant resilience under salt stress. This multi-kingdom synergistic mechanism for alleviating stress provides a new paradigm for developing smart agricultural inputs that target the plant holobiont to improve crop resilience.}, }
@article {pmid41938562, year = {2026}, author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F}, title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {864-876}, pmid = {41938562}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.<br><br>MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), &#x3b1;- and &#x3b2;-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.<br><br>RESULTS: &#x3b1;-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, &#x3b2;-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.<br><br>CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.}, }
@article {pmid41938768, year = {2026}, author = {Xue, Z and Han, Q and Han, H and Yan, L and Ma, X and Ji, P and Wang, B and Zhang, L and Wang, L and Liu, G}, title = {Mechanisms of fetal growth restriction in gestational cholestasis: role of gut microbiota and placental redox.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1815498}, pmid = {41938768}, issn = {2297-1769}, abstract = {INTRODUCTION: Intrahepatic cholestasis of pregnancy (ICP) is a cholestatic liver disorder associated with substantial fetal morbidity, including preterm birth, fetal distress, and even intrauterine demise. Although prior studies have documented structural and transcriptional alterations in the placenta during ICP, the mechanistic underpinnings linking maternal cholestasis to adverse fetal outcomes remain incompletely elucidated.<br><br>METHODS: In this study, a murine model of ICP was established by feeding pregnant C57BL/6 mice a 0.1% DDC (3,5-dicarboxylic acid-1,4-dihydrocollidine) diet from E0.5 to E18.5. We assessed fetal growth and employed multi-omics approaches, including placental transcriptome sequencing, maternal gut microbiome profiling, and serum/placental metabolome analysis.<br><br>RESULTS: Placental transcriptome sequencing revealed that ICP significantly downregulated the expression of antioxidant-related genes including Mgst1, Gstt1, Ggt1, Gpx8, Gstk1, and GSTA4 leading to reduced total antioxidant capacity in placental tissue and elevated levels of malondialdehyde (MDA), a marker of lipid peroxidation. Furthermore, ICP disrupted the maternal gut microbiota, resulting in decreased production of antioxidant microbial metabolites such as valeric acid and erythritol. This deficiency further aggravated oxidative damage in the placenta.<br><br>DISCUSSION: Collectively, our findings uncover a novel gut microbiota-placenta axis driven by cholestasis, which contributes to fetal IUGR. The maternal cholestasis induces gut dysbiosis, which diminishes the production of valeric acid and erythritol. The deficiency of these metabolites, coupled with a direct suppression of the placental Nrf2/Keap1 antioxidant signaling pathway by cholestasis, leads to placental oxidative stress. This oxidative damage impairs placental function, ultimately resulting in fetal growth restriction. Disrupting this pathogenic cycle may offer a promising therapeutic strategy for preventing or treating ICP-related reproductive disorders.}, }
@article {pmid41930959, year = {2026}, author = {Horinouchi, M}, title = {Identification of the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings in steroid degradation by Comamonas testosteroni TA441.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0233125}, doi = {10.1128/aem.02331-25}, pmid = {41930959}, issn = {1098-5336}, abstract = {Comamonas testosteroni TA441 is a model aerobic steroid-degrading bacterium whose sterane degradation pathway has been elucidated in the greatest detail to date. Similar pathways have been identified in many genera of bacteria, including both proteobacteria and actinobacteria, such as Mycobacterium tuberculosis. However, the genes encoding the C9-hydrogenase for 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid (9,17-DOHNA, also known as HIP) and the 7α-dehydratase essential for initiating β-oxidation of the B-, C-, and D-rings had not been identified. In this study, we identified these missing genes, located adjacent to the chsE1E2H1H2ltp2 cluster involved in C17 side-chain degradation, and designated them scdB and scdH, respectively. This finding completes the elucidation of all degradation steps of 9,17-DOHNA prior to D-ring cleavage. AlphaFold models showed that ScdB and at least five hydrogenases/dehydrogenases involved in steroid degradation in TA441 share a similar dimer structures with Rossmann fold motif. In contrast, ScdH was predicted to form a homohexameric structure similar to ScdY and ScdN, involved in B-, C-, and D-ring degradation in TA441. Furthermore, AlphaFold modeling revealed that SteC, the dehydratase responsible for removing the C12β-hydroxyl group from 9,17-DOHNA derivatives, exhibits strong structural similarity to BaiE, the bile acid 7α-dehydratase of Clostridium scindens JCM 10418/VPI 12708, despite sharing only ~28% amino acid sequence identity.IMPORTANCEResearch on bacterial aerobic steroid degradation began more than 70 years ago, initially to produce intermediates for steroid drug synthesis. Recently, this field has gained renewed attention due to its implications for human health-for example, the role of cholesterol import and degradation in the persistence of Mycobacterium tuberculosis H37Rv within chronically infected lungs. Comamonas testosteroni TA441 serves as a key model organism for elucidating aerobic steroid degradation, with pathways for cleavage of the A-, B-, C-, and D-rings already well established. The functions and structures of the enzymes identified in TA441 display striking similarities to those in actinobacteria, such as M. tuberculosis. In this study, we identified two enzymes indispensable for initiating β-oxidation of the B-, C-, and D-rings, thereby filling the last remaining gaps for initiating this pathway. Our AlphaFold-based structural analysis of these enzymes not only provides new insights into the steroid metabolism of M. tuberculosis but also broadens understanding of the ecological and physiological significance of bacterial steroid degradation.}, }
@article {pmid41930960, year = {2026}, author = {Nan, F and Song, H and Sun, M and Cui, L and Bian, Z and Yin, J and Lin, Z and Wang, Y}, title = {Hijacking competitor-derived signals: RcsB/C drives Lysobacter enzymogenes to exploit farnesol for enhanced antifungal capacity.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0030426}, doi = {10.1128/aem.00304-26}, pmid = {41930960}, issn = {1098-5336}, abstract = {Microbial antagonism is a fundamental ecological process that shapes community composition and maintains ecosystem balance. However, the molecular signals, such as cross-kingdom interactions between bacteria and fungi in natural environments, remain largely unexplored. Lysobacter enzymogenes is a widespread predatory bacterium that produces the antifungal secondary metabolite heat-stable antifungal factor (HSAF), which enables interactions with diverse fungi. Here, we investigated the interkingdom interactions between L. enzymogenes and the environmental fungus Candida krusei, both of which are widely distributed, to elucidate the bacterial-fungal communication. We found that the antagonistic effect of bacteria-fungi was significant under both contact and non-contact co-culture conditions, indicating the involvement of diffusible metabolites. Given that farnesol is a common quorum-sensing (QS) molecule in Candida, metabolite profiling combined with exogenous addition and biosynthesis inhibition experiments demonstrated that farnesol functions as a cross-kingdom signal regulating HSAF production and bacterial antagonism. Further mechanistic analysis of the intrinsic mechanism revealed that the two-component system (TCS) RcsB/C in L. enzymogenes can sense farnesol and activate the production of HSAF through the MarR family regulators, mediating the antagonistic pathway. In addition, our work identified the key amino acid residues in RcsC of L. enzymogenes responsible for recognizing farnesol. In summary, we report the bacterial TCS involved in farnesol sensing and reveal a novel bacterial-fungal antagonistic mechanism, in which L. enzymogenes "hijacks" a fungal QS molecule to enhance its antifungal capacity, uncovering a previously unrecognized strategy of cross-kingdom communication.IMPORTANCEBacteria and fungi frequently interact in shared habitats, yet the chemical cues that shape these cross-kingdom relationships remain poorly defined. Farnesol is a well-known quorum-sensing molecule in Candida, but its ecological roles beyond fungal communication are unclear. Here, we show that Lysobacter enzymogenes directly senses fungal-derived farnesol through the RcsB/C two-component system, which activates the downstream regulator MarR-2 and induces the production of the antifungal metabolite heat-stable antifungal factor (HSAF). This signal hijacking strategy allows L. enzymogenes to convert a fungal communication molecule into a cue that strengthens its antagonistic capacity. We further identify key amino acid residues in RcsC responsible for farnesol recognition, revealing the bacterial two-component system (TCS) known to detect this molecule. These findings expand the functional scope of fungal quorum-sensing signals, uncover a previously unrecognized mechanism of interkingdom antagonism, and provide insights with potential applications in microbiome-based biocontrol.}, }
@article {pmid41930968, year = {2026}, author = {Cheng, D and Luo, Z and Ning, W and Heath, SL and Gisslen, M and Price, RW and Adekunle, R and Salman, T and Johnson, D and McKinnon, JE and Ndhlovu, LC and Hossain, R and Hu, W and Jiang, W}, title = {Systemic translocation of Staphylococcus aureus promotes autoimmunity: implications in autoantibody-mediated poor immune reconstitution from antiretroviral therapy in HIV.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0196525}, doi = {10.1128/jvi.01965-25}, pmid = {41930968}, issn = {1098-5514}, abstract = {In 2017, our group first demonstrated that autoimmunity contributes to HIV pathogenesis, even without autoimmune disease. This concept is now broadly recognized, exemplified by the role of autoimmunity in severe COVID-19. In people with HIV (PWH) on suppressive antiretroviral therapy (ART), anti-CD4 autoantibodies may impair CD4+ T-cell recovery, though the mechanisms driving their production remain unclear. Building on evidence from our group and others that Staphylococcus aureus and its peptidoglycan (PGN) promote autoimmunity, we investigated their contribution to anti-CD4 IgG in HIV. Plasma from 32 ART-naive PWH, 53 ART-treated PWH, and 32 HIV-negative controls was analyzed for IgG autoantibodies and markers of S. aureus translocation using protein array and ELISA. EcoHIV mice were injected intraperitoneally with saline, S. aureus PGN, or Bacillus subtilis PGN. PGN structures were compared by mass spectrometry. Among 87 autoantibodies, 40% were elevated in ART-naive PWH and largely normalized by ART; however, anti-CD4 IgGs remained elevated in PWH on ART. Anti-CD4 IgG levels inversely correlated with CD4+ T-cell counts in ART-treated PWH and positively with markers of S. aureus translocation. In mice, S. aureus PGN induced anti-CD4 IgGs, reduced frequency of CD4+ T cells among total gut T cells, and promoted surface IgG binding and apoptosis in CD4+ T cells. S. aureus and its PGN translocation may drive anti-CD4 autoimmunity and hinder immune recovery in PWH on suppressive ART, highlighting S. aureus colonization as a therapeutic target and supporting the development of competitive probiotic interventions.IMPORTANCECurrently, no treatment is available for improving CD4+ T-cell recovery in people with HIV (PWH) on suppressive antiretroviral therapy (ART). Up to 20% of PWH on ART fail to restore peripheral CD4+ T-cell counts to levels observed in healthy individuals, a condition associated with increased morbidity and mortality and representing a major unmet challenge in HIV clinical care. Our study demonstrates that systemic Staphylococcus aureus translocation contributes to autoimmunity and impaired immune reconstitution in a subset of PWH on suppressive ART. These findings identify a previously unrecognized mechanism of immune failure and support a novel therapeutic strategy combining probiotics with ART to enhance immune recovery and reduce HIV-associated morbidity and mortality.}, }
@article {pmid41931049, year = {2026}, author = {Rosen, CJ and Ingelfinger, JR}, title = {GLP-1 Receptor Agonists.}, journal = {The New England journal of medicine}, volume = {394}, number = {13}, pages = {1313-1324}, doi = {10.1056/NEJMra2500106}, pmid = {41931049}, issn = {1533-4406}, mesh = {Humans ; *Cardiovascular Diseases/etiology/metabolism/prevention &amp; control ; *Diabetes Mellitus, Type 2/complications/drug therapy/metabolism ; Glucagon-Like Peptide 1/agonists/metabolism ; *Glucagon-Like Peptide-1 Receptor Agonists/adverse effects/pharmacology/therapeutic use ; Hypoglycemic Agents/adverse effects/pharmacology/therapeutic use ; Incretins/metabolism ; *Obesity/complications/drug therapy/metabolism ; *Renal Insufficiency/etiology/metabolism/prevention &amp; control ; Anti-Obesity Agents/adverse effects/pharmacology/therapeutic use ; Disease Progression ; Gastric Emptying/drug effects ; Glucagon/metabolism ; Gastrointestinal Microbiome/drug effects ; Satiety Response/drug effects ; Randomized Controlled Trials as Topic ; Medication Adherence ; }, abstract = {Glucagon-like peptide-1 (GLP-1) receptor agonists are incretin analogues that promote glucose-mediated insulin release and are used to treat type 2 diabetes mellitus and obesity. GLP-1 receptor agonists and GLP-1 and glucose-dependent insulinotropic peptide agonists have several mechanisms of action, including reduction of gastric emptying, inhibition of glucagon secretion, beneficial changes in the intestinal microbiome, and direct effects on hypothalamic nuclei to enhance satiety (which promotes weight loss). Beyond the impressive effects of GLP-1 receptor agonists on blood glucose levels and body weight, large-scale randomized, controlled trials have shown that GLP-1 receptor agonists reduce cardiovascular risk and slow progression to renal failure in persons at high risk and those with type 2 diabetes. Adverse side effects from GLP-1 receptor agonists are mostly gastrointestinal but may also include loss of muscle and bone mass. Questions remain about long-term adherence, weight regain after discontinuation of treatment, and the functional implications of the loss of muscle and bone mass. Recent and ongoing targeted studies suggest the possibility of additional uses for GLP-1 receptor agonists.}, }
@article {pmid41931118, year = {2026}, author = {Ansari, S and Purohit, KJ and Shelke, AB and Shah, M and Nkhoma, IA and Navale, AM and Wakchaure, R}, title = {Microbiota-driven mechanisms in multisystem diseases: integrative evidence across cardiovascular, metabolic, neurological and autoimmune disorders.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41931118}, issn = {1572-9699}, mesh = {Humans ; *Autoimmune Diseases/microbiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; *Cardiovascular Diseases/microbiology ; *Nervous System Diseases/microbiology ; *Metabolic Diseases/microbiology ; *Microbiota ; Animals ; }, abstract = {The human microbiota represents one of the body's most influential biological systems, engaging in constant metabolic, immunological, and neuroendocrine communication with the host. Disruption of this intricate ecosystem, or dysbiosis, has emerged as a fundamental determinant in the onset and progression of numerous chronic diseases. This review consolidates contemporary evidence on how alterations in microbial composition, metabolite production, and barrier integrity contribute to pathophysiological changes across multiple organ systems. Gut-derived metabolites-including short-chain fatty acids, bile acid derivatives, trimethylamine-N-oxide, and lipopolysaccharide-serve as key mediators linking microbial imbalance to systemic inflammation, metabolic dysfunction, autoimmunity, and neurodegeneration. We outline the mechanistic pathways through which dysbiosis promotes hypertension, atherosclerosis, obesity, type 2 diabetes, Parkinson's disease, Alzheimer's disease, rheumatoid arthritis, inflammatory bowel disease, asthma, chronic obstructive pulmonary disease, urinary tract infections, and chronic kidney disease. Particular emphasis is placed on the gut-brain, gut-lung, and gut-kidney axes, which facilitate bidirectional immune and metabolic signalling between the intestine and distant tissues. Additionally, the review highlights emerging therapeutic interventions aimed at restoring microbial homeostasis, including targeted dietary strategies, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and microbiome-directed pharmacological approaches. Collectively, the evidence positions the microbiota as a central regulator of human health and disease, offering a compelling platform for next-generation diagnostic and therapeutic innovation. Advancing mechanistic understanding of host-microbe interactions will be essential to developing personalized microbiome-based strategies capable of preventing, mitigating, or reversing disease across diverse clinical contexts.}, }
@article {pmid41931121, year = {2026}, author = {Liu, B and Wan, SH and Zhang, YT and Lin, JH and Ke, XC and Lin, WH and Zhan, MX}, title = {Gut microbiome remodeling across hepatocellular carcinoma progression and transarterial chemoembolization is associated with therapeutic response and prognosis.}, journal = {Clinical and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10238-026-02137-z}, pmid = {41931121}, issn = {1591-9528}, support = {2023A1515012588 and 2022A1515220092//Guangdong Basic and Applied Basic Research Foundation/ ; 2022B1515020010//Guangdong Basic and Applied Basic Research Foundation/ ; 82472084//the National Natural Science Foundation of China/ ; 82272103//the National Natural Science Foundation of China/ ; 2021B1212040004//the Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment/ ; }, }
@article {pmid41931829, year = {2026}, author = {Venkitaraman, AR}, title = {Proteostasis Deregulation by Metabolism Drives the Hallmarks of Cancer.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051424-052148}, pmid = {41931829}, issn = {1545-4509}, abstract = {Cancer cells acquire hallmark behaviors through adaptations that extend beyond genetic and epigenetic changes. Proteostasis-the biochemical network governing protein synthesis, folding, trafficking, and degradation-is a fundamental, yet underappreciated, mediator of these adaptations that merits consideration as a hallmark-enabling mechanism. Metabolic alterations impose proteotoxic stress, globally rewire protein homeostasis, and selectively modulate key oncogenic and tumor suppressive proteins. A unifying framework is proposed wherein metabolic deregulation of proteostasis operates throughout carcinogenesis: early, by enhancing accumulation of premalignant clones bearing cancer-driving somatic mutations in response to environmental and systemic metabolic stress, and later, by buffering proteotoxic stress to sustain malignant growth in hostile tissue environments. This perspective connects cancer risk with genetic background, diet, microbiome-derived metabolites, and metabolic disease, introduces metabolic bypass of tumor suppression as an alternative to classical genetic models, and highlights the metabolism-proteostasis interface as a promising target for cancer prevention and therapy.}, }
@article {pmid41931987, year = {2026}, author = {Dang, W and Li, W and Dong, F and Huang, Y and He, S and Zhu, Y}, title = {Microbial metabolites: Bridging the gut-brain divide in ischemic stroke.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128510}, doi = {10.1016/j.micres.2026.128510}, pmid = {41931987}, issn = {1618-0623}, abstract = {The Microbiota-Gut-Brain Axis (MGBA) has recently crystallized into a focal frontier spanning neuroscience and microbiology, illuminating the intricate reciprocity between intestinal microbes and the central nervous system. Stroke, a devastating and life-threatening cerebrovascular disorder, is now recognized to have its onset, progression, and long-term outcome intimately entwined with MGBA dynamics. Accumulating empirical literature substantiates the existence of intimate bidirectional gut-brain signaling circuits, wherein the gut microbiome functions as a central modulator. This microbial consortium not only orchestrates neuroinflammatory cascades following cerebral insult, but also bio-transforms dietary and host-derived substrates into multifunctional metabolites that exert both local and systemic bioactivity. Emerging evidence suggests that individual microbial metabolites and their secondary derivatives may serve as candidate signaling intermediaries, mediating the transduction of microbial cues into neurovascular responses. Accordingly, the present review provides a forward synthesis of how the MGBA intersects with ischemic stroke pathobiology, focusing on elucidating the therapeutic potential and strategies of gut microbial metabolites in ischemic stroke. It provides theoretical insights and translational prospects for gut-derived metabolites as therapeutic targets.}, }
@article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, }
@article {pmid41932098, year = {2026}, author = {Zhang, M and Xiong, W and Shao, R and Wang, Z and Shen, Z and Zhou, Q and Du, G}, title = {Disrupted Salivary Fungal Community in Patients With Oral Lichen Planus.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109546}, doi = {10.1016/j.identj.2026.109546}, pmid = {41932098}, issn = {1875-595X}, abstract = {INTRODUCTION AND AIMS: Oral lichen planus (OLP), a chronic inflammatory oral mucosal disorder with malignant potential, has been associated with oral microbial dysbiosis. While bacterial community alterations in OLP are well-documented, the fungal community architecture and ecological dynamics, particularly within salivary microbiota, remain poorly characterised.<br><br>METHODS: Saliva samples were collected from 30 participants and stratified into 3 cohorts: 10 healthy controls (HC), 10 reticular OLP (R-OLP) patients and 10 erosive OLP (E-OLP) patients. The fungal community profile was assessed using internal transcribed spacer (ITS) sequencing, complemented by multi-dimensional analytical approaches, including diversity metrics, co-occurrence network construction and functional prediction.<br><br>RESULTS: Significant diversity disparities distinguished fungal communities across groups. Taxonomically, Pseudozyma and Simplicillium demonstrated reduced abundance in OLP patients versus HC, while Pyronema was exclusive to OLP cohorts. Fungal ecological networks in OLP exhibited increased density compared to HC. Linear discriminant analysis effect size (LEfSe) analysis identified Pseudozyma as an HC-associated biomarker and Pyronema as an E-OLP discriminant, while predictive models highlighted Pseudozyma and Simplicillium as effective group stratifiers. FUNGuild profiling revealed predominant saprotrophic activity across all groups, with decreased pathotroph-symbiotroph guild representation in OLP patients.<br><br>CONCLUSIONS: Salivary fungal communities in OLP exhibit structural and compositional alterations. Through integrated analyses of relative abundance, random forest modelling and LEfSe, this study indicated that 3 fungal taxa may be as potential biomarkers for distinguishing OLP from HC. Among these, Pseudozyma and Simplicillium showed characteristics suggesting a possible probiotic role, while Pyronema, with its detection limited to OLP and absence in HC, may be associated with the disease.<br><br>CLINICAL RELEVANCE: The fungal profile observed in this study, comprising the potentially beneficial taxa Pseudozyma and Simplicillium as well as the OLP-linked Pyronema, offers new directions for developing noninvasive diagnostics and microbial-targeted therapies for OLP.}, }
@article {pmid41932183, year = {2026}, author = {Liu, L and Liu, L and Li, A and Liu, Z and Xue, S and Li, J and Mao, Y}, title = {Robust gut microbiota as a key protective barrier for Ruditapes philippinarum survival following an extreme-rainfall disturbance.}, journal = {Marine environmental research}, volume = {218}, number = {}, pages = {108033}, doi = {10.1016/j.marenvres.2026.108033}, pmid = {41932183}, issn = {1879-0291}, abstract = {Gut microbiota is critical for host health, yet its role in buffering filter-feeding bivalves against acute habitat disturbance remains poorly understood. Here, the Manila clam Ruditapes philippinarum was used as a model to investigate how an extreme rainfall event reshaped microbial communities in the gut and surrounding habitat (water and sediment), with sampling conducted before and 10 and 30 days after the event. Extreme rainfall caused mass mortality and markedly disrupted host-associated microbiota. Surviving clams harbored gut microbiota with higher diversity and richness, enrichment of putatively beneficial taxa (e.g., Actinomycetota, Bacteroidota, Verrucomicrobiota, and Bacillus), reduced abundance of the opportunistic pathogen Vibrio, and increased network complexity and stability, accompanied by enrichment of functional potentials related to energy metabolism, signal transduction, and stress adaptation. Notably, gut community assembly shifted toward greater stochasticity, broader niche breadth, and reduced dispersal limitation during recovery, indicating a reassembly pattern that balances compositional stability with adaptive flexibility. Together, these results highlight gut microbiota robustness and assembly plasticity as key mechanisms linking extreme-rainfall disturbance to clam resilience, providing insights for microbiome-informed management to support sustainable bivalve aquaculture.}, }
@article {pmid41932251, year = {2026}, author = {Huang, H and Yin, J and Xu, C and Gu, HY}, title = {The role of the gut-spinal axis in immune-metabolic coupling after spinal cord injury.}, journal = {International immunopharmacology}, volume = {178}, number = {}, pages = {116581}, doi = {10.1016/j.intimp.2026.116581}, pmid = {41932251}, issn = {1878-1705}, abstract = {Spinal cord injury (SCI), representing a devastating trauma to the central nervous system (CNS), is often accompanied by complex immune responses and metabolic dysregulation, significantly affecting patients' functional recovery and quality of life. In recent years, the gut-spinal axis, as an important pathway connecting the gut microbiome and the CNS, has emerged as a pivotal area of investigation regarding the pathological mechanisms of SCI. Changes in the gut microbiome modulate inflammatory responses and tissue repair processes after SCI by regulating immune system activation and metabolic pathways. However, the specific mechanisms by which the gut-spinal axis mediates the interplay between immune and metabolic processes after SCI have not been fully elucidated. This article summarizes the structural and functional characteristics of the gut-spinal axis, as well as the gut microbial imbalance, immune activation, and metabolic regulation induced by SCI. It focuses on how the gut-spinal axis mediates the interaction between immunity and metabolism, thereby influencing the pathological progression and repair potential of SCI. By integrating basic and clinical research findings, it aims to offer a theoretical framework for the comprehensive regulatory mechanisms of immunity and metabolism in SCI and to explore innovative therapeutic strategies targeting the gut-spinal axis.}, }
@article {pmid41932357, year = {2026}, author = {Winston, JA and Jennings, R and Randolph, NK and Welton, M and Partridge, E and Schreeg, M and Yaxley, PE and Rudinsky, AJ}, title = {Fecal microbiota transplantation dosing regimen accelerates clinical resolution in canine parvovirus infection: a novel spectrum-of-care approach.}, journal = {Journal of the American Veterinary Medical Association}, volume = {}, number = {}, pages = {1-9}, doi = {10.2460/javma.25.11.0764}, pmid = {41932357}, issn = {1943-569X}, abstract = {OBJECTIVE: To evaluate the efficacy of a novel spectrum-of-care fecal microbiota transplant (FMT) dosing regimen as an adjunctive therapy for canine parvovirus (CPV).<br><br>METHODS: 27 client-owned dogs naturally infected with CPV were enrolled from March to November 2023 in a prospective, double-blinded, placebo-controlled clinical trial. Patients were randomized into FMT-treated (n = 19) or placebo-treated (8) groups. Along with conventional treatments, CPV-infected dogs were administered FMT (single FMT enema, then 14 days of oral lyophilized FMT capsules) or placebo (single saline enema, then 14 days of oral placebo capsules) at admission. During hospitalization, dogs were monitored daily including fecal, clinical severity, and medication scores. Feces and serum were collected at admission, day 4, day 7, day 14, and day 21 for quantification of CPV viral shedding and immune response (bead-based multiplex of cytokines/chemokines). The primary outcome variable was length of hospitalization.<br><br>RESULTS: Interim analysis revealed that placebo-treated dogs had excessive study withdrawals due to worsening clinical status when compared to FMT-treated dogs (37.5% compared to 0%, respectively), leading to ethical discontinuation of the placebo arm. Fecal microbiota transplant-treated dogs had significantly reduced hospitalization length and medications required for treatment (maximum medication score) compared to placebo-treated dogs. Fecal microbiota transplant did not reduce fecal viral shedding or elicit a host immune response.<br><br>CONCLUSIONS: This novel FMT dosing regimen (single enema FMT followed by oral capsular FMT), designed to be feasible for inpatients or outpatients, accelerated clinical recovery from CPV.<br><br>CLINICAL RELEVANCE: In-house and commercially available FMT products were effective in CPV-infected dogs, thus broadening the spectrum of care available to these patients.}, }
@article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00976-y}, pmid = {41932913}, issn = {2055-5008}, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, }
@article {pmid41933092, year = {2026}, author = {Han, M and Liu, X and Li, G and Li, P}, title = {Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70335}, doi = {10.1111/1758-2229.70335}, pmid = {41933092}, issn = {1758-2229}, support = {32260652//The National Natural Science Foundation of China/ ; }, mesh = {*Ralstonia solanacearum/physiology/genetics/pathogenicity ; *Plant Diseases/microbiology/prevention &amp; control ; *Adaptation, Physiological ; Quorum Sensing ; Virulence ; Soil Microbiology ; }, abstract = {The Ralstonia solanacearum species complex (RSSC) ranks among the most destructive plant pathogens worldwide, due to its broad host range, extensive geographic distribution and remarkable environmental adaptability. Its persistence in soil and colonization of plant vascular tissues severely limits the effectiveness of conventional chemical control, posing significant challenges for disease management. This review highlights recent advances in understanding the environmental adaptation mechanisms of RSSC. Key topics include the dynamic evolution of pathogenicity, niche-specific survival strategies and virulence regulation mediated by quorum sensing, and complex interactions with surrounding microbial communities that shape its behaviour and fitness. We further provide a comprehensive assessment of current control strategies from an ecological perspective, encompassing physical, chemical, genetic, agronomic and microbial approaches, with critical evaluation of their mechanisms, potential and limitations. Meanwhile, we discuss the major challenges in bacterial wilt management and outline future directions, with an emphasis on multi-omics-informed precision breeding, microbiome engineering and intelligent integrated disease management (IDM). These emerging strategies hold promise for the sustainable and effective long-term control of bacterial wilt disease caused by RSSC.}, }
@article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44972-w}, pmid = {41933095}, issn = {2045-2322}, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, }
@article {pmid41933198, year = {2026}, author = {Ondreičková, K and Böhmer, M and Rusňáková, D and Kubáňová, M and Szemes, T and Pániková, L and Oxikbayev, BK and Mukasheva, D and Janiga, M}, title = {Microbial community structure across freshwater ecosystem types in a high-altitude region, Zhongar Alatau, Kazakhstan.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41933198}, issn = {1573-0972}, support = {101160008//European Union's Horizon Europe research and innovation programme/ ; AP26102759//Ministry of Education and Science of the Republic of Kazakhstan/ ; }, }
@article {pmid41933201, year = {2026}, author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB}, title = {Unbinned contigs expand known diversity in the global microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41933201}, issn = {2058-5276}, support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.}, }
@article {pmid41933264, year = {2026}, author = {Ma, Y and Li, X and Luo, Y}, title = {Microbiome-driven innovations for climate-resilient crop production.}, journal = {Nature food}, volume = {}, number = {}, pages = {}, pmid = {41933264}, issn = {2662-1355}, support = {41991335//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, }
@article {pmid41933289, year = {2026}, author = {Lawther, K and Tapio, I and Vera-Ponce de León, A and Aho, VTE and Huws, SA and Dimonaco, NJ}, title = {A curated database of rumen ciliate protozoal 18S rRNA gene sequences for metataxonomic applications.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01420-y}, pmid = {41933289}, issn = {2730-6844}, abstract = {OBJECTIVES: Protozoa are key members of the rumen microbiome playing significant roles in nutrient cycling and methane production, yet are understudied. As rumen metataxonomic studies increasingly incorporate protozoal primers, the lack of curated dedicated reference databases limits accurate classification. This dataset was developed to address that gap and support future protozoa-focused rumen microbial analyses.<br><br>DATA DESCRIPTION: The curated dataset comprises 228 rumen ciliate protozoal 18S rRNA gene sequences sourced from publicly available datasets. Sequences were processed to remove redundancy and standardise naming. The final database spans 23 families, 53 genera, and 100 species, and is suitable for use in metataxonomic pipelines, including QIIME2. It provides a valuable resource for researchers aiming to improve taxonomic resolution of protozoal communities in rumen environments.}, }
@article {pmid41933306, year = {2026}, author = {Adamczak, M and Pokora, P and Kaczmarczyk, M and Gojowy, D and Wierzbicka-Woś, A and Cembrowska-Lech, D and Kolonko, A and Łoniewski, I and Więcek, A}, title = {Intestinal microbiome and acute transplanted kidney rejection - results of a single-center, case-control study.}, journal = {BMC nephrology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12882-026-04951-9}, pmid = {41933306}, issn = {1471-2369}, }
@article {pmid41933371, year = {2026}, author = {Yao, T and Fan, M and Hao, Z and Jiang, Z and Li, X and Wang, S and Xu, Z}, title = {Gordonibacter-associated regulatory T cell dysfunction and S100A11-mediated neural impairment in Hirschsprung's disease: a microbiota-immune-neural axis.}, journal = {Cell &amp; bioscience}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13578-026-01562-7}, pmid = {41933371}, issn = {2045-3701}, support = {PL2024H140//Natural Science Foundation of Heilongjiang Province/ ; 24ZX008//Pediatric Special Project of the Sixth Affiliated Hospital of Harbin Medical University/ ; ZL2024H001//Key Project of the Joint Fund of the Natural Science Foundation of Heilongjiang Province/ ; }, abstract = {BACKGROUND: Hirschsprung's disease (HSCR) is a congenital disorder characterized by intestinal aganglionosis. Despite evidence linking gut microbiota and immune cells to various gastrointestinal diseases, their role in HSCR pathogenesis remains poorly understood. We investigated associations between gut microbiota composition, immune cell phenotypes, and neural impairment in HSCR patients.<br><br>RESULTS: Mendelian randomization analysis identified associations between Gordonibacter species and elevated HSCR risk (OR&#x2009;=&#x2009;2.74, 95% CI 1.42-5.28), potentially mediated through CD28&#x207a;CD39&#x207a; regulatory T cells. Multi-omics profiling revealed notable S100A11 upregulation in HSCR tissues. CD28&#x207a;CD39&#x207a; Tregs from HSCR patients exhibited functional alterations, including reduced suppressive capacity alongside elevated S100A11 production. Both CD4&#x207a; T cells and CD68&#x207a; macrophages expressed S100A11 by immunohistochemistry. S100A11 treatment activated RAGE-NF-&#x3ba;B signaling in vitro, accompanied by suppression of neural developmental markers (SOX10, RET, PHOX2B) and impaired neuronal migration. Serum S100A11 showed diagnostic potential (AUC&#x2009;=&#x2009;0.947). Microbiome profiling demonstrated differential bacterial enrichment, while antibiotic depletion experiments indicated microbiota-dependent modulation of immune-neural interactions.<br><br>CONCLUSION: Our findings link gut microbiota alterations, immune dysregulation, and neural developmental impairment in HSCR, implicating S100A11-RAGE-NF-&#x3ba;B signaling as a pathway deserving mechanistic investigation.}, }
@article {pmid41933391, year = {2026}, author = {Liu, Y and Liu, J and Niu, D and Hu, L and Kou, F and Jiao, Y and Cao, W and Liu, Q and Fu, X and Hu, C and Tong, J and Xiong, H and Wang, Y}, title = {16S rRNA gene sequencing reveals distinct intratumoral bacterial microbiome signatures between CT indeterminate benign and early-stage malignant pulmonary lesions.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08078-1}, pmid = {41933391}, issn = {1479-5876}, }
@article {pmid41933403, year = {2026}, author = {Dugény, E and Ceolotto, L and Franch, R and Pesce, G and Alvarez, E and Esposti, E and Mazzariol, S and Centelleghe, C}, title = {Optimizing cetacean blow collection methods under controlled conditions: implications for further non-invasive UAV-based sampling of the cetacean respiratory microbiome in the wild.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00555-8}, pmid = {41933403}, issn = {2524-4671}, support = {CN_00000033//NextGenerationEU/ ; ECS00000043//NextGenerationEU/ ; }, }
@article {pmid41933494, year = {2026}, author = {Yang, X and Gao, S and Kong, X and Gao, F and Xu, Q}, title = {Host Filtering Overrides Environmental Heterogeneity in Shaping Sea Cucumber Gut Microbiomes.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70294}, doi = {10.1111/1462-2920.70294}, pmid = {41933494}, issn = {1462-2920}, support = {2025FY101004//Science and Technology Fundamental Resources Investigation Program/ ; 2022YFD2401305//National Key Research and Development Program of China/ ; 2025-73//Hainan Postdoctoral Scientific Research Foundation/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Sea Cucumbers/microbiology ; Ecosystem ; Phylogeny ; }, abstract = {Gut microbiomes play critical roles in host physiology and ecological contributions of sea cucumbers in tropical coral reefs. However, the relative importance of host filtering versus environmental factors in gut microbiome assembly remains poorly quantified in natural populations. Using 16S rRNA gene amplicon sequencing and sediment physicochemical analyses, this study characterized gut microbiomes of three co-occurring sea cucumber species (Holothuria atra, Holothuria edulis and Stichopus chloronotus) across heterogeneous habitats. Despite significant spatial variation in sediment properties and microbial communities, all three sea cucumber species maintained species-specific and stable gut microbiomes across sites. Although source tracking identified sediment as the primary microbial reservoir, variation partitioning revealed that host filtering far overrode environmental heterogeneity, with sediment physicochemical properties explaining a negligible fraction (< 1%) of community variation. Each host harboured distinct functional taxa, and most dominant genera showed no significant correlations with sediment properties. These results support a 'host as filter and sediment as source' pattern, indicating that host-mediated selection can filter microbes from distinct source pools to establish a conserved gut microbiome largely independent of environmental variation. By retaining microbial taxa with functional potentials, sea cucumbers may ensure consistent contributions to organic matter degradation and nutrient cycling regardless of environmental fluctuations.}, }
@article {pmid41933499, year = {2026}, author = {Tonanzi, B and Massimi, A and Di Pippo, F and Petruccioli, M and Rossetti, S and Crognale, S}, title = {Unveiling Microbial Communities: Methodological Biases in DNA Extraction and 16S rRNA Sequencing Skew Microbial Profiles in Anaerobic Fermentation.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70297}, doi = {10.1111/1462-2920.70297}, pmid = {41933499}, issn = {1462-2920}, mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics/isolation &amp; purification ; Anaerobiosis ; Fermentation ; *Bacteria/genetics/classification/isolation &amp; purification ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Modern molecular analyses have revolutionized the study of microbial communities, yet DNA extraction and sequencing remain critical sources of bias. This study investigated the impact of seven different DNA extraction protocols and two 16S rRNA hypervariable regions (V1-V3 and V3-V4) on the profiling of a complex anaerobic fermentative biomass selected for medium-chain fatty acids production. Microscopic analysis established a baseline community dominated by Actinobacteria (53% ± 2%) and Firmicutes (47% ± 3%). The results demonstrate that Kit1 and Kit5 provided the highest DNA yields (up to 603 ng/μL) and the most effective recovery of these hard-to-lyse phyla, although they introduced a slight taxonomic bias toward Actinobacteria. In contrast, protocols relying on intensive chemical lysis without robust mechanical disruption (Kit4) significantly underestimated total bacterial abundance and showed the lowest purity. 16S rRNA gene sequencing revealed that the V3-V4 region provided higher alpha-diversity and a more balanced representation of the community core compared to V1-V3, which was more susceptible to extraction-related variability and overrepresented the genus Olsenella. Our multi methodological approach reveals significant biases introduced by both extraction technique and 16S rRNA gene region. This evidence highlights that protocol optimization is mandatory for achieving an accurate and comprehensive characterization of microbial ecosystems.}, }
@article {pmid41933506, year = {2026}, author = {Qiu, CW and Zhang, S and Gao, ZF and Chen, ZH and Zhang, C and Ali, MA and Wu, F}, title = {First Tetraploa Genome and Multi-Omics Analysis Reveal Key Plant-Microbe-Soil Interactions for Salt Tolerance and Yield Improvement of Wheat.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.70663}, pmid = {41933506}, issn = {1467-7652}, support = {32161143035//National Natural Science Foundation of China/ ; BP0618021//the 111 Project of China/ ; FT210100366//Australian Research Council/ ; WSU2303-001RTX//Grains Research and Development Corporation/ ; }, abstract = {Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.}, }
@article {pmid41933614, year = {2026}, author = {Abdollahi, S and Vajhadin, F and Rafiei, A and Tamrin, SH and Daniel, SD and Banoei, MM and Zarin, B and Sen, A and Kim, K and Sanati-Nezhad, A}, title = {On-Chip modeling of drug-gut interactions in Oral drug delivery.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {115864}, doi = {10.1016/j.addr.2026.115864}, pmid = {41933614}, issn = {1872-8294}, abstract = {The gastrointestinal tract is a dynamic ecosystem where biophysical forces, enzymatic gradients, and microbial metabolism converge to govern the fate of orally administered therapeutics. These multifactorial interactions-spanning shear stress, mucus transport, and microbial metabolism-collectively shape absorption, transformation, and therapeutic response. Such complexity drives the wide interindividual variability in oral pharmacokinetics and pharmacodynamics, challenging predictive modeling and formulation design. Capturing these intertwined processes requires experimental systems that bridge the physiological fidelity of human tissue with the analytical control of engineered models. Microphysiological Gut-on-a-Chip (GoC) platforms have emerged as promising tools that reconstruct human intestinal architecture and function with high precision. These devices integrate living epithelia, peristaltic motion, oxygen and nutrient gradients, immune and microbial co-cultures, and on-chip sensing within precisely engineered microenvironments. They enable direct observation and quantification of luminal-mesenchymal communication, barrier regulation, and metabolite exchange under physiologically relevant flow. This review delineates how GoC technology is advancing oral drug delivery by bridging biology, microengineering, and pharmacology. We summarize advances across three therapeutic domains-small-molecule drugs, macromolecular and biopharmaceutical agents, and microbiome-interacting therapeutics-highlighting how GoCs now recapitulate absorption, enzymatic metabolism, immune modulation, and microbial transformation in human-relevant contexts. By merging organ-level physiology with analytical precision, GoCs establish a unified platform for predicting oral bioavailability and systemic exposure. As these systems evolve toward sensor-integrated, multi-omics, and AI-enabled designs, they are poised to become the mechanistic backbone of next-generation preclinical drug discovery and personalized oral therapeutics.}, }
@article {pmid41933765, year = {2026}, author = {He, Y and Wang, Z and Xu, Z and Wang, H and Yuan, L and Xu, X and Deng, W}, title = {Regulatory effects of natural polysaccharides on skin wound repair through modulation of immune-microbiome interactions.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {151732}, doi = {10.1016/j.ijbiomac.2026.151732}, pmid = {41933765}, issn = {1879-0003}, abstract = {Chronic non-healing wounds pose a significant clinical challenge, driven by dysregulation of the "inflammation-immune-microbiome" triad. Traditional "debridement-anti-infection-coverage" approaches fail to break the vicious cycle of dysbiosis and immune dysfunction. Leveraging structural diversity and bioactivity, natural polysaccharides provide a versatile platform for multi-targeted intervention. This review systematically explores the mechanisms through which polysaccharides modulate the wound immune microenvironment, restructure microbial communities, and facilitate barrier repair. This interaction enables precise regulation of macrophage polarization, particularly the promotion of the M2 phenotype, as well as neutrophil function and adaptive immunity, thereby alleviating chronic inflammation. Moreover, polysaccharides utilize a variety of mechanisms to impact the microbiome, including direct antimicrobial effects through electrostatic interactions and prebiotic support that promotes the colonization and metabolism of beneficial bacteria. This review also explores advancements in intelligent delivery systems, such as microenvironment-responsive hydrogels, discusses challenges in clinical translation, and considers future directions that incorporate single-cell multi-omics, microbiota-based personalization, organ-on-a-chip models, and phage-polysaccharide synergistic therapies. This work offers a theoretical foundation and translational perspective for the development of next-generation polysaccharide-based strategies for chronic wound management.}, }
@article {pmid41933826, year = {2026}, author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D}, title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128041}, doi = {10.1016/j.envpol.2026.128041}, pmid = {41933826}, issn = {1873-6424}, abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.}, }
@article {pmid41933853, year = {2026}, author = {Rao, X and Zhou, R and Li, W and Chai, X and Zhang, H}, title = {Pulmonary Microbiota is a Hidden Link between Lung Cancer Development and Microenvironment: Potential for Future Immune Therapeutic Strategies.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105308}, doi = {10.1016/j.critrevonc.2026.105308}, pmid = {41933853}, issn = {1879-0461}, abstract = {Lung, as a vital interface with the external environment, hosts a diverse microbiota that plays a significant role in lung cancer development. The dual role of pulmonary microbiota is characterized by its potential to trigger chronic inflammation(precursor of cancer), and its ability to stimulate anti-tumor immune responses. In lung cancer patients, the pulmonary microbiota often exhibits reduced bacterial diversity and over representation of pathogenic bacteria. Distinct pathological types of lung cancer, and clinical stage of lung cancer were correlates with variations in microbial diversity. Particular focus on its influence on the immune microenvironment have also been delved. Including immune cells, inflammatory signaling pathways, microbiota-metabolic interactions, and modulation of the programmed cell death protein 1(PD-1)/ programmed death-ligand 1 (PD-L1) checkpoint, which is crucial for tumor immune evasion. Understanding these interactions is essential for optimizing lung cancer immunotherapy strategies. For instance, antibiotics may reduce the efficacy of immune checkpoint inhibitors (ICIs), especially in lung cancer patients with high PD-L1 expression or EGFR-mutant NSCLC. Additionally, new therapeutic interventions, such as microbiome-targeted therapies or probiotics, are suggested to enhance the efficacy of ICIs. By uniquely integrating clinical correlations with mechanistic insights on immune microenvironment, this may render pulmonary microbiota to be potential therapeutic strategies for future immunotherapy treatments.}, }
@article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.005}, pmid = {41934012}, issn = {1878-4380}, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, }
@article {pmid41934098, year = {2026}, author = {Sweeney, CJ and Bottoms, M and Hutcheson, K and Schulz, L}, title = {Dose response OECD 216 studies for agrochemicals.}, journal = {Integrated environmental assessment and management}, volume = {}, number = {}, pages = {}, doi = {10.1093/inteam/vjag057}, pmid = {41934098}, issn = {1551-3793}, abstract = {The nitrogen transformation test, as described by Organisation for Economic Co-operation and Development (OECD) test guideline 216, forms the basis of the current European risk assessment to assess the impacts of pesticides on the soil microbiome. This guideline contains both a two-dose threshold approach and a dose response study design, for use with agrochemicals and non-agrochemicals respectively. Recent proposals have suggested the use of a dose response study design for agrochemical risk assessment. However, differences in the principles underpinning the threshold and dose response study protocols including the method of endpoint calculation, study length and interpretation of stimulatory versus inhibitory responses, necessitate careful consideration of how to appropriately perform and interpret dose response OECD 216 studies for pesticides. Our study explores these considerations, through the conduct of dose response OECD 216 nitrogen transformation tests on four agrochemicals (dicyandiamide, nitrapyrin, dinoseb acetate and a fludioxonil metabolite). A comparison of four potential methods for endpoint calculation revealed this has little impact on the ecotoxicological inference derived from dose response OECD 216 studies. Hormetic responses were present for two of the four compounds tested, and for these compounds, the system had not reached a steady state over the 28-day study period. Test extensions beyond the 28-day test period defined in the dose response study may therefore need to be considered, as is currently implemented in the two-dose threshold approach. Furthermore, as dose response studies allow for consideration of the full ecotoxicological response over a range of concentrations, we suggest that dose response OECD 216 studies for agrochemicals should focus on inhibitory and not stimulatory responses. Finally, our work has shown that dose response OECD 216 studies are possible for agrochemicals, and their use offers a sensible approach to improving the European soil microbial risk assessment.}, }
@article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {7}, pages = {e70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, }
@article {pmid41934308, year = {2026}, author = {He, L and Zhong, Q and Zhang, X and Li, T}, title = {The effects of cetylpyridinium chloride mouthwash combined with triamcinolone acetonide on oral microbiota and the Th17/Treg balance in patients with oral lichen planus.}, journal = {Pakistan journal of pharmaceutical sciences}, volume = {39}, number = {6}, pages = {1708-1720}, doi = {10.36721/PJPS.2026.39.6.162.1}, pmid = {41934308}, issn = {1011-601X}, mesh = {Humans ; *Lichen Planus, Oral/drug therapy/immunology/microbiology ; *Mouthwashes/administration &amp; dosage/therapeutic use/adverse effects ; Female ; Male ; *T-Lymphocytes, Regulatory/drug effects/immunology ; Middle Aged ; *Th17 Cells/drug effects/immunology ; *Triamcinolone Acetonide/administration &amp; dosage/therapeutic use/adverse effects ; Adult ; *Cetylpyridinium/administration &amp; dosage/adverse effects/therapeutic use ; *Microbiota/drug effects ; Treatment Outcome ; Drug Therapy, Combination ; *Mouth/microbiology/drug effects ; *Anti-Inflammatory Agents/administration &amp; dosage ; Cytokines ; }, abstract = {BACKGROUND: Oral lichen planus (OLP) is a chronic inflammatory disease associated with oral microbiome imbalance and immune dysregulation.<br><br>OBJECTIVES: To evaluate the effects of CPC mouthwash combined with triamcinolone acetonide on oral microbiota and Th17/Treg balance in erosive OLP patients.<br><br>METHODS: This study involved 80 patients with erosive OLP from January 2023 to January 2025. They were divided into: A control group treated with triamcinolone acetonide and a combination group treated with triamcinolone acetonide plus cetylpyridinium chloride mouthwash. After 4 weeks, primary outcomes included clinical efficacy, visual analog scale (VAS) pain scores, changes in signs and erosive area, oral salivary bacteria detection rate, Th17/Treg ratio, serum adipokine chemerin and cytokine levels (IL-17, TNF-&#x3b1;, IL-10) and OHIP-14 scores. Secondary outcomes were adverse reaction incidence and recurrence rates during follow-up.<br><br>RESULTS: The combination group showed better outcomes after 4 weeks of treatment. The total effective rate was 95%, higher than the control group's 80% (P=0.022). The combination group had superior pain relief (P=0.024), better mucosal repair (P=0.002) and a significant decrease in erosive area (P=0.021). It also had lower oral detection rates of Staphylococcus and Candida albicans (P<0.05). Immunologically, the combination therapy significantly reduced serum levels of chemerin, Th17 cells, Th17/Treg ratio, IL-17 and TNF-&#x3b1; (P<0.001), while increasing Treg cells and IL-10 levels (P=0.003), indicating stronger anti-inflammatory and immune-balancing effects. The combination group showed a greater reduction in the OHIP-14 score (P < 0.001), indicating improved oral health-related quality of life. No significant difference in adverse reactions was observed (P>0.05) and all were mild. The combination group had a lower recurrence rate within 3 months post-treatment, although the difference was not statistically significant (P=0.521).<br><br>CONCLUSION: The combination of cetylpyridinium chloride mouthwash with triamcinolone acetonide effectively regulates the oral microbiota structure and restores the Th17/Treg immune balance in OLP patients.}, }
@article {pmid41934511, year = {2026}, author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM}, title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41934511}, issn = {1572-9699}, mesh = {*Chitosan/administration &amp; dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; }, abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.}, }
@article {pmid41934548, year = {2026}, author = {Cui, K and Chen, J and Kuang, M and Yang, H and Bu, Z and Xiong, X and Liu, X and Hu, Y and Wang, R and Chen, Y and Xu, T and Zhu, Y}, title = {Integrated Physiological and Omics Analyses Reveal Endophytic Streptomyces Regulates N and P Uptake, Utilization, and Crop Productivity Enhancement.}, journal = {Physiologia plantarum}, volume = {178}, number = {2}, pages = {e70858}, doi = {10.1111/ppl.70858}, pmid = {41934548}, issn = {1399-3054}, support = {ZR2024QD159//Natural Science Foundation of Shandong Province/ ; 32172497//National Natural Science Foundation of China/ ; 32400100//National Natural Science Foundation of China/ ; CSTB2023NSCQ-MSX0852//Natural Science Foundation of Chongqing City/ ; 502251012//Yuelushan Laboratory Breeding Program/ ; }, mesh = {*Streptomyces/physiology/metabolism ; *Nitrogen/metabolism ; *Phosphorus/metabolism ; Plant Roots/microbiology/metabolism ; *Endophytes/physiology/metabolism ; Rhizosphere ; *Crops, Agricultural/growth &amp; development ; Soil Microbiology ; }, abstract = {The inherent deficiency of available nitrogen (N) and phosphorus (P) in acidic soils severely limits productivity in agriculture and forestry. While plant-beneficial microorganisms offer a sustainable solution, the mechanisms by which endophytic actinobacteria regulate N and P absorption and utilization remain largely unexplored. In this study, we characterize Streptomyces sp. CoH27, an endophyte isolated from Camellia oleifera, which exhibits pronounced abilities in N fixation and insoluble P solubilization. Inoculation with CoH27 significantly promoted the growth of C. oleifera across different ages and propagation types, as evidenced by enhanced root architecture, improved photosynthetic parameters, and increased N and P absorption and utilization efficiencies. Physiological analyses revealed that CoH27 colonization upregulated the activity of key enzymes involved in organic acid synthesis and N assimilation in roots, thereby enhancing rhizosphere P mobilization and plant N utilization. Furthermore, CoH27 reshaped the rhizosphere microbiome, increasing bacterial diversity and the abundance of beneficial taxa, while reinforcing microbial networks. The driving effect of nutrient cycling was evidenced with enriched abundance of microbial genes involved in P solubilization (phnA, ppa) and N metabolism (nasA, narB, amoA, nxrA). Concurrently, transcriptomics identified the upregulation of critical transporter genes (CoPHT1;4, CoNRT2.5) and transcription factors in CoH27-inoculated roots, orchestrating improved N and P uptake and assimilation. The efficacy of CoH27 was further validated in Brassica napus L. and Capsicum annuum L., underscoring its potential as a versatile microbial inoculant to enhance sustainable crop production in acidic soils.}, }
@article {pmid41934839, year = {2026}, author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B}, title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141959}, doi = {10.1016/j.jhazmat.2026.141959}, pmid = {41934839}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.}, }
@article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, }
@article {pmid41934884, year = {2026}, author = {Macpherson, CV and Daisley, BA and Drosdowech, SM and Meers, JA and Raine, NE and Allen-Vercoe, E}, title = {Anthropogenic stressors drive microbiome assembly: A global meta-analysis of bumble bees.}, journal = {The Science of the total environment}, volume = {1029}, number = {}, pages = {181748}, doi = {10.1016/j.scitotenv.2026.181748}, pmid = {41934884}, issn = {1879-1026}, abstract = {Bumble bees (Bombus spp.) play a vital role in the provision of ecosystem services that benefit humans through crop pollination and supporting natural plant biodiversity. While their ecological function is well studied, the microbial communities within their gut are only beginning to be recognized for their contributions to bee health and resilience. To better understand these communities, we conducted a meta-analysis of 814 gut samples from 15 studies across 9 countries. This analysis confirmed Snodgrassella, Lactobacillus, Bifidobacterium, Bombilactobacillus, and Gilliamella as core gut taxa, and proposed the addition of Neisseriaceae_unclassified and Orbaceae_unclassified. Human-altered environments were identified as the most influential factor shaping microbiota composition, with indoor versus outdoor rearing showing the strongest effect. Outdoor bees collectively hosted 253% more genera and exhibited higher microbial richness, connectivity, and stability. In contrast, indoor bees showed reduced diversity and the loss of multiple environmentally-associated taxa. Based on these patterns, we propose a "captivity-sensitive core" of twelve taxa, including Frischella, Apilactobacillus, Staphylococcus, and Acinetobacter. These findings establish a robust reference for the bumble bee gut microbiome and highlight how anthropogenic environments alter microbial community structure, with implications for insect pollinator health, management, and conservation.}, }
@article {pmid41934901, year = {2026}, author = {Usmani, A and Siddiqui, MA and Kumar, D and Gowri, S and Webster, TJ and Faiyazuddin, M}, title = {Next 5 years in autoimmunity: predictive diagnostics, immune signatures, and personalized immune therapy.}, journal = {International immunopharmacology}, volume = {179}, number = {}, pages = {116530}, doi = {10.1016/j.intimp.2026.116530}, pmid = {41934901}, issn = {1878-1705}, abstract = {Autoimmune diseases are experiencing a conceptual transformation in the traditional system of phenotypical classification to a more molecularly stratified system. The next five years suggest that immunological and metabolic signals, such as autoantibody patterns, epitope-spreading patterns, and inflammatory signals of microbiome interactions, will frequently predict clinical illness making the preclinical period a critical predictive and intervention time. Simultaneously, single-cell and multi-omic profiling are being used to discover molecular endotypes and pathogenic immune programs which can more effectively explain the heterogeneity of autoimmune diseases. Such insights are also incorporated more and more with computational methods, such as digital immune modeling, to allow for individual risk assessment and disease prediction. The combination of these advancements is hastening the shift toward precision immunology, where predictive diagnostics and targeted immune-modulating therapies can be implemented sooner and more successfully. This review synthesizes the major mechanistic innovations over the past few years and describes how predictive biomarkers, molecular endotyping, and novel treatment regimens in the coming years are likely to transform the diagnosis and treatment of autoimmune diseases.}, }
@article {pmid41935031, year = {2026}, author = {Grassi, L and Heye, F and Proesmans, K and Abatih, E and Van Daele, A and Lahousse, L and Crabbé, A}, title = {Bacteria of the lung microbiome and health biomarkers in chronic airway disease: a systematic review and meta-analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00967-z}, pmid = {41935031}, issn = {2055-5008}, support = {12X6322N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {The lung microbiome is increasingly recognized as a key contributor to the development and progression of chronic airway diseases. While these conditions are typically associated with reduced microbial diversity and pathogen overgrowth, emerging evidence suggests that non-pathogenic bacteria may influence clinical outcomes. However, inconsistent findings across studies have made it difficult to determine their exact role in disease pathophysiology. To identify potentially beneficial members of the lung microbiome, we conducted a systematic review and meta-analysis of clinical studies investigating the association between non-pathogenic bacterial genera or species and clinico-pathological features in individuals with asthma, bronchiectasis, chronic obstructive pulmonary disease and cystic fibrosis. For the meta-analysis, data from different diseases were combined. Our analysis revealed that several bacteria in the lung microbiome were significantly associated with improved lung function and/or reduced airway inflammation across diseases. Although causal relationships cannot be established due to the absence of interventional studies, our findings highlight promising candidates for functional characterization and therapeutic exploration. Considerable heterogeneity in study design and reporting underscores the need for standardized methods and validation in relevant experimental models to advance our understanding of the lung microbiome in chronic airway diseases and inform the development of effective microbiome-based interventions.}, }
@article {pmid41935059, year = {2026}, author = {Bodkhe, R and Sankaran, K and Shapira, M}, title = {Caenorhabditis elegans populations shape their microbial environment.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00975-z}, pmid = {41935059}, issn = {2055-5008}, abstract = {Nematodes represent one of the most abundant and ecologically significant taxonomic groups on earth, playing diverse roles in the cycling of organic matter. However, little is known about their effects on their microbial environment. To explore such effects, we took advantage of the bacteriovore free-living nematode Caenorhabditis elegans, which has been shown to assemble a characteristic gut microbiome from different microbial environments. Worm populations (initially germ-free) were raised in several microbially-distinct natural-like environments emulating the environment from which C. elegans are often isolated, allowing worms to go through four generations encompassing the typical boom-to-bust population growth cycle. Samples from worms, their environments, and from control environments without worms were analyzed using next-generation 16S rRNA gene sequencing. Data analysis showed that microbial diversity increased in the environment, either when worms were present or not, but that trajectories of change were different depending on the presence of worms. Importantly, the presence of worms led with time to convergence in the composition of their microbial environments, particularly affecting the abundance of members of bacterial families that are part of the C. elegans gut microbiome. Our findings reveal that C. elegans not only responds to environmental microbial changes but also shapes them, suggesting new roles for nematodes in modulating environmental microbial diversity and ecosystems.}, }
@article {pmid41935114, year = {2026}, author = {Jia, Z and Meng, Y and Wang, W and Behm, J and Cai, FM and Mishra, S and Xia, S and Liu, S and Yang, X}, title = {Differential responses of termite gut bacterial and fungal community to tropical forest conversion.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09939-7}, pmid = {41935114}, issn = {2399-3642}, support = {41977057//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32201421//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Land-use change significantly impacts biodiversity, but its effects on the gut microbiomes of soil invertebrates remain poorly understood. We investigated how forest conversion to rubber plantations alters bacterial and fungal diversity, composition, and function in termite guts within a biodiversity hotspot Xishuangbanna, China. Our results showed that termites from natural forests harbored higher gut bacterial diversity than those from plantations, with effects varying across host species. Fungal diversity was shaped primarily by host species identity, with Odontotermes yunnanensis exhibiting the highest diversity index. While termite species solely governed bacterial community composition, both termite species and forest type shaped fungal composition. Fungal community variation correlated with local soil properties, whereas bacterial variation only associated with soil pH. Termites shared 17% of core gut bacteria (e.g., Bacillus, Pseudomonas, Mycobacterium) but 100% of fungi with the environment. Co-occurrence networks exhibited species-specific responses to forest conversion. Host species (Ancistrotermes and Odontotermes) predicted bacterial functional potential, but both forest type and host species influenced fungal functional potential. These findings demonstrate that termite gut microbiome responses to land-use change are multifaceted and taxon-specific, highlighting their role in ecosystem functional resilience under anthropogenic disturbance.}, }
@article {pmid41935132, year = {2026}, author = {Łopucki, R and Stępień-Pyśniak, D and Wójciak, J and Pacan, M and Jurczyk, S and Kuźniar, A}, title = {Early-life gut microbiota differentiation in sympatric wild raptors.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47288-x}, pmid = {41935132}, issn = {2045-2322}, abstract = {The establishment of the gut microbiota during early life plays a crucial role in host physiology and development, yet remains poorly understood under natural conditions, particularly in wild raptors. Limited access to free-living nestlings constrains our understanding of how host species identity, parental trophic ecology (shaping dietary microbial input and nutrient availability), and environmental factors structure early-life microbiota. Here, we investigated the gut microbiota of nestlings of two sympatric raptor species, the white-tailed eagle (Haliaeetus albicilla) and the lesser spotted eagle (Clanga pomarina), which differ in parental foraging ecology (fish/waterbird vs. small mammal-based diet). Using non-invasive fecal sampling during routine ringing, we characterized gut microbiota composition and predicted functional potential, and tested the effects of host species, geographic distance between nests, and within-nest variability. Gut microbiota composition differed markedly between species, with clear separation of microbial communities and higher alpha diversity in white-tailed eagle nestlings. In contrast, geographic distance between nests had a limited influence on microbiome structure, while pronounced inter-individual and within-nest variability was observed, highlighting the importance of individual-specific and potentially stochastic processes during early microbiome assembly. Predicted functional profiles also differed between species, with enrichment of amino acid biosynthesis pathways in white-tailed eagles and carbohydrate-related pathways in lesser spotted eagles. No dysbiosis-like microbiome profiles were detected in either species, providing a baseline for future comparative studies. Overall, our findings demonstrate strong species-level differentiation in early-life gut microbiota in wild raptors, in the context of contrasting trophic ecology, while local environmental variation appears to be of secondary importance.}, }
@article {pmid41935154, year = {2026}, author = {Pandey, K and Parmar, A and Vilas, S and Gosai, H and Mistry, H and Singh, KS and Roy, M and Dholpuria, S and Patel, RB}, title = {Weissella as a core member of the Gir cow milk microbiome: functional insights.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41935154}, issn = {1572-9699}, mesh = {Animals ; *Milk/microbiology ; Cattle ; *Weissella/genetics/isolation &amp; purification/classification/physiology ; *Microbiota ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Female ; }, abstract = {Gir cow (Bos indicus) milk is widely valued for its nutritional quality, digestibility, and A2 β-casein content; however, the microbial determinants contributing to these attributes remain insufficiently characterized. In this study, dominant lactic acid bacteria (LAB) associated with Gir cow milk were isolated and evaluated using an integrated phenotypic and genome-based approach to elucidate their functional relevance. Raw milk samples were analyzed to isolate LAB, which were characterized through morphological, biochemical, and molecular analyses. Predominant isolates were identified as Weissella cibaria and Weissella confusa. Selected isolates exhibited strain-dependent tolerance to acidic pH, bile salts, and phenolic stress, along with auto-aggregation ability, cholesterol assimilation, and antagonistic activity against enteric pathogens. Survival under simulated gastrointestinal conditions was further validated by viable cell count analysis. Whole-genome sequencing of W. cibaria revealed a high-quality draft genome of approximately 2.43 Mb with a GC content of 44.97%, assembled into 21 contigs, encoding 2,282 protein-coding sequences, 11 rRNA genes, and 72 tRNA genes. Functional annotation indicated enrichment of genes associated with carbohydrate metabolism, stress adaptation, and membrane transport, while screening confirmed the absence of known virulence determinants and transferable antibiotic resistance genes, supporting its safety profile. The consistent predominance of Weissella spp. in Gir cow milk suggests a breed-associated microbial signature that may contribute to the functional characteristics of this indigenous dairy system. Collectively, these findings position Weissella as a promising functional component of the Gir cow milk microbiome and provide a genomic framework supporting its potential application in probiotic and functional dairy research.}, }
@article {pmid41935253, year = {2026}, author = {Liu, K and Zhang, Z and Su, Y and Ma, X and Wang, J and Yang, Q and Nie, Q and Mo, Z and Zhou, H and Zouboulis, CC and Guo, D and Liu, Z and Yang, X}, title = {Lactobacillus-derived extracellular vesicles provide multi-target acne treatment by enriched proteins and skin microbiota protection.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04291-8}, pmid = {41935253}, issn = {1477-3155}, support = {2024YFA0918500//National Key R&amp;D Program/ ; }, abstract = {Numerous studies have highlighted the therapeutic potential of probiotics in acne. Given the complex and multifactorial nature of the disease, probiotic-based multi-target therapies may be promising. Additionally, due to their non-replicative and nanosized characteristics, probiotic-derived extracellular vesicles might provide a safer and more efficient alternative. Here, we selected three anti-acne targets-Propionibacterium acnes (P. acnes) inhibition, anti-inflammatory effects, and sebum suppression-for high-throughput screening, identifying Lactobacillus plantarum 5b4m2 with multi-target anti-acne potential. Next, we isolated 5b4m2-derived EVs (LP-EVs) and discovered that they retain the anti-acne potential of the parental bacteria while exhibiting superior skin permeability. Further studies in P. acnes-induced acne mice demonstrated that LP-EVs significantly alleviated inflammatory symptoms such as redness and swelling and effectively inhibited the colonization of P. acnes, leading to enhanced therapeutic efficacy. Then, proteomic analysis identified nine enriched proteins in LP-EVs directly associated with acne improvement, including mucus-binding protein, cell wall hydrolase, lipase, and thioredoxin. Correspondingly, pathway changes in the host were revealed by transcriptomic analysis, such as the chemokine signaling pathway, lipid metabolism, and tissue tight junctions. Moreover, LP-EVs effectively maintain the skin microbiota balance, which may also contribute to acne improvement. Collectively, our study offers a new perspective on probiotic-based multi-target strategies, which may facilitate the treatment of acne and other skin diseases in the future.}, }
@article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03152-y}, pmid = {41935274}, issn = {1743-422X}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.<br><br>METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.<br><br>RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.<br><br>CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, }
@article {pmid41935303, year = {2026}, author = {He, W and Gao, M and Ren, Q and Wang, M and Zhou, S and Liu, Q and Chu, K and Qin, Y and Fan, Y and Zou, H and Cui, Y and Shu, Y and Wang, X}, title = {Causal relationship between GM, immune cells and esophageal adenocarcinoma: a mediation analysis based on MR.}, journal = {Journal of cardiothoracic surgery}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13019-026-03984-3}, pmid = {41935303}, issn = {1749-8090}, support = {LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; LKZ2022019//Jiangsu Commission of Health/ ; 2025M782034//Supported&#xa0;by&#xa0;China&#xa0;Postdoctoral&#xa0;Science&#xa0;Foundation/ ; }, }
@article {pmid41935333, year = {2026}, author = {Qi, X and Jin, D and Olimi, E and Chen, X and Cernava, T}, title = {What do we know about the seed microbiome?.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41935333}, issn = {2049-2618}, support = {2024YFD1501602//National Key Research and Development Program of China/ ; doi.org/10.55776/J4753//Austrian Science Fund/ ; CXTD[2025]041//Guizhou Provincial Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities (111 Program)/ ; }, mesh = {*Seeds/microbiology/growth &amp; development ; *Microbiota ; Germination ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The seed microbiome supports plant health and increases resilience under adverse environmental conditions. Seeds are also an important vector for transgenerational transfer of the plant microbiota. Even though research over the last decade has provided valuable insights into the functional roles of seed-associated microbes, these important members of the plant microbiome remain underexplored. This review systematically highlights recently discovered key functions of the seed microbiota. It covers taxonomic composition and diversity across plant species, transmission mechanisms, functional roles in germination and seedling establishment, growth promotion, and stress resistance. The review also addresses methodological challenges and highlights critical open questions regarding assembly, spatial compartmentalization, and translation into applications. Further research into seed microbiomes has the potential to not only increase the sustainability in plant production but also to increase food security in a changing climate. Reaching such outcomes will be facilitated by mechanistic studies that will disclose the remaining secrets of plant-microbe interplay at the very first developmental stage of most plants that nowadays inhabit Earth. Video Abstract.}, }
@article {pmid41935339, year = {2026}, author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R}, title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00885-9}, pmid = {41935339}, issn = {2524-6372}, abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.<br><br>RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.<br><br>CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.}, }
@article {pmid41935342, year = {2026}, author = {Herlemann, DPR and Riedinger, DJ and Fenández-Juárez, V and Delgado, LF and Andersson, AF and Pansch, C and Riemann, L and Bengtsson, MM and Gyraite, G and Reusch, TBH and Katarzyte, M and Kube, S and Martin, G and Rakowski, M and Labrenz, M}, title = {Generalist phyllosphere taxa dominate microbial communities on macrophytes across a natural salinity gradient.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00881-z}, pmid = {41935342}, issn = {2524-6372}, abstract = {BACKGROUND: Shallow coastal habitats are characterized by diverse macrophytes and often feature steep abiotic gradients, including salinity variations, which can shape the leaf- surface epi-microbiome (phyllosphere). To elucidate the effect of salinity and host identity on the phyllosphere of aquatic macrophytes in shallow water, we sampled the leaf surface microbiota across a salinity range of 6-15. Samples included the eelgrass Zostera marina, as well as the Eurasian water milfoil (Myriophyllum spicatum), muskgrass (Chara spp.), and sago pondweed (Stuckenia pectinata) in the brackish Baltic Sea during the summer of 2022. Microbial communities were characterized using 16S and 18S rRNA gene amplicon sequencing.<br><br>RESULT: As hypothesized, the phyllosphere bacterial and protist community composition was distinct from the surrounding seawater microbiome. Typically associated taxa included the genera Loktanella, Pseudorhodobacter, the methylotrophic genus Methylotenera, unclassified Synechococcales, and Rhodobacteriaceae. Protist genera such as Picochlorum were consistently detected across all macrophyte hosts, while Cocconeis, Cyclotella, Mondous and unclassified Bacillariophyceae were present in all phyllospheres except Chara spp. Both, salinity and host species significantly influenced the composition and prevalence of the microbiota, primarily through shifts in the abundance of typical phyllosphere taxa. However, only 4-11% of phyllosphere taxa were uniquely associated with a specific salinity or macrophyte host.<br><br>CONCLUSIONS: Our results demonstrate that aquatic macrophytes harbor a distinct and characteristic phyllosphere microbiome. The low proportion of host- or salinity specific taxa suggests that the most abundant members of this community are generalists, broadly adapted to the phyllosphere niche rather than being narrowly specialized. This implies that the presence of the macrophyte itself, providing a stable, nutrient-rich surface, exerts a stronger deterministic influence on the microbial community than the host identity or salinity fluctuations. Consequently, the phyllosphere appears relatively resilient to environmental variability, particularly salinity fluctuations. This highlights the robust nature of host-microbiome interactions and their importance for conservation of aquatic macrophyte ecosystems.}, }
@article {pmid41935395, year = {2026}, author = {Theodosis-Nobelos, P and Papagiouvanni, I and Protopappas, AA and Papagiouvannis, G}, title = {Pathophysiology of CLD: Oxidative Stress and Antioxidant Mechanisms that may Limit its Progression.}, journal = {Endocrine, metabolic &amp; immune disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715303441513260220055400}, pmid = {41935395}, issn = {2212-3873}, abstract = {INTRODUCTION: Chronic liver disease (CLD) represents a progressive condition culminating in fibrosis and, ultimately, cirrhosis or hepatocellular carcinoma. A growing body of evidence implicates oxidative and nitrosative stress as key mediators in the pathogenesis of CLD.<br><br>OBJECTIVE: This review aims to summarize the role of oxidative stress in CLD progression and to highlight therapeutic strategies targeting redox imbalance and related signaling pathways.<br><br>METHODS: Relevant literature from preclinical and clinical studies was reviewed, with emphasis on mechanisms of oxidative and nitrosative stress, signaling pathways involved in fibrogenesis, and emerging therapeutic interventions targeting redox imbalance and the gut-liver axis.<br><br>RESULTS AND DISCUSSION: Reactive oxygen and nitrogen species contribute to hepatocyte damage, hepatic stellate cell activation, and extracellular matrix accumulation. Mitochondrial dysfunction, endoplasmic reticulum stress, and disrupted redox homeostasis induce tissue injury and fibrogenesis. Various signaling pathways, including Nrf2/Keap1, AMPK/SIRT1, JNK, PI3K/Akt/mTOR, and TGF-&#x3b2;/SMAD, serve as critical links between oxidative imbalance and fibrotic progression. The antifibrotic potential of antioxidants such as vitamin E, lipoic acid, berberine, and polyphenolic compounds is increasingly validated in preclinical and clinical studies. Additionally, modulation of NOX enzymes and support of endogenous defenses offer promising therapeutic avenues. The gut-liver axis and microbial dysbiosis further exacerbate redox disturbance, underscoring the systemic nature of liver injury. Probiotic and prebiotic therapies have shown hepatoprotective effects in NAFLD models.<br><br>CONCLUSION: In conclusion, targeting oxidative stress and its associated pathways represents a compelling strategy to attenuate or even reverse liver fibrosis, presenting a promising therapeutic strategy that could be integrated into clinical practice.}, }
@article {pmid41935448, year = {2026}, author = {Hemati, S and Mohsenipour, Z}, title = {Immune exhaustion in bacterial infections: mechanisms, consequences, and therapeutic implications.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {30}, number = {3}, pages = {105809}, doi = {10.1016/j.bjid.2026.105809}, pmid = {41935448}, issn = {1678-4391}, abstract = {T-cell exhaustion, a well-characterized phenomenon, has historically been studied in the context of viral and oncological diseases. However, its relevance to chronic bacterial infections has only recently garnered attention. This review summarizes emerging evidence suggesting that bacterial pathogens can induce immune exhaustion through a variety of mechanisms. Additionally, we explore how bacterial biofilms, immune-privileged niches, and regulatory T-cell expansion contribute to persistent immune dysfunction. The article further examines the consequences of immune exhaustion, including secondary infections, antibiotic resistance, and microbiome dysbiosis, which are often underappreciated aspects of chronic immune impairment. Therapeutic strategies targeting these exhaustion pathways, such as immune checkpoint blockade, metabolic reprogramming, and microbiome modulation, are also discussed. We emphasize the need to consider chronic bacterial infections not as static conditions but as dynamic processes that interact with and suppress the immune system. Thus, understanding the mechanisms behind immune exhaustion highlights the importance of developing therapies that restore immune function, rather than solely relying on traditional antimicrobial treatments.}, }
@article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {}, number = {}, pages = {101848}, doi = {10.1016/j.jhepr.2026.101848}, pmid = {41935631}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.<br><br>METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.<br><br>RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.<br><br>CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.<br><br>CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.}, }
@article {pmid41935802, year = {2026}, author = {Kwak, MJ and Park, B and Choi, H and Hong, W and Mun, D and Son, SH and Choi, YS and Pathiraja, D and Eor, JY and Ryu, S and Kim, JK and Whang, KY and Jeong, KC and Choi, IG and Kim, Y}, title = {Gut microbial extracellular vesicles modulate the development of metabolic dysfunction-associated steatohepatitis through the gut-liver axis.}, journal = {Pharmacological research}, volume = {227}, number = {}, pages = {108184}, doi = {10.1016/j.phrs.2026.108184}, pmid = {41935802}, issn = {1096-1186}, abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) represents a growing global health challenge due to its propensity to progress to irreversible hepatic disorders, including fibrosis, cirrhosis, and carcinoma. This study aimed to investigate the role of gut microbiota in the pathogenesis of MASH. We identified Romboutsia hominis as a key contributor to MASH progression, exacerbating hepatic lipid accumulation and inflammation via the tumor necrosis factor-α (TNF-α) signaling pathway. Conversely, Akkermansia muciniphila and its extracellular vesicles (EVs) mitigated MASH by reducing hepatic lipid deposition through lipid biosynthesis-related genes downregulation. Furthermore, by integrating gut microbiota profiles and serum biomarkers using a machine learning approach, we achieved over 90% accuracy in noninvasive MASH diagnosis. These findings elucidate critical mechanisms within the gut-liver axis and suggest novel therapeutic and diagnostic strategies targeting gut microbiota and their functional EVs for MASH.}, }
@article {pmid41935870, year = {2026}, author = {Genkel, V and Zaripova, Y and Sluchanko, A and Lebedev, E and Kuznetsova, A and Saenko, A and Pykhova, L and Sumerkina, V and Nikushkina, K and Savochkina, A and Kupriyanov, S and Shaposhnik, I and Dolgushina, A}, title = {Ultrasound-measured visceral adipose tissue thickness and carotid atherosclerosis in patients with inflammatory bowel diseases.}, journal = {Obesity research &amp; clinical practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.orcp.2026.03.001}, pmid = {41935870}, issn = {1871-403X}, abstract = {BACKGROUND AND AIM: Visceral obesity plays a pivotal role in initiating and sustaining chronic systemic inflammation through complex interactions involving adipose tissue dysfunction, insulin resistance, immune system activation, and gut microbiome composition. Visceral obesity is also hypothesized to contribute to the development and progression of extraintestinal manifestations and complications in inflammatory bowel disease (IBD). The aim was to evaluate the interrelationships between ultrasound-measured visceral and subcutaneous adipose tissue thickness with carotid artery atherosclerosis indicators in IBD patients.<br><br>METHODS AND RESULTS: The study included 90 patients with IBD aged 40-64 years. All patients underwent duplex ultrasound scanning of the carotid arteries with measurement of carotid plaque burden indicators. Ultrasound measurements of subcutaneous and visceral adipose tissue thickness (ATT) were performed: minimal subcutaneous adipose tissue thickness (mSATT), maximal preperitoneal adipose tissue thickness (mPATT), periumbilical subcutaneous adipose tissue thickness (PSATT), visceral abdominal adipose tissue thickness, peri- and pararenal adipose tissue thickness. Ultrasound-derived indicators of visceral obesity (mPATT and abdominal ATT), but not BMI or WC, were associated with an increased odds ratio for the presence of carotid plaque after adjustment for sex and age. Both mPATT and abdominal ATT demonstrated positive correlations with apoB concentration, LDL-C, sdLDL, eLDL-TG, and inverse correlations with adiponectin concentration.<br><br>CONCLUSION: In patients with IBD aged 40-64 years, visceral adipose tissue thickness measured by ultrasound and WC were associated with the carotid plaque burdens. Ultrasound-measured mPATT and abdominal ATT, but not BMI and WC, were independently associated with carotid atherosclerosis in patients with IBD.}, }
@article {pmid41936070, year = {2026}, author = {Duan, H and Ning, Z and Sun, Z and Guo, T and Sun, Y and Figeys, D}, title = {MetaDIA: A DDA-free Database Reduction Strategy for DIA Human Gut Metaproteomics.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzag029}, pmid = {41936070}, issn = {2210-3244}, abstract = {Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a substantial challenge, as it involves matching peptides to mass spectra within an enormous search space for complex and unknown samples. This poses difficulties for both the accuracy and the speed of identification. Specifically, analysis of data-independent acquisition (DIA) datasets has relied on libraries constructed from prior data-dependent acquisition (DDA) results. However, this method is resource-intensive, consumes samples, and limits identification to peptides previously identified. These limitations restrict the application of DIA in metaproteomics research. We introduced a novel strategy to reduce the search space by utilizing species abundance and functional abundance information from the microbiome to score each peptide and prioritize those most likely to be detected. Using this strategy, we have developed and optimized a workflow called MetaDIA for the analysis of microbiome data generated by DIA, which operates independently of DDA assistance. Our approach successfully created a smaller, yet sufficient database for DIA data search in metaproteomics. The results demonstrated strong consistency with the traditional DDA-based library approach at both protein and functional levels. MetaDIA is readily accessible as an open-source project hosted on GitHub (https://github.com/northomics/MetaDIA).}, }
@article {pmid41936460, year = {2026}, author = {Calbet, A}, title = {Gut Microbiomes of Marine Zooplankton: Consequences for Host Performance, the Biological Carbon Pump, and Prokaryote Biogeography.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70271}, doi = {10.1111/1462-2920.70271}, pmid = {41936460}, issn = {1462-2920}, support = {PID2023-150548NB-I00//MICIU/AEI/10.13039/5011 00011033/ ; //ERDF/EU/ ; //Consejo Superior de Investigaciones Cient&#xed;ficas/ ; }, mesh = {Animals ; *Zooplankton/microbiology/physiology ; *Gastrointestinal Microbiome ; *Carbon/metabolism ; Bacteria/metabolism/classification/genetics ; }, abstract = {Marine zooplankton are a link between primary producers and higher trophic levels and play a pivotal role in organic matter export via diel vertical migration and faecal-pellet production. Molecular surveys have revealed each individual as a holobiont hosting dense, taxonomically structured microbiomes in the gut, on the cuticle, and within feeding structures. These microbial partners expand dietary breadth through carbohydrate-active enzymes, supply limiting vitamins, detoxify xenobiotics, and may buffer thermal and oxidative stress, thereby influencing host fitness and the fate of particulate organic carbon. Experimental studies show intact microbiomes often enhance growth or fecundity, with effects amplified under vitamin limitation or toxin exposure. In contrast, gut and pellet-associated respiration can substantially reduce the carbon content of pellets within hours to days, depending on temperature and microbial composition. Vertical migrators also transport live bacteria and viruses below the thermocline, potentially seeding mesopelagic niches and affecting remineralization patterns. Despite these influences, zooplankton holobionts remain largely absent from biogeochemical models. This minireview synthesises current understanding of microbiome assembly and plasticity, their contributions to host performance and carbon export, and their role in microbial dispersal, underscoring the need to integrate holobiont traits into Earth-system models to better predict ecosystem responses to warming and deoxygenation.}, }
@article {pmid41928315, year = {2026}, author = {Defazio, G and Lorusso, E and De Robertis, M and Mello, T and Galli, A and Pesole, G and Fosso, B}, title = {Machine learning-based assessment of the healthy human gut mycobiota landscape using ITS1 DNA metabarcoding data.}, journal = {BioData mining}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13040-026-00532-6}, pmid = {41928315}, issn = {1756-0381}, support = {H93C22000560003//Regione Puglia/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; }, abstract = {The human gut microbiome plays a critical role in maintaining host health and homeostasis, and current literature suggests a bidirectional relationship between microbiome ecology and host well-being. DNA metabarcoding has emerged as a powerful tool for investigating microbiome imbalances (i.e., dysbiosis). While the prokaryotic microbiome has been extensively studied, the fungal counterpart - or mycobiome - remains largely unexplored, despite its recognized role from the perinatal stage onward. Here, we present a comprehensive survey based on DNA metabarcoding analysis of approximately 1,500 publicly available ITS1 samples. This survey integrates conventional statistical approaches with Machine Learning (ML) methods coupled with explainable Artificial Intelligence (XAI). ML models successfully predicted host health status with accuracies exceeding 80%, and fungal genera such as Eurotium, Aureobasidium, Candida, and Cutaneotrichosporon emerged as key classification features. This study introduces a cutting-edge multiview analytical framework applied to publicly available mycobiome data, highlighting the potential of fungal community profiling as a non-invasive tool to support health diagnostics.}, }
@article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02392-y}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.<br><br>RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.<br><br>CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, }
@article {pmid41928384, year = {2026}, author = {Valdez-Palomares, F and Noriega, LG and Reyes-Romo, D and Canizales-Quinteros, S and Nambo-Venegas, R and Salinas-Lara, C and Tovar-Palacio, A and Menjivar, M and Peña-Espinoza, B and Ortiz, G and Palacios-González, B}, title = {Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2651984}, doi = {10.1080/19490976.2026.2651984}, pmid = {41928384}, issn = {1949-0984}, mesh = {Animals ; Male ; *Fecal Microbiota Transplantation/adverse effects ; Mice ; Gastrointestinal Microbiome ; Humans ; Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; *Growth Disorders/microbiology/therapy/metabolism ; Child ; *High Fructose Corn Syrup/adverse effects/administration &amp; dosage ; Bacteria/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Obesity/etiology/metabolism ; *Metabolic Diseases/etiology ; }, abstract = {Stunting, or impaired child growth due to poor nutrition and infections, is characterized by a low height-for-age and affects 48%-56% of school-aged children worldwide. It is associated with later weight gain and chronic diseases. The gut microbiome in undernourished children may increase obesity risk if they are exposed to high-calorie environments. To investigate this, we assessed whether the intestinal microbiome of stunted children elevates obesity risk upon exposure to an obesogenic environment. Fecal microbiota transplantation (FMT) was performed using pooled stools from healthy (n = 6) or stunted (n = 6) school-aged children from a low-income cohort in Mexico. Eight-week-old male C57BL/6 mice underwent bowel cleansing with polyethylene glycol (PEG), followed by weekly intragastric FMT for 4 weeks. The mice were subsequently fed either a control diet (CT) or a high-fat, high-fructose corn syrup diet (HFFr, including 15% HFCS-55) for 15 weeks. Metabolic outcomes were assessed through body composition, indirect calorimetry, oral glucose tolerance test, insulin tolerance test, and histological analysis of visceral adipose tissue. The microbiota composition was evaluated by 16S rRNA V3-V4 hypervariable region sequencing, and the predicted functional capacity was analyzed using PICRUSt2. FMT from stunted children increased susceptibility to diet-induced obesity, visceral adipose tissue hypertrophy, and insulin resistance. In contrast, FMT from healthy children promoted energy expenditure and visceral adipose tissue hyperplasia, conferring a protective effect against diet-induced obesity and insulin resistance in the mice. Healthy-FMT led to sustained enrichment of Akkermansia and Parabacteroides, whereas stunting-FMT increased Proteobacteria, Veillonella, Desulfovibrionaceae, and Bifidobacterium. Microbial‒phenotypic correlations showed that Akkermansia and Parabacteroides were negatively correlated with fasting glucose, body weight, and fat mass, and positively correlated with postprandial RER, VO2, and lean mass. In conclusion, stunting-FMT recipient mice showed a higher risk of obesity and metabolic issues in an obesogenic environment. Healthy-FMT confers metabolic resilience, characterized by increased abundance of taxa such as Akkermansia and Parabacteroides, which are linked to enhanced energy expenditure, improved glucose metabolism, and favorable adipose tissue structure.}, }
@article {pmid41928387, year = {2026}, author = {Houshyar, Y and Zhang, F and Tavakoli, P and Grimm, MC and Hold, GL}, title = {Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653288}, doi = {10.1080/19490976.2026.2653288}, pmid = {41928387}, issn = {1949-0984}, mesh = {Humans ; *Virome ; *Mycobiome ; *Inflammatory Bowel Diseases/microbiology/therapy/virology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/virology ; *Fungi/classification/genetics/isolation &amp; purification ; Animals ; Fecal Microbiota Transplantation ; *Viruses/classification/genetics/isolation &amp; purification ; Bacteria/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing-remitting disorder of the gastrointestinal tract characterized by immune dysregulation, epithelial barrier dysfunction, and microbial imbalance. While bacterial dysbiosis, including depletion of short-chain fatty acid (SCFA) producers and enrichment of pathobionts, is well characterized, the gut virome and mycobiome remain comparatively neglected. Both exhibit high variability and are constrained by sequencing bias, contamination, and incomplete reference databases, leaving much of the viral and fungal diversity unresolved. Emerging evidence links fungal and viral dysbiosis to IBD pathogenesis, including Candida overgrowth, loss of Saccharomyces, expansion of Caudoviricetes phages, and detection of eukaryotic viruses such as Cytomegalovirus and Epstein-Barr virus in inflamed mucosa. These alterations disrupt barrier integrity, modulate immune signaling, and interact with bacteria and archaea in cross-kingdom networks that amplify inflammation. Translationally, the virome and mycobiome are now recognized as therapeutic targets, inspiring interventions from pre/probiotics and synbiotics to precision phage therapy and microbiota-based transplantation, including fecal virome transplantation (FVT) and fecal microbiota transplantation (FMT). This review recognizes the challenges and opportunities of studying these neglected kingdoms, reframes IBD dysbiosis and highlights new directions for biomarker discovery and multikingdom microbiota-directed therapies.}, }
@article {pmid41928627, year = {2026}, author = {Bong, SHS and Teh, KKJ and Wong, VW}, title = {Therapeutic Landscape Evolution: From Lifestyle Interventions to Precision Pharmacotherapy.}, journal = {Clinical and molecular hepatology}, volume = {}, number = {}, pages = {}, doi = {10.3350/cmh.2026.0125}, pmid = {41928627}, issn = {2287-285X}, abstract = {Steatotic liver disease (SLD) is a growing global epidemic, with metabolic dysfunction-associated steatotic liver disease (MASLD) now the most common chronic liver disease worldwide and closely linked to adverse cardiovascular outcomes. Lifestyle modification remains the cornerstone of management, with the Mediterranean diet as the preferred dietary intervention and emerging evidence supporting additional dietary and exercise strategies. Pharmacotherapy has advanced rapidly in recent years, with two U.S. Food and Drug Administration-approved options, resmetirom and semaglutide, for noncirrhotic metabolic dysfunction-associated steatohepatitis (MASH) with moderate-to-advanced fibrosis, alongside multiple agents in development targeting different disease mechanisms. In metabolic dysfunction- and alcohol-associated liver disease (MetALD), evidence remains limited, but management essentially focuses on alcohol cessation and optimization of cardiometabolic risk factors, with resmetirom, incretin-based therapies, and fibroblast growth factor (FGF)-21 analogues representing promising therapeutic agents that have yet to be fully evaluated in clinical trials. The field is increasingly moving toward a precision medicine paradigm integrating pharmacologic and lifestyle interventions, tailored to disease phenotype, genetic risk, and gut microbiome. Key challenges include heterogeneity in treatment response, assessment of alcohol intake, and real-world implementation barriers. This review summarizes current and emerging therapies and highlights the role of precision medicine in advancing individualized care across the SLD spectrum.}, }
@article {pmid41928791, year = {2026}, author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A}, title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9142184/v1}, pmid = {41928791}, issn = {2693-5015}, abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.}, }
@article {pmid41928923, year = {2026}, author = {Lesperance, DNA and Padhi, S and Macro, J and Olson, S and Stanwood, E and Kannan, K and Graveley, B and Rogina, B and Broderick, NA}, title = {Microbiome contribution to Indy longevity in Drosophila.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714291}, pmid = {41928923}, issn = {2692-8205}, abstract = {UNLABELLED: Reduction in the Indy (I'm not dead yet) gene, a plasma membrane citrate transporter, in Drosophila and its homolog in worms extends lifespan by promoting metabolic homeostasis. Indy reduction delays the onset of aging-associated pathology in the fly midgut, including preservation of intestinal barrier integrity and intestinal stem cell homeostasis. Gut microbiota has broad impacts on host metabolism, health, and aging. Age-related dysbiosis impairs intestinal barrier function and drives mortality. However, the underlying mechanisms that link increased microbial load to frailty and negative effects on health remain mostly unclear. Here we show that Indy heterozygote flies have significantly lower bacterial load and increased diversity during aging compared to controls. However, the presence of the microbiome was not required for Indy lifespan extension, though removal of microbes did enhance the effects of Indy reduction on longevity, suggesting potential interactions between the microbiome and Indy . Indy down-regulation was linked to reduced expression of the JAK/STAT signaling ligands Upd3 and Upd2 in the midgut of young flies, which likely contributes to preserved intestinal stem cell homeostasis. Altogether, our results suggest that Indy reduction impacts microbiome load and composition, which preserves gut homeostasis and extends lifespan through impacts on JAK/STAT signaling pathway.<br><br>SIGNIFICANCE STATEMENT: Indy is a fly homologue of mammalian SLC13A5 (mSLC13A5) plasma membrane citrate transporter, a central metabolic regulator involved in health, longevity, and disease. Reduction of fly Indy gene activity preserves metabolic and intestinal stem cell homeostasis and extends longevity. Gut microbiota impacts host metabolism, health, and aging. Here we show that Indy reduction prevents age-associated increases in bacterial load and expression of the JAK/STAT signaling ligands Upd3, and Upd2, while maintaining microbiome diversity. These changes likely slow activation of epithelial cell turnover in the gut and contribute to downstream lifespan effects. As the role of INDY and microbiome are conserved across organisms, our study provides a framework to study underlying mechanisms of the effects of reduced Indy and the microbiome on health and longevity.}, }
@article {pmid41928970, year = {2026}, author = {Rock, RR and Alexander, M and Noecker, C and Trepka, KR and Upadhyay, V and Ortega, EF and Ramirez, L and Siewert, L and Olson, CA and Halsey, T and Pröbstel, AK and Baranzini, SE and Turnbaugh, PJ}, title = {Female-enriched Eggerthella lenta drives neuroinflammation and IFN-γ via host receptor TLR2.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.16.711194}, pmid = {41928970}, issn = {2692-8205}, abstract = {UNLABELLED: Women are at increased risk of autoimmune diseases, including multiple sclerosis (MS); however, the degree to which sex differences in the gut microbiota impact autoimmunity remains largely unexplored. Our 27-cohort meta-analysis revealed 60 sex-associated gut bacterial species. Leveraging an independent clinical cohort, we demonstrate that female-enriched species significantly associate with MS status and clinical disability (EDSS). Top female-enriched species Eggerthella lenta drove disease in the experimental autoimmune encephalomyelitis (EAE) MS model, consistent with brain and gut lamina propria T cell infiltration and MS-associated T helper (Th) signatures. E. lenta induced intestinal Th1 and Th17 in healthy mice, independent of bacterial viability. Mechanistically, we demonstrate that TLR2 directly drives E. lenta -induced IFN-γ production in Th cells and is necessary for exacerbation of EAE. Together, we identify a causal host-microbe axis contributing to sex differences in autoimmunity and provide a framework for evaluating sex as a biological variable in human microbiome research.<br><br>HIGHLIGHTS: 27-cohort meta-analysis identifies a robust sex-signature in human gut microbiota.Female-enriched species are associated with MS risk and severity. Female-enriched Eggerthella lenta exacerbates the EAE model. E. lenta impacts neuroinflammation via toll-like receptor 2.}, }
@article {pmid41929040, year = {2026}, author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ}, title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714183}, pmid = {41929040}, issn = {2692-8205}, abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.<br><br>IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.}, }
@article {pmid41929113, year = {2026}, author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R}, title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714056}, pmid = {41929113}, issn = {2692-8205}, abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.}, }
@article {pmid41929228, year = {2026}, author = {Lester, BA and Kelly, C and Henry, SN and Elias, IP and Cevenini, SE and Hendrickson, MR and Park, T and Ashley, TD and Beltz, JM and Milner, JP and Pickrell, AM and Morton, PD}, title = {Germ-free piglets display variable neuroinflammatory-like perturbations in prefrontal cortical microglia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.22.713463}, pmid = {41929228}, issn = {2692-8205}, abstract = {UNLABELLED: Communication between gut microbiota and immune cells within the brain is essential for neurotypical development. Specifically, microglia are known to play a key role in regulating and supporting neural progenitor stem cell production during brain development, and are sensitive to changes in the maternal gut microbial composition during perinatal development. Here, we employed a germ-free (GF) porcine paradigm to examine how the absence of the microbiome affects microglial dynamics during a key epoch of brain development. We utilized automated software to evaluate microglial density and morphology across three developmentally significant regions: the ventricular/subventricular zone (VZ/SVZ), the prefrontal subcortical white matter (PFCSWM), and layers II/III of the prefrontal cortex (PFCII-III). We found no significant differences in microglial morphology or density in the VZ/SVZ or PFCSWM. In contrast, the PFCII-III of P16 piglets exhibited an increase in microglia density paired with morphologies indicative of an activated/reactive functional state. Notably, these effects were identified with no overall changes in microglial density in any of the regions assessed. Transcriptomics on RNA isolated from the PFCII-III revealed a significant upregulation of genes related to neuroinflammation, in agreement with a region-specific microglial and immune response in the absence of microbial colonization during postnatal development. Together, these findings build on the limited knowledge available on how microbiota influence brain development in large animal model organisms with high similarities to human brain anatomy and developmental trajectories.<br><br>SIGNIFICANCE STATEMENT: The prefrontal cortex of porcine display unique, ramified microglia which are sensitive to germ-free conditions whereby they display alterations in morphology with a more transcriptionally reactive signature. These findings indicate that microglia are regionally sensitive to stimuli in the periphery, and studies in lissencephalic mammalian models may not be directly correlative to other higher-order species. The neuroanatomical heterogeneity of microglia across species is informative and understudied, but necessary, to draw conclusions on the array of perturbations spanning neurodevelopmental trajectories in health and disease.}, }
@article {pmid41929259, year = {2026}, author = {Baird, AW}, title = {Coordinated regulation of colonic fluid and mucus secretion.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1757501}, pmid = {41929259}, issn = {1663-9812}, abstract = {The human colon, unlike the small intestine which is relatively sterile, contains a diverse microbiome which contributes to host metabolism. The luminal environment is constantly changing and responds to epithelial absorption and secretion which occurs as motility is regulated by longitudinal and circular smooth muscle. Mucous gels are crucial to lubrication and maintenance of an unstirred layer which separate the epithelium from the lumen. Gel-forming mucins are produced and released by goblet cells and become hydrated, although the source of water is not definitively understood. The purpose of this review is to summarize regulation of water movements across the colonic epithelium, goblet cell secretion of mucus and to consider how these distinct processes are functionally coupled.}, }
@article {pmid41929306, year = {2026}, author = {Kramer, M and Belleau, P and Tortora, SC and Deschenes, A and Founta, K and Gurjao, C and Yueh, B and Goodwin, S and Gee, D and Subhash, S and Barbi, M and Chung, C and Ozler, K and Eskiocak, O and Izar, B and Geiger, H and Chu, TR and Goldstein, Z and Winterkorn, L and Araneo, A and Whelan, RL and Rivadeneira, D and Fox, S and Kandel, A and Ozay, F and Talabong, DJA and Lanipekun, O and Talus, H and Zeng, J and Rishi, A and Chambwe, N and Robine, N and Boyd, J and Krasnitz, A and Beyaz, S and McCombie, WR and Martello, LA}, title = {Integrative Genomic, Transcriptomic, and Microbiome Profiles of Colon Cancer by Ancestry Provide Insights into Molecular Distinctions.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.26349226}, pmid = {41929306}, abstract = {Colorectal cancer (CRC) incidence, tumor biology, and clinical outcomes differ by patient ancestry, yet African ancestry (AFR) populations remain underrepresented in genomic and microbiome studies. Here, we comprehensively characterized genomic, transcriptomic and microbiome features of AFR and European ancestry (EUR) colon cancer patients residing in New York City and Long Island. While confirming known drivers from other large CRC studies, our AFR to EUR comparison of somatic variation also revealed a possible enrichment of functional KRAS variants in AFR tumors. Colon cancer genomes in patients in this study also exhibit distinct patterns of DNA copy number variation, correlating with consensus molecular subtypes. Fusobacterium nucleatum-positive tumors were enriched for co-occurring oral taxa, suggesting an organized oral microbial structure within the tumor microenvironment. Our findings highlight ancestry-associated differences in somatic mutation, copy number variation, and tumor microbiome composition, underscoring the urgent need to expand AFR representation in genomic studies to uncover population-specific determinants of CRC risk and to develop treatment strategies that reflect the full diversity of patients affected by this disease.}, }
@article {pmid41929401, year = {2026}, author = {Bokemeyer, B and Plachta-Danielzik, S and Helwig, U and Beuchert, P and Schreiber, S}, title = {Competence network inflammatory bowel diseases in Germany: 25 years of interdisciplinary and cross-sectoral research and knowledge transfer across all levels of IBD care.}, journal = {Therapeutic advances in gastroenterology}, volume = {19}, number = {}, pages = {17562848261431187}, pmid = {41929401}, issn = {1756-283X}, abstract = {The Competence Network Inflammatory Bowel Diseases (Kompetenznetz Darmerkrankungen) was established in Germany in 1999 through a 10-year funding programme by the German Ministry of Education and Research. It was created to address the growing gap between the rising prevalence and therapeutic complexity of inflammatory bowel disease (IBD) and the fragmented care structures and isolated academic initiatives of the time. The network's continuing mission is to improve care for patients with Crohn's disease and ulcerative colitis by more closely integrating clinical practice, translational science and patient involvement. This review summarises the history, governance, registries, biobanking, clinical trials, educational programmes and collaborations of the Competence Network IBD. Over the past 25 years, the Competence Network IBD has established prospective national registries (e.g. RUN-CD, RUN-UC, VEDO-IBD and FilgoColitis), developed pragmatic real-world cohorts (TARGET and GeCer) and contributed to the UMBRELLA-IBD data warehouse of the Competence Network IBD in Germany. The network played a central role in creating the German IBD DNA collection and supported the Kiel University biobank, both of which link biospecimens with longitudinal clinical data to support genetic and microbiome research. It also conducts and coordinates multicentre clinical trials and has supported the development of the German evidence- and consensus-based IBD guidelines. With more than 800 members from university centres, community practices, nursing and patient organisations, it now provides a robust platform for research and knowledge transfer across all levels of IBD care. The Competence Network IBD demonstrates how long-term interdisciplinary and cross-sectoral collaboration can improve the management of chronic inflammatory diseases. By integrating research infrastructures with education and patient involvement, the network serves as a scalable and sustainable model for national and international collaboration in IBD.}, }
@article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/physiology ; Metagenomics ; Aged ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, }
@article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, }
@article {pmid41929503, year = {2026}, author = {Pisa, CM and Verrone, A and Mazuy, M and Ientile, L and Rigante, D and Esposito, S}, title = {Gut microbiota alliance to shape sceneries of familial Mediterranean fever: a scoping review detailing difference between children and adults.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1814103}, pmid = {41929503}, issn = {1664-3224}, mesh = {Humans ; *Familial Mediterranean Fever/microbiology/immunology/drug therapy ; *Gastrointestinal Microbiome/immunology ; Child ; Adult ; Dysbiosis/immunology ; Colchicine/therapeutic use ; Age Factors ; Pyrin/genetics ; }, abstract = {Familial Mediterranean fever (FMF) is the most common monogenic autoinflammatory disease worldwide and a key-model to illustrate dysregulation of innate immunity, etiologically determined by pathogenic variants in the MEFV gene, encoding pyrin, leading to uncontrolled interleukin-1β and interleukin-18 release. Despite its genetic basis, FMF shows marked clinical heterogeneity in all-aged patients, mostly in children, suggesting a role of potential environmental modifiers which are far to be exactly unraveled. Recent medical literature has increasingly illuminated the importance of gut microbiota in maintaining overall health and immune functions, and its contribution has been claimed also to explain both FMF inflammatory activity and heterogeneous disease expression. This narrative review summarizes current evidence on the interaction between gut microbiota and FMF, with a specific focus on differences between children and adults. Pediatric studies dedicated to FMF have reported intestinal dysbiosis in terms of reduced microbial diversity and depletion of short-chain fatty acid-producing bacteria, with subsequent enrichment of pro-inflammatory taxa: such alteration could modulate pyrin-inflammasome activation and contribute to systemic inflammation, disease phenotype, and response to colchicine or to other drugs specifically used in colchicine-resistant FMF. Geographic and lifestyle factors may shape intestinal microbiota composition early in life, reinforcing the relevance of gut flora and confirming its activity as a crucial tessera to determine FMF sceneries, mostly in children, and a potential target for future add-on therapeutic strategies. In addition, colchicine therapy appears to partially remodel the gut microbiome, empowering a local beneficial anti-inflammatory microbial profile.}, }
@article {pmid41929505, year = {2026}, author = {Zhang, Y and Xiao, X and Guo, J and Lei, X and Xiong, W and Wang, S and He, Y and Lei, C and Hu, X}, title = {Multidimensional regulatory mechanisms and translational potential of epigenetic networks in the rheumatoid arthritis disease course.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1792863}, pmid = {41929505}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Rheumatoid/genetics/immunology/metabolism ; *Epigenesis, Genetic ; MicroRNAs/genetics ; DNA Methylation ; Animals ; *Gene Regulatory Networks ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic synovitis that may progress to irreversible joint destruction and disability, thereby substantially impairing quality of life. RA results from complex interactions among genetic predisposition, environmental exposures, and immune dysregulation; however, current therapies are not curative, and many patients continue to experience pain, morning stiffness, and recurrent inflammation. In recent years, epigenetic mechanisms have emerged as key modulators of RA heterogeneity and disease persistence. Reversible regulatory layers-including non-coding RNAs, RNA modifications, DNA methylation, histone modifications, and microbiota-host interactions-provide a conceptual framework linking environmental cues to cell-type-specific inflammatory programs. This review summarizes recent advances in the epigenetic regulation of RA and outlines six interconnected dimensions. (1) miRNA-mediated post-transcriptional regulation: dysregulated miRNAs reshape inflammatory circuits and promote synovial activation through regulatory hubs. (2) RNA m[6]A modification: aberrant m[6]A remodeling alters immune metabolism and inflammatory gene expression, thereby reinforcing pathogenic responses. (3) DNA methylation: genome-wide profiling of synovium reveals differentially methylated loci that may activate disease-relevant pathways. (4) Histone modification and chromatin remodeling: altered activity of histone-modifying enzymes (e.g., HDACs) modulates inflammatory transcriptional programs and may contribute to epigenetic memory. (5) Hypoxia-driven metabolic-epigenetic crosstalk: hypoxia-inducible factors (HIFs) coordinate metabolic adaptation and inflammatory amplification; for example, HIF-1α supports the FLSs under hypoxic conditions. (6) Microbiome-epigenome interactions: gut microbial metabolites (e.g., butyrate) regulate immune homeostasis, partly by promoting follicular regulatory T cell (TFR) differentiation and restraining inflammation. Collectively, these findings indicate that epigenetic networks exert multilevel control over RA pathogenesis and highlight translational opportunities for targeted epigenetic interventions, including RNA methylation modulators, DNA methyltransferase inhibitors, and histone deacetylase-directed strategies.}, }
@article {pmid41929571, year = {2026}, author = {Seenivasan, R and Pachiyappan, JK and Marimuthu, A and Halagali, P and Kuppusamy, G and Nayak, PG and Tippavajhala, VK}, title = {Gut microbiota shifts in spaceflight: a case study evidence and countermeasures for microbial homeostasis.}, journal = {3 Biotech}, volume = {16}, number = {4}, pages = {152}, pmid = {41929571}, issn = {2190-572X}, abstract = {The gut microbiota is a crucial component in maintaining overall human health since it has been found to influence not only metabolism but also neurobehavioral function and immunity. The extreme conditions of space, for example, cosmic radiation, microgravity, and confinement, can severely disrupt the functioning and alter the composition of gut microbiota. In fact, this will predispose the immune system to be dysfunctional, lead to psychological and metabolic disorders that are accompanied by a decrease in the diversity of beneficial microbes and change in the pattern of metabolite production. The spaceflight analog and ground, based studies have produced important findings concerning the mechanisms and reasons for gut microbial dysbiosis in extreme conditions. Different research works have been carried out, such as dietary intervention and high fiber to support the growth of healthy microbes. Further, advanced microbial monitoring using wearable sensors to identify the microbial and proinflammatory biomarkers will mitigate dysbiosis and safeguard the crew's health for longer-duration missions. This wearable sensor will not only help monitor astronauts' microbial status continuously, but it will also provide a significant feature for designing personalized dietary plans and probiotic supplements. This article provides a comprehensive understanding of astronaut health, including disturbances to the gut microbiome during space travel, space-analogue studies conducted by many researchers to unravel mechanisms, countermeasures to stabilize the gut microbiome, and its prospects.}, }
@article {pmid41929684, year = {2026}, author = {Chen, C and Wang, P and Tong, G and Chen, R and Shen, Y and Wu, X and Liang, W and Pu, J}, title = {The structure of rhizosphere microbial and endophytic communities of Coptis chinensis var. brevisepala: variations across different ecological niches.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1785609}, pmid = {41929684}, issn = {1664-302X}, abstract = {Coptis chinensis var. brevisepala is a valuable traditional Chinese medicinal plant, whose resources are severely depleted due to long-term overexploitation. However, the associations between its rhizosphere microbiome and habitat soil properties, as well as the composition and functions of endophytes, remain unclear. This study employed high-throughput sequencing to characterize rhizosphere microbial communities of C. chinensis var. brevisepala from four distribution sites, analyze their correlations with soil chemical properties, and explore the differences and functional traits of endophytic communities in distinct tissues (leaves, rhizomes, fibrous roots). A total of 177 core bacterial genera and 146 core fungal genera were detected in rhizosphere soils of the four sites. The dominant bacterial phyla were Proteobacteria, Acidobacteriota, and Actinobacteriota, with norank_f_Xanthobacteraceae and Bradyrhizobium as the dominant genera. The dominant fungal phyla were Ascomycota and Basidiomycota, with Paraboeremia and Saitozyma as the dominant genera. Soil chemical properties exerted significant effects on both bacterial and fungal communities in the rhizosphere, among which soil pH and total nitrogen (TN) were the key drivers shaping rhizosphere microbial communities. For endophytes, 29 bacterial phyla (596 genera) and 12 fungal phyla (653 genera) were identified, with significant differences in diversity, richness, and dominant genera across tissues; leaves harbored the highest endophytic diversity. Functional prediction indicated that endophytic fungi were dominated by saprotrophy-related functional genes, and KEGG secondary functional annotation uncovered the presence of antimicrobial-related genes. This study clarifies the rhizosphere microbiome ecological traits and tissue-specific endophytic characteristics of C. chinensis var. brevisepala, providing a scientific basis for screening beneficial microorganisms to facilitate the restoration and reconstruction of this endangered medicinal plant.}, }
@article {pmid41929693, year = {2026}, author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z}, title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729476}, pmid = {41929693}, issn = {1664-302X}, abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.<br><br>METHODS: Vaginal swabs (sPTB, n&#x202f;=&#x202f;37; term, n&#x202f;=&#x202f;62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.<br><br>RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p&#x202f;<&#x202f;0.05), and distinct community structure (PERMANOVA p&#x202f;<&#x202f;0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC&#x202f;=&#x202f;0.82), and a multi-metabolite model improved classification (AUROC&#x202f;=&#x202f;0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.<br><br>CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.}, }
@article {pmid41929779, year = {2026}, author = {Mishra, P and Prescott, SL and Logan, AC}, title = {The gut is guilty! Will legalomics transform forensic and legal psychology?.}, journal = {Frontiers in psychology}, volume = {17}, number = {}, pages = {1739593}, pmid = {41929779}, issn = {1664-1078}, abstract = {Multiple lines of converging research are supporting the idea that gut microbes play an outsized role in human cognition and behavior. Here in this perspective article, we argue that emergent gut-brain-microbiota research, and associated advances in multi-omics technologies, are destined to be of high-level relevance to forensic and legal psychology. After summarizing neural, immune, endocrine, and metabolic channels by which gut ecosystems can modulate behavior-relevant brain states, and discussing causal inferences from microbiota-transfer and adjacent human evidence, we present auto-brewery syndrome as a bounded legal precedent for microbiome-mediated impairment. The available evidence allows for a visualized future in which legalomics-the disciplined use of microbiome and omics evidence in prevention, treatment, competency, mitigation, risk assessments, reintegration care, correctional health, and professional wellness-is in the prevue of forensic and legal psychology. Framed by neurorights, we offer a series of ideas for future directions, with possible ways to strengthen research within ethical frameworks. Using auto-brewery syndrome as an example, we argue that the legalome offers forensic and legal psychology a way to calibrate, rather than replace, biopsychosocial judgement. Microbial signatures and legalomics-reliably obtained and narrowly construed-might one day help us judge more justly.}, }
@article {pmid41929949, year = {2026}, author = {Zhang, Q and Almanie, L and Ouyang, Y and Cheng, Z and Zhang, H}, title = {From routine periodontal therapy to Alzheimer's disease early detection: A scoping review.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261421629}, pmid = {41929949}, issn = {2542-4823}, abstract = {An epidemiological association has been observed between periodontitis and Alzheimer's disease (AD); however, salivary and blood assays often show low specificity. Periodontal tissues and fluids, which are routinely removed and discarded during periodontal treatment, may be collected to offer matrices useful for the early detection of AD. This study aimed to map current preclinical and clinical evidence on biomarkers measured in periodontal tissues and fluids for the early detection of AD and organize them within an AD-specificity pyramid anchored to brain-relevant endpoints. Following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Extension for Scoping Reviews) guidance, we searched PubMed, Scopus, and Web of Science (January 1, 2015-August 31, 2025) for preclinical and clinical studies measuring AD-relevant biomarkers in periodontal matrices. The protocol was pre-registered (OSF DOI: 10.17605/OSF.IO/EDVU9; August 20, 2025). Two reviewers extracted the data, and other two independently verified them. The findings were organized using a four-tier AD-specificity pyramid. Results: Fourteen studies met the inclusion criteria. The biomarkers from the included studies were clustered into microbiome features, molecular signals, and genetic/transcriptomic findings. Evidence ranged from Tier-1 contextual inflammation/pathogens to Tier-4 core-pathology adjacency; five studies incorporated clinical/biological anchoring, with cerebrospinal fluid amyloid-β positivity providing the most brain-relevant anchor. Periodontal matrices are practicable, high-signal sources for AD-relevant biomarkers. However, translational validation linking periodontal biomarkers to brain endpoints is needed to assess the feasibility of multi-tier and chairside panels for early AD detection as part of routine periodontal care.}, }
@article {pmid41929953, year = {2026}, author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE}, title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261436287}, pmid = {41929953}, issn = {2542-4823}, abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.<br><br>OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.<br><br>METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.<br><br>RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (&#x3b5;4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.<br><br>CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.}, }
@article {pmid41930197, year = {2026}, author = {Wu, J and Jiang, C}, title = {The authors respond to feedback on Cancer Cell-Memory Macrophage Hybrid Theory for metastatic cancer cells.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1780597}, pmid = {41930197}, issn = {2234-943X}, abstract = {We have recently hypothesized that the hematogenous metastatic cancer cell of solid tumors is a hybrid between a primary cancer cell and a memory/trained macrophage (doi: 10.3389/fonc.2024.1412296). The hybrid cell respectively acquires mutator phenotype and overgrowth/hyperplasia property from the primary cancer cell and migratability/metastability from the memory/trained macrophage. We name this hypothesis Cancer Cell-Memory Macrophage Hybrid Theory. Since the publication of the article, a number of questions related to this Theory have been raised by colleagues in the oncology community, including intratumoral microbes and microbiomes/microbiotas, oncolytic viruses and bacteria, human papilloma virus vaccines, anti-cancer effects of γδ T-cells, and immune checkpoint inhibitors. The current article is prepared to address these issues. Additional to resolving questions like "Why metastatic cancer cells enter dormancy and can recur via stem-like self-renewal?", the Cancer Cell-Memory Macrophage Hybrid Theory distinguishes itself from other carcinogenesis and metastasis hypotheses/theories by offering answers to many puzzling clinical features including metastasis of seemingly malignant parasitic cells within the human body, intracellular microbes (including viruses, bacteria, fungi, and parasites) within cancer cells, paradoxal effects (recurrence vs. regression) of microbes on cancer, contradictory immune effects of human papilloma virus vaccines between young and adult/senior females, and immune context-dependent effects (stimulatory and inhibitory) of T-lymphocytes on cancer cells. The Theory also predicts that quantitatively and functionally dampening innate macrophages that have hybridized with cancer cells (i.e., cancer cell-memory macrophage hybrids), should be explored as a fundamental anti-cancer strategy. The Theory further forecasts how to prepare an organotropic/tumoritropic Coley's toxin-like anti-cancer microbe, which could potentially circumvent direct injection of microbial preparations into a tumor. A testable experiment that uses zebrafish larva models can potentially either validate or falsify the Theory.}, }
@article {pmid41930211, year = {2026}, author = {Blagov, AV and Sazonova, MD and Ryzhkova, AI and Karagodin, VP and Popov, MA and Budnikov, EY and Ravani, AL and Orekhov, AN and Sazonova, MA and Arkhipenko, YV}, title = {Analysis of the use of monoclonal antibodies in the treatment of Crohn's disease.}, journal = {Antibody therapeutics}, volume = {9}, number = {2}, pages = {101-118}, pmid = {41930211}, issn = {2516-4236}, abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease with increasing global prevalence, significantly impacting patients' quality of life and healthcare costs. The introduction of monoclonal antibodies has revolutionized CD management, offering targeted therapy against specific inflammatory pathways. This review systematically analyzes the current state of monoclonal antibody therapy, including anti-TNF-α agents (infliximab, adalimumab, certolizumab pegol), anti-integrin antibodies (vedolizumab), and anti-cytokine therapies (ustekinumab, risankizumab). Despite remarkable therapeutic advances, significant limitations persist, including primary non-response (20%-40%), secondary loss of response (13%-20% annually), immunogenicity, safety concerns, and substantial economic burden. We propose evidence-based strategies to address these challenges, including therapeutic drug monitoring, combination therapy, and personalized medicine approaches. Furthermore, we identify promising novel therapeutic targets such as IL-36, IL-17C, SMAD7, TL1A, complement components, and microbiome-related factors. Targeting two or more specific targets simultaneously appears to be a promising direction of research for the development of bi- and polyspecific monoclonal antibodies capable of interfering with multiple pathological pathways in CD. The integration of advanced antibody engineering, personalized medicine, and innovative delivery systems represents the future direction for overcoming current limitations. Achieving sustained remission for all patients through safe, effective, and accessible therapeutic interventions remains the ultimate goal in CD management.}, }
@article {pmid41930263, year = {2025}, author = {Du, YC and Wang, D and Song, YQ and Zheng, QS and Wang, L}, title = {Arbuscular mycorrhizal fungi regulate the peanut rhizosphere microbiome to alleviate salinity stress and enhance yield.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1739241}, pmid = {41930263}, issn = {1664-302X}, abstract = {Salt stress threatens peanut yield by impairing physiological performance and disrupting rhizosphere microbial community stability. To investigate how arbuscular mycorrhizal fungi (AMF) mediate plant-microbe interactions under salt stress, researchers conducted a controlled pot experiment with four treatments: non-salt control (CK), AMF inoculation (A), salt stress (S; 100 mM sodium chloride), and combined AMF inoculation under salt stress (SA), with five biological replicates in each group. Plant growth traits, yield, and rhizosphere bacterial community were assessed at different peanut growth stages. AMF inoculation significantly increased peanut biomass, chlorophyll content, and yield, both under salt and non-salt stress conditions. Salt stress significantly reduced bacterial richness and community evenness, while AMF partially restored α-diversity and reshaped bacterial community composition. Functional predictions indicated that AMF enriched nitrogen cycling pathways such as nitrate reduction and nitrogen fixation. Furthermore, AMF promoted a more complex and stable bacterial community under salt stress, characterized by enhanced synergistic effects among key taxa, including Actinobacteria, Firmicutes, and Proteobacteria. Overall, AMF inoculation enhanced plant performance and rhizosphere bacterial resistance, highlighting its potential as an effective ecological strategy for improving peanut yield in saline-alkali agricultural ecosystems.}, }
@article {pmid41930266, year = {2026}, author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag041}, pmid = {41930266}, issn = {2730-6151}, abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.}, }
@article {pmid41930333, year = {2026}, author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T}, title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.}, journal = {MedComm}, volume = {7}, number = {4}, pages = {e70705}, pmid = {41930333}, issn = {2688-2663}, abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.}, }
@article {pmid41930403, year = {2026}, author = {Ai, Y and Zhu, T and Gan, J}, title = {Parental autoimmune diseases and offspring's allergic disease: A systematic review and meta-analysis.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {4}, pages = {e70335}, pmid = {41930403}, issn = {1399-3038}, mesh = {Humans ; *Autoimmune Diseases/epidemiology ; Female ; *Hypersensitivity/epidemiology ; Asthma/epidemiology ; *Parents ; Male ; Child ; Rhinitis, Allergic/epidemiology ; }, abstract = {Epidemiological studies have reported an increased risk of allergic diseases in children born to parents with autoimmune diseases (AIDs); however, the mechanisms underlying this association remain unclear. We conducted a systematic review and meta-analysis to explore the relationship between parental AIDs and allergic diseases in offspring. EMBASE, Web of Science, and PubMed databases were searched for articles published up to December 1, 2025. AIDs in both mothers and fathers were included. Allergic outcomes included asthma, eczema, and allergic rhinitis. A random-effects model was used to synthesize the data. Twelve studies were included in the final analysis, and the methodological quality ranged from moderate to high. Maternal AIDs (of any type) were associated with an increased risk of asthma (odds ratio (OR) 1.25, 95% confidence interval (CI): 1.09-1.43), eczema (OR 1.30, 95% CI: 1.13-1.50), and allergic rhinitis (OR 1.04, 95% CI: 1.02-1.07) in offspring. Paternal AIDs were also associated with a higher risk of asthma (OR 1.16, 95% CI: 1.06-1.27) and eczema (OR 1.13, 95% CI: 1.02-1.26) in offspring. This systematic review and meta-analysis demonstrate that parental AIDs are associated with an increased risk of asthma and eczema in children. However, the available evidence is limited by potential bias in case ascertainment and inadequate adjustment for confounding factors. Larger high-quality studies are needed to confirm these findings and to elucidate the underlying genetic and microbiome-related mechanisms. Such evidence may facilitate early identification and targeted prevention or management of allergic diseases in children of parents with AIDs.}, }
@article {pmid41930490, year = {2026}, author = {Herrera, MJ and Khanna, A and Jones, JA and Betancur-R, R and Rohner, PT}, title = {Diet Outweighs Vertical Transmission in Shaping Dung Beetle Larval Gut Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {7}, pages = {e70336}, pmid = {41930490}, issn = {1365-294X}, support = {//University of California, San Diego/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Coleoptera/microbiology/growth &amp; development ; Larva/microbiology ; *Diet ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Cattle ; }, abstract = {The microbiome is central to host development and adaptation, yet the balance between vertical and environmental acquisition, and how hosts shape surrounding microbial communities, remains poorly understood. Dung beetles rely on microbial symbionts to extract nutrients from vertebrate dung, with part of their microbiome vertically inherited via a maternal faecal pellet. However, the relative importance of vertical versus horizontal transmission is unclear. We examined this in the gazelle dung beetle (Digitonthophagus gazella), rearing larvae on brood balls made of dung from grass-(high-quality), hay-(low-quality) or silage-fed (a novel fermentable energy-rich diet) cattle, with or without maternal microbes. We integrated measures of gut morphology with 16S rRNA amplicon sequencing to assess host development and the gut microbiome. Diet significantly influenced overall size, hindgut area, and microbiome composition. Silage-dung fed larvae had more even and taxonomically rich microbiomes, with higher microbial diversity in individuals reared with maternal microbes. Diet explained ~26% of the variation in microbial composition, while the vertical transmission of microbes only explained 3%. Vertical transmission only slightly increases microbial species richness and relative hindgut area but did not influence overall microbial diversity. The larval brood ball contributed 40%-50% of the hindgut microbiome, while maternal microbes contributed < 0.05%. These findings demonstrate that horizontal acquisition through diet is the dominant force shaping larval gut microbiomes, while vertical inheritance plays a minor but detectable role in enhancing richness and gut development. More broadly, this work reinforces the importance of examining host-microbiome-environment interactions in ecological and evolutionary contexts.}, }
@article {pmid41930642, year = {2026}, author = {Xu, S and Guo, G and Gao, J and Fang, Z and Chai, L and Gao, Y and Liu, J and Wang, J and Siqinbateer,  and Zhang, L}, title = {Systematic Identification and Characterization of Causal Risk Genes Implicated in Colorectal Cancer by Integrating GWAS, eQTL, and mQTL Data.}, journal = {Current drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113894501444884260130225445}, pmid = {41930642}, issn = {1873-5592}, abstract = {INTRODUCTION: Knowledge of the mechanisms through which common single-nucleotide polymorphisms (SNPs) modulate colorectal cancer (CRC) susceptibility is central to elucidating the molecular basis of this disease. Genome-wide association studies (GWAS) reveal noncoding SNPs influencing CRC susceptibility, yet their functional mechanisms, particularly through gene expression dysregulation, DNA methylation alterations, and interactions with gut microbiota, remain uncharacterized. Through integrative analysis, systematically exploring the effects of genetic variations on gene expression heterogeneity, DNA methylation, and gut microbiome is expected to yield potential biomarkers for early diagnosis and intervention of CRC.<br><br>METHODS: An integrative framework is developed to prioritize causal risk genes at CRC-associated GWAS loci, applying the SMR&amp;HEIDI (Summary-data-based Mendelian randomization and heterogeneity in dependent instruments) and TSMR (Two-sample Mendelian Randomisation) methods. The findings were validated via gene expression and TF binding affinity.<br><br>RESULTS: 10 tissue-specific gene-SNP pairs, 3 blood eQTL-gene pairs, 26 gene-CpG-SNP regulatory modules, and 39 microbiota-associated gene-SNP pairs are identified. A few potential regulatory influences on CRC development associated with genes and variants, such as POU5F1B and rs10797801, were identified. Moreover, the genetic variants disrupted TF binding affinity while only a few promoted the binding of transcription factors (TFs).<br><br>DISCUSSION: The data integration enabled us to prioritize genes according to different regulatory mechanisms, such as gene expression and DNA methylation, and bridge the gap between statistical associations and biological functionality.<br><br>CONCLUSION: Multi-omics integration reveals some causal risk genes and variants implicated in CRC. These findings offer novel insight into the molecular mechanisms underlying CRC susceptibility and provide valuable clues for diagnosis and therapeutic intervention strategies.}, }
@article {pmid41930694, year = {2026}, author = {Yuhan, W and Zhiru, C and Yu, D and Ruiqing, Z and Guangtao, P and Jie, X}, title = {Research Progress on the Synergistic Role of Gut Microbiota and Exosomal miRNAs in the Treatment of Androgenetic Alopecia.}, journal = {Current topics in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115680266424195251211072643}, pmid = {41930694}, issn = {1873-4294}, abstract = {INTRODUCTION: Androgenetic alopecia (AGA), a widespread condition marked by the gradual shrinkage of hair follicles, involves complex pathogenic mechanisms. Recently, a growing body of research has begun to uncover the influence of gut microbial communities and exosomederived microRNAs (miRNAs) in hair follicle regulation. Although current findings remain preliminary, they point toward a potential interplay between intestinal microbiota and exosomal signaling pathways, which may offer novel therapeutic avenues. This review seeks to dissect the biological contributions of gut microbiota and exosomal miRNAs to the onset and progression of AGA, aiming to inform future clinical approaches through an integrative perspective.<br><br>METHODS: We performed a comprehensive literature search (2018-2025) in PubMed, Web of Science, and CNKI. Studies were selected based on predefined criteria focusing on gut microbiota, exosomal miRNAs, and their roles in AGA pathogenesis.<br><br>RESULTS: Gut microbiota contribute to hair follicle health by modulating host immune responses, metabolic pathways, and the skin microbiome, thereby enhancing follicular stem cell activity. Exosomes, as key mediators of intercellular communication, transport miRNAs that play essential roles in regulating the hair growth cycle. These miRNAs can counteract follicular miniaturization by targeting specific suppressor molecules.<br><br>DISCUSSION: The gut microbiota may influence the composition and functional properties of exosomes, thereby exerting indirect regulatory effects on hair follicle dynamics. These findings provide new insights into potential therapeutic strategies for AGA.<br><br>CONCLUSION: Gut microbiota and exosomal miRNAs may synergistically influence the progression of AGA through interconnected metabolic, immune, and microbial skin axes. Targeted modulation of the "microbiota-miRNA axis" could represent a novel, multidimensional approach for AGA treatment. Nevertheless, the precise molecular crosstalk and signaling cascades underlying these phenomena remain largely unresolved, warranting more targeted experimental investigations.}, }
@article {pmid41930951, year = {2026}, author = {Everett, BA and Prindle, A}, title = {AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.}, journal = {mBio}, volume = {}, number = {}, pages = {e0023126}, doi = {10.1128/mbio.00231-26}, pmid = {41930951}, issn = {2150-7511}, abstract = {UNLABELLED: Aromatic amino acids-tryptophan, tyrosine, phenylalanine, and histidine-are essential for bacterial growth and are among the most energetically expensive metabolites to synthesize. Despite this cost, it has been recently shown that bacteria possess exporters for these amino acids. Here, we identify aexB (formerly yvjA) as a gene encoding a novel aromatic amino acid exporter in Bacillus subtilis. Using a transposon-based screen, we found that aexB overexpression confers resistance to the toxic tryptophan analog 5-fluorotryptophan. Additional analog screens revealed that AexB also promotes tolerance to toxic derivatives of tyrosine, phenylalanine, and histidine but not non-aromatic amino acids. LC-MS analysis showed that AexB specifically exports aromatic amino acids, and co-culture assays confirmed that overexpression of aexB can support the growth of aromatic amino acid auxotrophs. Furthermore, overexpression of aexB impaired growth when intracellular tryptophan was limiting. On the other hand, deletion of aexB exacerbated growth defects under excess tryptophan conditions, likely due to feedback inhibition of aromatic amino acid synthesis pathways. Our findings reveal that AexB is an aromatic amino acid exporter that functions as a metabolic safety valve.<br><br>IMPORTANCE: Identification and characterization of amino acid exporters is a broadly relevant topic. Amino acid synthesis is energetically costly, and thus functional relevance for their export is unintuitive. Identification of the molecular components that allow export may offer new engineering opportunities to improve biomanufacturing and metabolic engineering. Characterization of these exporters may also provide a more complete understanding of the human microbiome where amino acids, especially tryptophan, have been established as nodes of crosstalk between host and microbiota.}, }
@article {pmid41930957, year = {2026}, author = {Benucci, GMN and Garcia-Barreda, S and Sanchez, S and Marco, P and De Miguel, AM and Le Tacon, F and Marozzi, G and Baciarelli Failini, L and Eslick, H and Elliott, TF and Deveau, A and Murat, C and Donnini, D and Bonito, G}, title = {Mycorrhizal competition release and microbial dynamics in native and non-native Tuber melanosporum habitats.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0022526}, doi = {10.1128/aem.00225-26}, pmid = {41930957}, issn = {1098-5336}, abstract = {Truffles in the genus Tuber (Pezizales) are among the few ectomycorrhizal taxa successfully cultivated worldwide. Australia has recently become one of the top producers of Tuber melanosporum, a high-valued black truffle native to Europe. Truffle co-introductions in the Southern Hemisphere with their Northern Hemisphere plant symbionts are hypothesized to benefit from reduced ectomycorrhizal competition and natural enemies. In this study, we tested whether T. melanosporum in Australia experiences competition release by sampling soils and truffles across France, Spain, Italy, and Australia. Fungal and prokaryotic communities in truffle plantations were assessed in native (European) and non-native (Australian) habitats through ITS and 16S rDNA amplicon sequencing from soil and truffles. Community composition was primarily structured by site of origin and secondarily by presence of brûlé, vegetation-free area induced by truffle production of plant-growth inhibiting compounds, with significant interactions indicating site-dependent brûlé effects. European soils showed higher fungal richness outside the brûlé, with higher evenness overall and for ectomycorrhizal fungi only outside brûlé. T. melanosporum showed higher abundance in Australia, with significant differences restricted to outside the brûlé. Overall, ectomycorrhizal fungi in European soils had more than four times the taxa and higher diversity compared to Australian soils. Among the main competitors, Tomentella, Inocybe, and Trichophaea co-dominated in Europe, versus Scleroderma, Hebeloma, and Tarzetta in Australia. Despite differences in soil microbiomes, bacterial communities within T. melanosporum truffle ascocarps were strikingly similar across sites and continents and were dominated by Bradyrhizobium. Despite high site-level variation, our results support the competition release hypothesis, with reduced enemies benefiting T. melanosporum colonization outside the brûlé in Australia.IMPORTANCEThis study provides the first cross-hemisphere analysis of the truffle microbiome, comparing native and non-native soils and truffles from Europe and Australia. We demonstrate that the remarkable success of Tuber melanosporum cultivation in Australia is compatible with ecological release from competitors, which favors its development outside the brûlé. At the same time, we reveal striking cross-hemispheric similarities in truffle-associated bacterial communities, consistently dominated by Bradyrhizobium. These findings highlight both the novelty and transcontinental relevance of our work, offering new perspectives on fungal ecology and truffle cultivation.}, }
@article {pmid41927455, year = {2026}, author = {Seo, JI and Koh, A and Lim, S and Yoo, HH}, title = {The 3M roles of the gut microbiome in pharmacotherapy for diabetes: mediator, modifier, and marker.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tem.2025.12.006}, pmid = {41927455}, issn = {1879-3061}, abstract = {The rising global prevalence of type 2 diabetes mellitus (T2DM) presents major challenges to healthcare systems; thus, more effective treatment strategies are urgently needed. In this context, the growing recognition of the gut microbiome's role in T2DM pharmacotherapy has shifted attention toward integrating microbiome-derived mechanisms to optimize drug response. This review proposes a structured '3M' framework that classifies the gut microbiome's roles in T2DM pharmacotherapy into three translational categories: mediator of drug action, modifier of therapeutic response, and marker for predicting efficacy or intolerance, based on recent clinical and mechanistic insights. Together, these insights support a translational framework that may guide the integration of microbiome-informed strategies into future T2DM pharmacotherapy.}, }
@article {pmid41927536, year = {2026}, author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J}, title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.}, journal = {Nutrition &amp; diabetes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41387-026-00418-w}, pmid = {41927536}, issn = {2044-4052}, abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.<br><br>METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.<br><br>RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs&#x2009;>&#x2009;0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.<br><br>CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.}, }
@article {pmid41927585, year = {2026}, author = {Song, J and Tang, S and Guo, Y and Hong, C and Song, T}, title = {The gut-heart dialogue: an epigenetic perspective on myocardial infarction.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00974-0}, pmid = {41927585}, issn = {2055-5008}, support = {No. 20250602055RC//Jilin Province Science and Technology Department/ ; }, abstract = {Myocardial infarction (MI) remains a leading cause of global mortality, with adverse cardiac remodeling and heart failure presenting persistent metabolic and clinical challenges. While traditional pharmacotherapies have improved outcomes, there is an urgent need to elucidate how lifestyle and nutritional factors influence disease progression. Emerging evidence underscores the critical interplay between natural bioactive compounds (e.g., dietary fibers, polyphenols), the gut microbiota, and host metabolic regulation. This review systematically clarifies the "gut microbiota-epigenetic axis" as a pivotal mechanism linking nature-derived bioactives to cardiac repair. We delineate how the gut microbiota transforms specific bioactives into functional metabolites, such as short-chain fatty acids (SCFAs) from fibers and urolithin A from ellagitannins, which act as potent epigenetic modulators. These microbial metabolites remodel the epigenetic landscape of the host heart via histone modification and DNA methylation, thereby regulating gene networks governing inflammation, energy metabolism, and fibrosis. Synthesizing evidence from in vivo animal studies and clinical observations, we explore therapeutic strategies centered on natural bioactives, including high-fiber dietary interventions and polyphenol supplementation, alongside probiotics and postbiotics. By integrating the metabolic potential of the gut microbiome with epigenetic regulation, this review offers novel insights into how natural bioactive compounds can be leveraged for precision prevention and therapeutic strategies in myocardial infarction.}, }
@article {pmid41927589, year = {2026}, author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, &#x10c; and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H}, title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71145-0}, pmid = {41927589}, issn = {2041-1723}, abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.}, }
@article {pmid41927609, year = {2026}, author = {Duffy, EP and Sterrett, JD and Hale, LH and Ward, JO and Saba, LM and Frank, DN and Bachtell, RK and Ehringer, MA}, title = {Oxycodone self-administration and genetic background exert community-specific effects in the gut microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41666-1}, pmid = {41927609}, issn = {2045-2322}, }
@article {pmid41927721, year = {2026}, author = {Nakamaru, K and Ito, T and Shimogama, T and Shijimaya, T and Tahara, T and Yamazaki, J and Orino, A and Masuda, M and Nakayama, S and Ikeura, T and Naganuma, M}, title = {Distinct difference of pancreatic tissue-specific microbiome in autoimmune pancreatitis and pancreatic ductal adenocarcinoma.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44821-w}, pmid = {41927721}, issn = {2045-2322}, support = {22K16032//JSPS KAKENHI Grant-in-Aid for Young Scientists/ ; }, abstract = {Autoimmune pancreatitis (AIP) is a form of chronic pancreatitis that may be difficult to distinguish from pancreatic ductal adenocarcinoma (PDAC). Emerging evidence suggests the substantial involvement of gut microbiome dysbiosis in various disorders, including pancreatic diseases. This study investigates the differences in pancreatic tissue-specific microbiomes between AIP and PDAC. Pancreatic tissues were obtained from patients with type 1 AIP (n = 17) or PDAC (n = 24) via ultrasound-guided tissue acquisition and subjected to 16S rRNA sequencing. The sequences were used to determine the bacterial alpha diversity and characterize the microbiome structures related to different sample groups. The pancreatic microbiome in PDAC exhibited increased bacterial alpha diversity compared to that in AIP. The abundances of 16 bacteria were significantly different between the AIP and PDAC groups, and most of them (15/16) were increased in PDAC relative to that in AIP. The bacterial index calculated using these bacteria had a favorable discriminative ability for these different groups, with an area under the curve value of 0.91. Functional analysis demonstrated that the pentose phosphate pathway, gondoate biosynthesis, and several pathways related to adenosine biosynthesis were positively associated with the bacterial index. The findings from this preliminary study indicate that pancreatic microbiome, as a new diagnostic alternative, may potentially help with the differential diagnosis of AIP and PDAC.}, }
@article {pmid41927746, year = {2026}, author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA}, title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46933-9}, pmid = {41927746}, issn = {2045-2322}, support = {SRUG2204254606//National Research Foundation/ ; }, abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.}, }
@article {pmid41927935, year = {2026}, author = {Gao, W and Wang, X and Shi, Y and Wu, G and Zhou, M and Lin, X}, title = {Retraction Note: Predictable regulation of gut microbiome in immunotherapeutic efficacy of gastric cancer.}, journal = {Genes and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41435-026-00397-z}, pmid = {41927935}, issn = {1476-5470}, }
@article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12920-026-02359-w}, pmid = {41928235}, issn = {1755-8794}, }
@article {pmid41928236, year = {2026}, author = {Gschwendtner, S and Kovacevic, D and Gaede, KI and Herzmann, C and Overmann, J and Schloter, M and Krauss-Etschmann, S}, title = {Longitudinal dynamics and site-specific recovery of the human respiratory microbiome following smoking cessation.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03644-z}, pmid = {41928236}, issn = {1465-993X}, }
@article {pmid41920180, year = {2026}, author = {Thomas, CE and Loroña, NC and LaBrie, SD and Curtis, KR and Yin, H and Ma, N and Randolph, TW and Qu, C and Huyghe, JR and Thomas, S and Hsu, L and Koehne, AL and Nayemi, S and Ammar, H and Kahsai, OJ and Redwood, D and Li, CI and Li, L and Peters, U and Figueiredo, JC and Thomas, TK and Phipps, AI and Hullar, MAJ}, title = {The phylum Fusobacteriota is associated with CRC-specific mortality: Results from the Translational Research Program in Cancer Differences across Populations.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-25-1580}, pmid = {41920180}, issn = {1538-7755}, abstract = {BACKGROUND: The microbiome is an important component of the tumor microenvironment implicated in colorectal cancer (CRC). However, its relationship with CRC-specific mortality remains unclear.<br><br>METHODS: We included 581 participants with CRC (167 African American, 176 Alaska Native, 118 Hispanic, 120 non-Hispanic White) from the Translational Research Program in Cancer Differences across Populations (TRPCDP). We sequenced the V4 region of the 16S rRNA bacterial gene using DNA extracted from formalin-fixed paraffin embedded tumors. 204 participants died of CRC and 377 did not die of CRC. Participants who died of CRC were matched to participants who did not die of CRC during follow-up by age, sex, tumor site, tumor stage, year of diagnosis, and population group. Logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between bacterial presence with CRC-specific mortality, adjusting for matching factors and tissue macrodissection status.<br><br>RESULTS: Individuals who died from CRC were 1.71 times as likely to have bacteria from the Fusobacteriota phylum present in their tumors (OR=1.71, 95% CI: 1.19-2.47). Associations with Fusobacteriota were strongest among African American participants (OR=2.36, 95% CI: 1.14-4.99) compared to other populations, however this different was not statistically significant (OR range = 1.05-1.38, Pinteraction = 0.697). Candidate pathways of pyruvate fermentation to acetate and lactate II and peptidoglycan biosynthesis I were associated with higher odds of CRC death.<br><br>CONCLUSIONS: Fusobacteriota was significantly associated with CRC-specific mortality with noted differences across populations.<br><br>IMPACT: This finding highlights the tumor microbiome as a candidate for further investigation into CRC outcome disparities.}, }
@article {pmid41920710, year = {2026}, author = {Wan, Y and Alessa, HB and Guasch-Ferré, M and Tobias, DK and Lee, KH and Manson, JE and Willett, WC and Sun, Q and Hu, FB}, title = {Intake of Fiber From Different Food Sources and Type 2 Diabetes Risk: An Integrated Analysis of Epidemiological and Multiomic Data.}, journal = {Diabetes care}, volume = {}, number = {}, pages = {}, doi = {10.2337/dc25-2957}, pmid = {41920710}, issn = {1935-5548}, support = {/NH/NIH HHS/United States ; //Novo Nordisk Foundation/ ; }, abstract = {OBJECTIVE: To examine the association between fiber from various food sources and type 2 diabetes (T2D) risk, as well as the molecular profiles involved.<br><br>RESEARCH DESIGN AND METHODS: Using data from three large prospective U.S. cohorts comprising 195,222 participants observed for up to 34 years, we evaluated the association between fiber from various food sources and T2D risk. We also assessed the association between fiber intake, plasma metabolic biomarkers, and a metabolomic profile indicative of T2D risk. Additionally, we examined gut microbial features related to fiber intake and the T2D metabolomic profile.<br><br>RESULTS: During follow-up, we documented 18,369 incident T2D cases. Higher intakes of total fiber (hazard ratio [HR] comparing extreme quintiles 0.88; 95% CI 0.82, 0.94), cereal fiber (HR 0.77; 95% CI 0.73, 0.82), and fruit fiber (HR 0.82; 95% CI 0.78, 0.87) were each associated with a lower T2D risk. Greater intakes of total fiber, cereal fiber, and fruit fiber, but not vegetable fiber, were linked to more favorable plasma profiles of insulinemic, lipid, and inflammatory biomarkers and a metabolomic profile indicative of a lower T2D risk. We also identified multiple gut microbial species, such as Faecalibacterium prausnitzii, Ruminococcus lactaris, and Gemmiger formicilis, along with relevant butyric acid-producing enzymes, all of which were associated with higher fruit fiber intake and a metabolomic profile indicating a lower likelihood of T2D development.<br><br>CONCLUSIONS: Higher intakes of total, cereal, and fruit fiber are associated with a lower risk of T2D and a more favorable metabolic profile, with the gut microbiome potentially contributing to the beneficial association of fruit fiber.}, }
@article {pmid41920740, year = {2026}, author = {Mingolelli, G and Subedi, P and Bonitatibus, S and Johnson, JJ and Henke, M}, title = {Metabolism by ex vivo cultures of human stool increases the activity of coumarin, a widespread antioxidant from herbal supplements.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117199}, doi = {10.1016/j.celrep.2026.117199}, pmid = {41920740}, issn = {2211-1247}, abstract = {Host and microbiome metabolism of bioactive compounds can alter their efficacy. Herbal supplements contain many bioactive compounds, but their metabolism by gut microbes and the effects on efficacy remain poorly understood. To gain clarity, we investigate coumarin, an antioxidant in food, cosmetics, and supplements and a scaffold for diverse bioactive compounds. In this study, we characterize coumarin metabolism by the human gut microbiome, which produces 3,4-dihydrocoumarin and melilotic acid. We characterize this pathway in the culturable microbiota from 9 stool donors with liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics and microbiome profiling. We discover that 17 microbiome species metabolize coumarin and that the E. coli gene nemA is necessary for coumarin reduction. In antioxidant assays, melilotic acid is more potent than coumarin, suggesting that this pathway may impact bioactivity, with possible contributions to supplement efficacy. Further characterization may provide insights on the metabolic fate of coumarins and contributions of the microbiome to their efficacy.}, }
@article {pmid41920780, year = {2026}, author = {Donovan, SM}, title = {Human Milk Oligosaccharides Support Coordinated Microbiome and Immune Development and Function in Infancy.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-15}, doi = {10.1159/000549867}, pmid = {41920780}, issn = {1421-9697}, abstract = {BACKGROUND: Human milk contains functional ingredients that shape the microbiome and immune development of infants. Human milk oligosaccharides (HMOs) are among the largest and most diverse components of human milk. Their heterogeneity enables unique structure-function relationships that contribute to their physiological effects. This narrative review will focus on how HMOs directly and indirectly protect the infant from pathogens and educate the immune system.<br><br>SUMMARY: Preclinical research, observational studies, and intervention trials demonstrate that HMOs provide multilayer modulation of host defense and immune development. HMOs are soluble glycans that are acetylated, sialylated, or fucosylated, which mediate their interactions with viruses and bacteria to reduce infectivity. Additionally, HMOs enhance pathogen exclusion by promoting intestinal cell maturation, mucin production, and barrier function. Moreover, HMOs directly interact with immune cells through binding to carbohydrate recognition domains. HMOs promote the growth of beneficial bacteria, particularly Bifidobacterium longum subspecies infantis, which is also immunomodulatory. Lastly, HMOs are fermented to short-chain fatty acids, which lower the pH of the intestinal lumen, providing further antimicrobial defense.<br><br>KEY MESSAGES: Breastfed infants have a reduced risk of infectious disease compared to non-breastfed infants, attributable in part to the high concentration and structural diversity of HMOs. Clinical trials using formulas supplemented with synthetic human-identical milk oligosaccharides (HiMOs) have demonstrated benefits to adaptive and innate immunity, reduced infections, increased bifidobacteria, and reduced pathogenic bacteria. These benefits are amplified in formulas containing higher concentrations and greater varieties of HiMOs. However, the clinical benefit of routinely supplementing term infant formulae with HiMOs remains unsettled due to variability across existing clinical trials. Further research in healthy infants focused on short- and long-term immune outcomes is needed.}, }
@article {pmid41920852, year = {2026}, author = {Kim, H and Kim, S and Kimbrel, JA and Morris, MM and Mayali, X and Buie, CR}, title = {Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference.}, journal = {PLoS computational biology}, volume = {22}, number = {4}, pages = {e1014102}, doi = {10.1371/journal.pcbi.1014102}, pmid = {41920852}, issn = {1553-7358}, abstract = {Multidimensional scaling (MDS) is a widely used dimensionality reduction technique in microbial ecology data analysis that captures the multivariate structure of the data while preserving pairwise distances between samples. While improvements in MDS have enhanced the ability to reveal group-specific data patterns, these MDS-based methods require prior assumptions for inference, limiting their application in general microbiome analysis. In this study, we introduce a new MDS-based ordination method, "F-informed MDS," which configures the data distribution based on the F-statistic, the ratio of dispersion between groups sharing common and different characteristics. Using semisynthetic datasets, we demonstrate that the proposed method is robust to hyperparameter selection while maintaining statistical significance throughout the ordination process. Various quality metrics for evaluating dimensionality reduction confirm that F-informed MDS is comparable to state-of-the-art methods in preserving both local and global data structures. Its application to a diatom-associated bacterial community suggests the role of this new method in interpreting the community's response to the host. Our approach offers a well-founded refinement of MDS that aligns with statistical test results, which can be beneficial for broader multidimensional data analyses in microbiology and ecology. This new visualization tool can be incorporated into standard microbiome data analyses.}, }
@article {pmid41920977, year = {2026}, author = {Flower, S and Gruvstad Melén, A and Seidler, K}, title = {Investigating the Link between the Intestinal Microbiome and Th17/Treg Dysregulation in Hashimoto's Thyroiditis, and the Therapeutic Potential of Vitamin D.}, journal = {Journal of the American Nutrition Association}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/27697061.2026.2644894}, pmid = {41920977}, issn = {2769-707X}, abstract = {Objective:Autoimmune disease (AD) has become a leading cause of illness in the twenty-first century, with autoimmune thyroid disease at the forefront of these conditions. Hashimoto's thyroiditis (HT) shares many features with other ADs, including associations with gastrointestinal symptoms linked to intestinal dysbiosis (ID). However, the pathogenesis of HT remains incompletely understood, particularly the role of specific T cell lymphocyte activity. The primary objective of this review was to investigate links between ID and HT pathogenesis, focusing on the relationship between a specific cluster of differentiation 4 (CD4) T cell subsets including T helper 17 (Th17) and regulatory T cells (Treg). A secondary aim was to explore whether vitamin D supplementation may serve as a viable intervention in managing HT, given existing research demonstrating links between Vitamin D status, HT pathogenesis and ID. Methods:A systematic literature search was conducted in PubMed using predefined inclusion/exclusion criteria across three tranches. A search of the review literature pertaining to thyroid autoimmunity, HT and the intestinal microbiome identified 21 papers for inclusion. A mechanistic literature search covering animal, in vitro and human studies on HT, autoimmunity, ID, intestinal microbiota, intestinal permeability (IP) and Th17 yielded 43 papers. A final search of human studies examining vitamin D status or supplementation in relation to ID, IP, Th17 and interleukin (IL)-17 identified 45 relevant papers. Accepted studies were critically appraised and synthesized in a narrative analysis.Results:Evidence across the included studies suggests an association between ID and pathogenesis of HT. Increased IP and alterations in Th17/Treg balance emerged as key contributing mechanisms. Vitamin D status was also associated with immune modulation, particularly involving Th17 activity, and was strongly linked to both ID and HT pathogenesis.Conclusions:ID may play a contributory role in HT pathogenesis through immune modulation involving CD4+ T cell subsets. Vitamin D supplementation demonstrates potential as an adjunctive strategy; however, further targeted human studies are required to clarify causality and therapeutic efficacy.}, }
@article {pmid41921305, year = {2026}, author = {Teixidó Mulet, M and Veas Rodriguez, J and Terán, E and Piñol, M and Vilardell, F and Iglesias, M and Hierro, C and Calvo, M and Matias-Guiu, X and Salud, A and Tabernero, J and Montal, R}, title = {Biomarker-guided immunotherapy in gastric cancer: current insights and future perspectives.}, journal = {Cancer treatment reviews}, volume = {145}, number = {}, pages = {103124}, doi = {10.1016/j.ctrv.2026.103124}, pmid = {41921305}, issn = {1532-1967}, abstract = {Gastric and gastroesophageal junction adenocarcinoma (GC) is a biologically challenging malignancy associated with suboptimal clinical outcomes due to limited effective treatment options. The recent incorporation of immune checkpoint inhibitors (ICIs) into therapeutic algorithms has improved the clinical prospects of subsets of GC patients. However, responses to anti-PD-1/PD-L1 agents remain highly heterogeneous, with only some patients deriving long-term benefits. This variability highlights the importance of identifying optimal biomarkers to enhance patient selection, thereby enabling tailored immunotherapy strategies. Whereas microsatellite instability has demonstrated a potent capacity for predicting immunotherapy benefits in GC, other predictive biomarkers, such as PD-L1 expression, remain suboptimal. Advances in gene expression and epigenetic profiling, liquid biopsy approaches, gut microbiome characterization, and artificial intelligence-driven multimodal algorithms applied to multi-omics or digital pathology are key drivers for the comprehensive characterization of the GC tumour microenvironment (TME), which could be used for better treatment selection. Similarly, elucidating the complex tumour-immune interplay with these technologies will be crucial for the success of novel immunotherapeutic approaches under clinical development, by evaluating alternative immune pathways alone or in combination with current actionable targets of GC. The current review aims to give an overview of the current immunotherapeutic landscape in GC, evaluate standard-of-care and emerging biomarkers of immunotherapy response, and discuss the translational potential of incorporating multi-omic and AI-derived biomarkers into biomarker-enriched clinical decision-making frameworks.}, }
@article {pmid41921320, year = {2026}, author = {Huang, DQ and Zhou, S and Jia, Y and Yan, Y and Lu, H}, title = {Deciphering pharmaceutical resistance in sulfur-driven autotrophic denitrification: an integrated multi-omics artificial intelligence-driven structural biology approach.}, journal = {Water research}, volume = {298}, number = {}, pages = {125834}, doi = {10.1016/j.watres.2026.125834}, pmid = {41921320}, issn = {1879-2448}, abstract = {Sulfur-driven autotrophic denitrification (SdAD) is a promising low-carbon technology for nitrogen removal; however, its stability and adaptive mechanisms under pharmaceutical stress remain poorly understood. In this study, ibuprofen (IBU) was used as a representative pharmaceutical to investigate the response of an SdAD system. Throughout the 210-day operational period, the system demonstrated exceptional functional robustness, maintaining high sulfide (97.46 ± 3.18%) and inorganic nitrogen (99.17 ± 4.34%) removal efficiencies across IBU concentrations ranging from environmentally relevant levels to elevated shock loads (100-2000 μg/L). Underpinning this macroscopic stability, community-level analyses revealed that instead of succumbing to inhibition, the SdAD microbiome actively reorganized its composition and topological structure to accommodate the selective pressure. This adaptation was characterized by enhanced microbial diversity and stress-induced network modularity (particularly at 100-500 μg/L), alongside strengthened cooperative interactions between sulfur-oxidizing bacteria and denitrifiers. To unravel the specific molecular drivers of this resilience, we integrated AlphaFold-based structural modeling with machine learning-coupled molecular docking. This enabled us to resolve the three-dimensional structure of sulfide: quinone oxidoreductase (SQR) and perform the first structure-function analysis of SQR within an SdAD context under pharmaceutical stress, revealing that arginine residues serve as key interaction hotspots for IBU binding. Consistent with this binding mechanism, multi-omics data further corroborated a systemic adjustment involving the coordinated regulation of sulfur oxidation genes and the transcriptional upregulation of arginine biosynthesis pathways. Overall, these findings shed light on how the SdAD community mitigates pharmaceutical toxicity through a multi-tiered strategy involving ecological network reorganization and metabolic compensation. Methodologically, this work highlights the value of integrating artificial intelligence-driven structural biology with multi-omics analyses to decode the mechanisms of contaminant resistance in biological wastewater treatment systems.}, }
@article {pmid41921321, year = {2026}, author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ}, title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.}, journal = {Water research}, volume = {298}, number = {}, pages = {125784}, doi = {10.1016/j.watres.2026.125784}, pmid = {41921321}, issn = {1879-2448}, abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.}, }
@article {pmid41921531, year = {2026}, author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, QL}, title = {Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.}, journal = {Journal of breath research}, volume = {}, number = {}, pages = {}, doi = {10.1088/1752-7163/ae5a51}, pmid = {41921531}, issn = {1752-7163}, abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated by Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.}, }
@article {pmid41921618, year = {2026}, author = {Khajanchi, BK and Grocholl, J and Alam, M and Hasan, NA and Wang, H and Hughes, S}, title = {Colonization of Salmonella Newport and Microbiome Analyses of Bulb Onions Grown in Artificially Contaminated Soil at Lab-Scale Under a Controlled Environment.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100769}, doi = {10.1016/j.jfp.2026.100769}, pmid = {41921618}, issn = {1944-9097}, abstract = {INTRODUCTION: Several multistate Salmonella outbreaks in the United States have been linked to bulb onions. In this study we investigated the extent of Salmonella colonization on bulb onions grown in contaminated soil.<br><br>PURPOSE: The study evaluated the colonization potential and microbial community dynamics of Salmonella Newport on bulb onions grown in artificially spiked soil.<br><br>METHODS: Red bulb onions were grown from seed, and resultant seedlings were transplanted into pots containing soil. Soil surface was spiked with S. Newport at transplant and again two weeks before harvest. Three inoculum levels [10[2] (low), 10[4](medium), 10[6] (high) CFU per 200 g soil] of Salmonella Newport were investigated in triplicate, with three unspiked controls. Three independent trials were conducted using two different soil types. Microbiome analyses were performed on the bulb onions and soil from the high inoculum group in Trial 1 (field topsoil) at 0 h, 1 h, and 24 h pre-enrichment. Results Salmonella was detected in one high-inoculum bulb onion in Trial 1 (field topsoil) and in all high-inoculum onions in Trials 2 and 3 (Miracle-Gro soil). Among the medium inoculum groups, all onions in Trial 2, one in Trial 3, and none in Trial 1 were positive for Salmonella. No onions in the low inoculum group were Salmonella-positive. Microbiome analysis of control and Salmonella-spiked high inoculum field topsoil samples and associated bulb onions revealed that bacterial community composition remained stable at 0 h and 1 h pre-enrichment but underwent notable shifts after 24 h. Bacterial diversity decreased following 24 h of pre-enrichment, with increased dominance of Proteobacteria and Firmicutes. However, Salmonella spiking had minimal or no effect on microbiome dynamics. Significance These findings provide insights into the colonization capability of Salmonella Newport on bulb onions in different soil types and associated microbial community shifts after 24h pre-enrichment.}, }
@article {pmid41921761, year = {2026}, author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S}, title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.}, journal = {Diabetes research and clinical practice}, volume = {235}, number = {}, pages = {113232}, doi = {10.1016/j.diabres.2026.113232}, pmid = {41921761}, issn = {1872-8227}, abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.}, }
@article {pmid41921818, year = {2026}, author = {Ziade, I and McDermott, MM and O'Riordan, KJ and Cryan, JF and Schneider, E}, title = {The microbiome and eating disorders: a new framework at the interface of interoception and reward.}, journal = {Neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neuroscience.2026.03.050}, pmid = {41921818}, issn = {1873-7544}, abstract = {Accumulating evidence suggests that the gut microbiome can modulate brain and behaviour including those relevant to eating behaviours and reward signalling through the dynamic communication pathways of the microbiota-gut-brain-axis. Emerging evidence links altered gut microbial composition to disordered eating patterns, implicating the gut microbiome as a possible mechanism underlying eating disorders, as well as a potential therapeutic target for these conditions. In this review, we synthesise evidence across preclinical and clinical research to propose an integrated framework wherein the gut microbiome, interoception and reward circuits may interact to shape disordered eating behaviours. We firstly explore how microbial signals modulate homeostatic and reward feeding systems via vagal afferents, neurotransmitter modulation and immune-neural pathways, and how these signals converge in brain regions implicated in reward systems and interoception. Particular attention is given to how these interactions may occur in under- and over-eating phenotypes of disordered eating. The therapeutic potential of microbiota-targeted interventions to modulate eating disorder-induced dysregulations in interoception and reward signalling is discussed. Combined evidence suggests a paradigm shift in the etiological considerations of eating disorders is warranted taking into account dysregulations of gut microbiota and its effects on reward processing and interoceptive signalling. Specifically, we propose that EDs are underpinned by dysregulations of gut microbiota, reward processing and interoceptive signalling, rather than neurobehaviour alone. The novel, integrated, and transdiagnostic framework posited in this review could represent a conceptual shift in the aetiological understanding of eating disorders with the potential to derive new neurobiological targets for intervention.}, }
@article {pmid41921920, year = {2026}, author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB}, title = {Virulence and antimicrobial resistance profiling of Klebsiella pneumoniae isolated from foxes in northern China.}, journal = {Microbial pathogenesis}, volume = {215}, number = {}, pages = {108476}, doi = {10.1016/j.micpath.2026.108476}, pmid = {41921920}, issn = {1096-1208}, abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.}, }
@article {pmid41922110, year = {2026}, author = {Bhat, A and Chaudhary, S and Kumari, A and Sharma, S and Sarin, SK and Maras, JS}, title = {Aspirin reprograms platelet signaling and the intrahepatic microbiome to suppress RyR2-driven inflammation and fibrosis in preclinical chronic liver disease.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {198}, number = {}, pages = {119296}, doi = {10.1016/j.biopha.2026.119296}, pmid = {41922110}, issn = {1950-6007}, abstract = {Platelet deactivation by aspirin possibly helps in regression of liver fibrosis, though the mechanisms are unclear. We administered aspirin in a murine model of liver fibrosis and studied molecular signatures associated with fibrosis regression; both in vivo (murine model/ patients) and in vitro. Increase in intrahepatic PF4, p-selectin, PDGFR-β levels (platelet activation) correlated with increase in liver fibrosis (p < 0.05, r[2]>0.3). Aspirin reduced the number and activation of intrahepatic platelets, inflammation and fibrosis (p < 0.05). Platelet deactivation using aspirin in murine model increased autophagy, glutathione, energy metabolism and decreased arachidonic acid and butanoate metabolism (p < 0.05). Aspirin modulated liver microenvironment and showed decrease in intrahepatic immune cell activation (blood transcription module) which correlated with histidine and tryptophan metabolism (r2 > 0.5, p < 0.05). The intrahepatic microbiome post-aspirin showed increased abundance of Firmicutes (Ruminococcaceae, Lachnospiraceae, and Clostridiaceae) and improved functionality (p < 0.05). Aspirin caused decreased expression of Ryanodine-receptor-2 (RyR2), Arginase-1 and Kynurenine-3-monooxygenase, which correlate with reduction in α-SMA and degree of hepatic fibrosis (r2 > 0.75; p < 0.05). In addition, pan specific blocking of RyR2 by carvedilol/flecainide markedly inhibited HSC activation and proliferation in-vitro by reducing Ca[2+] overload, ER/mitochondrial stress (p < 0.05). Further, RyR2 blockade in HSCs reduced its activation by activated platelet secretome or TGFβ1 (p < 0.05). CONCLUSIONS: Platelet deactivation using aspirin regresses hepatic fibrosis by decreasing intrahepatic platelet accumulation/activation, inflammation and modulation of intrahepatic microbiome. Induction of RyR2 is critical for fibrosis development and pharmacological inhibition of RyR2 could ameliorate liver fibrosis.}, }
@article {pmid41922261, year = {2026}, author = {Adebayo, AA and Babalola, OO}, title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70325}, pmid = {41922261}, issn = {1758-2229}, support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {*Daucus carota/microbiology/growth &amp; development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.}, }
@article {pmid41922263, year = {2026}, author = {Hosogaya, N and Fukui, S and Takazono, T and Fukushima, K and Morio, R and Irifune, S and Morimoto, S and Nakada, N and Yoshida, M and Takeda, K and Ide, S and Iwanaga, N and Nemoto, K and Izumikawa, K and Yatera, K and Yanagihara, K and Mukae, H}, title = {Hypoalbuminemia and reduced sputum microbiome diversity associated with antibiotic treatment failure in nursing and healthcare-associated pneumonia.}, journal = {Drug discoveries &amp; therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.5582/ddt.2026.01005}, pmid = {41922263}, issn = {1881-784X}, abstract = {Nursing and healthcare-associated pneumonia (NHCAP) pose significant challenges in older populations, yet factors predicting antibiotic treatment failure remain elusive. This exploratory secondary analysis of a multicenter phase IV trial aimed to identify the clinical and microbiome predictors of treatment failure in patients with NHCAP treated with lascufloxacin. Among the 56 evaluable patients (median age 86 years; cured n = 44, not cured n = 12), paired sputum and tongue samples were analyzed using 16S ribosomal RNA gene clone library sequencing. Alpha diversity was assessed using the Shannon index, Simpson index, observed richness, and Pielou's evenness, whereas beta diversity was calculated using Bray-Curtis dissimilarity and visualized by principal coordinate analysis. Serum albumin was significantly lower in not cured patients (3.0 vs. 3.5 g/dL, p = 0.0497) and emerged as the strongest predictor of treatment failure in univariate logistic regression (odds ratio 0.18, 95% confidence interval 0.05-0.73, p = 0.016). Sputum Pielou's evenness showed a comparable predictive ability (odds ratio 0.010, p = 0.047). The overall microbiome community composition did not differ according to the outcome. Notably, patients with hypoalbuminemia (< 2.85 g/dL) exhibited significantly reduced sputum alpha diversity (Shannon p = 0.034, Simpson p = 0.025, Pielou's evenness p = 0.010). A simple risk stratification combining hypoalbuminemia and denture use identified a high-risk subgroup with markedly elevated treatment failure rates (75.0% vs. 12.5%, p = 0.001). These findings suggest an interconnected pathophysiology linking nutritional status and respiratory microbiome stability in patients with NHCAP. Nutritional status and oral health may be modifiable targets for improving treatment outcomes in high-risk patients.}, }
@article {pmid41922553, year = {2026}, author = {Cloud, RE and Irwin, P and Muturi, EJ and Cáceres, CE}, title = {Characterizing the Microbiome and Prevalence of Wolbachia in Culex pipiens Complex and Culex restuans Mosquitoes in the Midwest United States.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02750-1}, pmid = {41922553}, issn = {1432-184X}, support = {DEB - 1754115//National Science Foundation/ ; DEB - 1754115//National Science Foundation/ ; DBI - 2022049//Genomics and Eco-evolution of Multi-scale Symbioses Institute/ ; }, }
@article {pmid41922622, year = {2026}, author = {Chan, E and Chan, WH and Kerr, G and Archer, SK and Jardé, T and Engel, RM and Gould, JA and Amarasinghe, SL and Rutten, EL and D'Adamo, GL and Gulliver, EL and Gearing, LJ and Forster, SC and Giles, EM and Abud, HE}, title = {Patient-derived intestinal organoids as a model for site-specific mucosal bacterial interactions in paediatric inflammatory bowel disease.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46184-8}, pmid = {41922622}, issn = {2045-2322}, support = {1188689//National Health and Medical Research Council of Australia/ ; 1188689//National Health and Medical Research Council of Australia/ ; }, abstract = {Inflammatory bowel disease (IBD) is secondary to an abnormal immune response to the microbiota. To study this, models of host-microbe interactions that represent mucosal bacterial communities and inter-patient diversity are required. Human intestinal organoids (HIOs) are an established model to investigate epithelial responses. Here, we describe a technique of culturing bacteria directly from the sites of inflammation in IBD, while simultaneously sampling host tissue. We generated HIOs from a cohort of newly diagnosed paediatric IBD patients, without confounding treatments or comorbidities, and explored their response to site-specific bacteria. A unique biobank of matched HIOs and cultured mucosa-attached bacteria was established from 27 paediatric patients. Transcriptional profiling revealed differential gene expression between control and IBD-derived organoids. We used microinjection to introduce bacteria to the apical surface of the epithelium, to determine the effect of bacteria on host epithelial cells. We measured survival and growth of bacteria within the HIOs and tested several related bacterial isolates for their impact on the epithelium. An isolate from a control patient stimulated inflammatory signalling pathways but this was not observed in response to a closely related isolate originating from an IBD patient. This study demonstrates the feasibility of isolating bacteria and generating organoids from the same biopsy tissue, to explore personalised host-microbe interactions. The microinjections, while labour-intensive, demonstrate that closely related bacteria can induce very different epithelial responses, with downstream implications for immune response. This highlights the importance of understanding host-microbe interactions in a strain- and site-specific manner and developing techniques for personalised microbiome-based therapeutics.}, }
@article {pmid41922662, year = {2026}, author = {Liu, B and Huang, X and Chang, C and Wan, X and Liu, M and Li, R and Li, J and Li, Q and Tao, Y}, title = {Toward microbiome-assisted remediation: Vanadium-titanium magnetite mining reshapes cropland soil chemistry and rhizosphere microbiomes.}, journal = {Crop health}, volume = {4}, number = {1}, pages = {}, pmid = {41922662}, issn = {2948-1945}, support = {2024NSFSC1202//Natural Science Foundation of Sichuan Province/ ; 25FTZLCL0012//Open Projects of the Sichuan Provincial Key Laboratory for Critical Strategic Materials of Vanadium and Titanium/ ; TYNSYS-2023-Z-03//Open Projects of the Sichuan Provincial University Key Laboratory for Solar Energy Technology Integration and Application Promotion/ ; Z3785//the start-up funds provided by Chengdu University/ ; }, abstract = {Vanadium-titanium magnetite (VTM) mining can modify cropland soils and root-associated microbiomes with implications for crop health. However, how crop rhizosphere microbiomes reorganize under VTM-derived stress-particularly when bacteria and fungi are considered together-remains poorly understood. In the Hongge district (Panzhihua, China), we sampled bulk soils and rhizospheres of lettuce, rapeseed, and pea from croplands within the VTM mining influence zone (mining-impacted fields) and paired croplands outside the zone (reference fields). We measured soil chemistry and profiled bacterial and fungal communities using 16S rRNA and ITS amplicon sequencing, respectively. Mining-impacted soils generally showed a VTM geochemical imprint, neutral-alkaline pH, and reduced plant-available P and K. Bray-Curtis-based ordinations indicated a clear separation between mining-impacted and reference rhizospheres, and taxonomic profiles suggested host-dependent reassembly of both bacterial and fungal communities. Putative functional profiling suggested a shift toward stress-accommodation processes, and fungal guild assignments tended to tilt toward saprotrophic/endophytic categories. Mantel analyses identified pH as one of the strongest correlates of community turnover, whereas structural equation modeling was consistent with nutrient availability (available N/P/K composite) explaining a substantial portion of the VTM effect; the composite total-metal-load axis (Fe/V/Ti/Zn) showed limited explanatory power, especially for fungi. Together, these field-based, two-kingdom signals link VTM-altered soil chemistry to rhizosphere restructuring in edible crops and provide actionable indicators for crop health management.}, }
@article {pmid41922722, year = {2026}, author = {Neufert, C and Neurath, MF}, title = {Pathophysiology of colitis-associated colorectal cancer.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {41922722}, issn = {1759-5053}, abstract = {Colitis-associated colorectal cancer (caCRC) is a subset of lower gastrointestinal tract malignancies that occurs in patients with inflammatory bowel disease (IBD), such as ulcerative colitis and Crohn's disease. The global prevalence of IBD is increasing, putting more individuals at risk of developing caCRC. The pathophysiological mechanisms that underlie the initiation and growth of caCRC remain to be fully elucidated. Nevertheless, studies have provided novel insights into the pathophysiology of caCRC, underscoring the distinguishing characteristics of caCRC compared with sporadic forms of CRC. In this Review, we describe the key mechanisms that drive caCRC. Starting from a clinical perspective and highlighting key features of the tumour epithelium, we discuss typical caCRC-related characteristics among subtypes of CRC, with a particular focus on the role of stromal cells in the tumour microenvironment. In addition, we review the contributions of immune cells to tumour control versus tumour promotion, and how signals from the gut microbiome might influence tumour development in caCRC. We also discuss various aspects of the pathophysiological heterogeneity of caCRC. Finally, we outline potential implications for therapy, and how these findings could be translated into future strategies of personalized medicine targeting caCRC.}, }
@article {pmid41922727, year = {2026}, author = {Klinhom, S and Kunasol, C and Sriwichaiin, S and Kerdphoo, S and Chattipakorn, N and Chattipakorn, SC and Thitaram, C}, title = {Development of gut microbiota composition in captive Asian elephants: a year-long analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46586-8}, pmid = {41922727}, issn = {2045-2322}, support = {59/2565//The CMU Presidential Scholarship and Chiang Mai University/ ; N42A660301//The Distinguished Research Professor Grant from the National Research Council of Thailand/ ; RSA6280095//Thailand Research Fund/ ; }, abstract = {The establishment of gut microbiota is vital for the health and development of elephant calves, especially during their first year of life. This study investigates the transformation of the gut microbiome in captive Asian elephant calves, focusing the influence of maternal milk and subsequent dietary transitions on microbial colonization. A single meconium was collected at birth, followed by monthly fresh fecal samples during the first year. Mothers' fecal samples were also collected when calves reached three months of age. Gut microbiota profiling was conducted using 16 S rRNA gene sequencing. Meconium exhibited a diverse microbiota with moderate richness at birth. Richness subsequently declined in the monthly fecal samples, reaching its lowest point by three months of age. Firmicutes, Actinobacteriota, and Bacteroidota were the dominant bacterial phyla throughout the first year. A major shift was observed around 7 to 8 months of age with emergence of the archaeal genus Methanobrevibacter from phylum Euryarchaeota, which subsequently declined by 11 to 12 months. By this age, the calf microbial community had become more similar to that of adult elephants; however, species richness and diversity remained lower, indicating that microbial maturation was still ongoing. These findings advance our understanding of gut microbiota development in elephant calves and underscore the critical role of dietary management in promoting gut health and survival, providing essential data for captive conservation and management strategies.}, }
@article {pmid41922879, year = {2026}, author = {Dou, S and Shen, J and Wang, C and Ma, G and Fu, G and Fu, L and Cong, B and Li, S}, title = {Forensic analysis of environmental and skin microbiome differences in college dormitories based on 16 S rRNA.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {41922879}, issn = {1437-1596}, support = {82572154//National Natural Science Foundation of China/ ; 30705010060//HeBei Medical University Postdoctoral Fund/ ; }, }
@article {pmid41923122, year = {2026}, author = {Li, M and Cui, J and Qu, R and Liu, R and Sun, Y and Li, P and Liu, J and Low, A and Huang, X and Gan, F and Xu, ZZ}, title = {Porphyromonas gingivalis induces intestinal inflammation through gingipain-dependent gut microbiome dysbiosis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02389-7}, pmid = {41923122}, issn = {2049-2618}, support = {2025AHGXZK40069//Natural Science Foundation of Education Department of Anhui Province/ ; }, abstract = {BACKGROUND: Porphyromonas gingivalis (Pg), a key pathogen in periodontitis, is implicated in various systemic diseases such as pancreatic cancer and Alzheimer's disease. However, as a periodontal pathogen that can directly enter the lower gastrointestinal tract via saliva, its potential impact on the gut microbiome, intestinal inflammation, and its underlying mechanisms remains largely elusive.<br><br>RESULTS: Here, we observed that oral administration of Pg exacerbates intestinal inflammation in mice by inducing gut microbiome dysbiosis, increasing Th17 cells and the release of pro-inflammatory cytokines. Inhibition of Th17 activity with GSK805 or an anti-IL-17A blocking antibody mitigated this inflammatory response, highlighting the mediating role of Th17 cells. Gingipains, the virulence factors of Pg, played a crucial role in this process. Sequential knockout of gingipain genes revealed a gradual reduction in inflammatory phenotypes, with statistically significant alleviation observed when all three gingipain genes were deleted. Co-housing experiments showed that gut microbiota remodeling effectively protected against Th17-driven inflammatory response. Furthermore, immunization with inactivated Pg effectively prevented gut microbiome dysbiosis and Th17 cell-mediated inflammation.<br><br>CONCLUSION: Our findings suggest that Pg may exacerbate intestinal inflammation, potentially via its gingipain virulence proteases, which are linked to gut microbiota dysbiosis and enhanced Th17-mediated immune responses. These results suggest that gingipains could be promising targets for further investigation in Pg-associated intestinal disorders. Video Abstract.}, }
@article {pmid41923148, year = {2026}, author = {Mogouong Tambue, J and Yager, C and Bushley, KE}, title = {Associations between phloem microbiota and metabolomes in three North American ash species (Fraxinus spp.) susceptible to emerald ash borer (Agrilus planipennis).}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00884-w}, pmid = {41923148}, issn = {2524-6372}, support = {DEB 2030036//National Science Foundation/ ; }, abstract = {BACKGROUND: Microorganisms play crucial roles in the survival and fitness of their plant and insects hosts, including invasive species. The emerald ash borer (Agrilus planipennis, Fairmaire; EAB) is an invasive insect from Asia. It represents a significant threat to North American forest ecosystems, causing widespread mortality in susceptible native ash (Fraxinus) species. While previous studies have shown differences in specific plant defense metabolites between susceptible North American ash species and their more resistant Asian counterparts, widely targeted metabolite profiles and their interactions with phloem microbiota in response to EAB infestation has thus far received little attention. This study aimed to profile microbial communities associated with ash phloem and EAB larval guts and their relationship to ash phloem metabolites in three native susceptible North American ash species: F. pennsylvanica (green ash), F. nigra (black ash) and F. americana (white ash).<br><br>RESULTS: Using metabarcoding to characterize the microbial communities associated with the larval gut and host tree phloem and widely targeted metabolomics to establish the first global metabolomic profile of phloem in these ash species, we examined interspecies differences in profiles and associations of ash phloem microbiota and metabolites in relation to EAB infestation. Multivariate analysis revealed that fungal communities were distinct in all ash species, while F. pennsylvanica (green ash) harbored bacterial communities distinct from black ash. Only black ash showed a phloem profile significantly associated with EAB attack symptoms and had the largest number of differentially abundant bacterial taxa. In contrast, larval gut bacterial communities from green ash were distinct from those in other ash species. Green ash displayed a distinct global metabolite profile from the other two species and had the highest number of differentially regulated metabolites, while black ash had the least. Green and white ash shared a strong upregulation of terpenoid compounds, several of which were among compounds significantly associated with microbial communities in green ash phloem or the EAB larval gut.<br><br>CONCLUSIONS: Our results provide the first comparative analysis of phloem-associated microbial communities and metabolomes across three susceptible North American ash species and their response to EAB. We found that microbiota and metabolites in green ash showed a distinct response to EAB infestation from the other ash species and we identified specific metabolites exhibiting significant correlations with microbial communities in ash phloem or the EAB larval gut. These findings contribute novel insights into interspecies variability in host-associated microbial communities and metabolomes and their response to an invasive insect.}, }
@article {pmid41923164, year = {2026}, author = {Kiplimo, D and Sánchez, AM and Ramakrishnan, DK and Wicaksono, WA and Mwirichia, R and Teixidó, N and Berg, G and Abdelfattah, A}, title = {Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00880-0}, pmid = {41923164}, issn = {2524-6372}, support = {PID2020-117607RR-I00 (ENVIRONAPPLE)//University of Lleida and IRTA predoctoral UdL-IRTA Sponsored Fellowship 2021, Spanish 'Agencia Estatal de Investigaci&#xf3;n' (AEI), European Regional Development Fund (ERDF), 2021 SGR 01477 grant and the CERCA Programme from the 'Generalitat de Catalunya'/ ; }, abstract = {BACKGROUND: In recent years, there has been increasing concerns about antibiotic resistance. Although studies have investigated resistance in food-associated bacteria, fresh produce microbes remain underexplored as potential hub of resistance genes capable for horizontal transfer to human via consumption. To this end, we tested the antibiotic resistance profiles of bacterial isolates recovered from Golden Reinders and Mandy apple cultivars. We aimed to investigate the effects of orchard-cultivar combinations and microbial lifestyle on the antibiotic resistance profiles. The apples (Golden Reinders and Mandy) were sampled from four separate orchards (EEL-Lleida, Esterri, Fruits-de-Ponent and Gotarta) in Spain. We used combination of culture-dependent and whole genome sequencing approaches to analyse the antibiotic resistance profiles.<br><br>RESULTS: A total of 516 bacterial isolates were screened for susceptibility against seven different classes of antibiotics. Results showed that 272 isolates were resistant to at least one antibiotic. From those, 203 were epiphytes and 95 classified as endophytes (isolated from surface-sterilized apple peels), whereas 26 isolates were shared between the groups. The resistance profiles varied across the antibiotics, with over 50% of the isolates exhibiting resistance to tetracycline, quinolones and cephalosporins. In contrast, none of the isolates showed resistance to imipenem. Whole genome sequencing (WGS) was performed on 18 isolates, however, only 10 genomes passed quality-control thresholds and were included in subsequent resistome analyses. We found ARGs encoding resistance to 14 main antibiotic classes, with the majority of the confirmed resistances attributed to multidrug resistance (MDR). Only few target-specific ARGs were annotated, including (Rif)iri (rifampicin), lnu(A) (lincomycin) and FosD (Fosfomycin). Pantoea agglomerans possessed higher number of ARGs, while Staphylococcus arlettae exhibited notable prevalence of plasmid-encoded ARGs.<br><br>CONCLUSION: Overall, the study highlights the prevalence of antibiotic resistance in apple microbiomes. The presence of multidrug-resistance (MDR) genes further underscores the persistent threat of 'antibiotic resistance', underlining the necessity for deeper insight into antibiotic resistance within food chain.}, }
@article {pmid41923171, year = {2026}, author = {Delgadillo-Ordoñez, N and Schwarzenberg, A and Zhang, H and Beenham, L and Bensaddek, D and Raimundo, I and Terraneo, T and Benzoni, F and Peixoto, RS}, title = {Coral color morphs exhibit distinct microbial and proteomic profiles linked to stress and immune mechanisms in a changing ocean.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02391-z}, pmid = {41923171}, issn = {2049-2618}, abstract = {BACKGROUND: Coral phenotypic plasticity facilitates acclimation and adaptation to environmental variability. Coral species often display a variety of color morphs, yet key biological and ecological implications of such phenotypic variation remain underexplored. Here, we present the first proteomic and untargeted lipidomic and metabolomic survey to explore the biological characteristics and potential ecological significance of different color morphs (pink and brown) of healthy Pocillopora verrucosa sampled along a latitudinal gradient.<br><br>RESULTS: Our multi-omic approach elucidated distinct mechanisms associated with these dominant color morphs. We discovered bacterial indicators specific to each morph: putative pathogens such as Salmonella, Escherichia-Shigella, and carotenoid-producing Gemmatimonas were notably associated with the pink morph, whereas the brown morph was associated with potentially beneficial bacteria, such as Lysobacter, Acinetobacter, and Endozoicomonas. Despite these microbiome differences, the lipidome and metabolome of P. verrucosa were surprisingly homogeneous across colors and locations, suggesting similar metabolic performances during summer conditions. Key polar and apolar lipid classes, such as fatty acids, glycerophosphocholines, and retinoids, were prevalent. Notably, our proteomic analysis revealed morph-specific expressions, with pink morphs exhibiting enhanced levels of GFP-like proteins, Ankyrin, and the enzyme pullulanase, suggesting novel putative&#xa0;protective roles. In contrast, the brown morphs showed a higher abundance of heat shock proteins, indicating putative differential stress response capabilities.<br><br>CONCLUSION: This comprehensive study provides the first proteomic survey of P. verrucosa and identifies key physiological pathways and trade-offs linked to color morphs, which can further contribute to enhancing our understanding of coral resilience in the face of climate change.<br><br>SIGNIFICANCE STATEMENT: Understanding the phenotypic plasticity of corals is crucial for uncovering mechanisms of resilience in warming oceans, yet the biological significance of coral color morphs still needs to be explored. Using an innovative multi-omic approach (proteomics, lipidomics, and metabolomics), we provide the first comprehensive analysis of differences between pink and brown morphs of Pocillopora verrucosa. Our data reveal key taxa, potentially pathogenic or beneficial, associated with each morph, and suggest different strategies for each color morph to cope with heat stress, either expressing proteins involved in UV protection and heterotrophic activity or enhanced levels of heat stress resilience and DNA repair. These findings offer insights into the phenotypic plasticity of coral color morphs and their differential responses to climate change. Video Abstract.}, }
@article {pmid41923274, year = {2026}, author = {Slaughter, M and Sung, CH and Suchodolski, JS and Pilla, R and Torres, C and Lappin, MR}, title = {EXPRESS: Oral administration of Enterococcus lactis strain SF68 speeds the recovery of amoxicillin-clavulanate-induced dysbiosis in cats.}, journal = {Journal of feline medicine and surgery}, volume = {}, number = {}, pages = {1098612X261441923}, doi = {10.1177/1098612X261441923}, pmid = {41923274}, issn = {1532-2750}, abstract = {OBJECTIVES: In a previous study, Torres-Henderson et al. (2017), the probiotic Enterococcus lactis strain SF68 was clinically shown to lessen amoxicillin-clavulanate associated diarrhea. The cause or mechanism as to why this clinical benefit occurred, however, was unknown. The cause or mechanism as to why this clinical benefit occurred, however, was not apparent in that study. Since the completion of that work, a new feline dysbiosis index (DI) has been developed and new information concerning the microbiome and bile acid metabolism has been published. The objective of this study was to assess changes in the feline DI and fecal bile acid metabolism to explain how this probiotic lessened amoxicillin-clavulanate-associated diarrhea.<br><br>METHODS: Prospective, randomized, placebo-controlled, double-blinded study. 27 healthy, young, adult, purpose-bred cats were used for a previous study. Cats were randomized into the probiotic (13 cats) or placebo (14 cats) group. Each cat received amoxicillin-clavulanate for 7 days at a standard dose and either the probiotic or placebo for 14 days. Fecal samples from all cats were obtained at baseline, day 7 and day 14. All samples were frozen at -80&#xb0;C until assessed. Targeted qPCR assays were then used to determine the fecal feline DI and unconjugated fecal bile acid concentrations were measured at each time point.<br><br>RESULTS: An antibiotic-induced shift in fecal microbiota and unconjugated bile acids was observed, with the probiotic group showing normalization of the feline DI and increased secondary bile acids on Day 14 compared to the placebo group (P = 0.0322).<br><br>CONCLUSIONS AND RELEVANCE: The probiotic E. lactis strain SF68 lessened amoxicillin-clavulanate-associated clinical signs of disease at least in part from the positive effects on the selected microbiota and bile acid metabolism. These findings support supplementing this probiotic to cats that have a clinical need for amoxicillin-clavulanate treatment.}, }
@article {pmid41923440, year = {2026}, author = {Wang, P and Liu, X and Sun, W and Dong, X and Tan, J and Chen, M and He, J and Ali, A and Wu, L and Shao, K}, title = {Network Pharmacology Combined With Gut Microbiome and Serum Metabolomics Reveals the Therapeutic Mechanisms of Hydroxysafflor Yellow A in Diabetic Kidney Disease.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e2131566}, pmid = {41923440}, issn = {2314-6753}, support = {SH2023073//Zhenjiang Science and Technology Innovation Fund (Key R&amp;D Program-Social Development) Project/ ; YK2024116//Scientific Research Project of Yancheng Municipal Health Commission/ ; MS2022126//Project of Jiangsu Provincial Science and Technology Development Plan for Traditional Chinese Medicine/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Diabetic Nephropathies/drug therapy/metabolism/blood/microbiology ; Metabolomics ; *Chalcone/analogs &amp; derivatives/pharmacology/therapeutic use ; *Quinones/pharmacology/therapeutic use ; Male ; Mice ; Oxidative Stress/drug effects ; *Network Pharmacology ; Kidney/drug effects/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/metabolism/complications ; Mice, Inbred C57BL ; }, abstract = {Diabetic kidney disease (DKD) is a severe complication of diabetes, primarily driven by chronic inflammation, oxidative stress, and gut microbiota dysbiosis. Hydroxysafflor yellow A (HSY), a bioactive compound derived from Carthamus tinctorius L., demonstrates promising renoprotective effects. However, its mechanisms, especially through modulation of the gut-kidney axis, remain poorly understood. This study employed a combination of network pharmacology, a high-fat diet/streptozotocin-induced type 2 diabetic mouse model, 16S rRNA sequencing, and serum metabolomics to explore the therapeutic mechanisms of HSY. Renal function, oxidative stress, inflammation, and gut microbiota composition were evaluated. HSY significantly alleviated renal injury by reducing blood glucose, creatinine, and urea nitrogen levels (p < 0.05), while enhancing renal antioxidant enzyme activity (GSH, SOD, CAT). Inflammatory markers (TNF-α, IL-1β) and AGE-RAGE signaling were suppressed. Analysis of the gut microbiota revealed that HSY enriched SCFA-producing genera (e.g., Lactobacillus, Alloprevotella) and decreased the abundance of Schaedlerella. Serum metabolomics further indicated that HSY modulated riboflavin metabolism, linoleic acid metabolism, and steroid hormone biosynthesis, thereby linking microbial metabolites to renal protection. Spearman correlation analysis revealed strong associations between specific gut microbiota (e.g., Prevotella) and serum metabolites (e.g., eicosapentaenoic acid). HSY mitigates DKD by targeting AGE-RAGE-mediated inflammation, oxidative stress, and gut microbiota dysbiosis while correcting metabolic disturbances. This study offers a novel multi-omics approach to understanding HSY's renoprotective effects, highlighting its potential as a therapeutic agent for DKD.}, }
@article {pmid41923466, year = {2026}, author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC}, title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70324}, pmid = {41923466}, issn = {1758-2229}, support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; }, mesh = {*Phytophthora/genetics/isolation &amp; purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; }, abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.}, }
@article {pmid41923582, year = {2026}, author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A}, title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e9317962}, pmid = {41923582}, issn = {2314-6753}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; }, abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.}, }
@article {pmid41923586, year = {2026}, author = {Oh, Y and Lee, H and Jang, S}, title = {Emerging synthetic biology-assisted technologies for overcoming antibiotic resistance: CRISPR-Cas, bacteriophage, microbiome, and metabolic engineering-based solutions.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {3}, pages = {e2512002}, doi = {10.71150/jm.2512002}, pmid = {41923586}, issn = {1976-3794}, support = {//National Research Foundation of Korea/ ; RS-2025-02214910//Ministry of Science and ICT/ ; //Incheon National University/ ; }, mesh = {*CRISPR-Cas Systems ; *Synthetic Biology/methods ; *Bacteriophages/genetics ; *Metabolic Engineering/methods ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; *Bacteria/drug effects/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance has become a critical global health challenge due to the decreased efficacy of existing antibiotics and the emergence of multidrug-resistant pathogens. In particular, the rapid horizontal transfer of resistance genes and the diverse mechanisms by which bacteria acquire resistance have significantly undermined the effectiveness of conventional therapeutic strategies, revealing fundamental limitations in current infectious disease management. In this context, synthetic biology provides a promising framework to overcome the limitations of conventional antibiotics by integrating engineering principles with bioengineering approaches, thereby enabling precise and programmable control of biological processes. These synthetic biology-based approaches offer substantial potential for developing sustainable and highly specific antimicrobial strategies. This review comprehensively examines recent advances in synthetic biology-assisted antimicrobial strategies, including CRISPR-Cas systems, bacteriophage engineering, microbiome engineering, and metabolic engineering-driven antibiotic discovery. Collectively, these approaches represent a precision antimicrobial paradigm that enables selective targeting of resistant bacteria while preserving microbiome homeostasis. These strategies also provide new directions for limiting resistance dissemination and guiding the development of next-generation therapeutics.}, }
@article {pmid41923590, year = {2026}, author = {Liu, Z and Hui, C and Zhang, G and Yang, H and Wang, Y and Shi, Y and Wang, C and Liu, Y and Gao, X and Wen, Y}, title = {Tanshinones from Salvia miltiorrhiza alleviate ulcerative colitis via reprogramming the gut microbiota-metabolite axis.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2026054}, pmid = {41923590}, issn = {1745-7270}, abstract = {The anti-inflammatory properties of the traditional herb Salvia miltiorrhiza Bunge are well-established, yet its precise mechanism of action in ulcerative colitis (UC) remains unclear. Herein, we evaluate the therapeutic potential of four major tanshinones-tanshinone IIA (Tan IIA), miltirone, neocryptotanshinone, and dihydrotanshinone I-in a murine dextran sulfate sodium (DSS)-induced colitis model. Our results show that tanshinones effectively alleviate disease severity, suppress systemic and local inflammation, and restore intestinal barrier integrity. Integrated multi-omics analysis reveals that the therapeutic efficacy originates from a comprehensive reprogramming of the gut microbiota-metabolite axis. Specifically, tanshinones reverse colitis-associated dysbiosis and rectify metabolic disturbances in linoleic acid metabolism, bile acid biosynthesis, and amino acid utilization. Correlation network analysis identifies key functional modules linking beneficial microbes (e. g., Akkermansia) to anti-inflammatory lipid mediators and associating pathobionts (e . g., Desulfovibrio) with disrupted bile acid metabolism. Notably, supplementation with Akkermansia muciniphila synergizes with Tan IIA to amplify barrier restoration and metabolic normalization. Our findings establish that tanshinones ameliorate UC through microbiota-driven metabolic reprogramming, wherein the restructured microbial community actively shapes a therapeutic metabolic output. This work elucidates a metabolite-mediated mechanism of action and positions tanshinones as promising microbiome-targeting therapeutics for inflammatory bowel disease.}, }
@article {pmid41923636, year = {2026}, author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.011}, pmid = {41923636}, issn = {1934-6069}, abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.}, }
@article {pmid41923890, year = {2026}, author = {Willis, DN and Dubberke, ER and Hayashi, RJ and Tarr, PI and Haslam, DB and Hink, T and Luo, J and Tao, Y and Padhye, A and Hall, EM and Storch, GA}, title = {Clostridioides difficile Colonization and Infection in Pediatric Oncology and Stem Cell Transplant Patients.}, journal = {Open forum infectious diseases}, volume = {13}, number = {4}, pages = {ofag149}, pmid = {41923890}, issn = {2328-8957}, abstract = {BACKGROUND: Pediatric oncology and hematopoietic stem cell transplant (HSCT) patients have elevated risk for Clostridioides difficile infection (CDI), which can prolong hospitalization and delay chemotherapy. Colonization is an important prelude to symptomatic CDI. We sought to characterize colonization status in these patients.<br><br>METHODS: We retrospectively studied 276 stools longitudinally collected over 34 months from 32 HSCT and 12 oncology patients treated at a single tertiary center. Specimens were cultured for C difficile and compared by whole genome sequencing. The fecal microbiome was characterized by 16S rRNA gene sequencing.<br><br>RESULTS: Baseline cultures were positive in 16 (50%) HSCT patients and 2 (12%) oncology. On subsequent samples, 64% of patients who were initially negative acquired colonization: 8 of 15 (53%) HSCT and 8 of 10 (80%) oncology. Nine clonal strains and 25 multilocus sequence types were identified by whole genome sequencing, with 4 clones found in both cohorts. Nine patients had different strains at different time points. Seven clonal strains were found in multiple patients. Seven (15.9%) patients had symptomatic CDI. C difficile-positive stools had greater microbial diversity than negative stools in both the oncology cohort (Simpson diversity index, 0.07; 95% CI, .01-.14; P = .03) and the HSCT cohort (0.15; 95% CI, .07-.24; P < .001).<br><br>CONCLUSIONS: C difficile acquisition and colonization are common in pediatric oncology and HSCT patients. The high prevalence of clonally related strains in multiple patients suggests that asymptomatic patients may be important reservoirs of this pathogen and lead to symptomatic CDI in some patients. Gut microbial composition may influence the risk of colonization.}, }
@article {pmid41924284, year = {2026}, author = {Tao, YL and Wu, XX and Wang, JR and Liu, M and Liu, YN and Lian, YQ and Liang, ZY and Zhu, SF}, title = {The microbiome: regulating anti-tumor immunity.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1781872}, pmid = {41924284}, issn = {1664-3224}, mesh = {Humans ; *Neoplasms/immunology/microbiology/therapy ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Tumor Microenvironment/immunology ; }, abstract = {Microorganisms distributed throughout the human body have always been a complex ecosystem that has long coexisted with other organisms. They are involved in essential key links, such as nutrient absorption, energy regulation, metabolism, toxin clearance, and immune regulation. With a deeper understanding of the microbiome, many studies have shown that the microbiome is also actively involved in the occurrence and development of tumors. The core mechanism of dysregulated microorganisms and their derivatives in the treatment response and toxicity management of tumors is the regulation of the immune function. This article explores the evolution of the microbiome and its impact on the immune function during tumor progression, and focuses on analyzing cutting-edge treatment strategies targeting the microbiome, as well as future research directions and challenges in clinical translation.}, }
@article {pmid41924305, year = {2026}, author = {Kerff, F and Mühlematter, C and Adamov, A and Fast, D and Plüss, S and Zimmermann, P and Kurth, S and Bokulich, NA}, title = {The gut microbiota and sleep in infants: a focus on diurnal rhythmicity patterns.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2649096}, pmid = {41924305}, issn = {2993-3935}, abstract = {Emerging evidence supports a bidirectional relationship between the gut microbiome and sleep, which is partly mediated by the microbiota‒gut‒brain axis. Infancy is a critical window for the establishment of both the gut microbiome and sleep regulation, which we hypothesize to be linked across both short (diurnal) and long (monthly) time scales. In this longitudinal study, we investigated associations between gut microbiota development and sleep patterns in 20 infants at 2, 4, and 6 months of age (n = 163 samples). Infants were continuously monitored across 48-h sampling periods. The gut microbiota profiles were characterized using 16S rRNA gene sequencing; gut melatonin concentrations were measured; sleep data were collected via wearable actimetry, 24-h parent-reported sleep diaries, and the Brief Infant Sleep Questionnaire; and parenting style and behavioral development were assessed. In some infants, bacterial diversity followed diurnal rhythmic patterns. While bacterial rhythmicity was not significantly associated with sleep rhythmicity, infants with higher microbial alpha diversity showed more robust sleep patterns. Infant age emerged as the strongest predictor of gut microbial diversity and melatonin levels. Our findings suggest that gut microbial establishment may support the maturation of sleep‒wake rhythms in early infancy. Further research is needed to elucidate mechanistic roles of the gut microbiome in sleep development.}, }
@article {pmid41924306, year = {2026}, author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D}, title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2622259}, pmid = {41924306}, issn = {2993-3935}, abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.}, }
@article {pmid41924307, year = {2026}, author = {Bhagavata Srinivasan, SP and Kendig, MD and Hasebe, K and Kaakoush, NO and Morris, MJ and Leigh, SJ}, title = {Cafeteria diet exposure, and not weight gain propensity, impacts gut microbiota of rats - a within laboratory meta-analysis.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2649442}, pmid = {41924307}, issn = {2993-3935}, abstract = {Preclinical studies have implicated the microbiota in body weight control, but its translation to humans remains uncertain, partly owing to methodological variability in assessing the relationship between diet-induced obesity and microbiota composition. We performed an internal meta-analysis to determine whether the propensity for diet-induced obesity, defined by relative weight gain due to a high-fat, high-sugar "cafeteria" diet, is associated with changes in microbiota composition. We collated fecal microbiome data from 12 studies using our validated model of diet-induced obesity (208 male and 74 female Sprague-Dawley rats; 3.5-13 weeks of chow (control) or cafeteria diet) and determined whether the alpha diversity and composition of the gut microbiota differed between obese-prone and obese-resistant rats. We found consistent effects of cafeteria diet exposure on the microbiota, with marked changes in overall composition, and reduced microbial richness and evenness. Furthermore, specific obesity-associated microbial genera, such as Bacteroides and Blautia, were enriched by the cafeteria diet. Critically, alpha diversity measures and the gut microbiota composition did not differ between obese-prone and obese-resistant rats in either diet group. Our findings suggest that while the microbiota is substantially altered by cafeteria diet intake, these changes appear unrelated to individual susceptibility to weight gain, highlighting the role of additional host factors in modulating diet-induced obesity.}, }
@article {pmid41924422, year = {2026}, author = {Nazarova, V and Kamzayeva, N and Ukybassova, T and Kozhakhmetov, S and Kushugulova, A}, title = {Systems analysis of the HPV-microbiome-biofilm triad.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1767224}, pmid = {41924422}, issn = {2235-2988}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Microbiota ; Female ; *Papillomavirus Infections/microbiology/virology/immunology ; Dysbiosis/microbiology ; *Papillomaviridae/physiology ; Vagina/microbiology/virology ; Uterine Cervical Neoplasms/virology/microbiology ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) remains the leading cause of cervical cancer worldwide, however, its pathogenesis cannot be sufficiently explained by viral factors alone. Accumulating evidence highlights the critical role of cervicovaginal microbiome composition and biofilm formation in shaping viral persistence, epithelial barrier disruption and carcinogenic progression.<br><br>METHODS: This systems-based integrative synthesis analyzed peer-reviewed literature published between January 2000 and July 2025, retrieved from PubMed and Google Scholar with additional records identified through backward citation screening. The collected data were synthesized to construct a conceptual model of the HPV-microbiome-biofilm triad and to evaluate its clinical and biological implications.<br><br>RESULTS: The analysis indicates that depletion of Lactobacillus-dominated communities and expansion of anaerobic taxa, particularly Gardnerella vaginalis, are associated with biofilm development, chronic inflammation and immune modulation. These interrelated processes form self-reinforcing feedback loops that promote HPV persistence and reduce therapeutic efficacy. Microbiome dysbiosis and biofilm formation were further linked to impaired epithelial integrity, altered cytokine signaling pathways and clinically relevant phenotypes including immune escape, metabolic shifts and treatment non-responsiveness.<br><br>DISCUSSION: This systems perspective challenges reductionist pathogen-centered models and emphasizes the importance of integrating microbiome profiling and biofilm dynamics into cervical cancer risk stratification and therapeutic strategies. The coupled interactions between microbial communities, host immunity and viral persistence underscore the cervicovaginal ecosystem as an active regulator of disease progression rather than a passive bystander. Incorporating ecosystem-based parameters into clinical decision-making may enhance prognostic assessment and improve treatment outcomes, particularly in low- and middle-income countries where high HPV prevalence coincides with increased microbiome vulnerability.<br><br>https://www.crd.york.ac.uk/PROSPERO/, identifier CRD420251208178.}, }
@article {pmid41924474, year = {2026}, author = {Li, M and Dai, L and Yang, Y and Chen, S and Ma, J and Feng, P}, title = {Jinzhi and fecal microbiota transplantation: a comparative review of historical and modern microbial therapeutics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1700764}, pmid = {41924474}, issn = {1664-302X}, abstract = {Since its formal introduction in 1958, fecal microbiota transplantation (FMT) has gained prominence. However, challenges remain in standardizing protocols and optimizing efficacy. This review provides a systematic comparison between the historical practice of Jinzhi and modern FMT, focusing on their preparation methodologies. We hypothesize that specific, underexplored features of Jinzhi preparation could inform and refine current FMT practices. Specifically, we propose that the utilization of adolescent donors, underground low-temperature fermentation, and the careful consideration of seasonal timing, all integral to Jinzhi's traditional protocol, may offer novel insights and testable hypotheses for enhancing microbial diversity, functionality, and therapeutic stability in FMT. By bridging this ancient wisdom with modern microbiome science, we aim to outline a novel and actionable framework for developing the next generation of microbiota-based therapeutics, urging future research to empirically test these historically inspired hypotheses.}, }
@article {pmid41924483, year = {2026}, author = {Niu, Y and Wang, C and Kuang, Y and Ma, X and Nan, S and Zhang, P and Lu, Q and Qi, Y and Nie, C and Wu, Y and Zhang, W}, title = {Multi-omics insights into triticale silage as a sustainable alternative to corn silage in heifer diets.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761287}, pmid = {41924483}, issn = {1664-302X}, abstract = {BACKGROUND: Intensive ruminant production systems rely heavily on corn silage (CS) as a primary forage source; however, its resource-intensive cultivation and environmental constraints necessitate the development of sustainable alternatives.<br><br>METHODS: In a 90-day feeding trial, 24 growing heifers were assigned to diets in which CS was replaced by triticale silage (TS) at 0, 25, 50%, or 100% (DM basis). Growth performance, rumen fermentation, ruminal fatty acid (FA) profiles, and integrated rumen microbiome-metabolome interactions were evaluated.<br><br>RESULTS: A 25% substitution (TS25) as the optimal level, maintaining growth performance comparable to the control while achieving the lowest feed cost of gain. TS25 improved rumen fermentation (lower A: P and high total VFA), promoted more efficient nitrogen utilization (higher MCP with lower ammonia N), and enriched functionally relevant bacteria associated with fiber degradation and fermentation (e.g., Ruminococcus, Prevotella, and Rikenellaceae_RC9_gut_group). Consistently, TS inclusion shifted ruminal lipid metabolism, increasing UFA proportions and elevating PUFA (TS25 and TS50 increased PUFA by 15.2 and 23.7% vs. control), alongside metabolomic signals indicating upregulation of linoleic acid metabolism and aromatic amino acid biosynthesis pathways. In contrast, TS substitution &#x2265;50% reduced DMI and ADG, impairing feed utilization.<br><br>CONCLUSION: Partial replacement of CS with TS at 25% provides a practical, data-supported strategy to improve economic efficiency while maintaining productivity and promoting favorable rumen microbial-metabolic features. This feeding approach may be applicable in water-limited or double-cropping regions, where TS can enhance forage system sustainability without compromising heifer growth.}, }
@article {pmid41924563, year = {2026}, author = {Santoyo, G and Kumar, A and Orozco-Mosqueda, MDC and de Oliveira Mendes, G}, title = {Editorial: Role of endophytic/symbiotic fungi in plant growth promotion and disease suppression.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1820241}, pmid = {41924563}, issn = {2673-6128}, }
@article {pmid41924635, year = {2026}, author = {Graspeuntner, S and Lupatsii, M and Hamala, N and Masuch, A and Depenbusch, M and Pfeffer, I and Schultze-Mosgau, A and Eggersmann, TK and Rupp, J and Griesinger, G}, title = {Vaginal microbial community state types fail to predict IVF outcomes, whereas Ureaplasma parvum and Lactobacillus iners are negative predictors of implantation, clinical pregnancy, and live birth.}, journal = {Human reproduction open}, volume = {2026}, number = {2}, pages = {hoag018}, pmid = {41924635}, issn = {2399-3529}, abstract = {STUDY QUESTION: Are previously proposed vaginal microbial community state types (CSTs) valid predictors of IVF success, or do alternative microbial signatures provide stronger associations?<br><br>SUMMARY ANSWER: Previously proposed CSTs as predictors of implantation, clinical pregnancy, and live birth were not confirmed, while an interaction between Ureaplasma parvum and Lactobacillus iners emerged as a strong negative predictor.<br><br>WHAT IS KNOWN ALREADY: Infertility affects 17% of the global population. Only one-third of treatment cycles of assisted reproductive technologies result in embryo implantation, and even fewer lead to clinical pregnancy or live births. While early findings have spurred the development of microbiome-based tests for success prediction, evidence on supporting their reliability remains inconclusive.<br><br>STUDY DESIGN SIZE DURATION: This prospective, single-centre study aimed to validate existing, and identify better, microbial predictors of infertility treatment outcomes. A cohort of 266 infertile female patients (age 18-45&#x2009;years) undergoing a frozen-thawed embryo transfer cycle in an anovulatory regimen (i.e. a cycle with transfer of an embryo following a previous oocyte retrieval, fertilization, and freezing of embryos) was recruited for the study within&#xa0;a timeframe from May 2017 to March 2019.<br><br>The female, infertile patients, aged 18-45&#x2009;years, were undergoing routine care. Vaginal swabs were taken prior to embryo transfer and subjected to DNA isolation for 16S-based microbiota analysis. Extended demographic and treatment data were recorded. Clinical outcomes were defined as: (i) implantation, confirmed by a positive hCG test, (ii) clinical pregnancy, and (iii) live birth (defined as the birth of a viable infant). Sequencing data were processed in mothur following established pipelines, and microbial composition (taxonomy) as well as microbial diversity (dissimilarity analyses) were determined using the open-source software R. A prediction model for implantation success was built using binary logistic regression based on abundance of putatively predictive microbial taxa.<br><br>This study suggests that vaginal microbial CSTs, alpha-diversity, and the ratio of dominant Lactobacillus species do not correlate in statistical terms or in a clinically meaningful manner with implantation and clinical pregnancy (as a surrogate for endometrial receptivity) or with live birth (as a surrogate for ongoing pregnancy viability). However, Ureaplasma parvum and Lactobacillus iners abundances were identified as negative predictors of embryo implantation, clinical pregnancy, and live birth. A subset of women colonized by these taxa experienced drastically reduced embryo implantation and completely failed to achieve clinical pregnancy or give birth to live offspring, suggesting a potential role of these organisms in implantation failure and reproductive outcome, independent of other influencing factors such as age, oestradiol levels, endometrial thickness etc.<br><br>LARGE SCALE DATA: The raw sequencing data used for this manuscript are publicly available at the European Nucleotide Archive under accession number PRJEB107113.<br><br>This study is a single-centre study warranting further validation cohorts. Given the variable nature of the vaginal microbiota, sample sizes need to be enlarged for better refinement of the analyses. Further, the underlying mechanistical basis of our findings is yet elusive and clinical translation has yet to be established.<br><br>While this novel association warrants confirmation, the results caution against reliance on previously suggested CSTs as predictors, and highlight the need for refined, reproducible microbiome-based diagnostics in reproductive medicine.<br><br>Financial support was received from the University of L&#xfc;beck and the German Center of Infection Research. M.L., A.M., I.P., M.D., and J.R. declare no conflicts of interest. S.G. discloses personal fees from Organon outside the submitted work. T.K.E. discloses honoraria from Ferring; travel support from Ferring, Merck, Theramex, and Gedeon-Richter; and receipt of equipment/materials/laboratory analyses (to institution) from Arthrex, Besins, Merck, and Abbott outside the submitted work. N.H. discloses personal fees from Gedeon Richter, Ferring, and Merck. G.G. reports that his institution received grants or contracts from Besins, Merck, Abbott, Ferring, and Theramex. He has received personal consulting fees, support for travel fees and meeting attendance, and honoraria for lectures or educational events from Organon, Ferring, Merck, Gedeon-Richter, Theramex, Abbott, ReproNovo, Igyxos, OxoLife, Philipps, ReprodWissen, PregLem, Guerbet, Roche, IBSA, and Besins. He also received support for travel and meeting attendance from Merck, Organon, Ferring, Theramex, Gedeon-Richter, and Abbott. Additionally, he holds unpaid leadership positions as a member of the ESHRE Working Group on RIF, the ESHRE Working Group on clinical KPI, and the ESHRE guideline development group on ovarian stimulation. A.S.-M. reports consulting fees and speaker's fees from Merck, Theramex, and Gedeon-Richter as well as travel support from Merck, Theramex, Gedeon-Richter, IBSA, Ferring, and MSD.}, }
@article {pmid41924822, year = {2026}, author = {Gamage, MAGNDMA and Dissanayake, WMN and Yi, YJ}, title = {Response of the mTOR signaling pathway to the reproductive dysfunction of dysbiosis-induced male mice.}, journal = {Reproductive biology}, volume = {26}, number = {2}, pages = {101213}, doi = {10.1016/j.repbio.2026.101213}, pmid = {41924822}, issn = {2300-732X}, abstract = {The mammalian target of rapamycin (mTOR) signaling pathway plays a key role in coordinating several cellular activities in response to environmental signals, thereby influencing metabolism and reproduction. This study aimed to determine the role of mTOR signaling pathway in testicular dysfunction caused by intestinal microbiome imbalance. An antibiotic mixture containing ampicillin, neomycin sulfate, vancomycin, and metronidazole was administered orally to mice for four weeks, and subsequently serum, and tissues were obtained following sacrifice. Glucose, cholesterol, and sex hormone levels were measured in the serum, and real-time PCR was performed using extracts of the ileum and testis to determine the expression of genes associated with pro-inflammatory cytokines, mTOR signals and testosterone synthesis. The levels of glucose and sex hormones in the serum of antibiotic-induced dysbiosis (WD) mice were significantly decreased, while the cholesterol levels were elevated (p < 0.05). The mRNA expression of IL-1β, IL-6 and TNF-α significantly increased in the testis of the WD group (p < 0.05 &amp; p < 0.01), while testosterone synthesis, such as the expression of 3β-HSD and P450scc decreased (p < 0.05). Immunofluorescence revealed the localization of mTOR in the mid-piece and tail of the epididymal spermatozoa. The mRNA expression of mTOR signaling pathway, including Mtor, Raptor, p53, PI3K, Akt1, P70s6k, and Rheb, was significantly upregulated in the testis of the WD group (p < 0.05). Consequently, antibiotic-induced dysbiosis in male mice led to increased secretion of pro-inflammatory cytokines in the testis, decreased serum sex hormone levels, and impaired sperm quality, all of which could be associated with altered regulation of the mTOR signaling pathway.}, }
@article {pmid41925161, year = {2026}, author = {Bergemann, CM and Jameson, LE and Kenny-Ganzert, IW and Huayta, J and Castellano-Escuder, P and Sarkar, A and Ilkayeva, OR and Sherwood, DR and Hirschey, MD and Meyer, JN}, title = {Caenorhabditis elegans fed native gut microbiota have altered bioenergetic pathway utilization impacting mitochondrial function and susceptibility to pollutants.}, journal = {Environmental science. Processes &amp; impacts}, volume = {}, number = {}, pages = {}, pmid = {41925161}, issn = {2050-7895}, support = {P42 ES010356/ES/NIEHS NIH HHS/United States ; R01 ES034270/ES/NIEHS NIH HHS/United States ; R35 GM118049/GM/NIGMS NIH HHS/United States ; T32 ES021432/ES/NIEHS NIH HHS/United States ; }, abstract = {The gut microbiome can influence host health by facilitating digestion, immune function, and xenobiotic metabolism. Microbial metabolites can influence mitochondrial function by shifting bioenergetic pathways, potentially altering sensitivity to mitochondrial toxicants. However, mechanisms through which the gut microbiota can alter mitochondrial function and susceptibility to mitochondrial toxicity are not well characterized. We used the model organism Caenorhabditis elegans and the microbiome kit CeMbio, a characterized collection of native gut commensals, to explore the interactions between gut microbiota, mitochondrial function, and chemical susceptibility. C. elegans grown on selected bacterial strains had varying levels of steady-state whole-body ATP, with an ∼3 fold difference between the highest and lowest strains, as well as 2- and 3-fold changes in antioxidant and mitochondrial unfolded protein gene induction. Further, C. elegans grown on selected bacterial strains showed differential sensitivity to short-term exposure to chemicals that inhibit mitochondrial electron transport chain Complexes I, II, and V, and fatty acid oxidation. To test mechanistically how microbiome-mediated sensitivities could result in chemical susceptibility, we carried out follow-up experiments using the Complex I inhibitor rotenone. We found that C. elegans grown on BIGb0170 (Sphingobacterium multivorum) had much higher lethality after 24- and 48-hour exposures than when grown on MYb10 (Acinetobacter guillouiae), MYb11 (Pseudomonas lurida), and OP50 (Escherichia coli) strains. Metabolomic analysis revealed that C. elegans grown on BIGb0170 had lower amounts of triglycerides and acylcarnitines. ATP levels were partially rescued by supplementing BIGb0170 with pyruvate. This work suggests that BIGb0170 can impact mitochondrial function through changes in metabolite abundance, which can increase sensitivity to the Complex I inhibitor rotenone.}, }
@article {pmid41925202, year = {2026}, author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Cohen, NA and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N}, title = {Phage-display immunoprecipitation sequencing reveals distinct antibody signatures against bacterial flagellins associated with treatment response in Crohn's disease.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000001030}, pmid = {41925202}, issn = {2155-384X}, abstract = {OBJECTIVES: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.<br><br>METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index [HBI]>4 or fecal calprotectin [FCP]>150&#x3bc;g/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22 and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.<br><br>RESULTS: Using PhIP-Seq analysis, only the anti-flagellin antibodies library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (HBI&#x2264;4 and FCP&#x2264;150) versus non-remission at all time points (p<0.05). Of the 55 anti-flagellin antibodies analyzed, 15 showed consistent >1.5-fold over-representation in non-remission samples, with high conservation of amino-acid sequences and targeting of Clostridiales, Lachnospiraceae, or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while non-remission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semi-essential amino acids biosynthesis (q<0.05).<br><br>CONCLUSIONS: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.}, }
@article {pmid41925227, year = {2026}, author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y}, title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag068}, pmid = {41925227}, issn = {1751-7370}, abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.}, }
@article {pmid41925420, year = {2026}, author = {Leroy, S and Roméo, B and Belaid, A and Brest, P and Marquette, CH and Vouret-Craviari, V and Hofman, V and Hofman, P and Mograbi, B}, title = {Harnessing the lung microbiome for precision management of fibrotic lung disease.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2026.02.002}, pmid = {41925420}, issn = {1471-499X}, abstract = {Interstitial lung diseases, particularly idiopathic pulmonary fibrosis (IPF), have dismal prognoses, with a median survival of 3-5 years, owing to a lack of early biomarkers or effective treatments. This review highlights the lung microbiome as a key biological factor in IPF pathogenesis and a promising therapeutic target. Elevated burdens of pathogenic bacteria, including Streptococcus and Staphylococcus, in bronchoalveolar lavage fluid correlate with accelerated progression and higher mortality. These bacteria release toxins and activate Th17-driven inflammation, providing mechanistic links to alveolar injury and fibrosis. Host genetics and systemic factors, including oral-gut-lung interactions, further shape disease progression. Although antibiotic trials have been unsuccessful, embracing the microbiome as an active participant in IPF may open unprecedented opportunities for personalized interventions.}, }
@article {pmid41925447, year = {2026}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {The rhizosphere microbiome as a decentralized immune system.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.006}, pmid = {41925447}, issn = {1878-4380}, abstract = {Plant immunity should be reconsidered beyond the boundaries of the plant genome. We propose that the rhizosphere microbiome may function analogously to a decentralized immune system, contributing adaptive defenselike properties and memory effects. In this forum article, we discuss how this perspective reframes immunity as an emergent property of plant-microbiome interactions, shifting the focus from a solitary host toward an integrated holobiont.}, }
@article {pmid41925964, year = {2026}, author = {Oriquat, G and H, M and Maharana, L and Dhyani, A and Al-Hasnaawei, S and Singh-Chauhan, A and Arora, V and Sharma, J and Sadeghi-Samarjan, R}, title = {The Gut Microbiome in Amyotrophic Lateral Sclerosis: Emerging Mechanisms and Therapeutic Potential.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {41925964}, issn = {1559-1182}, mesh = {*Amyotrophic Lateral Sclerosis/microbiology/therapy ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Dysbiosis ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder marked by progressive loss of motor neurons and a median survival of 2 to 3 years after symptom onset. Despite advances in genetics, particularly the identification of mutations in C9ORF72, SOD1, and TDP 43, substantial variability in disease onset and progression remains unexplained. Mounting evidence points to the gut microbiome as a potential modifier of ALS biology. Microbial communities within the intestine influence systemic and central immune responses, energy metabolism, and the bioavailability of nutrients and therapeutic agents. Animal studies reveal that dysbiosis contributes to intestinal barrier dysfunction, immune activation, and altered metabolite production, while supplementation with beneficial metabolites such as butyrate or nicotinamide can delay disease progression and extend survival. Human studies, though inconsistent in their findings, consistently identify microbial imbalances and loss of diversity in subsets of patients. The gut-brain axis provides a plausible framework for these effects, as microbial products can signal through endocrine, neural, and immune pathways to influence central nervous system function. Beyond motor decline, microbiota alterations may also contribute to non-motor symptoms such as depression, anxiety, and gastrointestinal dysfunction, further shaping quality of life. While methodological variability complicates interpretation, integration of microbiome research with host genomics and metabolomics offers a path toward precision medicine. Targeting microbial composition and function may ultimately represent a novel therapeutic approach capable of modifying both disease biology and patient outcomes in ALS.}, }
@article {pmid41926038, year = {2026}, author = {Haykal, D and Flament, F and Balooch, G and Mora, P and Kovylkina, N and Calixto, LS and Mercurio, DG and Sachdev, M and Sundaram, H}, title = {Integrative Dermatology for Longevity: The Synergy of Topical and Internal Approaches.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {41926038}, issn = {2193-8210}, abstract = {Skin aging reflects both intrinsic biological decline and extrinsic influences collectively known as the skin exposome, including ultraviolet (UV) radiation, air pollution, psychosocial stress, fatigue, sleep disruption, and suboptimal lifestyle behaviors. These factors contribute to cumulative molecular and structural damage, positioning the skin as both a visible marker of whole-body aging and a target for longevity strategies. This review examines the validity of an integrative "In and Out" approach, combining topical treatments, such as retinoids, peptides, antioxidants, and exosome-based formulations, with internal nutraceuticals including NAD[+] precursors, collagen peptides, polyphenols, and microbiome modulators. By targeting key hallmarks of aging, oxidative stress, inflammation, and epigenetic changes, this dual-modality model has the potential to promote skin regeneration, enhance aesthetic and functional outcomes, and contribute to broader health span optimization. Emerging tools such as skin aging clocks, biomarker-driven personalization, and artificial intelligence (AI)-guided interventions further strengthen this paradigm, establishing a scientifically grounded, preventive, and personalized framework that redefines the role of dermatology in the context of longevity. Personalized strategies that integrate diagnostic tools, lifestyle coaching, and tracking technologies allow for adaptive, dynamic strategies both internally and externally.}, }
@article {pmid41926198, year = {2026}, author = {Grotzinger, H and Martínez-García, M and Miller, EC and Stelzer, IA and Collado, MC and Jacobs, EG}, title = {The Maternal Brain in Context: Systemic Physiological Changes Across Pregnancy.}, journal = {Annual review of neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-neuro-102124-043515}, pmid = {41926198}, issn = {1545-4126}, abstract = {During pregnancy, the maternal body undergoes profound, coordinated physiological adaptations to support the developing fetus, including major shifts in immune regulation and dramatic changes in the vascular system. Accompanying these peripheral adaptations, recent longitudinal studies in humans point to significant remodeling of the nervous system, occurring in lockstep with increases in gonadal hormone production. To understand the neural adaptations tied to pregnancy and the postpartum period, a holistic approach is essential-one that accounts for changes across multiple peripheral systems. In this review, we consider the impact of the endocrine, cardiovascular, microbiome, and immune systems on the maternal brain. By adopting this integrative approach, we aim to better understand the biological pathways that shape the maternal brain during normative pregnancies and those marked by adverse events.}, }
@article {pmid41926522, year = {2026}, author = {Chen, Y and Zhou, D and Tu, Y and Wang, Y}, title = {Analysis of the Impact of Preterm Premature Rupture of Membranes (PPROM) on Maternal and Infant Outcomes and Countermeasures.}, journal = {International journal of women's health}, volume = {18}, number = {}, pages = {534571}, pmid = {41926522}, issn = {1179-1411}, abstract = {OBJECTIVE: This study aimed to analyze the risk factors for Preterm Premature Rupture of Membranes (PPROM) and evaluate the impact of the timing of antibiotic administration on maternal and neonatal outcomes.<br><br>METHODS: A retrospective cohort study was conducted involving 480 pregnant women (240 with PPROM and 240 without PPROM) hospitalized between January 2021 and December 2022. Maternal data, genital microbiome profiles, and pregnancy outcomes were collected and compared. Within the PPROM group, patients were subdivided into an Early Treatment group (received intravenous cefuroxime sodium within 12&#xa0;hours of membrane rupture, n=120) and a Late Treatment group (received antibiotics after 12&#xa0;hours, n=120). Statistical analyses were performed using SPSS 22.0.<br><br>RESULTS: Genital infections (73.8% vs 20.4%, p<0.001) and gestational diabetes mellitus (GDM; 53.3% vs 22.9%, p<0.001) were significantly more prevalent in the PPROM group and were identified as independent risk factors (Genital infections: OR=3.895; GDM: OR=11.166). The PPROM group had worse outcomes, including a higher cesarean section rate (39.2% vs 25.8%, p=0.002) and higher incidences of neonatal asphyxia (4.2% vs 0.4%, p=0.006) and sepsis (2.5% vs 0%, p=0.040). Compared to the Late Treatment group, the Early Treatment group demonstrated significantly lower rates of intrauterine infection (1.67% vs 7.50%, p<0.05), cesarean section (30.0% vs 48.3%, p<0.05), neonatal asphyxia (0.83% vs 7.50%, p<0.01), and neonatal sepsis (0% vs 5.00%, p<0.05).<br><br>CONCLUSION: Genital tract infections and GDM are significant risk factors for PPROM. Early administration of antibiotics within 12&#xa0;hours of membrane rupture is associated with substantially improved maternal and neonatal outcomes, underscoring its critical importance in clinical management.}, }
@article {pmid41926667, year = {2026}, author = {Chen, Y and Duan, R and Zhang, C and Li, G and Ji, X and Zhang, Q and Pei, F and Wang, K and Duan, L}, title = {Maternal Preconception Antibiotic Exposure Disrupts Microbial Succession: A Transgenerational Risk for Offspring Gut Mucosal Immaturity and Colitis Susceptibility.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e16931}, doi = {10.1002/advs.202516931}, pmid = {41926667}, issn = {2198-3844}, support = {2021YFA1301300//National Key R&amp;D Program of China/ ; 82470578//National Natural Science Foundation of China/ ; 7254451//Beijing Natural Science Foundation/ ; }, abstract = {The early-life microbiome plays a pivotal role in host development and lifelong health. Maternal factors are increasingly recognized as crucial in shaping offspring microbiome. However, how maternal preconception perturbations affects offspring health remain unclear. Thus, we combined animal and clinical data to elucidate whether preconception microbial perturbations disrupt microbial succession and increase offspring susceptibility to colitis. In animals, preconception antibiotic exposure induced long-lasting disruptions in offspring microbial ecology, through enhanced maternal-offspring microbial transmission, altered microbial developmental trajectories, and increased selective pressures during microbial community assembly. Ultimately, these alterations resulted in persistent gut mucosal immaturity and heightened susceptibility to colitis in adulthood. Complementary clinical studies revealed concordant alterations in gut microbiome and metabolome of children with inflammatory bowel disease (IBD) and their seemingly healthy mothers, characterized by pro-inflammatory taxa and metabolites. Notably, mothers of IBD children reported significantly higher antibiotic exposure than controls, which was also associated with enhanced maternal-offspring microbial transmission and increased selective pressures during microbial community assembly. Our findings reveal a potential intergenerational mechanism in which preconception perturbations are associated with disrupted microbial succession, transgenerational propagation of gut mucosal immaturity, and susceptibility to colitis. These results underscore the importance of judicious antibiotic use during the often-overlooked preconception period.}, }
@article {pmid41926670, year = {2026}, author = {Chen, F and Yu, Y and Cai, X and Lin, J and Liang, R and Kang, R and Tang, D and Liu, J}, title = {Immune Checkpoint Inhibitors and Immunomodulators for Cancer Immunotherapy: Insights Into Resistance and Therapeutic Strategies.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e21355}, doi = {10.1002/advs.202521355}, pmid = {41926670}, issn = {2198-3844}, support = {32500653//National Natural Science Foundation of China/ ; 20261A031076//Guangzhou Health Science and Technology Young Talents Cultivation Program/ ; 2025M782596//China Postdoctoral Science Foundation/ ; GZC20251317//Postdoctoral Fellowship Program of China Postdoctoral Science Foundation/ ; 2024A03J0895//Guangzhou Municipal Science and Technology Bureau/ ; }, abstract = {Cancer immunotherapy has redefined cancer treatment. However, the molecular and cellular basis of immune evasion and therapeutic resistance remains incompletely understood. Early immune checkpoint inhibitors have delivered significant clinical benefit, but their efficacy and durability remain limited in many patients. These limitations have driven the exploration of next-generation immune checkpoints and additional regulatory pathways that shape tumor-immune interactions. Recent advances have broadened the immune checkpoint landscape and revealed new targets. These targets operate within interconnected networks shaped by tumor-intrinsic alterations, microenvironmental cues, the microbiome, and neuroimmune crosstalk. The application of emerging technologies has enabled high-resolution dissection of immune-tumor dynamics, providing a technological foundation for improving clinical outcomes through precise patient stratification and intervention. Furthermore, distinct regulated cell deaths, including apoptosis, ferroptosis, pyroptosis, necroptosis, and alkaliptosis, are increasingly recognized as critical modulators of antitumor immunity. Harnessing these mechanisms offers a rational path toward designing targeted and controllable therapeutic strategies that enhance the efficacy and durability of cancer immunotherapy.}, }
@article {pmid41926812, year = {2026}, author = {Santana, DAD and Rolinski, F and Trombetta, LG and Göhringer, RMD and Lipinski, LC and Weber, SH and Sotomaior, CS and Ollhoff, RD}, title = {Humic acid supplementation modulates ruminal and fecal microbial communities in lamb.}, journal = {Research in veterinary science}, volume = {205}, number = {}, pages = {106166}, doi = {10.1016/j.rvsc.2026.106166}, pmid = {41926812}, issn = {1532-2661}, abstract = {The gastrointestinal microbiome affects the health and productivity of animals. Modifying these traits with additives may enhance their effects, making it a relevant strategy. This study investigated the effects of humic acids (HA) on the ruminal and fecal microbiomes of lambs and its potential adherence to ruminal mucosa. Twenty weaned Hampshire Down crossbred lambs aged 102.1 ± 6.6 days with an average body weight of 24.2 ± 3.5 kg were randomly allocated into two groups. Control group was fed a basal diet without HA, and treatment group was fed a basal diet with commercial HA at a dose of 500 mg/kg BW/day for 56 days. At the end of the experiment, ruminal and fecal samples were analyzed using 16S rRNA gene sequencing, and ruminal mucosal tissue from the slaughtered lambs was evaluated using histology and scanning electron microscopy (SEM). The addition of HA to the feed of lambs increased the relative abundance of the genus Bifidobacterium and decreased the genus Lachnospiraceae CAG-127 in the ruminal microbiome of lambs. Furthermore, an increase in the relative abundance of the genera Acutalibacteraceae UBA5905 and Lachnospiraceae VUNI01, along with a reduction in the order Campylobacterales and the genus Acutalibacteraceae CAG-180 was observed in the fecal microbiome. HA was not found in the ruminal mucosa of lambs, as determined by histology or SEM. HA supplementation modulated the ruminal and fecal microbiomes of lambs by reducing harmful and increasing beneficial bacteria, highlighting its potential as a functional feed additive to support ovine gut health.}, }
@article {pmid41926825, year = {2026}, author = {Ali Ahmad, F and Salam, DA}, title = {Microbial community dynamics and functional potential in response to organic micropollutants in river sediments.}, journal = {Marine pollution bulletin}, volume = {229}, number = {}, pages = {119679}, doi = {10.1016/j.marpolbul.2026.119679}, pmid = {41926825}, issn = {1879-3363}, abstract = {Freshwater river sediments are increasingly exposed to complex mixtures of anthropogenic contaminants, yet the ecological repercussions on indigenous microbial communities -the main drivers of biogeochemical cycling- remain poorly understood. Previous investigations have focused primarily on contaminant occurrence, with no integrated assessment linking sediment contamination to microbial community structure and function. The objective of this study is to characterize the microbiome of the Upper Litani River Basin and to determine how chronic inputs of pharmaceuticals and aromatic hydrocarbons influence taxonomic composition, diversity, and predicted metabolic functions. 54 sediment samples were collected across nine locations during consecutive wet and dry seasons. Target organic micropollutants were quantified in the river sediments using validated analytical methods, and spatiotemporal patterns in microbial composition and metabolic functional potential were determined using amplicon sequencing. Across all samples, 45 phyla were identified, with Pseudomonadota, Bacillota, and Actinomycetota consistently being the dominant taxa. At the genus level, microbial communities were dominated by Acinetobacter, Exiguobacterium, Proteiniclasticum, Planococcus, and Clostridium sensu stricto. Variations in microbial community structure were correlated with the occurrence and concentrations of specific organic micropollutants detected in the sediments, namely with the pharmaceuticals ibuprofen, clomipramine and atenolol, as well as the hydrocarbons o-xylene and toluene. Functional predictions revealed a microbiome highly oriented toward chemoheterotrophic metabolism, underscoring the community's response to persistent organic enrichment. Collectively, these results demonstrate that pollutant concentrations and chemical profiles act as a major ecological force that shapes sediment microbial community dynamics and metabolic function in impacted freshwater ecosystems.}, }
@article {pmid41926978, year = {2026}, author = {Masson, L and Radzey, N and Abrahams, AG and Ngcapu, S and McKinnon, L and Jaspan, HB}, title = {The vaginal microbiome and HIV acquisition risk.}, journal = {The lancet. HIV}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2352-3018(26)00032-9}, pmid = {41926978}, issn = {2352-3018}, abstract = {Non-optimal vaginal bacteriomes, vulvovaginal candidiasis, and sexually transmitted infections have been associated with increased risk of HIV acquisition in multiple clinical studies. However, there are still major gaps in our understanding of the role of the vaginal microbiome in HIV acquisition risk and non-bacterial components of the vaginal microbiome are not well characterised. Additionally, the functional interactions between the vaginal microbiome and its host that can result in increased risk of HIV acquisition are not fully understood. Better vaginal microbiome diagnostics and therapeutics feasible for implementation in settings with insufficient financial, human, and infrastructural resources are needed, and the effects of vaginal microbiome interventions on HIV risk need to be clinically evaluated. Progress is being made towards effective interventions through advanced omics technologies and improved in-vitro models that more accurately represent the complexity of the female genital tract. However, continued research and investments are needed to address this important women's health issue.}, }
@article {pmid41927358, year = {2026}, author = {Cummings, LC and Freedman, SD}, title = {Increased gastrointestinal cancer risk in cystic fibrosis: Screening, prevention, and future directions.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.03.024}, pmid = {41927358}, issn = {1873-5010}, abstract = {The marked improvement in life expectancy from advances in treatment for cystic fibrosis has focused attention on diseases of aging. Cystic fibrosis (CF) is associated with increased risk for digestive system malignancies, including colorectal cancer and pancreaticobiliary cancers. Although risk factors for gastrointestinal malignancy include solid organ transplant and older age, people with CF may present with cancer at a younger age than the general population. Potential mechanisms for increased digestive cancer susceptibility include the underlying genetic defect, dietary patterns, or alterations in the gut microbiome. The impact of cystic fibrosis transmembrane regulator modulator therapies on gastrointestinal cancer risk remains unclear. Our review summarizes the previously published consensus screening recommendations for colorectal cancer, which endorsed starting colonoscopy at age 30 in patients with history of transplant and at age 40 in patients without a transplant. Recent work evaluating the use of non invasive testing for colorectal cancer is reviewed. We propose screening practices for non-colorectal cancers based on the limited evidence to date. We discuss potential preventative approaches and conclude with future directions to improve our ability to address this growing problem. Future work should focus on a greater understanding of the underlying mechanisms of pathogenesis at a molecular level, clinical risk factors for gastrointestinal malignancies at a population level, and preventative strategies.}, }
@article {pmid41927378, year = {2026}, author = {Cai, Z and Han, C}, title = {Letter to the Editor re: "Age-related changes in the urinary microbiome of healthy Japanese children".}, journal = {Journal of pediatric urology}, volume = {}, number = {}, pages = {105884}, doi = {10.1016/j.jpurol.2026.105884}, pmid = {41927378}, issn = {1873-4898}, }
@article {pmid41742032, year = {2026}, author = {Zhang, J and Dai, Y and Mustafa, A and Li, L and Li, Y and Sun, T and Chen, M and Yang, H and Ma, J}, title = {Terracing influences soil microbial assembly in citrus orchards: stochastic processes dominate community dynamics in a karst sloping land.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41742032}, issn = {1471-2180}, support = {GUIKE AB22080071//Guangxi Key Research and Development Program/ ; AA20161002//Science and Technology Major Project of Guangxi/ ; }, abstract = {BACKGROUND: Terracing is a key soil conservation practice in karst citrus orchards, yet its long-term effects on rhizosphere microbial community assembly remain poorly understood, especially the relative influence of deterministic (e.g., environmental filtering) versus stochastic processes (e.g., dispersal limitation).<br><br>RESULTS: We investigated rhizosphere soil microbial communities along a terrace chronosequence (0&#x2013;12&#xa0;years) in the Lijiang River Basin using MiSeq sequencing and metabolomics, with null model analysis employed to assess community assembly processes. Terrace age did not significantly affect microbial &#x3b1;-diversity, but was associated with subtle changes in community composition: Proteobacteria, a copiotrophic group, decreased slightly, while Chloroflexi, an oligotrophic group, increased modestly. These shifts suggest a weak trend toward lower soil nutrient availability rather than a clear successional reorganization. Microbial diversity and structure were significantly correlated with soil stoichiometric ratios and available phosphorus (p&#x2009;<&#x2009;0.05). Terracing also affected microbial network complexity and potential function. Potential functional profiling and metabolome data revealed that L-glutamine, a key nitrogen source, was negatively correlated with potential catabolic nitrate reduction (p&#x2009;<&#x2009;0.05). This relationship was most pronounced at the Y5 phase (peak diversity/network complexity), suggesting accelerated L-glutamine utilization tightly coupled with enhanced potential for dissimilatory nitrate reduction to maximize nitrogen-use efficiency during the successional climax. Notably, stochastic processes explained over 96% of the microbial assembly. Bacterial communities were primarily driven by homogenizing dispersal, while fungal communities followed undominated processes.<br><br>CONCLUSION: The prominence of stochasticity in our results complements current understanding of agricultural microbiome assembly, particularly emphasizing its vital role in fragile karst environments. We propose that optimizing terrace rotation intervals (e.g., every 5-year) could be a practical strategy to enhance nitrogen-cycling efficiency and support sustainable nutrient management in karst citrus cultivation.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04811-4.}, }
@article {pmid41749104, year = {2026}, author = {Baz, L}, title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41749104}, issn = {1471-2164}, abstract = {BACKGROUND: Archaea are a major domain of life that inhabit diverse and often extreme environments, contributing to biogeochemical cycles and participating in nutrient cycling within plant rhizospheric soils. This study applies metagenomic whole-genome shotgun sequencing to characterize the archaeal component of the rhizospheric microbiome associated with the wild plant species Moringa oleifera in Saudi Arabia.<br><br>RESULTS: Based on KEGG-annotated enzymes, Thaumarchaeota and Euryarchaeota emerged as the predominant archaeal phyla in the rhizosphere, with higher abundance than in bulk soil. The most abundant archaeal enzymes were assigned to metabolic pathways related to nitrogen and sulfur metabolism, carbon transformations, and responses to oxidative stress, indicating a putative contribution to nutrient turnover and stress-related functions. Network analysis further identified archaeal chemotaxis-related regulators and two-component sensor kinases linked to the root&#x2013;soil interface. Key enzymes detected included urease, glutamine synthetase, thiosulfate sulfurtransferase, and catalase-peroxidase.<br><br>CONCLUSIONS: These findings suggest that archaeal communities form a distinct functional module within the M. oleifera rhizosphere, potentially influencing soil nutrient dynamics and plant performance. The chief limitation is reliance on DNA-based metagenomic data from a single site and time point, without multi-omics or detailed soil characterization, restricting temporal and ecological generalization. Nonetheless, the dataset provides a genome-scale view of archaeal functional potential and offers testable directions for future experimental and process-oriented studies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12700-3.}, }
@article {pmid41896654, year = {2026}, author = {Li, Y and Fu, W and Xiang, Z and Zhao, M and Xie, X and Guo, W and Zhou, Y and Zheng, M and Yang, J}, title = {Characteristics of gut microbiota and metabolites in patients with metabolic dysfunction-associated steatotic liver disease and colorectal adenoma.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41896654}, issn = {2045-2322}, support = {2021J0252//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2025J0270//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2024B010//Innovation Fund for Postgraduate Education of Kunming Medical University/ ; 202501AY070001-088//Science and Technology Plan Project of Yunnan Provincial Department of Science and Technology/ ; 82160106//National Natural Science Foundation of China/ ; }, abstract = {UNLABELLED: Metabolic dysfunction-associated steatotic liver disease (MASLD) has become one of the most prevalent chronic liver conditions worldwide, with its incidence steadily rising. However, the underlying mechanisms linking MASLD to colorectal adenoma remain unclear, and the role of gut microbiota and metabolites in this association requires further investigation. This study aims to characterise the gut microbiota and metabolites in patients with MASLD and colorectal adenoma. A cohort of 58 MASLD patients was enrolled and stratified into two groups based on colorectal adenoma status: the MASLD with colorectal adenoma group (M-CA group, n = 30) and the MASLD without colorectal adenoma group (M-NCA group, n = 28). The gut microbial ecosystem in the M-CA group showed significant dysregulation, evidenced by a decreased Gut Microbiome Health Index (GMHI) and significantly increased Microbiome Dysbiosis Index (MDI). Linear Discriminant Analysis Effect Size (LEfSe) identified 75 differentially abundant microbial taxa between groups, with Bacteroides vulgatus, Bacteroides ovatus, uncultured bacterium of norank genus of Muribaculaceae family, Muribaculaceae, and norank of Muribaculaceae family being significantly enriched in the M-CA group, representing potential microbial biomarkers for this cohort. Partial Least Squares Discriminant Analysis (PLS-DA) screened 116 differential metabolites. When combined with Random Forest (RF), Support Vector Machine (SVM) and Least Absolute Shrinkage and Selection Operator (LASSO) machine learning algorithms, 16 significantly identified biomarkers were discovered. The joint analysis of both omics revealed that variations in differential metabolite levels were associated with changes in specific microbiota abundances. Kyoto encyclopedia of genes and genomes (KEGG) functional prediction analysis indicated that the coordinated alterations in metabolites and microbiota may collectively influence multiple metabolic pathways, including lipid metabolism, xenobiotics biodegradation and metabolism, amino acid metabolism, carbohydrate metabolism, biosynthesis of other secondary metabolites and nucleotide metabolism. This study revealed that patients with MASLD and colorectal adenoma exhibited significant alterations in the gut microbiota composition and metabolic profile, indicating potential impacts on associated metabolic pathways. These findings provided novel insights and a foundation for future research into potential intervention strategies for this clinical complication.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45782-w.}, }
@article {pmid41915463, year = {2026}, author = {Yasavoli-Sharahi, H and Shahbazi, R and Alsadi, N and Sahebi, NB and Cuenin, C and Cahais, V and Chung, FF and Herceg, Z and Matar, C}, title = {Lentinula edodes Cultured Extract Intake at Puberty Mitigates Inflammatory Signals at the Mammary Glands by the Involvement of Epigenetic Mechanisms in BALB/c Mice.}, journal = {The breast journal}, volume = {2026}, number = {1}, pages = {e2122220}, doi = {10.1155/tbj/2122220}, pmid = {41915463}, issn = {1524-4741}, support = {532223-18//Natural Sciences and Engineering Research Council of Canada/ ; 2019-01497//AHCC Research Association, and New Frontiers in Research Fund-Exploration (NFRF/ ; //University of Ottawa/ ; }, mesh = {Animals ; Female ; Mice ; Mice, Inbred BALB C ; *Epigenesis, Genetic/drug effects ; DNA Methylation/drug effects ; *Mammary Glands, Animal/drug effects/metabolism ; Lipopolysaccharides ; *Shiitake Mushrooms/chemistry ; Sexual Maturation ; MicroRNAs/metabolism ; *Inflammation ; }, abstract = {Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages like puberty may lead to gut microbiome dysbiosis and epigenetic dysregulation in mammary glands, affecting gene expression and potentially elevating breast cancer susceptibility in adulthood. Although LPS's adverse impacts on intestinal and brain functions are well-documented, its effects on mammary glands remain underexplored. Using an immunocompetent BALB/c mouse model, we administered an acute LPS dose (1.5 mg/kg body weight) during puberty. The study evaluated the long-term consequences of LPS exposure alone and combined with AHCC (Lentinula edodes cultured extract, 2 g/kg body weight/day) on DNA methylation patterns, cytokine profiles, and microRNA expression in mammary glands at 9 weeks of age. Analyses included DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing. Pubertal LPS exposure produced persistent molecular dysregulation in mammary glands, including differential DNA methylation (> 5% change vs. control; FDR-adjusted p < 0.05), elevated inflammatory mediators, and altered microRNA expression. Differentially methylated regions were enriched in regulatory features, with decreased methylation at transcription start sites, promoters, and 5' UTRs of genes implicated in mammary development and oncogenic signaling (including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb) in the LPS group, whereas the AHCC + LPS group exhibited a shift toward hypermethylation at these loci (approximately 5%-10% decrease). Inflammatory profiling showed increased IL-17A/F (∼2-fold vs. control; p < 0.05), while microRNA analyses indicated reduced let-7a/c (∼30% vs. control; p < 0.05). Notably, miR-130a and miR-34a increased ∼1.5-fold across all treatment groups relative to control. Pubertal LPS exposure induces enduring epigenetic and inflammatory changes in mammary glands that may heighten breast cancer risk. AHCC's mitigating role indicates potential for dietary interventions to counteract these effects.}, }
@article {pmid41915473, year = {2026}, author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C}, title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117166}, doi = {10.1016/j.celrep.2026.117166}, pmid = {41915473}, issn = {2211-1247}, abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.}, }
@article {pmid41915616, year = {2026}, author = {Wei, Y and Ji, X and Mao, Y and Liu, Y and Li, Y}, title = {Gut Microbiome, Immune Cells, and Heart Failure: A Multi-Omics Mendelian Randomization Study.}, journal = {Cardiology}, volume = {}, number = {}, pages = {1-14}, doi = {10.1159/000550655}, pmid = {41915616}, issn = {1421-9751}, abstract = {INTRODUCTION: The global burden of heart failure is escalating, marked by persistently rising prevalence, incidence, and mortality. The emerging hypothesis that the gut microbiome, as a modifiable factor, influences HF pathogenesis through immune modulation.<br><br>METHODS: To examine the causal relationship, we conducted two-sample Mendelian randomization (MR) analyses using summary genetic data, which was obtained from genome-wide association studies (GWASs) of gut microbial taxa, immune cells, and HF. Single-cell RNA sequencing data and single-nucleus RNA sequencing from chronic heart failure and healthy samples were extracted for investigation. Expression quantitative trait loci (eQTL) MR analysis was used to integrate HF GWAS with eQTL from heart to confirm potential genes. We performed functional enrichment analysis to enrich their functions.<br><br>RESULTS: The analysis revealed that genus Blautia (p = 0.0287), genus Corynebactrium (p = 0.022), genus Demequina (p = 0.0064), genus Enterococcus (p = 0.0307), genus Eubacterium (p = 0.0234), genus F0482 (p = 0.0107), genus Leclercia (p = 0.0026), genus Prevotellamassilia (p = 0.0444), and genus Ruminococcus were causally linked to a higher risk of HF, while genus CAG-125 (p = 0.0443), genus CAG-245 (p = 0.0116), genus Fournierella (p = 0.0326), genus Roseibacillus (p = 0.028) protective factors for HF. Among differential microflora, genus Leclercia was significantly related to higher level of HVEM on terminally differentiated CD4+T-cell count (p = 0.0058). Moreover, HF patients underwent obviously increased NK/T cells. We identified positive association of EIF3A, RPL5, SLC25A51, HERC5, SUSD3, ZNF292, ZNF655, and DNAJC9 with increased risk of HF, whereas the expression of RMC1, CAMK2G, RPS26, ATP5PO displayed protective effect against HF by eQTL MR analysis; they were mainly enriched in myc-Targets-V1, IFN-&#x3b3;-response, IFN-&#x3b1;-response, PI3K/AKT/mTOR signaling, TGF-beta signaling, allograft rejection, notch signaling pathways, angiogenesis, epithelial mesenchymal transition, UV-response-DN, hedgehog signaling, myogenesis.<br><br>CONCLUSION: Our multi-omics MR study uncovered the causality of gut microbiome on immune cells and HF. Genus Leclercia-related changes in T cells may present as a viable focus for HF. This offers new insights into mechanisms and therapy of gut microbiome-mediated HF.}, }
@article {pmid41915730, year = {2026}, author = {Negahban, M and Msaada, K}, title = {Beyond the crop: the role of medicinal and aromatic plants in soil carbon sequestration and nitrogen cycling.}, journal = {International journal of environmental health research}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/09603123.2026.2653197}, pmid = {41915730}, issn = {1369-1619}, abstract = {Medicinal and aromatic plants (MAPs) play a critical yet underexplored role in enhancing soil functionality through their unique phytochemical interactions and ecological adaptability. This review synthesizes current research on how MAPs influence soil carbon sequestration and nitrogen cycling, positioning them as multifunctional agents in sustainable agroecosystems. Unlike conventional crops, MAPs release complex secondary metabolites, such as flavonoids, alkaloids, terpenoids, and phenolics, which modulate microbial diversity, enzymatic activity, and nutrient transformation. These compounds shape the rhizosphere microbial communities, facilitate nitrogen fixation and mineralization, and contribute to soil organic matter (SOM) stabilization through rhizosphere priming and humus formation. Integrated approaches, such as intercropping, agroforestry, and organic amendments, enhance these benefits, while mitigating allelopathic effects and improving carbon and nitrogen fluxes. This review further explores technological innovations including remote sensing (RS), biochar applications, and nanotechnology, which support MAP-based climate-resilient agriculture. Case studies across diverse geographies demonstrate MAPs' potential to restore degraded soils, reduce greenhouse gas emissions, and improve phytochemical yields. Overall, MAPs offer a promising model for regenerative, low-input farming systems that align ecological integrity with economic viability. By actively engineering the soil environment, MAPs emerge not only as botanical resources but also as ecological catalysts in the transition to sustainable agriculture.}, }
@article {pmid41916054, year = {2026}, author = {Pongmanee, K and Rassmidatta, K and Lee, TY and Lin, JS and Chaosap, C and Adeyemi, KD and Ruangpanit, Y}, title = {Influence of synbiotic supplementation on performance, fecal consistency, cecal microbiome, and egg quality of hens during late laying phase.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106851}, doi = {10.1016/j.psj.2026.106851}, pmid = {41916054}, issn = {1525-3171}, abstract = {Hens in the late laying phase often experience age-related physiological constraints that may reduce production efficiency, eggshell quality, and welfare. This study evaluated the effects of dietary synbiotic supplementation on laying performance, egg quality, fecal characteristics, and the cecal microbiome of late-phase laying hens. A total of 240 Lohmann Brown hens (50 weeks old) were distributed into 20 replicates and randomly assigned to a corn-soybean control diet or the same diet supplemented with 100 mg/kg synbiotic (SYNLAC Prime®) for 22 weeks. Synbiotic supplementation did not affect egg production or egg mass but significantly reduced feed intake (P = 0.036). It also improved eggshell quality by decreasing the proportion of cracked eggs (P = 0.014) and increasing eggshell weight (P = 0.049) and shell thickness (P = 0.031). Fecal score and moisture content were not affected; however, synbiotic-fed hens showed lower fecal ammonia concentration (P = 0.033). Synbiotic supplementation increased both alpha and beta microbial diversity in the cecum. While microbial composition at higher taxonomic levels was largely unchanged, the relative abundances of Ruminococcaceae and Lachnospiraceae increased, whereas those of Bacteroidaceae and Clostridiaceae decreased. At the genus level, synbiotic supplementation increased Faecalibacterium, Ruminococcus, and Lactobacillus, while reducing Bacteroides and Alistipes. Functional prediction analysis indicated that synbiotic supplementation upregulated 12 cecal metabolic pathways and downregulated two pathways. Overall, synbiotic supplementation improved eggshell quality, promoted beneficial gut microbial populations, and reduced fecal ammonia emissions, suggesting its potential as a dietary strategy to support productivity and gut health in hens during the late laying phase.}, }
@article {pmid41916081, year = {2026}, author = {Machado, P and Mazahery, H and Black, LJ and Tremlett, H and Daly, A and Pham, NM and Tessema, GA and Zhu, F and Banwell, B and Bar-Or, A and Marrie, RA and Bernstein, CN and Mirza, AI and Yeh, EA and Waubant, E and O'Mahony, J and Dunlop, E and , }, title = {Higher ultra-processed food consumption is associated with higher likelihood of paediatric-onset multiple sclerosis.}, journal = {Multiple sclerosis and related disorders}, volume = {109}, number = {}, pages = {107159}, doi = {10.1016/j.msard.2026.107159}, pmid = {41916081}, issn = {2211-0356}, abstract = {BACKGROUND: Diets are increasingly dominated by ultra-processed foods, which have been linked to several chronic diseases. Emerging evidence suggests an association between ultra-processed food consumption and inflammatory diseases, including multiple sclerosis (MS).<br><br>OBJECTIVE: To assess associations between consumption of ultra-processed foods and paediatric-onset MS (PoMS).<br><br>METHODS: We used data from the microbiome sub-study of the Canadian Pediatric Demyelinating Disease Network Study for PoMS cases (symptom onset aged <18 years) and unaffected controls. Data on consumption of ultra-processed foods (defined within the Nova system) were derived from dietary intake data collected using the Block Kids Food Screener. Dietary contribution of ultra-processed foods (% of total grams consumed per day) was estimated. Logistic regression models were used to examine associations between ultra-processed food consumption (continuous and tertiles) and likelihood of PoMS. Models were adjusted for age at dietary data collection, sex, race, region of residence, and total energy intake.<br><br>RESULTS: Dietary data were collected from PoMS participants (females=57, males=23) aged 5-28 years and controls (females=30, males=16) aged 8-26 years. Each additional 10% in ultra-processed food consumption was associated with a 35% higher odds of being a PoMS participant (adjusted odds ratio [aOR]=1.35, 95% CI 1.05, 1.73). Participants in the highest (versus lowest) tertile for ultra-processed food consumption had over five times higher odds of being a PoMS participant (aOR=5.30, 95% CI 1.36, 20.70).<br><br>CONCLUSION: Participants with PoMS reported greater consumption of ultra-processed foods compared to unaffected peers. More comprehensive longitudinal dietary histories are required to better understand this observation.}, }
@article {pmid41916092, year = {2026}, author = {Qiu, C and Jie, W and Qian, Y and Lu, X and Chen, Y and Si, M}, title = {Ageing of the Oral Mucosa: Mechanisms and Consequences.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109482}, doi = {10.1016/j.identj.2026.109482}, pmid = {41916092}, issn = {1875-595X}, abstract = {Oral mucosal ageing represents a fundamental reprogramming of the tissue microenvironment, a dynamic process that underlies the functional decline and heightened disease susceptibility observed in the elderly. This review synthesises current evidence to reconceptualise oral mucosal ageing as an active reprogramming of the tissue microenvironment, delineating the interplay between structural, molecular, and immunological changes, and exploring how these alterations drive functional decline and increase susceptibility to age-related oral diseases. Through a comprehensive analysis of experimental and clinical studies from human and animal models, we demonstrate that the ageing process fundamentally transforms the oral mucosa. Key findings include structural changes such as epithelial atrophy, extracellular matrix remodelling, and salivary gland degeneration, driven molecularly by genomic instability, accumulation of proinflammatory senescent cells, stem cell exhaustion, and dysregulated stress responses. These are compounded by an immunological state of 'inflammaging' and functional decline in innate and adaptive immunity, further exacerbated by shifts in the oral microbiome. Collectively, these deficits lead to impaired regeneration, diminished sensory function, and reduced salivary secretion, creating a permissive landscape for chronic oral diseases. In conclusion, oral mucosal ageing is a dynamic process of microenvironmental reprogramming driven by cellular senescence, immunosenescence, and structural decay. This actively underpins the heightened vulnerability to oral disease in the elderly, providing a mechanistic foundation for developing targeted interventions to preserve oral health in ageing populations.}, }
@article {pmid41916240, year = {2026}, author = {Wen, S and Liu, J and Lin, B and Li, N and Diao, X}, title = {Aging enhances the ecological toxicity of polyethylene microplastics to marine medaka larvae (Oryzias melastigma).}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129493}, doi = {10.1016/j.jenvman.2026.129493}, pmid = {41916240}, issn = {1095-8630}, abstract = {Microplastics (MPs), widely distributed in marine environments, pose urgent ecological risks as emerging contaminants. However, current ecological risk assessments are largely based on the commercially produced MPs, which poorly represent in natural settings. Here, we simulated the natural aging of polyethylene MPs (PE-MPs) using ultraviolet radiation (UV) and Fenton reactions, characterized the resultant physicochemical changes, and assessed their ecological toxicity in marine medaka larvae over a 30-day exposure experiment. Short-term aging via UV and Fenton reactions primarily altered the physical properties of PE, including surface morphology, hydrophobicity, and Zeta potential. Both original and aged PE induced intestinal damage and oxidative stress in the larvae, indicating that aged PE retains its toxicity. In contrast, aged PE significantly altered the microbial community structure in the fish intestines: Roseibacillus was significantly enriched in the UV-aged polyethylene (UVPE) exposure group, while Ruegeria and Pseudomonas were enriched in the Fenton-aged polyethylene (FPE) exposure group. Functional predictions of the intestinal microbial communities indicated that exposure to FPE resulted in the upregulation of metabolism-related functions, whereas exposure to UVPE significantly downregulated similar functions. Such upregulation likely reflects microbiome reprogramming under stress rather than improved health. Overall, our study demonstrated that aged PE exhibited pronounced toxicity to marine fish and their larvae by altering gut microbiota, and thus significantly impacting energy metabolism and nutrient absorption, leading to detrimental effects on their growth and development. These findings further underscore the enhanced ecological toxicity effects of aged MPs on marine organisms, highlighting the need for better assessments of the adverse impacts of MPs in marine environments.}, }
@article {pmid41916289, year = {2026}, author = {Chen, S and Wang, Y and Chen, B and Hou, X and Liu, S and He, S and Qi, J and Peng, Z and Pan, H and Liang, C and Wei, G and Jiao, S}, title = {Diversity-triggered 2-naphthoic acid exudation recruits keystone microbial taxa to promote soybean drought tolerance.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.002}, pmid = {41916289}, issn = {1934-6069}, abstract = {Rhizosphere microbiomes are essential for plant growth and stress tolerance, yet how microbial diversity shapes drought resilience in soybean remains unclear. Here, we demonstrate that high rhizosphere microbial diversity, generated via dilution-to-extinction manipulation of soil microbiome diversity, improves soybean performance under drought. Integrated metabolomic and transcriptomic analyses identify 2-naphthoic acid as a diversity-induced root exudate that accumulates exclusively under drought. This metabolite selectively recruits Sinorhizobium CS204 via chemotaxis and ATP-binding cassette (ABC) transporter-mediated uptake, as confirmed by in vitro substrate utilization assays and targeted mutant construction. Molecular docking and microscale thermophoresis reveal direct interactions between this metabolite and nitrogen-cycling proteins, enhancing denitrification and nitrogen fixation of S.CS204. Co-application of 2-naphthoic acid and S.CS204 significantly improves plant nutrient acquisition and photosynthesis under drought. Collectively, our study underscores the pivotal role of rhizosphere microbial diversity in triggering the exudation of root metabolites to recruit keystone taxa, establishing microbe-plant synergies that bolster drought tolerance.}, }
@article {pmid41916309, year = {2026}, author = {Cichy, A and Dewan, A and He, Z and Fitzgerald, C and Ratkowski, M and Krasewicz, J and Ozarkar, V and Kaye, S and Teng, T and Zhang, J and Feinstein, P and Bozza, T}, title = {A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2026.03.009}, pmid = {41916309}, issn = {1879-0445}, abstract = {Many species use microbiome-derived metabolites as chemosensory cues, yet the chemicals involved and the sensory pathways that detect and process them remain poorly understood. Trimethylamine (TMA) is a volatile metabolite that is produced by the gut microbiome and selectively accumulated in the urine of sexually mature male mice. Here, we show that TMA regulates inter-male aggression and social dominance by activating trace amine-associated receptor 5 (TAAR5) in the main olfactory system. In wild-type mice, early aggressive behavior during male-male encounters strongly predicts eventual social status: dominant males initiate more attacks, whereas subordinate males display more defensive behaviors. Deletion of TAAR5 eliminated this asymmetry, with dominant and subordinate mice showing similar levels of aggressive and defensive behaviors. Strikingly, restoring TAAR5 expression in olfactory sensory neurons (OSNs) rescued the behavioral asymmetry, indicating that this effect is mediated by the main olfactory system and arguing against contributions from proposed TAAR5 expression in the brain. Finally, pharmacological suppression of microbial TMA production reduced inter-male aggression, and this effect was reversed by painting treated males with TMA, showing that microbiome-derived TMA is the key volatile ligand for TAAR5 in this context. Taken together, our findings identify TMA as a critical olfactory cue that signals the presence of sexually mature males and facilitates social hierarchy formation. More broadly, our results demonstrate that a microbiome-derived metabolite can shape mammalian social interactions through the main olfactory system and uncover a previously unrecognized role for the TAAR family in regulating social behavior.}, }
@article {pmid41916434, year = {2026}, author = {Iachizzi, M and Zajac, N and Ruiz, JL and Güller, T and Rabin, R and Schalbetter, S and de Cillis, F and Moccia, MD and Cattaneo, A and Cryan, JF and Richetto, J}, title = {Probiotic treatment rescues behavioral deficits and gut microbial abnormalities induced by preconceptional stress in mothers and offspring.}, journal = {Brain, behavior, and immunity}, volume = {136}, number = {}, pages = {106571}, doi = {10.1016/j.bbi.2026.106571}, pmid = {41916434}, issn = {1090-2139}, abstract = {Depression and anxiety during pregnancy are major public health concerns with lasting consequences for mother and child. Although the gut microbiome contributes to stress and mood regulation, its role in preconceptional stress and transgenerational outcomes remains unclear. Here, we examined behavioral, microbial, and thalamic transcriptional effects of preconceptional social isolation rearing (SIR) in female mice and tested whether maternal probiotic supplementation mitigates these alterations. SIR females displayed increased anxiety-like and social-avoidant behavior, reduced gut microbial diversity, depletion of Odoribacter, Tuzzerella, and Alloprevotella, and enrichment of Bacteroides and Lachnospiraceae. A multispecies probiotic (Lactobacillus rhamnosus HN001, L. acidophilus La-14, Bifidobacterium lactis HN019) reversed these behavioral and microbial changes. Adult offspring of SIR dams showed sex-dependent behavioral deficits and microbial alterations partly reflecting maternal patterns. Prenatal SIR was associated with reduced thalamic Bdnf expression in offspring and altered Grin2a/2b selectively in males. In contrast, prenatal probiotic exposure exerted broader transcriptional effects and restored Bdnf levels in SIR offspring. SIR-induced increases in Lachnospiraceae were transmitted to offspring, whereas reductions in Ruminococcaceae were normalized by maternal probiotic treatment. Predicted functional profiling indicated sex-dependent modulation of microbial pathways related to tryptophan and central carbon metabolism. These findings demonstrate enduring transgenerational effects of preconceptional stress on the gut-brain axis and support maternal probiotic supplementation as a potential strategy to mitigate stress-induced dysregulation.}, }
@article {pmid41916460, year = {2026}, author = {Asiri, F and Kishk, M and Karam, H and Al-Muhanna, K and Al-Najdi, F and Al-Enezi, A and Al-Khalifah, N and Hejji, AB and Al-Salameen, F and Al-Salem, SM}, title = {Innovative soil seeding with waste-derived microbial inoculums: Enhancing plastic biodegradation and Revealing microbiome shifts.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134523}, doi = {10.1016/j.biortech.2026.134523}, pmid = {41916460}, issn = {1873-2976}, abstract = {Plastic waste accumulation in terrestrial ecosystems poses a global environmental challenge, demanding sustainable alternatives to conventional disposal. Aerobic biodegradation is promising, yet most studies rely on composting systems, often overlooking different polymer types and how seeding soil with waste-derived inoculums affect polymer breakdown. This study developed an innovative soil-seeding approach using microbe-rich inoculums derived from real waste streams: compost (Comp.), activated sludge (AS), plastic-contaminated soil (PCS), and oil-contaminated soil (OCS) to enhance biodegradation of starch, compostable bioplastic (CBP), and the mineralization of linear low-density polyethylene (LLDPE). Biodegradation was evaluated under controlled soil conditions, and microbial community responses were characterized through metataxonomic profiling. Starch exhibited the highest biodegradation (71-100%), followed by CBP (31-56%) and LLDPE mineralization (12-22%). OCS and PCS significantly enhanced CBP and LLDPE degradation, respectively, corresponding to differences in organic content and carbon-to-nitrogen ratios. Shifts in microbial composition revealed polymer-specific microbial drivers, including Bacilli (Bacillaceae, Paenibacillus) and Chaetomium for starch, and Actinobacteriota, Acidimicrobiia, Mycobacterium, and Nocardioides for CBP, particularly in OCS. LLDPE degradation remained low but was modestly improved in Comp- and PCS-amended soils. Overall, this study demonstrates that targeted soil-seeding with waste-derived inoculums can substantially influence polymer degradation and microbial succession, providing a practical strategy to accelerate biodegradation in natural soils and informing future sustainable plastic-management approaches.}, }
@article {pmid41916675, year = {2026}, author = {Boven, A and Vranken, H and Vlieghe, E and Boleij, A and Fall, K and Engstrand, L and Brusselaers, N}, title = {Commonly prescribed drugs as risk factors for Clostridioides difficile infections: a Swedish population-based case-control study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337629}, pmid = {41916675}, issn = {1468-3288}, abstract = {BACKGROUND: Clostridioides difficile infections (CDIs) are associated with antibiotic use, although the link with other drugs remains underexplored.<br><br>OBJECTIVES: To investigate the association between antibiotic and non-antibiotic drugs with microbiome-modulating activity on new occurrences of CDI.<br><br>DESIGN: We conducted a Swedish population-based case-control study from 2006 to 2019 including 42&#x2009;921 cases matched with 355&#x2009;159 population controls on age and sex, obtained from multiple linked Swedish registries. The effect of antibiotic and non-antibiotic use within 30 days from the index date on CDI occurrence was estimated using multivariable conditional logistic regression additionally with a lasso penalty. Models were adjusted for age and sex by design and for Charlson Comorbidity Index and concomitant drug use, providing adjusted ORs (aORs) with 95% CIs.<br><br>RESULTS: Antibiotics with the greatest CDI risk were lincosamides (aOR=31.4, 95% CI 27.9 to 35.3), combinations of penicillins (aOR=19.8, 95% CI 15.9 to 24.5), sulfonamides and trimethoprim, and cephalosporins, though no association for tetracyclines. Among non-antibiotic drugs, we found decreased risks of CDI for lipid-modifiers (aOR=0.8, 95% CI 0.8 to 0.8) and aspirin (aOR=0.8, 95% CI 0.7 to 0.8) and increased risks for antidiarrhoeals (aOR=7.3, 95% CI 6.8 to 7.8), corticosteroids (aOR=2.4, 95% CI 2.3 to 2.5), proton-pump inhibitors (PPIs) (aOR=1.8, 95% CI 1.7 to 1.8), nervous system drugs, constipation drugs, histamine H2-receptor antagonists, antidepressants, and beta blockers, but no significant risk for non-steroidal anti-inflammatory drugs.<br><br>CONCLUSIONS: We found varying effects of antibiotics on CDI, providing evidence for ongoing efforts in prudent prescribing decisions and antimicrobial stewardship. We confirmed PPI as a main risk factor for CDI and provided new evidence for other non-antibiotic drugs as potentially important risk factors considering their high prescription prevalence.}, }
@article {pmid41916943, year = {2026}, author = {Sailesh, SS}, title = {Association between soft drink consumption and depression mediated by gut microbiome: a perspective.}, journal = {East Asian archives of psychiatry : official journal of the Hong Kong College of Psychiatrists = Dong Ya jing shen ke xue zhi : Xianggang jing shen ke yi xue yuan qi kan}, volume = {36}, number = {1}, pages = {56-59}, doi = {10.12809/eaap25136}, pmid = {41916943}, issn = {2224-7041}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Carbonated Beverages/adverse effects ; *Depression/etiology/epidemiology/microbiology ; *Sugar-Sweetened Beverages/adverse effects ; Female ; }, abstract = {This perspective synthesises current evidence on the association between soft drink consumption and depression, with emphasis on the gut microbiome as a potential mediating mechanism. PubMed, Scopus, and Google Scholar were searched using the following terms: 'soft drinks', 'sugar-sweetened beverages', 'carbonated beverages', 'soda', 'depression', 'depressive symptoms', 'mental health', 'gut microbiome', 'microbiota', and 'gut-brain axis'. Peer-reviewed original articles published in English between January 2000 and October 2025 were included if they involved human participants of any age (sample size ≥50 for observational studies), assessed soft drink or sugar-sweetened beverage consumption, and measured depression diagnosis, depressive symptoms, or depression severity. Associations between soft drink consumption and increased depression risk were consistently shown across multiple study designs and populations. Evidence for artificially sweetened beverages was less consistent and suggested potentially distinct, non-sugar-related pathways. A multicentre cohort study of 932 participants revealed that soft drink consumption predicted the major depressive disorder diagnosis (odds ratio = 1.081), with stronger effects in women (odds ratio = 1.167). Eggerthella partially mediated the soft drink-depression association, explaining approximately 4% of the association. Soft drink consumption is associated with increased depression risk through multiple biological pathways involving inflammation, metabolic dysregulation, and gut microbiome alterations. Modest effect sizes suggest the involvement of multiple interconnected mechanisms. Public health interventions to limit sugar-sweetened beverage consumption are recommended to improve physical and mental health. Healthcare providers should consider dietary assessment and counselling as part of depression prevention and treatment strategies.}, }
@article {pmid41917102, year = {2026}, author = {Roy, M and Han, D and Lee, D and Kang, B and Choi, K}, title = {Cultivation system and plant health influence root-associated bacterial community structure and interaction networks in strawberry.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45642-7}, pmid = {41917102}, issn = {2045-2322}, support = {(RS-2023-00251252 and 2020R1A6A1A03047729)//National Research Foundation of Korea/ ; (RS-2025-02613089)//Rural Development Administration/ ; }, abstract = {Strawberry is cultivated in both soil-based field and substrate-based soilless hydroponic systems, yet how cultivation context shapes root-associated bacterial communities and their interaction architecture remains unclear. We compared root-associated bacterial communities from field root-associated soil and hydroponic root-adhering substrate under asymptomatic and symptomatic conditions using 16S rRNA gene amplicon sequencing. Cultivation system was the primary driver of community structure, clearly separating field and hydroponic samples. Field communities were enriched in Firmicutes and Actinobacteria, such as Bacillaceae and Nocardioidaceae, whereas hydroponic communities showed higher relative abundances of Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia, including Chitinophagaceae and Sphingomonadaceae. Differential abundance and Random Forest analyses revealed consistent enrichment of Bacillus-associated ASVs in field samples, whereas asymptomatic and symptomatic communities showed greater compositional differentiation in hydroponic than in field samples.. Co-occurrence network analysis further demonstrated that hydroponic communities contained more taxa and interactions but exhibited lower density and clustering compared to field communities, indicating reduced structural cohesion. These findings demonstrate that cultivation system strongly influences both the composition and structural organization of strawberry root-associated bacterial communities, with implications for microbiome-informed disease management in intensive production systems.}, }
@article {pmid41917200, year = {2026}, author = {Lee, YH and Lin, WJ and Tsai, MT and Lan, B and Chu, YL and Yang, JI and Sun, SJ}, title = {Context-dependent indirect effects mediate ecological transitions between parasitism and mutualism.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09945-9}, pmid = {41917200}, issn = {2399-3642}, support = {Academic Research-Career Development Project (Sprout Research Projects; 114L7869)//National Taiwan University (NTU)/ ; }, abstract = {Symbiotic interactions frequently shift along a mutualism-parasitism continuum, altering host fitness, population dynamics, and microbial community structure with ecological context. Here, we integrate field surveys, reciprocal breeding experiments, feeding assays, and microbiome profiling to dissect interactions between phoretic mite (Poecilochirus carabi), nematode (Rhomborhabditis regina), and their burying beetle host (Nicrophorus nepalensis) during reproduction. We show that high nematode densities reduce beetle offspring survival during metamorphosis, but co-occurring mites mitigate these costs by preying on nematodes and suppressing vertical transmission, thereby enhancing beetle fitness. Both mites and nematodes are equally effective at suppressing bacterial loads on carrion, but mites drive greater shifts in carcass microbiome composition. Carcasses exposed to both symbionts display the most pronounced shifts in bacterial communities, suggesting that inter-symbiont interactions have cascading effects on host-associated microbiota. Intriguingly, in the absence of nematodes, mites impose fitness costs on their beetle hosts. These results demonstrate that the net effects of mites on beetle fitness emerge largely through indirect, density-dependent interactions with nematodes and microbial competitors. By integrating macro-symbiont and microbiome perspectives, our study highlights how phoresy extends beyond passive dispersal to actively restructure host-symbiont networks, highlighting the overlooked potential of indirect effects in driving context-dependent mutualism within multisymbiotic systems.}, }
@article {pmid41917642, year = {2026}, author = {Gao, J and Ren, X and Hu, Y and Li, G and Yang, T and Xiao, J}, title = {New Trends and Challenges in Academic Research on Adolescent Growth and Development.}, journal = {Advances in experimental medicine and biology}, volume = {1505}, number = {}, pages = {411-420}, pmid = {41917642}, issn = {0065-2598}, mesh = {Humans ; Adolescent ; *Adolescent Development/physiology ; *Adolescent Health/trends ; Gastrointestinal Microbiome/physiology ; Epigenesis, Genetic ; *Biomedical Research/trends ; }, abstract = {Adolescence is a critical period for physical and psychological growth and development when individuals undergo a burst growth in physical size, hormonal re-adjustment, and brain development. In recent years, research studies have changed from descriptive growth charts toward focusing on the roles of multiple factors that affect adolescent health, including epigenetic regulators, genetic traits, social stressors, and gut microbiota. Compared to traditional factors like nutrition and hormones, environmental factors, personalized genomics, social media exposure, and gut-microbiome, etc. are increasing recognized as novel critical regulators of adolescent health. Currently, the goal of academic research in adolescence is to understand the interactions and underlying mechanisms of these factors and to develop targeted interventions for addressing adolescent health issues. Therefore, this chapter mainly discusses the new trends, key challenges, and translational research potential in these rapidly advancing field of adolescent growth and development.}, }
@article {pmid41917750, year = {2026}, author = {Yeh, GY and Wayne, PM and Mehta, D}, title = {Inside the Gut-Mind Connection: Mind-Body Medicine Meets the Microbiome Revolution.}, journal = {Journal of integrative and complementary medicine}, volume = {}, number = {}, pages = {27683605261438880}, doi = {10.1177/27683605261438880}, pmid = {41917750}, issn = {2768-3613}, }
@article {pmid41917988, year = {2026}, author = {Liu, M and Li, S and Cui, Y and Zhu, X and Wang, Z and Sun, H and Li, D and Liu, B and Shi, Y}, title = {Tryptophan metabolism mediated by the gut microbiota inhibits pyroptosis via the AhR signaling pathway to maintain intestinal epithelial homeostasis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02408-7}, pmid = {41917988}, issn = {2049-2618}, support = {CARS-34//Modern Agro-industry Technology Research System of China/ ; No. 244200510010//Science and Technology Innovation Leading Talent in Central Plains/ ; }, abstract = {BACKGROUND: The intestinal epithelial barrier protects the gut from pathogen invasion as well as exposure to food antigens and toxins. Increasing evidence has linked the gut microbiota to the function of the intestinal epithelial barrier. Fecal microbiota transplantation (FMT) can treat various intestinal diseases by reshaping the gut microbiota. However, the mechanisms by which FMT exerts its effects across different gastrointestinal conditions remain unclear. Moreover, its limitations are significant, including issues related to donor selection, the complexity of the microbiome, potential infection risks, inconsistent clinical responses, and ethical and legal considerations. Therefore, exploring the microbes and metabolites that mediate the effects of FMT as a replacement for traditional FMT is of great importance. In this study, we aim to investigate the gut microbiota and its metabolites to support the therapeutic role of FMT in intestinal barrier damage and elucidate its potential molecular mechanisms.<br><br>RESULTS: Our findings indicate that FMT prevents Lipopolysaccharide (LPS)-induced pyroptosis and damage to the colonic epithelial barrier. Mechanistically, FMT treatment reprograms the composition of gut microbiota, increasing the relative abundance of Lactobacillus reuteri and the levels of tryptophan metabolites (ILA, IAld, and IAA) in the colon, thereby inhibiting pyroptosis and protecting the intestinal epithelial barrier. Importantly, the AhR/NLRP3 axis is essential for the pyroptosis-inhibitory effects of Lactobacillus reuteri and its tryptophan metabolites.<br><br>CONCLUSIONS: Our results provide the first evidence that targeting the regulation of Lactobacillus reuteri and tryptophan metabolism is a promising strategy for inhibiting pyroptosis and improving intestinal epithelial homeostasis.}, }
@article {pmid41918066, year = {2026}, author = {Singh, N and DuBrock, HM and Prisco, SZ and Dai, Z and Zheng, Q and Fallon, MB and Thenappan, T and Ventetuolo, CE and Jose, A}, title = {The Importance of Liver-Lung Communication in Pulmonary Vascular Diseases.}, journal = {Comprehensive Physiology}, volume = {16}, number = {2}, pages = {e70140}, pmid = {41918066}, issn = {2040-4603}, support = {HL134625/HL/NHLBI NIH HHS/United States ; HL141268/HL/NHLBI NIH HHS/United States ; HL174007/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; HL158596/HL/NHLBI NIH HHS/United States ; HL162794/HL/NHLBI NIH HHS/United States ; HL170096/HL/NHLBI NIH HHS/United States ; HL169509/HL/NHLBI NIH HHS/United States ; HL16497/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; }, mesh = {Humans ; *Lung/physiology/physiopathology ; *Liver/physiology/physiopathology ; Animals ; Hepatopulmonary Syndrome/physiopathology ; *Lung Diseases/physiopathology ; Gastrointestinal Microbiome/physiology ; Hypertension, Pulmonary/physiopathology ; }, abstract = {In normal health, the liver and lungs enjoy a close anatomic, physiologic, and functional relationship. In the context of pulmonary vascular disease, however, there is accumulating evidence that the interplay between the gut microbiome, hepatic system, and pulmonary vasculature (so-called "gut-liver-lung" axis) plays an important role in driving disease pathogenesis and determining clinical outcomes. Despite recognizing the importance of the gut-liver-lung axis in pulmonary vascular disease however, little is known about the clinical characteristics, circulating factors, and physiologic pathways that mediate this important axis of communication. In this clinical and translationally focused review, we provide an overview of liver-lung communication in normal physiology, and contrast this with gut-liver-lung derangements in pulmonary arterial hypertension, portopulmonary hypertension, and hepatopulmonary syndrome. We conclude with identifying key gaps in knowledge that will need to be addressed in order to manipulate the gut-liver-lung axis to prevent worsening pulmonary vascular disease, develop novel therapeutics, and improve patient outcomes.}, }
@article {pmid41918094, year = {2026}, author = {Liu, Y and Liu, W and Pu, J and Wang, Y and Kang, Z and Zheng, H and Chang, W and Zheng, X and Yang, Q and Xu, H and Feng, Z and Dong, K and Li, J}, title = {Compositional disparities and potential pathogenic mechanisms of the ocular microbiome in cataract patients: insights from high-throughput sequencing.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05009-4}, pmid = {41918094}, issn = {1471-2180}, support = {2023L118//Science and Technology Innovation Program for Higher Education Institutions of Shanxi Province/ ; 2024149//Laboratory Special Project of the Health Commission of Shanxi Province/ ; B202201//Doctoral Fund Project of Shanxi Eye Hospital/ ; 2024NITFID303//Independent Research Program of the National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases/ ; }, }
@article {pmid41918359, year = {2026}, author = {Fairfield, H and Reagan, MR}, title = {Fiber: A New Myeloma Prevention Approach with Abundant Positive Effects.}, journal = {Cancer discovery}, volume = {16}, number = {4}, pages = {623-625}, doi = {10.1158/2159-8290.CD-26-0152}, pmid = {41918359}, issn = {2159-8290}, mesh = {Humans ; *Multiple Myeloma/prevention &amp; control/diet therapy ; *Dietary Fiber/administration &amp; dosage/therapeutic use ; Quality of Life ; Obesity/diet therapy/complications ; }, abstract = {In a recent study by Shah, Cogrossi, and colleagues, patients with overweight/obesity and pre-myeloma diseases (monoclonal gammopathy of undetermined significance or smoldering myeloma) were mailed 12 weeks of high-fiber meals, provided with nutritional counseling, and required to track their food intake and weight. The intervention was well tolerated and improved quality of life, metabolic health, gut microbiome composition, and immune system function while supporting stable or improved multiple myeloma disease trajectories. See related article by Shah et al., p. 697.}, }
@article {pmid41918498, year = {2026}, author = {Belhedi, M and Sghaier-Hammami, B and Hammami, SBM and Ben Slema, S and De Bellis, P and Somma, S and Nafati, H and Hibar, K and Abi Saad, C and Moretti, A and Masiello, M}, title = {Microbial biodiversity in Tunisian olive grove soils: a reservoir of phytopathogenic fungi and potential beneficial microorganisms.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1770745}, pmid = {41918498}, issn = {2673-6128}, abstract = {INTRODUCTION: Intercropping in olive orchards increases the risk of soil-borne fungal infections, particularly when associated crops are susceptible to the same pathogens. This study aimed to identify soil-borne microorganisms colonizing the roots and rhizosphere of olive trees in Tunisia intercropped with Solanaceae plants and to evaluate co-occurring bacterial communities for their potential to mitigate wilt disease and promote plant health.<br><br>MATERIAL AND METHODS: Endophytic fungi and bacteria were isolated from olive soils and roots collected from three olive orchards subjected to different intercropping systems. Fungal strains were molecularly identified at the species level using Internal Transcribed Spacer (ITS) and translation elongation factor 1-&#x3b1; (TEF1) gene sequencing, while bacterial strains were characterized by rep-PCR profiling and 16S rDNA sequencing. The pathogenicity of selected Fusarium strains was assessed by in vitro inoculation of detached olive leaves, olive twigs, and tomato seedlings. Antagonistic activity of bacterial strains against selected Fusarium species was evaluated using dual-culture assays, and bacteria-fungi interactions were further investigated by scanning electron microscopy (SEM).<br><br>RESULTS AND DISCUSSION: A total of 83 fungal and 40 bacterial strains were isolated. The fungal community was dominated by Fusarium species (62%), followed by Phoma (13%) and Alternaria (10%) species, while Verticillium dahliae was not detected at any site. The prevalence and virulence of Fusarium varied among olive groves, with the highest incidence observed at Sidi Bou Ali, where olive trees were intercropped with tomato, and the lowest at Kairouan, where potato intercropping was less frequent. Pathogenicity assays showed that 12 out of 15 of the tested Fusarium strains caused symptoms on both olive tissues and tomato seedlings. Bacterial communities were dominated by Bacillus species and Priestia megaterium. Bacillus species were particularly abundant at the site with the highest Fusarium pressure. The in vitro assay showed that several bacteria exhibited antagonistic activity against pathogenic fungi, with growth inhibition ranging from 8% to 68%, including volatile organic compound-mediated effects. SEM analyses revealed that Bacillus amyloliquefaciens inhibited fungal growth through biofilm formation and hyphal alteration.}, }
@article {pmid41918618, year = {2026}, author = {Her, TK and Pszczolkowski, VL and Chung, G and Woollett, LA and Alejandro, EU}, title = {Multiparity as a Key Variable in Metabolism and Pregnancy Research.}, journal = {Current opinion in physiology}, volume = {47}, number = {}, pages = {}, pmid = {41918618}, issn = {2468-8673}, support = {R01 DK136237/DK/NIDDK NIH HHS/United States ; }, abstract = {Parity is defined as the total number of pregnancies reaching ≥20 weeks of gestation. It is an important variable to consider in any metabolic studies involving maternal or offspring health, as multiparity has been identified as a potential driver of numerous aspects of reproduction, maternal-fetal programming, and the health of both maternal and offspring. Currently, it is understood that multiparity may increase the risk of maternal pregnancy complications, such as preeclampsia and gestational diabetes mellitus (GDM), which can have subsequent long-term effects on both the maternal and offspring. Although there are some differences in data between rodents and humans, multiparity has been shown to disrupt glucose homeostasis, decrease pancreatic beta-cell proliferation, alter cardiac hemodynamics, and change the composition of the gut microbiome. In this review, we discuss what is known in the current literature about the impact of multiparity on pregnancy outcomes, maternal health, and offspring health.}, }
@article {pmid41918694, year = {2026}, author = {Zheng, W and Liang, Y and Li, J}, title = {The neonatal lung microbiome: a dynamic determinant of respiratory health, disease, and novel therapeutics.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1770578}, pmid = {41918694}, issn = {2296-2360}, abstract = {The neonatal lung, once considered sterile, is now recognized to harbor a dynamic and complex microbiome that plays a critical role in respiratory health and disease. This review synthesizes current evidence on the composition, development, and functional impact of the lung microbiome in neonates, with a focus on its involvement in key respiratory disorders such as bronchopulmonary dysplasia, respiratory syncytial virus infection, neonatal acute respiratory distress syndrome, cystic fibrosis, and asthma predisposition. We place particular emphasis on the bidirectional communication along the gut-lung axis as a central mechanism, wherein intestinal microbiota and their metabolites modulate pulmonary immunity and inflammation. Emerging multi-omics studies that integrate microbial data with host metabolomic and immune profiles are highlighted for their role in deciphering disease-specific dysbiotic signatures and mechanistic pathways. Critically, this review advances the discussion beyond association by evaluating the translational potential of the microbiome as both a diagnostic biomarker and a therapeutic target. We provide a critical appraisal of innovative microbiome-targeted strategies-including probiotics, postbiotics, phage therapy, and bacterial lysates-and discuss the unique challenges and future directions for translating these approaches into safe, effective clinical interventions for vulnerable neonates. By bridging foundational science with clinical implications, this work aims to inform the development of novel, ecology-informed therapeutics to prevent and mitigate neonatal respiratory diseases.}, }
@article {pmid41918737, year = {2026}, author = {Edwards, JS and De Paris, K}, title = {Inflammation at the maternal-fetal interface: a perspective on interacting risk factors for preterm birth in sub-Saharan African women living with HIV.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1741921}, pmid = {41918737}, issn = {1664-3224}, mesh = {Humans ; Female ; Pregnancy ; *HIV Infections/immunology/drug therapy/complications/epidemiology/virology ; *Premature Birth/immunology/epidemiology/etiology ; Risk Factors ; Africa South of the Sahara/epidemiology ; *Inflammation/immunology ; Vagina/microbiology/immunology ; *Pregnancy Complications, Infectious/immunology/virology ; Microbiota/immunology ; Macrophages/immunology ; Infant, Newborn ; *Maternal-Fetal Exchange/immunology ; }, abstract = {Globally, approximately 10% of all babies are born prematurely. The vast majority of preterm births, defined as birth <37 weeks of gestation, occur in low- and middle-income countries (LMICs) in Asia and Africa. Furthermore, premature birth has become the leading cause of death in infants under the age of 5 years. Thus, to improve maternal and infant health outcomes, better diagnostics and intervention strategies are urgently needed. However, the multifactorial etiology of preterm birth provides a major obstacle in achieving this goal. A common factor to many adverse birth outcomes, including preterm birth, is aberrant immune activation at the maternal-fetal interface. The specific cause of immune activation, however, remains unknown. Both HIV and an anaerobe-rich vaginal microbiota have been independently identified as risk factors for preterm birth, and both factors also promote inflammation and immune activation at mucosal sites. The interplay of HIV and microbiota is widely acknowledged, although mostly in the context of the intestinal microbiome. This review will highlight how the regulatory function of macrophages at the maternal-fetal interface can be altered in response to HIV and antiretroviral therapy and to changes in vaginal microbiota. We proceed to discuss interactions between the various factors and propose a dual-hit model in which macrophages act as mediators of inflammation at the maternal-fetal interface in response to specific vaginal commensals and HIV infection in sub-Saharan African women with preterm birth outcomes.}, }
@article {pmid41918738, year = {2026}, author = {Lee, AR and Yang, SW and Lee, SY and Jeon, SB and Kang, HY and Choi, JW and Park, JH and Park, JH and Son, SB and Jeong, Y and Lee, JH and Kim, W and Cho, ML}, title = {Mitochondrial transplantation ameliorates experimental autoimmune encephalomyelitis by modulating the Th17/Treg balance and restoring metabolic homeostasis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1698136}, pmid = {41918738}, issn = {1664-3224}, mesh = {*Encephalomyelitis, Autoimmune, Experimental/therapy/immunology/metabolism/pathology ; Animals ; *Th17 Cells/immunology/metabolism ; *Mitochondria/transplantation/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Mice ; Humans ; Female ; Homeostasis ; Multiple Sclerosis/immunology/therapy/metabolism ; Oxidative Stress ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Spinal Cord/pathology/immunology/metabolism ; Disease Models, Animal ; Reactive Oxygen Species/metabolism ; }, abstract = {INTRODUCTION: Mitochondrial dysfunction has been increasingly implicated in the pathogenesis of multiple sclerosis (MS), contributing to oxidative stress, immune dysregulation, and neurodegeneration. Current therapies primarily target inflammation but do not adequately address mitochondrial impairment or progressive tissue damage. This study aimed to evaluate the therapeutic potential of mitochondrial transplantation in experimental autoimmune encephalomyelitis (EAE), a murine model of MS, by investigating its effects on immune modulation, mitochondrial function, and tissue integrity.<br><br>METHODS: EAE was induced in mice using myelin oligodendrocyte glycoprotein. Isolated mitochondria were administered intravenously, and clinical progression, spinal cord histology, immune cell populations, mitochondrial activity, fibrosis, and gut microbiota composition were assessed. Additionally, human peripheral blood mononuclear cells (PBMCs) from MS patients were co-cultured with mitochondria to examine ATP production, reactive oxygen species levels, and T cell differentiation.<br><br>RESULTS: Mitochondrial transplantation significantly reduced EAE severity, spinal cord inflammation, demyelination, and fibrosis. Treated mice showed increased regulatory T (Treg) cells, reduced T helper 17 (Th17) cells, improved mitochondrial biogenesis, and decreased oxidative stress. Gut microbiome analysis revealed beneficial compositional changes. In human PBMCs, mitochondrial transfer enhanced ATP synthesis, suppressed mitochondrial ROS, and promoted Treg differentiation while inhibiting pro-inflammatory cytokines.<br><br>DISCUSSION: Our findings suggest that mitochondrial transplantation restores mitochondrial function, rebalances immune responses, and mitigates neuroinflammation and fibrosis in EAE. This approach offers a novel therapeutic strategy for MS by addressing both metabolic and immunological drivers of disease progression.}, }
@article {pmid41918743, year = {2026}, author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F}, title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745166}, pmid = {41918743}, issn = {1664-3224}, mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; }, abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.<br><br>METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.<br><br>RESULTS AND DISCUSSION: On average, 23.29% &#xb1; 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% &#xb1; 17.88%), pyelonephritis (22.75% &#xb1; 12.91%), asymptomatic bacteriuria (18.17% &#xb1; 17.14%)] and 30.63% &#xb1; 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% &#xb1; 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.}, }
@article {pmid41918843, year = {2026}, author = {Huang, Q and Liang, Z and Cui, Y and Diao, J and Zhou, T and Shi, L and Deng, Z and Wang, R and Yuan, H and Chen, K and Du, Y and Chen, A and Chen, J and Xiao, W}, title = {Uremic Clearance Granules Regulate Immune Equilibrium via Gut Microbiome to Alleviate Chronic Renal Failure.}, journal = {Biomaterials research}, volume = {30}, number = {}, pages = {0342}, pmid = {41918843}, issn = {1226-4601}, abstract = {Chronic renal failure (CRF) is the common end point of various chronic kidney diseases, and there is currently no specific drug for CRF. Effectively halting its progression remains a clinical challenge. Gut microbiota disorders are a key factor influencing immune dysfunction in chronic kidney disease patients. Intervening in gut microbiota to improve immune regulatory function in patients could serve as a new strategy for treating CRF with Traditional Chinese Medicine. Uremic Clearance Granules (UCG), a Traditional Chinese Medicine formulation, effectively attenuate CRF progression, but their active components and mechanisms remain undefined. This study investigates how UCG mitigate CRF via coordinated regulation of gut microbiota, metabolites, and the T helper 17 cells / regulatory T cell axis. Using an adenine-induced CRF mouse model, we combined gut microbiota depletion, fecal microbiota transplantation, 16S rRNA sequencing, and metabolomics to delineate the gut-kidney interactions underlying UCG efficacy. Flow cytometry quantified immune cell profiles in blood, and microbial intervention experiments verified the therapeutic role of Bifidobacterium animalis (B. animalis). In this study, we found that UCG treatment alleviated renal injury, reduced intestinal permeability, and up-regulated intestinal barrier markers. Microbiota depletion and fecal microbiota transplantation demonstrated that UCG's renoprotective effects depend on gut microbial modulation. Specifically, UCG ameliorates CRF through gut-kidney axis remodeling by enhancing B. animalis abundance and sophocarpine, thereby rebalancing T helper 17/regulatory T immunity and preserving renal function. These findings identify a microbiota-dependent immunometabolic mechanism for UCG and highlight a potential therapeutic strategy for CRF via the drug-microbiota axis.}, }
@article {pmid41918857, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M}, title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20990}, pmid = {41918857}, issn = {2167-8359}, mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; }, abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.<br><br>METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.<br><br>RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.}, }
@article {pmid41918873, year = {2026}, author = {Duan, Y and Yang, M and Li, M and Sun, Y and Liu, S}, title = {Microbiome and metabolite signatures for cirrhosis to HCC risk stratification: progress, controversies, and gaps.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1793213}, pmid = {41918873}, issn = {2235-2988}, mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/metabolism/pathology/etiology ; *Liver Cirrhosis/microbiology/metabolism/complications/pathology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/microbiology/metabolism/pathology/etiology ; Fatty Acids, Volatile/metabolism ; Risk Assessment ; Disease Progression ; Dysbiosis ; Bile Acids and Salts/metabolism ; }, abstract = {The progression from cirrhosis to hepatocellular carcinoma (HCC) is a key outcome in the management of chronic liver disease. This process has a long incubation period and significant individual differences, making early warning still difficult. Clinical follow-up mainly relies on imaging examinations and alpha fetoprotein, but the ability to identify high risk precancerous states is limited. The imbalance of gut microbiota and its metabolites may occur earlier than the visible stage of tumors. They can affect barrier integrity, chronic inflammation, immune surveillance, and metabolic homeostasis through the gut liver axis, and participate in the formation of a pro tumor microenvironment. Therefore, such changes may provide more upstream risk stratification clues for the population with cirrhosis. This article summarizes previous research evidence and summarizes the common microbiome and metabolite characteristics of cirrhosis and high-risk populations, including a decrease in short chain fatty acid (SCFA) related symbiotic bacteria, an increase in inflammation related bacteria, bile acid spectrum shift, and other intestinal derived metabolite abnormalities. This article also outlines the key mechanisms that these features may correspond to, such as barrier damage and microbial translocation, immune suppression, etc. There are still significant uncertainties at present. The effect of SCFA is context dependent. Different etiologies, diets, medications, and complications can lead to significant confounding and affect cross cohort consistency. Subsequent research requires longitudinal cohort validation and the promotion of multi omics integration and the construction of interpretable predictive models to support clinical translation.}, }
@article {pmid41918874, year = {2026}, author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D}, title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1782744}, pmid = {41918874}, issn = {2235-2988}, mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; }, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.<br><br>METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.<br><br>RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-&#x3b1; and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.<br><br>DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.}, }
@article {pmid41918946, year = {2026}, author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG}, title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41918946}, issn = {2312-0541}, abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.<br><br>METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32&#x2005;weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and &#x3b1;-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).<br><br>CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.}, }
@article {pmid41918963, year = {2026}, author = {Athithan, P and Ishaq, SL and Allen-Vercoe, E and O'Doherty, KC}, title = {Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems.}, journal = {Sustainable microbiology}, volume = {}, number = {}, pages = {}, pmid = {41918963}, issn = {2755-1970}, support = {R15 DK133826/DK/NIDDK NIH HHS/United States ; }, abstract = {All organisms on the planet intrinsically rely on microbial ecosystems, and there are increasing calls from research communities to consider microbiota when administering personal or public health, ecosystem health, and the use of microbiota in personal or environmental health remediation, such as reducing the impacts of climate change, or protecting at-risk habitats which host rare microbiota. Through our collective work on the integral nature of microbiomes to host and environmental health, on health policy, and on the development of research and policy agendas, we have previously developed the concept of 'microbiome stewardship' and guidelines to promote consideration of microbial communities broadly or in specific scenarios. The practicality of stewarding one versus many microbiota is highly contextual, and will require different strategies for different scales of conservation. Here, we provide scientific arguments for the need for microbial stewardship, examples of possible solutions scaled to different ecological challenges or conservation goals, discourse on the logistical challenges which have been cited by research communities, and opportunities to use cutting-edge microbiome concepts and technology to implement large-scale interventions.}, }
@article {pmid41918966, year = {2026}, author = {Jiang, W and Liu, J and Chen, A and Zhao, T and Xu, Z and Xu, L and Du, Y and Guan, X and Ding, J and Liu, Y and Sun, D}, title = {Antimicrobial Peptides as Novel Ecological Approaches to Caries Prevention.}, journal = {Drug design, development and therapy}, volume = {20}, number = {}, pages = {592732}, pmid = {41918966}, issn = {1177-8881}, mesh = {*Dental Caries/prevention &amp; control/microbiology ; Humans ; *Antimicrobial Peptides/pharmacology/chemistry ; Biofilms/drug effects ; Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology/chemistry ; }, abstract = {Antimicrobial strategies have consistently been a central theme in caries prevention research. Due to their potent antibacterial properties and the potential for multifunctionality through sequence modification, antimicrobial peptides (AMPs) are emerging as promising candidates for anticaries therapeutics. Traditional investigations primarily focused on the broad-spectrum bactericidal efficacy of AMPs to eradicate cariogenic bacteria; however, this approach may inadvertently harm the beneficial oral microbiome. With advancing knowledge of oral microecology, the focus has progressively shifted towards ecological approaches. These strategies aim to selectively modulate cariogenic populations or the disease-associated microbiota while preserving microbial diversity and maintaining ecological balance, as demonstrated in multispecies biofilm models and sequencing-based microbiome analyses. Current innovations include targeting specific pathogens, regulating virulence factors, utilizing bio-responsive mechanisms within the cariogenic microenvironment, and disrupting dental plaque biofilms. This article reviews the current progress and limitations of antimicrobial peptide-based ecological approaches to caries control and offers valuable insights for the future design and optimization of antimicrobial peptides with microecology regulating effects or other promising functions aiding caries prevention.}, }
@article {pmid41918983, year = {2026}, author = {Weingarden, AR}, title = {Strengths and limitations of in vitro and animal models to advance understanding of human diet‒microbiome interactions.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2636336}, pmid = {41918983}, issn = {2993-3935}, abstract = {The gut microbiome is a critical mediator of human health. As the intestinal microbiota is far more metabolically diverse than humans, it plays a significant role in the digestion of food, particularly food components that are nutritionally inaccessible to the human host. While no system can fully recapitulate the in vivo interactions of food, the host, and the gut microbiome in the human body, in vitro and animal model tools are critical for studying these complex relationships. Here, we review many of the common in vitro and animal models used to manipulate and study how the gut microbiome affects and is affected by diet. We focus on colonic fermentation systems, with or without small intestinal contribution, bioreactors with both microbial and host epithelial cell components, and animal models that have been developed to study these relationships. We will review the limitations of these systems while also discussing new innovations that seek to address these limitations.}, }
@article {pmid41918985, year = {2026}, author = {Keskey, R and Meltzer, R and Toni, T and Hyoju, S and Cohn, E and Cao, J and Benjamin, A and Lam, A and Zaborin, A and Zaborina, O and Alverdy, J}, title = {Microbiota-accessible carbohydrates enhance gut microbiota stability and antibiotic resilience through production of quorum sensing molecule AI-2.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2646055}, pmid = {41918985}, issn = {2993-3935}, abstract = {Dietary fiber and fat shape the gut microbiota and human health, yet their role in modulating the response of the microbiota to antibiotics remains underexplored. We hypothesized that dietary fiber, independent of fat content, mitigates antibiotic-induced weight loss and diarrhea in a microbiota-dependent manner. Mice were fed refined diets varying in fat and fiber contents for 6 weeks, compared to a standard plant-based chow diet. Following antibiotic administration, fiber consumption independent of fat reduced diarrhea and weight loss. High-fiber diets increased Bacteroidetes and decreased Firmicutes and Proteobacteria prior to antibiotic exposure, all of which correlated with elevated cecal short-chain fatty acids (SCFAs). Fermentable fiber increased AI-2 quorum-sensing pathway activity and improved Firmicutes resiliency to antibiotics. Supplementation with AI-2 reduced antibiotic-induced weight loss in mice fed high-fat, low-fiber diets. These findings suggest that fermentable fiber alters the gut microbiota composition and function, enhancing microbial resiliency and host tolerance to antibiotics. Dietary supplementation with microbiota-accessible fiber increased AI-2 production, stabilized Firmicutes populations, and attenuated antibiotic-associated weight loss, independent of dietary fat content.}, }
@article {pmid41919041, year = {2026}, author = {Bizzarri, E and Proietti, S and Falconieri, GS and Caruso, C and Bertini, L}, title = {Exploring the molecular landscape of environmental responses in the Antarctic plant Colobanthus quitensis: insights from metatranscriptomic analysis.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1774223}, pmid = {41919041}, issn = {1664-462X}, abstract = {INTRODUCTION: The harsh environmental conditions of Antarctica significantly influence plant responses, impacting both defence mechanisms and developmental processes. Moreover, plant-associated microbial communities further modulate physiological functions, creating a complex network of interactions. This study aimed to investigate how local environmental conditions and plant-associated microbiota shape the transcriptomic landscape of the Antarctic plant Colobanthus quitensis.<br><br>MATERIALS AND METHODS: A comparative metatranscriptomic analysis was conducted on plants collected from three sites spanning a coastal-to-inland gradient of increasing climatic severity to investigate both the functional roles of differentially expressed plant genes and taxonomic profiling of the associated microbial community. In addition, the content of photosynthetic and protective pigments was quantified biochemically to assess whether environmental conditions influence the photosynthetic pathway.<br><br>RESULTS AND DISCUSSION: The results suggested that Site 2 (Puchalski Station) represents a particularly favourable microenvironment that optimises the physiological performance of C. quitensis, supporting enhanced homeostasis and the activation of multiple stress-response strategies. Furthermore, distinct variations in microbial community composition were observed across the sites, underscoring the interplay between local environment and plant-associated microbiota.<br><br>CONCLUSIONS: These findings highlight the sensitivity of C. quitensis to minor environmental changes and suggest that its associated microbiome could serve as an early-warning system for ecological change in Antarctica.}, }
@article {pmid41919346, year = {2025}, author = {Berretta, A and Schwab, C}, title = {Fermentation-driven interactions of gut microbes with their environment.}, journal = {Essays in biochemistry}, volume = {69}, number = {6}, pages = {}, doi = {10.1042/EBC20253057}, pmid = {41919346}, issn = {1744-1358}, mesh = {*Fermentation ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Butyrates/metabolism ; }, abstract = {The gut microbiome has gained a lot of attention in recent decades due to the multitude of interactions it has with the host. One of the main ways the microbiota communicates with the host is through the fermentation of dietary or host-derived nutrients. Fermentation of carbohydrates and amino acids yields structurally and compositionally different metabolites that have distinct functionality within the gut microbial community but also in the interaction with the host. The most abundant fermentation metabolites are the short-chain carboxylic acids acetate, butyrate, and propionate. While important contributions to host health have been attributed to these three, there are other compounds formed by fermentation whose relevance in the gut becomes increasingly recognized. In this essay, we will present how gut physiological properties relate to microbial fermentation capacity. We will introduce the diversity of fermentation pathways and relate functionality to the intrinsic properties of fermentation-derived metabolites. Finally, we will present strategies to restore disrupted fermentation activity.}, }
@article {pmid41919524, year = {2026}, author = {Jain, A}, title = {Advances in New Approach Methodologies for Assessing ADME Properties of Nano-formulations.}, journal = {Xenobiotica; the fate of foreign compounds in biological systems}, volume = {}, number = {}, pages = {1-36}, doi = {10.1080/00498254.2026.2653145}, pmid = {41919524}, issn = {1366-5928}, abstract = {Conventional animal models face ethical concerns and scientific limitations, as interspecies differences often fail to capture the unique pharmacokinetics of nanomaterials.This review highlights advances in Non-Animal Models, including organoid-based systems that replicate human tissue structure, microfluidic organ-on-chip platforms that mimic dynamic physiology, and computational approaches such as physiologically based pharmacokinetic (PBPK) modelling, molecular dynamics, and machine learning.Innovations such as vascularized organoids, multi-organ chip networks, and artificial intelligence-driven refinement are evaluated for their potential to improve predictive accuracy.Remaining challenges, including scalability, standardisation, and incorporation of immune and microbiome components, are critically discussed.By integrating technological advances with regulatory perspectives, this review underscores New Approach Methodologies as a transformative pathway toward more ethical, human-relevant, and predictive nanomedicine development.}, }
@article {pmid41919539, year = {2026}, author = {Liu, J and Sun, Y and Wu, J and Tang, S and Ding, G}, title = {[Comparative analysis of microbial communities in different oral ecological niches of preschool children].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {44}, number = {2}, pages = {197-205}, doi = {10.7518/hxkq.2025.2025285}, pmid = {41919539}, issn = {2618-0456}, mesh = {Humans ; Child, Preschool ; *Microbiota ; Child ; *Mouth Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; *Tongue/microbiology ; *Bacteria/classification/genetics ; *Tooth/microbiology ; *Dental Plaque/microbiology ; Male ; Mouth/microbiology ; }, abstract = {OBJECTIVES: This study aims to investigate the structural differences, dominant bacterial genera, and potential functions of microbial communities in different oral ecological niches (dorsal tongue, tooth surface, and buccal mucosa) of preschool children to clarify the influence of local microenvironments on microbial colonization and provide a theoretical basis for the microbiota-targeted regulation of pediatric oral diseases.<br><br>METHODS: A total of 105 plaque samples were collected from the dorsal tongue, tooth surface, and buccal mucosa of 35 healthy preschool children (aged 4-6 years). High-throughput sequencing of the 16S rRNA gene was performed to analyze the microbial community structure and alpha/beta diversity. Principal coordinate analysis, UPGMA clustering, and LEfSe analysis were used to identify niche-specific dominant genera. PICRUSt2 was applied to predict the potential metabolic functional profiles across niches.<br><br>RESULTS: Spatial hete-rogeneity in microbial composition and structure was observed across the three oral niches. Species richness was significantly higher on the tooth surface and buccal mucosa than on the dorsal tongue. The dominant phyla included Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Fusobacteria, and Patescibacteria. At the genus level, Actinomyces and Corynebacterium were enriched on the tooth surface, Veillonella was enriched on the dorsal tongue, and Streptococcus was predominant on the buccal mucosa. Beta diversity and clustering analyses confirmed distinct microbial community structures among the niches. LEfSe analysis identified several niche-specific genera. PICRUSt2 functional prediction revealed significant differences in amino acid metabolism, carbohydrate metabolism, cell motility, translation, signal transduction, immune system, infectious disea-ses, and membrane transport (P<0.05).<br><br>CONCLUSIONS: The dorsal tongue, tooth surface, and buccal mucosa in preschool children harbor distinct microbial communities with different taxonomic composition, diversity, and functional potential. The findings suggest that local microenvironmental factors shape oral microbiota and may contribute to the early onset of oral diseases. This study provides foundational data and theoretical insights for early microbiome-based risk assessment and personalized oral health interventions in children.}, }
@article {pmid41919541, year = {2026}, author = {Xu, Y and Wang, S and Zhou, J}, title = {[Oral homeostasis imbalance under hypoxia].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {44}, number = {2}, pages = {215-223}, doi = {10.7518/hxkq.2026.2025427}, pmid = {41919541}, issn = {2618-0456}, mesh = {*Homeostasis ; Humans ; *Hypoxia/physiopathology ; Mouth Mucosa/physiopathology ; Microbiota ; Salivary Glands/physiopathology ; Bone Remodeling ; }, abstract = {Hypoxia disrupts oral homeostasis through multiple interconnected pathways, including interference with tooth germ development, impairment of salivary gland function and salivary buffering capacity, compromise of the oral mucosal barrier, imbalance in jawbone and alveolar bone remodeling, and alterations in the diversity and functionality of the oral microbiome. These disturbances collectively contribute to the onset and progression of oral diseases. Moreover, disruption of oral homeostasis may, in turn, affect systemic homeostasis, increasing the risk of disorders in other organ systems through mechanisms involving inflammatory mediator release and microbial translocation. Here, we systematically review the effects and underlying mechanisms of hypoxia exposure on oral homeostasis, and further explore the interconnections between hypoxia-induced oral dysregulation and systemic homeostatic imbalance. This review aims to provide a comprehensive understanding of the regulatory networks linking oral and systemic homeostasis under hypoxia, thereby offering potential insights for maintaining homeostatic balance.}, }
@article {pmid41919563, year = {2026}, author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W}, title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.70091}, pmid = {41919563}, issn = {1522-7278}, abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.}, }
@article {pmid41919917, year = {2026}, author = {Mall, A and Rode, KJ and Marx, CJ}, title = {Evolution uncovers a general tradeoff between recovery after heat shock and growth at elevated temperatures.}, journal = {mBio}, volume = {}, number = {}, pages = {e0330525}, doi = {10.1128/mbio.03305-25}, pmid = {41919917}, issn = {2150-7511}, abstract = {Fitness tradeoffs between different environments enable the maintenance of microbial diversity. While the importance of tradeoffs is clear, it has been surprisingly difficult to predict which traits they will occur between and at how granular a level. For example, it is unclear whether performance between a constant versus pulsed exposure of the same stress tends to be positively correlated, independent of each other, or negatively correlated. Empirically, it has been shown that a critical feature structuring microbial communities is temperature. However, the compatibility between strategies to deal with different forms of heat stress is unclear. For instance, are strains that grow well at higher temperatures also stronger at withstanding heat shock? To understand how environmental microbes can adapt to better deal with heat stress, we performed an evolution experiment using a dominant phyllosphere microbe Methylobacterium extorquens in a regime of intermittent heat shock. We identified the genetic basis of adaptation, discovering a large number of loci capable of mediating adaptation to heat shock, many of which had not been previously linked to heat stress. Despite the genetic divergence among evolved isolates, we discovered a general tradeoff between heat shock resistance and growth at consistently elevated temperatures. We found this tradeoff was not limited to evolved isolates, but also represented across a sample of environmentally isolated Methylobacterium strains. These findings indicate a generic conflict between strategies to deal with heat shock recovery and growth at elevated temperatures, suggesting even variation in intensities of a stressor can drive diversity in microbial strategies.IMPORTANCEOne of the key forces shaping the microbial diversity in nature is temperature. However, temperature in ecological settings is variable, and it is unknown if strategies to deal with different intensities of high temperature are compatible or not. Using evolution experiments, we identify the genetic basis of adaptation to heat shock in Methylobacterium extorquens, a dominant member of the phyllosphere microbiome. We discover a number of genetic targets where beneficial mutations improve heat shock resistance, most of which have not been implicated with heat stress before. For both the evolved isolates and a set of environmentally isolated Methylobacterium strains, we discover a general tradeoff between recovery after heat shock and growth at elevated temperatures. While the strategies to deal with increasing temperatures have garnered significant interest, our results suggest that even different intensities of heat stress can select for distinct and incompatible strategies and can drive microbial diversification in ecological settings.}, }
@article {pmid41919968, year = {2026}, author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C}, title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0039226}, doi = {10.1128/aem.00392-26}, pmid = {41919968}, issn = {1098-5336}, abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.}, }
@article {pmid41920102, year = {2026}, author = {Bruyere, D and Delahaye, T and Nikkels, A and Herfs, M}, title = {Pathophysiology of cutaneous commensal human papillomaviruses.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.02.011}, pmid = {41920102}, issn = {1523-1747}, abstract = {Cutaneous human papillomaviruses (HPVs), particularly those of the β-genus, have traditionally been viewed as harmless constituents of the skin microbiome. However, a debate has emerged over the past few years regarding their possible contribution to cancer development. In immunocompetent hosts, commensal β-HPVs may contribute to immune education and cutaneous homeostasis. In contrast, under immunosuppression, their increased viral load (combined with UV-induced DNA damage) can promote early oncogenic events and facilitate cancer initiation, through a "hit-and-run" mechanism. This context-dependent behavior defines β-HPVs as dynamic modulators of skin health, capable of exerting protective or pathogenic effects within the cutaneous ecosystem depending on host and environmental factors.}, }
@article {pmid41731377, year = {2026}, author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M}, title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41731377}, issn = {1471-2180}, abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots.<br><br>RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma.<br><br>CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04837-8.}, }
@article {pmid41909894, year = {2025}, author = {Hensen, T and Ahmad, S and Kastenmüller, G and Kraaij, R and Ghanbari, M and Ikram, A and Kaddurah-Daouk, R and Thiele, I}, title = {In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2443171}, pmid = {41909894}, issn = {2993-3935}, support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, abstract = {The gut microbiome has become increasingly recognized for its role in the pathogenesis of Alzheimer's disease (AD) and is thought to influence AD pathogenesis via metabolic crosstalk with the host. However, mechanistic pathways connecting the gut microbiome to AD pathogenesis remain unknown. To explore potential mechanistic pathways in AD pathogenesis, we created host-microbiome whole-body metabolic models personalized with 16S rRNA microbiome data and predicted emergent metabolic contributions of gut microbiomes. We analyzed 63 metabolites in blood with previously known links with AD. These in silico predictions were then associated with major risk factors for AD in a cohort of 1,065 aging non-AD individuals and subsequently used to inform targeted analyses on serum metabolomics. Our analysis identified increased host-microbial production of L-arginine in older individuals. Lower production of deoxycholate correlated with the neuroprotective APOE E2 allele and it decreased with higher global cognition. Serum metabolomics from the same individuals of cholesterol products and bile acid metabolism corroborated the modeling predictions, suggesting a potential link between the APOE genotype and cognitive health. In conclusion, this study associated metabolic gut microbiome influences on human metabolism with risk factors for AD and identified cholesterol and bile acid metabolism to potentially link with AD pathogenesis.}, }
@article {pmid41909897, year = {2025}, author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M}, title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2527766}, pmid = {41909897}, issn = {2993-3935}, abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.}, }
@article {pmid41909899, year = {2025}, author = {Rozenberga, M and Saksis, R and Elbere, I and Birzniece, L and Briviba, M and Konrade, I and Klovins, J}, title = {Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2482771}, pmid = {41909899}, issn = {2993-3935}, abstract = {Recent studies propose the existence of a blood microbiome, but its composition, origin, and dynamics remain largely unresolved. In this pilot study, we analyzed the bacterial DNA present in the blood of 10 volunteers by comparing the taxonomic profiles of 16S rRNA gene sequences from skin, vaginal, oral, and fecal samples. After applying stringent decontamination protocols, we detected bacterial DNA in all blood samples, predominantly from the Pseudomonas genus. A key finding was the identification of 32 unique Amplicon Sequence Variants (ASVs) that were identical between blood and a single body site within individual participants, with no overlap between multiple body sites or across different participants. This participant-specific overlap suggests a true biological origin of bacterial DNA in blood, likely stemming from localized bacterial migration, such as from the skin. Additionally, 27.4% of the ASVs in blood were found in other body sites, with the highest overlap observed in skin samples. Furthermore, 25.3% of blood ASVs persisted after three months, suggesting a consistent pattern in the bacterial DNA composition detected in blood over time. These findings deepen our understanding of the blood microbiome and provide a basis for future research linking blood microbiota to health and disease phenotypes.}, }
@article {pmid41909901, year = {2025}, author = {Teo, Y and Lavrinienko, A and Albertos Torres, D and Asare, PT and Ruder, A and Dominguez-Bello, MG and Egli, A and Bokulich, NA and Vonaesch, P}, title = {Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2594958}, pmid = {41909901}, issn = {2993-3935}, abstract = {UNLABELLED: The gut microbiome plays a fundamental role in human health, prompting efforts to catalog and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cultivation remains essential for mechanistic studies and therapeutic development. However, best practices for long-term stool preservation remain limited. Here, we compared the stability of eight cryopreservation treatments for maintaining viable stool microbiota over a 1-y storage period at -80 °C (freezer) or at -196 °C (liquid nitrogen) using samples from infants, children, and adults. Combining cultivation on six media with 16S rRNA sequencing, we show that ultralow-temperature cryopreservation has a minimal impact on microbiota diversity compared to fresh cultures. Standard glycerol preservation and simple snap-freezing performed comparably to more complex and costly protocols, with all cultured samples retaining donor-specific microbiota profiles after long-term cryopreservation. The lack of strong treatment-specific effects on microbiota composition suggests a shared microbial response to freeze‒thaw stress favoring taxa with broad environmental tolerance. Our findings offer practical, low-cost strategies for stool biobanking.<br><br>IMPORTANCE: The cultivation of bacterial taxa from complex communities, such as those in fecal samples, is essential for mechanistic studies and the development of microbiota-based therapeutics, including defined consortia and individual probiotic strains. Such cultivation efforts typically rely on previously stored samples; however, systematic knowledge regarding long-term preservation strategies that ensure the viability and regrowth of constituent bacterial taxa remains limited. In this study, we systematically evaluated 16 distinct cryopreservation conditions to assess their efficacy in maintaining bacterial viability. Our results show that conventional glycerol-based preservation and simple snap-freezing are comparable in performance to more elaborate and cost-intensive protocols. Moreover, we identified the duration of sample transport prior to freezing as a critical determinant of post-thaw bacterial recovery. These findings provide valuable data on the relative effectiveness of various preservation methods and support the use of low-cost, easily implementable strategies that are particularly suitable for application in resource-limited settings.}, }
@article {pmid41909902, year = {2025}, author = {Andalib, KMS and Rodosy, FB and Habib, A}, title = {The living medicine inside us: in vitro therapeutic prospects of human gut bacteria.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2480093}, pmid = {41909902}, issn = {2993-3935}, abstract = {Gut microbial metabolism is intimately coupled to host health and disease. Recent knowledge on potential health benefits of gut microbiome lays the groundwork for development of novel therapeutic strategies. But how microbiota-derived metabolites impact on host-microbiome crosstalk remains untapped from therapeutic perspectives. In this study, six gut bacteria sourced from a fecal pool of forty healthy donors were cultured in three distinct growth media. Subsequently, the bacteria were identified through 16S rRNA gene sequencing and subjected to metabolite extraction to evaluate their anti-microbial, anti-oxidant and anti-thrombotic potential. Findings reveal strong anti-oxidant activities in the metabolic-extracts from all the isolates. Metabolites derived from Lactobacillus rhamnosus, Priestia flexa and Bacillus subtiilis inhibited the growth of clinically pathogenic strains Escherichia coli ATCC-8739, Salmonella typhi ATCC-1408 and Staphylococcus aureus ATCC-6538. Escherichia fergusonii originated metabolites demonstrated the highest efficacy in lysing blood clots compared to streptokinase. Additionally, extracts from all the isolates exhibited significant ability to delay coagulation time, competing with standard warfarin. Thus, the findings of our early-stage study provide novel insights into metabolomic functions of gut microbiota. This study underscores the significance of exploring these active metabolites for prospective therapeutic and clinical exploration at the intersection of drug discovery and live bio-therapeutics.}, }
@article {pmid41909904, year = {2025}, author = {Ramakrishnan, M and Cross, TL and Organski, AC and Saiprasad, SM and Simpson, AMR and Tancredi, DJ and Van Haute, MJ and Christensen, CM and Lewis, ZT and Auchtung, TA and Walter, J and Hutkins, R and Savaiano, DA}, title = {Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2508199}, pmid = {41909904}, issn = {2993-3935}, abstract = {Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, from the fecal sample of a human donor after consumption of galactooligosaccharides (GOS), a prebiotic derived from lactose. Therefore, it was hypothesized that iVS-1 might reduce symptoms associated with lactose maldigestion. Compared to other probiotic strains, iVS-1 had high β-galactosidase activity and reduced gas formation by fecal communities during in vitro fermentations of lactose or milk. A randomized placebo-controlled clinical trial was then conducted with 21 lactose maldigesters, randomized to receive either B. adolescentis iVS-1 (n = 11) or placebo (n = 10) daily for 2 weeks. Compared to the two-week run-in period, iVS-1 abundance was higher both at the end of the treatment period (p = 0.0005) and after the 2-week post-treatment period (p = 0.045). The iVS-1 group reported less overall daily symptoms during the treatment period when compared to placebo (p = 0.032) and had significant improvement for fecal urgency (p = 0.033) and diarrhea (p = 0.006). The metabolism of lactose, reduction of gas, and improvement of multiple gastrointestinal symptoms suggest that B. adolescentis iVS-1 may be an effective treatment for lactose intolerance. Trial Registration: The trial is registered at ClinicalTrials.gov (https://clinicaltrials.gov/study/NCT05668468).}, }
@article {pmid41909905, year = {2025}, author = {Chakraborty, J and Lanchenba Singh, N and Kumar Das, B}, title = {Gut microbiome and lung cancer: mechanisms, interactions, and dietary interventions.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2501313}, pmid = {41909905}, issn = {2993-3935}, abstract = {Lung cancer continues to claim countless lives globally. Several studies have shown that the gut microbiome is vital in maintaining healthy lung function through the gut-lung axis. A comparison between the gut microflora of healthy volunteers and lung cancer patients revealed that changes in the composition of gut microflora occur in lung cancer patients. The gut microflora may contribute to lung cancer by influencing immune reactions, inflammatory pathways, bacterial metabolites modulating host metabolism, microbiome dysbiosis, genotoxicity, virulence, and bacteria-induced epigenetic alterations. Thus, it may be assumed that maintaining a healthy gut microflora could help prevent lung cancer. Nutraceuticals are specialized products designed to support health and address specific nutritional needs. They contain ingredients like vitamins, minerals, probiotics, polyphenols, and herbs to reduce the risk or impact of certain illnesses. Nutraceuticals, including probiotics and polyphenols, play a role in preventing and treating various cancers, including lung cancer, by modulating the gut microbiome. This review examines the link between the gut microbiome and lung cancer, how it contributes to cancer development, and the impact of dietary interventions - particularly probiotics, polyphenols, and dietary fibers - on lung cancer prevention and treatment.}, }
@article {pmid41909906, year = {2025}, author = {Shibi Anilkumar, A and Thomas, SM and Veerabathiran, R}, title = {Gut microbial metabolites as a convergence point between autoimmunity and solid tumors.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2470805}, pmid = {41909906}, issn = {2993-3935}, abstract = {The human gut microbiome, a diverse community of trillions of microorganisms, is essential for controlling numerous bodily functions, such as metabolism, immune response, and epithelial barrier integrity. The gut microbiota comprises bacteria, viruses, fungi, and other microorganisms that affect human health, metabolic pathways, and immune responses. Dysbiosis, or the imbalance of gut microbial composition, has been linked to the pathogenesis of several ailments, including cardiovascular conditions, gastrointestinal conditions, allergies, obesity, autoimmune disorders, and tumors. The interaction between gut microbes and immune responses, mainly through Tregs cells and Th17 cells, underscores the microbiome's function in immune regulation. Furthermore, gut microbial metabolites act as signaling molecules and substrates for metabolic processes, impacting autoimmune disorders and cancer development. Recent research highlights the microbiome's potential role in cancer immunoediting, where gut microbial metabolites may either promote or suppress cancer progression by modulating inflammation and immunosuppression. This review delves into the critical functions of the gut microbiome, its influence on autoimmune disorders, and the emerging connection between gut microbial metabolites and cancer immunoediting, offering new insights into their impact on human health and disease.}, }
@article {pmid41909907, year = {2025}, author = {Ishii, C and Suzuki, M and Murakami, S and Song, I and Soejima, Y and Kato, M and Fukuda, S}, title = {Ecologically robust gut environment associated with personalized metabolic responses in a Japanese cohort.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2574930}, pmid = {41909907}, issn = {2993-3935}, abstract = {The gut microbiota produces numerous metabolites that affect host physiology. However, the effects of daily diet on human fecal metabolome profiles and their robustness are not well understood, and examinations of intra-individual stability over multiple time points are limited. Here, we investigated the robustness of the human intestinal environment through fecal metabolome and microbiome profiling in response to daily dietary fluctuations. We analyzed 176 fecal samples from 25 healthy Japanese individuals subjected to three dietary regimens, including heterogeneous and homogeneous diets. Fecal metabolome and microbiome profiles were unique to each individual. Further in-depth analyses of seven of these individuals showed that these profiles were stable despite daily dietary fluctuations in six individuals. In addition, random forest classification successfully predicted each subject's identity based on their metabolome profile. The correlation analysis also revealed that the food-metabolite and food-microbiome relationships were highly personalized. The findings from this study suggest that individual diet prior to sample collection is unlikely to influence the fecal metabolome and microbiome data to an extent that is not representative of the individual's "normal" condition, which may lower barriers to future research on the gut environment and its implications for host health.}, }
@article {pmid41909910, year = {2025}, author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J}, title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2570502}, pmid = {41909910}, issn = {2993-3935}, abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.}, }
@article {pmid41909911, year = {2025}, author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO}, title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2589861}, pmid = {41909911}, issn = {2993-3935}, abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.}, }
@article {pmid41910033, year = {2026}, author = {Jinato, T and Sikaroodia, M and Gilleveta, PM and Dissayabutra, T and Tangkijvanich, P and Bajaj, JS and Chuaypen, N}, title = {Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70358}, pmid = {41910033}, issn = {1440-1746}, support = {C2F//Second Century Fund/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; HEA_FF_68_159_3000_028//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF68//Fundamental Fund 2025/ ; B36G660004//Program Management Unit for Human Resources &amp; Institutional Development, Research and Innovation/ ; }, abstract = {BACKGROUND: Gut microbiota, microbial metabolites, and inflammatory cytokines play key roles in the pathogenesis of cirrhosis and hepatocellular carcinoma (HCC); however, data from Southeast Asia are limited. This study examined microbial composition, intestinal permeability, butyrate-related gene expression, and cytokine profiles in Thai patients with cirrhosis, with and without HCC.<br><br>METHODS: This cross-sectional study included 30 healthy controls, 33 patients with cirrhosis without HCC, and 44 patients with HCC (HCC-cirr). Fecal samples were analyzed using 16S rRNA sequencing. Microbial functional profiles were predicted using KEGG Orthology-based pathway inference. Gut permeability markers (intestinal fatty acid-binding protein [I-FABP] and lipopolysaccharide-binding protein [LBP]), butyrate-associated gene (BCoAT) expression, and cytokine profiles were assessed.<br><br>RESULTS: Alpha diversity (Chao1) was significantly lower in HCC-cirr patients than in healthy controls (p&#x2009;<&#x2009;0.001) and patients with cirrhosis (p&#x2009;=&#x2009;0.008). Beta diversity also differed significantly between HCC-cirr and controls (p&#x2009;=&#x2009;0.008). Ligilactobacillus, Catenibacterium, and Alloprevotella were enriched in the cirrhosis group, whereas HCC-cirr patients showed increased Ruminococcus gnavus and reduced butyrate producers (Coprococcus, Subdoligranulum). Functional prediction suggested pathway differences between cirrhosis and HCC-cirr, including folate, sulfur, tyrosine metabolism, and steroid biosynthesis. BCoAT expression was significantly decreased in HCC (p&#x2009;=&#x2009;0.006). Plasma LBP and I-FABP were significantly elevated in HCC-cirr (p&#x2009;=&#x2009;0.033, p&#x2009;<&#x2009;0.001), with I-FABP also higher than in cirrhosis (p&#x2009;=&#x2009;0.002). Proinflammatory cytokines (GM-CSF, IL-10, IL-18, IL-1&#x3b1;, IL-7, IL-8, and M-CSF) were elevated in HCC-cirr.<br><br>CONCLUSIONS: Among the Thai cohort, HCC with cirrhosis was associated with distinct gut microbial changes, reduced BCoAT expression, increased gut permeability, and cytokine alterations, highlighting the contribution of gut dysbiosis and microbial by-products to liver disease progression.}, }
@article {pmid41910132, year = {2026}, author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A}, title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019126}, doi = {10.1128/msystems.00191-26}, pmid = {41910132}, issn = {2379-5077}, abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.<br><br>IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.}, }
@article {pmid41910137, year = {2026}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0418725}, doi = {10.1128/spectrum.04187-25}, pmid = {41910137}, issn = {2165-0497}, abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.<br><br>IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20&#xb0;C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25&#xb0;C and 30&#xb0;C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.}, }
@article {pmid41910192, year = {2026}, author = {Saqib, S and Latousakis, D and Virtanen, S and Kalliala, I and Holster, T and Juge, N and Salonen, A}, title = {Exploratory analyses of cervicovaginal mucus O-glycan composition and microbiota profiles in unexplained infertility.}, journal = {Glycobiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/glycob/cwag023}, pmid = {41910192}, issn = {1460-2423}, abstract = {In addition to the specific causes of infertility, two components of the vaginal ecosystem, the vaginal microbiota and the cervicovaginal mucus (CVM), may be associated to reduced fecundity and the success of infertility treatments. The aim of this study was to explore the composition of the CVM O-glycans and vaginal microbiota in women with unexplained infertility. We collected CVM and vaginal swab samples during medically induced ovulation from 19 women with unexplained infertility. Mucin O-glycosylation profiles were generated through Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-ToF) mass spectrometry and taxonomic profiles of the vaginal microbiota through 16S rRNA gene amplicon sequencing. Altogether 57 O-glycan structures were identified, dominated by core 1 and 2 structures. A significant proportion, nearly 85%, of the glycans were fucosylated and five structures dominated the profiles, accounting for >50% of the glycans observed in most samples. The vaginal microbiota of the patients was dominated by Lactobacillus crispatus (79%), followed by Lactobacillus jensenii (32%) and Lactobacillus iners (21%) and Gardnerella vaginalis (5%, single sample). PERMANOVA analysis indicated significant associations between the glycan structures and dominant taxa (q = 0.0011, R2 = 0.37). This exploratory study provides initial insights into the composition and variation of CVM O-glycans in unexplained fertility and in relation to the vaginal microbiota composition, laying a groundwork for future research.}, }
@article {pmid41910204, year = {2026}, author = {Green, L and Marchesani, A and Joyner, JL}, title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag084}, pmid = {41910204}, issn = {1365-2672}, abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.<br><br>METHODS &amp; RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.<br><br>CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.}, }
@article {pmid41910238, year = {2026}, author = {Le, NNT and Xue, S and Mu, H and Wu, J and Xi, C and Marhaba, T and Zhang, W}, title = {Soil chemistry and microbiome modulation through water irrigation containing oxygen, hydrogen, and carbon dioxide nanobubbles.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0217325}, doi = {10.1128/aem.02173-25}, pmid = {41910238}, issn = {1098-5336}, abstract = {Nanobubble technology has shown considerable promise in sustainable agriculture due to its ability to enhance seed germination, plant growth, and soil quality without leaving harmful residues. While benefits are often attributed to improved soil aeration and soil texture changes (e.g., permeability), nanobubbles may also influence soil microbiome, an essential driver of plant health and nutrient cycling. This study systematically investigated how different nanobubble types-oxygen, hydrogen, and carbon dioxide-modulate soil chemistry and microbial community structure over a 4-week period. Multivariate analyses on microbiome taxonomic composition revealed distinct microbial responses to each gas type. Oxygen and hydrogen nanobubble treatments resulted in more pronounced shifts in microbial composition and functional potential compared to carbon dioxide nanobubbles. These shifts included enrichment of bacterial taxa associated with nutrient turnover, pollutant degradation, and pathogen suppression, such as Flavobacteriaceae, Comamonadaceae, Nannocystaceae, and Blastocatellaceae. Functional predictions showed that oxygen and hydrogen nanobubbles could promote metabolic pathways related to organic compound degradation and remediation of contaminated soil. Microbial network analysis further highlighted the beneficial impacts of nanobubbles on keystone taxa, such as Flavobacteriaceae, which in turn play pivotal roles in shaping soil ecosystem functions. Together, these findings demonstrate that gas-specific nanobubble irrigation can steer soil microbiome dynamics in ways that may enhance soil fertility, resilience, and crop productivity.IMPORTANCEThis study provides new insights into how nanobubble irrigation can be used to improve soil health and agricultural sustainability. By demonstrating that oxygen and hydrogen nanobubbles selectively enrich beneficial microbial taxa linked to soil nutrient turnover, pollution degradation, and pathogen suppression, this study identifies a promising approach to enhance plant growth and soil health through new nanobubble-driven processes. The detection of keystone taxa responsive to nanobubble treatments also reveals potential microbial mechanisms underlying the interactions between nanobubbles, soil, and plant health. Together, these findings highlight nanobubble irrigation as a novel and scalable strategy for microbiome engineering that could advance sustainable crop production and environmental stewardship. Furthermore, while prior studies have primarily focused on the microbial effects of air and oxygen nanobubbles, our study systematically examined and compared the impacts of less explored nanobubble types, specifically hydrogen and carbon dioxide, demonstrating the broad versatility of nanobubbles for diverse agricultural applications.}, }
@article {pmid41910252, year = {2026}, author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y}, title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0252325}, doi = {10.1128/aem.02523-25}, pmid = {41910252}, issn = {1098-5336}, abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.}, }
@article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0179025}, doi = {10.1128/msystems.01790-25}, pmid = {41910273}, issn = {2379-5077}, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.<br><br>IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, }
@article {pmid41910342, year = {2026}, author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D}, title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085625}, doi = {10.1128/msphere.00856-25}, pmid = {41910342}, issn = {2379-5042}, abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.<br><br>IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.}, }
@article {pmid41910441, year = {2026}, author = {Manti, M and Dimitriadis, K and Dri, E and Mavromoustakou, K and Vakka, A and Koutsopoulos, G and Tsioufis, P and Katsimichas, T and Siakavellas, S and Gazouli, M and Tsioufis, K}, title = {Transcatheter aortic valve implantation and gut microbiota: Rationale and design of the 'GUT-TAVI' cohort study.}, journal = {Science progress}, volume = {109}, number = {1}, pages = {368504261426427}, doi = {10.1177/00368504261426427}, pmid = {41910441}, issn = {2047-7163}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Transcatheter Aortic Valve Replacement/methods ; *Aortic Valve Stenosis/surgery/microbiology ; Prospective Studies ; Methylamines/blood ; Female ; Male ; Aged ; Cohort Studies ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Hemodynamics ; }, abstract = {ObjectiveAlterations in gut microbiota have been reported in patients with aortic valve stenosis (AVS), yet the impact of haemodynamic restoration following transcatheter aortic valve implantation (TAVI) on microbiota composition remains unclear. This study protocol describes a prospective cohort investigation designed to examine changes in gut microbiota and related metabolic markers after TAVI.Methods'GUT-TAVI' is a single-centre, prospective observational cohort study enrolling 40 adults with severe AVS undergoing TAVI. Stool samples will be collected at two timepoints (1 month to 1 day pre-TAVI and 3 months post-TAVI) for 16S-rRNA sequencing. Serum trimethylamine N-oxide (TMAO), standard biochemical markers, echocardiographic parameters, and dietary adherence scores will also be assessed. The primary endpoint is the change in gut microbiota composition following TAVI. Secondary analyses will examine associations between microbiota changes, haemodynamic parameters, and TMAO levels while accounting for potential confounders.ResultsAs a protocol, no results are yet available. Planned analyses include alpha- and beta-diversity comparisons, multi-variable modelling, sub-group analyses, and sensitivity analyses addressing antibiotic exposure and procedural variability.ConclusionsThis study may provide preliminary insights into how haemodynamic improvement after TAVI is associated with changes in gut microbiota and metabolic function. Findings may help inform future, larger-scale studies investigating the gut-heart axis in cardiovascular diseases.}, }
@article {pmid41910593, year = {2026}, author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , }, title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.}, journal = {Pancreas}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPA.0000000000002618}, pmid = {41910593}, issn = {1536-4828}, abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.<br><br>OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).<br><br>METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.<br><br>RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.<br><br>CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.}, }
@article {pmid41910796, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D}, title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41910796}, issn = {1573-7446}, abstract = {UNLABELLED: Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11259-026-11113-7.}, }
@article {pmid41910822, year = {2026}, author = {Kumar, V and Nautiyal, CS}, title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41910822}, issn = {1573-0972}, }
@article {pmid41910951, year = {2026}, author = {Dasgupta, S}, title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261419483}, doi = {10.1177/15578100261419483}, pmid = {41910951}, issn = {1557-8100}, abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.}, }
@article {pmid41911313, year = {2026}, author = {Odem, MA and Simbassa, SB and Alvarez, CF and Jeilu, O and Simar, SR and Bosserman, R and Dutta, S and Galdamez, W and Ayele, H and Hanson, BM and Proctor, DM and Krachler, AM}, title = {Shiga toxin increases intestinal transit to displace resident microbes and facilitate pathogen colonization.}, journal = {PLoS pathogens}, volume = {22}, number = {3}, pages = {e1014104}, doi = {10.1371/journal.ppat.1014104}, pmid = {41911313}, issn = {1553-7374}, abstract = {Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of food-borne illnesses, and disease severity correlates with the production of Shiga toxins. While clinical symptoms such as bloody diarrhea and haemolytic uremic syndrome have been attributed to Stx, its contribution to bacterial fitness is not well understood. Here, we demonstrate that Stx2 enhances STEC colonization of the zebrafish gut by facilitating the partial displacement of gut resident microbes. Infection with Stx2-producing STEC strains or direct exposure of fish to purified Stx2 induces alterations in the zebrafish microbiome structure, impacting several bacterial phyla and genera, notably Pseudomonads. We show that Stx2 is sufficient to facilitate these changes by accelerating intestinal transit, leading to increased expulsion of select gut microbes, including resident Pseudomonas species. Additionally, prokinetic drug treatment causes similar changes in gut transit and expulsion of Pseudomonas. Collectively, these findings detail a novel mode of action of Stx2 on the host, and shed light on its contribution to bacterial fitness within the host intestine.}, }
@article {pmid41911577, year = {2026}, author = {Kaplunova, V and Alioui, H and Griguschies, T and Müller, L and Joisten-Rosenthal, V and Lautwein, T and Metzger, S and Durán, P and Loo, E}, title = {Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media.}, journal = {The Plant journal : for cell and molecular biology}, volume = {126}, number = {1}, pages = {e70833}, pmid = {41911577}, issn = {1365-313X}, support = {390686111//Cluster of Excellence on Plant Sciences/ ; Wolf Frommer//Alexander von Humboldt-Stiftung/ ; 391465903/GRK 2466//Deutsche Forschungsgemeinschaft/ ; 458090666//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Soil/chemistry ; *Arabidopsis/growth &amp; development ; *Culture Media/chemistry ; Soil Microbiology ; Sucrose/metabolism ; Microbiota ; Plant Development ; }, abstract = {Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses of plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the absence of microbiota and soil edaphic factors on plant growth. The rapid advances in spatial omics call for accurate characterization of plants grown under conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media and on ArtSoil under various growth conditions. We showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type-specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to demonstrate its potential to decouple nutrient effects from microbiota in plant growth. We conclude that ArtSoil offers a more physiologically relevant alternative to conventional media for studying plant growth within a soil-like context.}, }
@article {pmid41911622, year = {2026}, author = {Naim, A and van Staaveren, N and Leishman, EM and Nicklas, AL and Tulpan, D and Forsythe, P and Harlander, A}, title = {Preference and behavioral responses to synbiotic supplementation via drinking water in laying hens under social stress.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106860}, doi = {10.1016/j.psj.2026.106860}, pmid = {41911622}, issn = {1525-3171}, abstract = {Synbiotics (SYN) have the potential to enhance animal health, but their efficacy depends on both biological impact and voluntary intake, particularly under stress, when hydration and gut support are critical. This study presents the first investigation of SYN supplementation delivered exclusively through drinking water in laying hens, evaluating both preference and behavioral responses, particularly feather pecking, during a period of social stress induced by repeated mixing of unfamiliar birds. A total of 226 White Leghorn hens (37 weeks old) were housed in enriched floor pens with simultaneous access to color-coded SYN-enriched and plain water containers. Following a 2-week associative learning phase and 1-week washout, hens entered a 6-week preference testing period encompassing pre-stress, stress, and post-stress phases. Water consumption was measured at the group level, while individual jug visits were tracked using RFID technology. Feather pecking was measured (10 min/day) and feather damage assessed according to severity. Hens showed a clear preference for SYN-enriched water, consuming significantly more than plain water (p < 0.0001). While overall intake remained stable, SYN consumption fluctuated across stress phases, with the strongest preference pre-stress and a modest decline during stress. Although hens with higher rates of severe feather pecking (SFP) visited SYN-enriched water more frequently than hens with lower rates (p = 0.0288), suggesting a potential coping mechanism, overall, SFP rates remained stable across all phases. Notably, the level of SFP observed during the pre-stress phase was already sufficient to cause progressive plumage deterioration, which continued throughout the study. The proportion of birds with severe feather damage rose from 39.4% to 53.5%, while those with intact plumage dropped from 37.6% to 19.9% over time. Thus, SYN supplementation via drinking water is feasible and preferred by laying hens, even under stress. These findings highlight the potential of nutraceuticals delivered through drinking water to influence hen behavior; however, the progressive plumage deterioration despite stable SFP rates suggests that SYN supplementation alone may be insufficient, underscoring the need for integrated management strategies.}, }
@article {pmid41912274, year = {2026}, author = {Dutton, CL and Goeckner, A and Goldwire, T and Grupstra, CGB and Houghtaling, D and Nonnamaker, LE and Subalusky, A}, title = {Bioreactors on the Move: How Animals Contribute to Microbial Community Coalescence and Shape Ecosystem Function.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70291}, doi = {10.1111/1462-2920.70291}, pmid = {41912274}, issn = {1462-2920}, support = {//Florida Atlantic University/ ; //University of Florida/ ; //United States National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Microbiota ; *Ecosystem ; *Bioreactors/microbiology ; Fishes/microbiology ; Oligochaeta/microbiology ; Bacteria/classification ; Soil Microbiology ; }, abstract = {Microbiome community coalescence-the mixing of separate microbial communities and their environments resulting in a novel community-represents an important but understudied ecological process at the animal-environment interface. Here, we propose that animals function as "mobile bioreactors" across landscapes, ingesting environmental microbes that undergo selective filtering within the animal gut that are then deposited back into the environment alongside the animal's native microbiota. This coalescence of animal and environmental microbiomes can significantly alter ecosystem processes including nutrient cycling, organic matter decomposition, and trophic interactions. We synthesize emerging evidence from terrestrial, freshwater, and marine ecosystems demonstrating how animal-facilitated microbial coalescence influences ecosystem functioning. Through case studies of hippos in African rivers, fish on coral reefs, and earthworms in soil, we illustrate how these coalescence events create novel microbial communities with distinct functional capabilities. We identify methodological approaches for investigating these phenomena and outline key knowledge gaps, particularly regarding the persistence of animal microbiota in environmental settings and their quantitative contribution to ecosystem processes. Here we highlight the importance of studying animal-environmental coalescence events with far reaching implications for our understanding of ecosystem processes, animal health, and environmental resilience.}, }
@article {pmid41912276, year = {2026}, author = {Luko-Sulato, K and Sulato, ET and Osman, JR and Nolasco-Jiménez, P and Morales, D and Rezende, GS and Rodrigues, CA and Maintinguer, SI and da Cunha, AF and Rosolen, V}, title = {Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70306}, doi = {10.1111/1758-2229.70306}, pmid = {41912276}, issn = {1758-2229}, support = {2021/06332-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/15396-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Wetlands ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Tropical Climate ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; }, abstract = {Characterisation of the microbial communities of two small tropical wetlands under two distinct hydrological regimes (permanent and seasonal), across a rainy and dry season was performed by 16S rRNA amplicon sequencing. We identified 48 bacterial phyla across the two wetland types, seasons and depths and 83% of the bacterial sequences consistently corresponded to six phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Proteobacteria and Verrucomicrobia. The seasonal wetland presented a predominance of Chloroflexi, Nitrospirae, Actinobacteria and Acidobacteria, whereas the permanent wetland showed higher relative abundances of Planctomycetes, Bacteroidetes, Proteobacteria and Firmicutes. Archaeal communities also differed, with Crenarchaeota predominating in the seasonal and Euryarchaeota in the permanent wetland. Microbial communities showed pronounced compositional shifts across wetland type, season and depth, while maintaining stable alpha diversity, with depth was the dominant driver. Functional inference suggested that aerobic ammonia oxidation, nitrate reduction and sulphur compound respiration were the predominant putative metabolic pathways in the seasonal wetland and methanogenesis, fermentation, dark hydrogen oxidation, nitrogen fixation, photoautotrophy, ureolysis and hydrocarbon degradation in the permanent wetland. The permanent wetland exhibited sparse correlation with environmental drivers, consistent with long-term saturation and chronic nutrient limitation, while the seasonal wetland presented influence of pH, nutrients and SOC on microbial community structure.}, }
@article {pmid41912342, year = {2026}, author = {Engelen, MPKJ and van der Meij, BS}, title = {Targeting muscle, mitochondria, and microbiome: nutritional and exercise strategies across wasting diseases and conditions.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {29}, number = {3}, pages = {211-213}, doi = {10.1097/MCO.0000000000001220}, pmid = {41912342}, issn = {1473-6519}, }
@article {pmid41912530, year = {2026}, author = {Jiang, J and Poulsen, CS and Boulund, U and Shah, S and Trivedi, U and Bhattacharyya, M and Neumann, AU and Dai, DLY and Petersen, C and Hoskinson, C and Moraes, TJ and Mandhane, PJ and Simons, E and Azad, MB and Subbarao, P and Bønnelykke, K and Chawes, B and Turvey, SE and Sørensen, SJ and Thorsen, J and Stokholm, J}, title = {Early life bacteria and sibling exposure associate with restoration of the infant gut microbiome after cesarean section.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71185-6}, pmid = {41912530}, issn = {2041-1723}, abstract = {Long-term gut microbiome perturbation following Cesarean section (CS) delivery has been associated with an increased risk of developing childhood asthma. Whether such CS-associated microbiome composition can be modulated by environmental exposures or ecological interactions, and thereby mitigate disease risk, is unclear. In the COPSAC2010 birth cohort (N = 700), we develop a restoration score quantifying the degree to which the 1-year gut microbiome resembled that of vaginally delivered infants. We identify predictors of this restoration score in the 1-week gut microbiome. In addition, having older siblings is linked to a higher restoration score, mediated by increased abundances of restoration-associated bacteria. The restoration score, including association with delivery mode, older siblings and later asthma as well as early bacterial drivers, is successfully replicated in the independent Canadian birth cohort, CHILD. These insights suggest that specific early-life bacteria and sibling exposure may support microbiome restoration and confer protective effects against asthma risk.}, }
@article {pmid41913243, year = {2026}, author = {Mancin, E and Casto-Rebollo, C and Maltecca, C and Ibañez-Escriche, N and Mantovani, R and Sartori, C and Tiezzi, F}, title = {Insights into pig resilience: the Microbiome-genetic connection.}, journal = {Porcine health management}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40813-026-00506-4}, pmid = {41913243}, issn = {2055-5660}, }
@article {pmid41913289, year = {2026}, author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P}, title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00828-2}, pmid = {41913289}, issn = {1757-4749}, abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.}, }
@article {pmid41913604, year = {2026}, author = {Wang, HY and Li, C and Pan, YP}, title = {[Imbalance and reconstruction of periodontal homeostasis: new perspectives on the pathogenesis, prevention and treatment of periodontitis].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {61}, number = {4}, pages = {445-451}, doi = {10.3760/cma.j.cn112144-20251209-00499}, pmid = {41913604}, issn = {1002-0098}, support = {2023YFC2506300//National Key R&amp;D Program of China/ ; }, abstract = {Periodontal homeostasis is a dynamic equilibrium based on healthy periodontal structures, a relatively stable oral microbiome, appropriately regulated host immunity, coordinated cellular metabolism, and a functional dentition with normal occluion. This review aims to systematically elucidate the key mechanisms underlying the maintenance and disruption of periodontal homeostasis. The dysregulation of microbiota and excessive immune activation mutually reinforce each other, serving as the core driving forces for the occurrence and progression of periodontitis. On this basis, a treatment approach oriented toward "re-establishing periodontal homeostasis" is proposed. Based on microbiota remodeling and structural reconstruction, combined with host immune regulation and immunometabolic intervention, emphasizing systemic risk factor management and functional dentition reconstruction, we aim to establish a personalized, precise, and sustainable new model for periodontal prevention and treatment.}, }
@article {pmid41913620, year = {2026}, author = {Wang, XY and Yao, YJ and Li, LL and Yan, FH}, title = {[From oral microbiome dysbiosis to renal injury: research advances in the mechanism of association between periodontitis and diabetic kidney disease].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {61}, number = {4}, pages = {582-588}, doi = {10.3760/cma.j.cn112144-20251112-00446}, pmid = {41913620}, issn = {1002-0098}, support = {82301100//National Natural Science Foundation of China/ ; BK20220198//Natural Science Foundation of Jiangsu Province/ ; 0224C001//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; YKK23177//Nanjing Foundation for Development of Science and Technology/ ; }, abstract = {Periodontitis, a chronic inflammatory disease driven by dysbiosis of the oral microbiome, has increasingly been recognized for its systemic impact beyond the oral cavity. Growing evidence links periodontitis to the onset and progression of diabetic kidney disease (DKD), suggesting that disturbances of oral microbial homeostasis may influence distant organs through systemic circulation or the oral-gut-kidney axis. Such interactions can trigger systemic inflammation, immune dysregulation, oxidative stress, and metabolic disturbances, thereby accelerating renal injury. This review summarizes recent advances on the potential mechanisms linking periodontitis to DKD progression and highlights the key role of oral microbial dysbiosis and related systemic effects.}, }
@article {pmid41913730, year = {2026}, author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A}, title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {65}, pmid = {41913730}, issn = {2732-5121}, abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.}, }
@article {pmid41913906, year = {2026}, author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y}, title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {590621}, pmid = {41913906}, issn = {1178-7074}, abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.}, }
@article {pmid41913928, year = {2026}, author = {Mulinde, T and Sousa, LGV and Castro, J and George, SD and Muzny, CA and Cerca, N}, title = {Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20902}, pmid = {41913928}, issn = {2167-8359}, mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Prevotella/genetics/isolation &amp; purification ; *Peptide Nucleic Acids/genetics ; Vagina/microbiology ; Sensitivity and Specificity ; Biofilms/growth &amp; development ; Adult ; }, abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women. It is associated with multiple adverse health outcomes in women including adverse pregnancy outcomes, an increased risk of pelvic inflammatory disease, infertility, and an increased risk of HIV and other sexually transmitted infections. BV is characterized by an imbalance in the vaginal microbiota, namely a decrease in protective Lactobacillus species and an overgrowth of facultative and strict anaerobic bacteria, leading to the development of a polymicrobial biofilm. Despite extensive research, the etiology of BV remains unclear, and its pathophysiology is not fully understood. It has been hypothesized that P. bivia, in combination with Gardnerella spp., plays an important role in the early development of the BV biofilm. We previously developed a peptide nucleic acid (PNA) probe specifically targeting P. bivia to investigate its role as a potential early colonizer. However, our recent findings have raised doubts about the specificity of this association, suggesting a broader involvement of other Prevotella species in incident BV (iBV).<br><br>METHODS: A new PNA probe targeting Prevotella spp. 23S rRNA was developed compared to the existing P. bivia-specific probe. This new probe was optimized in vitro through a variation of hybridization temperatures and times. Its performance was evaluated using a collection of 28 Prevotella strains representing 24 different species and 38 non-Prevotella spp. typically found in BV in order to assess its sensitivity and specificity. Both probes were tested on vaginal swab specimens from women with and without BV to assess the bacterial count and detection of Prevotella species.<br><br>RESULTS: In vitro validation demonstrated that the new Prevotella spp. probe achieved a specificity of 100% and sensitivity of 96%. As expected, its broader detection allowed identification of a wider range of Prevotella spp. compared to the P. bivia-specific probe, which was intentionally restricted to a single species. Application to clinical specimens revealed that the new probe identified a significantly higher count of Prevotella spp. in 6/9 (66.6%) BV-positive specimens compared to the P. bivia-specific probe. In 2/9 (22.2%) healthy control specimens, greater Prevotella spp. detection was also observed.<br><br>CONCLUSIONS: Our findings suggest that the involvement of Prevotella spp. in BV extends beyond P. bivia, implicating a wider range of species which could be present in the polymicrobial BV biofilm. The broader specificity of this new Prevotella spp. probe provides a valuable tool for future research on the vaginal microbiome and the pathogenesis of BV.}, }
@article {pmid41914163, year = {2026}, author = {Kozin, S and Kravtsov, A and Lyasota, O and Dorohova, A and Ivlev, V and Chikhirzhina, E and Moiseev, A and Nesterova, V and Babenkova, P and Popov, K and Fedulova, L and Dzhimak, S}, title = {Consumption of Water Similar to Martian Water in Terms of Deuterium Content by Mammals Leads to the Development of an Adaptation Syndrome and Activation of Protective Mechanisms Against Stress.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39086}, doi = {10.31083/FBE39086}, pmid = {41914163}, issn = {1945-0508}, support = {125011700394-5//State Task Force of the Southern Scientific Center of the Russian Academy of Sciences for 2025/ ; }, mesh = {Animals ; *Deuterium/analysis ; Rats, Wistar ; Rats ; *Adaptation, Physiological ; Male ; *Stress, Physiological ; Brain/metabolism ; *Water/chemistry ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Deuterium is unevenly distributed in natural waters, while the same applies to the content of deuterium in ice on Mars. Moreover, changes in the deuterium content of drinking water are known to affect the bodies of mammals. Thus, since plans are in place to send people to Mars in the coming years, understanding the effects of water with a Martian isotopic composition is necessary. Therefore, this study aimed to evaluate the impact of water with an increased deuterium content of 1200 ppm on the dynamics of indicators in the body of mammals.<br><br>METHODS: The study was conducted on Wistar rats. The metabolic profile of blood and the content of deuterium in it were studied in dynamics by days using nuclear magnetic resonance (NMR) spectroscopy. Additionally, the isotopic composition of brain tissue was studied in dynamics by days using isotope mass spectrometry. A further study was conducted on the functioning of the antioxidant system in blood plasma and brain tissue using PCR analysis, chemiluminescence, and biochemical analysis methods; the intestinal microbiome was also studied. The durations of the animal experiments were 31 (blood and brain study) and 38 (stress-protective activity study) days.<br><br>RESULTS: On day 23, the deuterium content in the blood plasma increased to 856 parts per million (ppm), and to 260 ppm in the brain on day 31. This increase led to an imbalance in the antioxidant/prooxidant processes. This effect was accompanied by shifts in the intensity of oxidative processes, alongside changes in enzyme activity and the expression of genes responsible for their synthesis, shifts in amino acid composition, and changes in the concentration of metabolites and microbiome molecules in the blood plasma. By the fifth and eighth days, the number of Bacteroides in the intestines had decreased by 14% and 21.8%, respectively, compared to the values measured on day zero of the experiment. Meanwhile, the population of Firmicutes-type bacteria increased by 12% and 16% on the fifth and eighth days, respectively, compared to the indicators measured on day zero of the experiment.<br><br>CONCLUSION: An increase in the concentration of deuterium in the body promotes the development of a stress reaction and the activation of compensatory mechanisms aimed at adaptation.}, }
@article {pmid41914171, year = {2026}, author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN}, title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39439}, doi = {10.31083/FBE39439}, pmid = {41914171}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.<br><br>METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.<br><br>RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).<br><br>CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.}, }
@article {pmid41914284, year = {2026}, author = {Wang, P and Ding, L and Lang, Z and Zhang, Y and Yu, Y}, title = {Therapeutic Modulation of the Gut Microbiome in Coronary Artery Disease: Current Evidence and Future Directions.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {3}, pages = {45081}, doi = {10.31083/FBL45081}, pmid = {41914284}, issn = {2768-6698}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Coronary Artery Disease/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Synbiotics/administration &amp; dosage ; Methylamines/metabolism ; Diet ; }, abstract = {The gut microbiome is increasingly recognized as a modifiable contributor to coronary artery disease (CAD). This narrative review integrates mechanistic and clinical evidence regarding short-chain fatty acids (SCFAs), trimethylamine-N-oxide (TMAO), and bile acids, and appraises therapeutic modulation via diet; probiotics, prebiotics, and synbiotics; fecal microbiota transplantation (FMT); and drug-microbiome interactions. SCFAs generally confer anti-inflammatory and lipid-regulatory effects, whereas bile acid signaling exhibits context-dependent metabolic actions. Findings regarding TMAO are inconsistent; in several cohorts, associations with cardiovascular risk become null or attenuated after adjustment for renal function (estimated glomerular filtration rate [eGFR]) and dietary patterns. Most interventional studies are small, use surrogate endpoints, and vary in strains and dosing, limiting certainty. Microbiome profiles differ across geographic regions, racial and ethnic groups, and dietary patterns, underscoring the need for stratified approaches. Routine FMT in CAD remains constrained by safety, feasibility, and ethical and logistical considerations. Overall, the microbiome represents a promising yet unproven therapeutic target in CAD. Future trials should standardize interventions, rigorously control for confounders, evaluate drug-microbiome interactions, and be adequately powered to detect clinical events to enable precision medicine.}, }
@article {pmid41914628, year = {2026}, author = {Fu, Y and Long, N and Sourn, P and Li, W and He, Z and Tan, W and Yuan, J and Chen, Y and Wu, J and Wang, S and Feng, L and Wang, Z and Ding, W}, title = {Distinct vaginal microbial signatures in pregnancies complicated by antiphospholipid syndrome: depletion of Lactobacillus johnsonii and enrichment of Bifidobacterium dentium.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0388225}, doi = {10.1128/spectrum.03882-25}, pmid = {41914628}, issn = {2165-0497}, abstract = {UNLABELLED: Antiphospholipid syndrome (APS) is a systemic autoimmune disease that contributes substantially to recurrent pregnancy loss, fetal death, intrauterine growth restriction, and preeclampsia, posing major threats to maternal and fetal health. These obstetric complications exhibit clinical similarities to those resulting from vaginal dysbiosis, yet the vaginal microbiota in APS pregnancies has not been systematically investigated. In this study, we characterized the vaginal microbiome in 33 pregnant women with APS and 90 healthy controls using 16S rRNA gene sequencing. We identified a unique microbial signature in APS pregnancies that differed from the commonly observed pattern of increased microbial diversity and Lactobacillus depletion seen in classical vaginal dysbiosis. Specifically, while overall alpha diversity and Lactobacillus dominance were preserved, we observed distinct compositional restructuring characterized by selective depletion of Lactobacillus johnsonii and marked enrichment of Bifidobacterium dentium. A logistic regression model integrating the relative abundances of these microbial biomarkers demonstrated robust diagnostic performance in differentiating pregnancies with APS from healthy pregnancies, with risk scores significantly correlating with clinical parameters and pregnancy outcomes. This study demonstrates that pregnant women with APS display a distinct vaginal microbiome pattern defined by species-specific compositional restructuring rather than global dysbiosis. These microbial alterations may contribute to APS-related pregnancy morbidity, highlighting vaginal microbial signatures as promising noninvasive biomarkers for risk stratification and potential therapeutic targets in obstetric APS management.<br><br>IMPORTANCE: Antiphospholipid syndrome (APS) is an autoimmune disease that causes recurrent miscarriage, fetal death, and pregnancy complications in women of reproductive age. While coagulation dysfunction is a known contributing factor, whether APS is accompanied by vaginal microbiota alterations and their role in adverse outcomes remains unclear. We discovered that pregnant women with antiphospholipid syndrome harbor a unique vaginal microbial community: they exhibit depletion of the protective species Lactobacillus johnsonii while showing enrichment of Bifidobacterium dentium, a bacterium typically found in the gut. Unlike typical vaginal infections that display widespread microbial dysbiosis, antiphospholipid syndrome induces only selective alterations in specific bacterial species. These microbial signatures correlated with hematological parameters and adverse pregnancy histories, including prior miscarriages. Our findings suggest that monitoring vaginal microbiota could provide a simple, noninvasive approach to identify high-risk pregnancies in women with antiphospholipid syndrome and may guide novel screening strategies for pregnancy-related disorders targeting the vaginal microbiome.}, }
@article {pmid41914631, year = {2026}, author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS}, title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219825}, doi = {10.1128/spectrum.02198-25}, pmid = {41914631}, issn = {2165-0497}, abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.}, }
@article {pmid41914733, year = {2026}, author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D}, title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0235725}, doi = {10.1128/aem.02357-25}, pmid = {41914733}, issn = {1098-5336}, abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.}, }
@article {pmid41914747, year = {2026}, author = {Franklin, S and Sahasrabhojane, P and Hayase, T and Hayase, E and Chang, C-C and Senapati, J and Desikan, SP and Kadia, T and Lorenzi, PL and Jenq, RR and Shelburne, SA and Galloway-Peña, J}, title = {Short-chain fatty acid-producing microbes differentiate non-infectious and infectious neutropenic fever in leukemia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0134325}, doi = {10.1128/msystems.01343-25}, pmid = {41914747}, issn = {2379-5077}, abstract = {UNLABELLED: Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruptions to treatment-related infections, it typically examines NF as the outcome, leaving a gap in understanding how the microbiome and metabolic factors distinguish infectious from non-infectious cases. Stool samples from acute myeloid leukemia patients were analyzed to characterize gut microbiome composition and fecal metabolites at baseline and at fever onset. Machine learning models, network analyses, and functional profiling were used to differentiate infectious NF vs non-infectious NF at baseline and at fever onset. The baseline model (area under the receiver operating characteristic [AUROC] = 0.769) identified higher levels of Akkermansia, Enterobacter, Escherichia-Shigella, and Flavonifractor as predictors of infectious NF, while Collinsella, Lachnospiraceae, Coprococcus, and acetic acid were linked to non-infectious cases. At fever onset, Enterococcus was enriched in infectious NF, whereas Gemella, Butyrate, Lachnospiraceae, Ruminococcaceae, and Eisenbergiella abundances favored non-infectious NF outcomes (AUROC = 0.752). Network analyses also revealed greater functional diversity and microbiome-metabolome connectivity in non-infectious cases at fever onset. This study suggests that gut microbiota and metabolites may serve as biomarkers for distinguishing infectious from non-infectious neutropenic fever, warranting further validation in larger cohorts.<br><br>IMPORTANCE: Our study tackles the challenge of managing neutropenic fever (NF) in immunocompromised patients whose numbers have increased due to various immunodeficiencies and treatments that suppress immune function. Fever is often the only sign of a serious infection in these patients, yet there are neither clear patterns linking risk factors to infection nor biomarkers reliable for ruling out non-infectious causes. As a result, febrile patients are typically empirically treated for major pathogens, even in the absence of confirmed infections, which propagates antimicrobial resistance and gut dysbiosis. Our research utilizes gut microbiome and targeted metabolomic profiling from two cohorts of patients with acute myeloid leukemia undergoing chemotherapy and employs a machine learning framework to distinguish between infectious and non-infectious NFs at baseline and upon fever onset.}, }
@article {pmid41914795, year = {2026}, author = {}, title = {Corrigenda to 'Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos'.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261432716}, doi = {10.1177/13872877261432716}, pmid = {41914795}, issn = {1875-8908}, }
@article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0035926}, doi = {10.1128/aem.00359-26}, pmid = {41914849}, issn = {1098-5336}, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, }
@article {pmid41914961, year = {2026}, author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W}, title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0258725}, doi = {10.1128/spectrum.02587-25}, pmid = {41914961}, issn = {2165-0497}, abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.}, }
@article {pmid41915085, year = {2026}, author = {Liang, J and Zang, S and Wang, Z and Zhang, R}, title = {Cancer and aging: complex associations and therapeutic targets.}, journal = {Molecular biomedicine}, volume = {7}, number = {1}, pages = {}, pmid = {41915085}, issn = {2662-8651}, support = {No. 202303021221201//Shanxi Provincial Basic Research Program/ ; }, mesh = {Humans ; *Aging/genetics/pathology ; *Neoplasms/therapy/pathology/genetics/metabolism/etiology ; Animals ; Cellular Senescence ; Genomic Instability ; Autophagy ; Epigenesis, Genetic ; Molecular Targeted Therapy ; }, abstract = {The incidence of cancer increases markedly with aging, and the two processes share underlying molecular mechanisms. In the context of global population aging and rising cancer incidence, nine convergent hallmark axes have been identified: genomic instability, epigenetic drift, inflammation-immunity imbalance, microbiome dysbiosis, metabolic reprogramming, telomere attrition, stem cell exhaustion, cellular senescence, and autophagy dysfunction. These hallmarks constitute an integrated regulatory network that operates synergistically, antagonistically, or through bidirectional feedback across molecular, cellular, and microenvironmental levels. Genomic instability, epigenetic remodeling, chronic inflammation, microbiome dysbiosis, and metabolic reprogramming in aging often act synergistically to promote tumorigenesis, whereas telomere attrition and stem cell exhaustion primarily exert antagonistic, tumor-suppressive effects. Cellular senescence and autophagy dysfunction display context-dependent dual roles. Importantly, this network framework has direct relevance to cancer therapeutics. Although chemotherapy, radiotherapy, and immunotherapy effectively suppress tumor progression, they frequently induce therapy-induced senescence, characterized by cell-cycle arrest and a senescence-associated secretory phenotype, thereby accelerating functional decline and increasing long-term toxicities in older patients. The proposed "synergistic-antagonistic-dual" framework linking aging and cancer not only helps explain the disproportionate cancer burden in older adults but also supports a "one drug, two targets" therapeutic paradigm. Targeting these shared pathways has delayed aging phenotypes and suppressed tumorigenesis in preclinical studies and early clinical trials, highlighting the potential of integrated interventions that concurrently address aging and cancer.}, }
@article {pmid41915167, year = {2026}, author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E}, title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02730-5}, pmid = {41915167}, issn = {1432-184X}, }
@article {pmid41915265, year = {2026}, author = {Volk, A and Mills, M and Chae, S and Lee, J}, title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41915265}, issn = {1614-7499}, abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.}, }
@article {pmid41915459, year = {2026}, author = {Gupta, RM and Ismail, HM and Siller, AF and Pesikoff, J and Devaraj, S and Balasubramanyam, A and Redondo, MJ}, title = {Impact of Body Size on Preclinical Type 1 Diabetes Development and Progression.}, journal = {Diabetes care}, volume = {}, number = {}, pages = {}, doi = {10.2337/dci25-0134}, pmid = {41915459}, issn = {1935-5548}, support = {3-SRA-2025-1738-S-B//Breakthrough Type 1 Diabetes/ ; }, abstract = {Type 1 diabetes arises from the interplay of genetic susceptibility and environmental exposures, leading to autoimmune β-cell destruction. Although disease-modifying therapies (DMTs) can delay progression to clinical (stage 3) type 1 diabetes, treatment responses remain inconsistent and transient. The marked heterogeneity of type 1 diabetes, shaped by age, sex, race/ethnicity, and genetic background, underscores the need to elucidate distinct mechanistic pathways. Among environmental contributors, obesity stands out as a compelling modifiable target. Data from The Environmental Determinants of Diabetes in the Young (TEDDY), Type 1 Diabetes TrialNet, and other longitudinal cohorts link BMI and adiposity to the onset of islet autoimmunity, progression through preclinical stages, and development of stage 3 type 1 diabetes. These associations are not uniform; heightened susceptibility to adiposity-related risk is seen among younger children, Hispanic populations, and individuals with specific HLA genotypes. Despite robust epidemiologic evidence, the biological pathways connecting elevated BMI to autoimmune β-cell destruction remain incompletely defined. Emerging data implicate a network of immunologic and metabolic disturbances, including insulin resistance, β-cell stress, chronic adipose tissue inflammation, altered adipokine signaling, and gut microbiome changes, that collectively heighten β-cell vulnerability, amplify autoreactive immune responses, and drive metabolic decompensation toward clinical disease. Elucidating these mechanisms and identifying related biomarkers are critical to advancing precision prevention. In future studies, investigators should evaluate whether modifying elevated BMI or targeting obesity-associated immunologic and metabolic pathways can alter the preclinical trajectory of type 1 diabetes. Such mechanistic understanding may help curb type 1 diabetes incidence and improve outcomes for populations most vulnerable to obesity-related risk.}, }
@article {pmid41907525, year = {2026}, author = {González-Valdivia, C and Tong, B and Hjalmarsson, S and Guðnadóttir, U and Wagner, N and Engstrand, L and Schuppe-Koistinen, I and Fransson, E and Prast-Nielsen, S and Brusselaers, N and Hugerth, LW}, title = {The gut microbiome in early pregnancy is associated with the severity of nausea and vomiting: a nested case‒control study.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2603861}, pmid = {41907525}, issn = {2993-3935}, abstract = {Approximately 70% of all pregnancies are affected by nausea and vomiting (NVP), yet the mechanisms controlling this phenomenon are not well known. Pregnancy hormones explain a large part of this effect, mostly through human chorionic gonadotropin and fetal production of GDF15, a hormone active in the brain stem. Still, there is a wide variation in the severity of symptoms, ranging from no nausea to severe vomiting requiring hospitalization (hyperemesis gravidarum). Here, we present a nested case‒control study within the large SweMaMi cohort, wherein 337 participants with severe NVP in early pregnancy were matched 1-to-1 with moderate and mild NVP, respectively. Subjects with more severe nausea had lower richness and diversity in their fecal microbiomes. Several taxa were significantly associated with NVP score, where the most extreme are a negative correlation with Lactobacillaceae and positive correlations with Bifidobacterium dentium and Puniceicoccaceae. Finally, higher NVP score was associated with a higher abundance of bacteria encoding for the neuroactive pathways of glutamine degradation, inositol synthesis, and lactate production. In conclusion, the gut microbiota was strongly associated with NVP. Further studies with direct interventions capable of restoring the early-pregnancy gut microbiome could open up new approaches for dealing with the most common symptom of early pregnancy.}, }
@article {pmid41907632, year = {2026}, author = {Russo, F and Tripodi, L and Caldora, F and Pandolfo, SD and Aveta, A and Nardelli, C and Imbimbo, C and Perdonà, S and Pastore, L and Castaldo, G}, title = {Identification of a weighted urinary microbial signature for bladder cancer discrimination.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1784501}, pmid = {41907632}, issn = {2234-943X}, abstract = {INTRODUCTION: Growing evidence from microbiome studies has demonstrated associations between dysbiosis and cancers, including bladder cancer (BCa). Our recent works on urobiome revealed a different microbial composition in BCa patients compared to controls. The aim of this work was to create a Weighted Composite Index (WCI) to distinguish BCa-affected patients (mBCa) from healthy controls (mHC) in a cohort of male aged over 50 years.<br><br>METHODS: Urobiome data from 51 subjects (27 mBCa and 24 mHC) were analyzed. Random Forest (RF) classifier was trained to identify genera and species which significantly contributed to discriminating between mBCa and mHC group. A weighted normalization approach was used to compute separate WCIs at genus and species levels and in-silico validation test were performed to assess the models' robustness.<br><br>RESULTS: the WCI was calculated for each patient at both genera and species levels, showing a significant difference between the two groups (p < 0.0001) in both comparisons. WCIs showed superior discriminative performances compared to any individual taxon used for the model construction. Despite the need for validation in larger independent cohorts, the in-silico validation pipeline showed a stable high sensitivity of the models.<br><br>CONCLUSIONS: Our findings identified a candidate urinary microbial signature in a biomarker discovery setting associated with bladder cancer. This hypothesis-generating approach may contribute to the identification of a non-invasive biomarker, which requires validation in larger, independent cohorts before clinical application.}, }
@article {pmid41907707, year = {2024}, author = {Teigen, LM and Kaiser-Powers, T and Matson, M and Elkin, B and Kabage, AJ and Hamilton, M and Vaughn, BP and Sadowsky, MJ and Staley, C and Khoruts, A}, title = {Contribution of Common Sulfur-Containing Substrates to Hydrogen Sulfide Production By Human Gut Microbiota Using an In Vitro Model Standardized For Bacterial Counts.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2361246}, pmid = {41907707}, issn = {2993-3935}, abstract = {Hydrogen sulfide (H2S) produced by human gut microbiota is highly toxic and implicated in pathogenesis of gastrointestinal tract disorders. Sulfur-containing amino acid (SAA) degradation is a major contributor to its production, but SAA degradation pathways have not been extensively characterized. In vitro model systems of fecal H2S production offer a basic method to help elucidate SAA degradation pathways, but the approach is not standardized. To address this, we used fecal microbiota separated from feces and standardized for bacterial counts to measure H2S production potential in response to different substrates in healthy controls (n = 6) with repeated sampling (three samples per participant). H2S production was highest with cysteine (mean = 16.7 ppm) compared to sodium sulfate (0.7 ppm) and taurine (0.8 ppm). Sodium-sulfate-driven H2S production negatively correlated with Ruminococcus (Spearman's ρ = -0.5) and cysteine-driven H2S production negatively correlated with Firmicutes (Spearman's ρ = -0.5). These findings, using a protocol controlling for confounding variables such as bacterial counts, validate previous findings of cysteine as a primary driver of H2S production. Finally, the inclusion of samples from two patients with UC allowed for the illustration of the potential of this approach to identify functional differences in specific disease states.}, }
@article {pmid41907708, year = {2024}, author = {Kaufman, P and O'Meara, KE and Hawrelak, J}, title = {Preventing chemotherapy-induced diarrhea and microbiota imbalances with prebiotics and probiotics in breast cancer treatment: A case report.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2379475}, pmid = {41907708}, issn = {2993-3935}, abstract = {Breast cancer (BC) is the second most common cancer in women in the United States. Of those diagnosed, 40-80% will undergo chemotherapy. Adverse effects of chemotherapy are chemotherapy-induced diarrhea (CID) and gut microbiota dysregulation. CID can lead to dehydration, metabolic acidosis, malnutrition, and gut dysbiosis. Antidiarrheal medications are the standard treatment of care; however, this has been shown to further contribute to gut dysbiosis, is not always effective in controlling diarrhea, and can lead to rebound constipation with the potential of pathogenic bacterial overgrowth. In this case report, we describe the experience of a patient-centered, personalized intervention with pre- and probiotics to preserve the microbiota and prevent CID. A 57-year-old postmenopausal female with BC undergoing adriamycin-cyclophosphamide (AC) and taxol-cyclophosphamide (TC) chemotherapies for invasive ductal carcinoma under the care of a cancer team wanted to refrain from using loperamide and instead use nutritional interventions and supplementation for preventing CID and maintaining gut health. This case report is a narrative report of the observed outcomes of one patient with BC after taking specific prebiotics and probiotics. The outcomes included the prevention of CID and other gastrointestinal adverse effects, and maintaining microbiota alpha-diversity, butyrate producing genera, and Bifidobacterium populations while inhibiting the overgrowth of Proteobacteria pathogenic bacteria.}, }
@article {pmid41907711, year = {2024}, author = {Varshney, N and Pandey, RK and Mishra, A and Kumar, S and Jha, HC}, title = {Aurora Kinase A: Integrating Insights into Cancer, Inflammation, and Infectious Diseases.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2419069}, pmid = {41907711}, issn = {2993-3935}, abstract = {Aurora kinase A (AURKA) is crucial in regulating cell division and maintaining genomic stability, making it significant in cancer biology. This review explores AURKA's structural and functional roles, emphasizing its involvement in cell cycle progression. Beyond cancer, AURKA emerges as a multifaceted player in host cell modulation, exerting influence over inflammatory responses, cell death mechanisms, and autophagy pathways. Moreover, recent research highlights its involvement in viral and bacterial infections. Numerous viruses, for their replication and assembly, modulate host cell cycle progression. Various viruses modulated AURKA to induce viral-mediated tumor. It also emerged as a key modulator in various gut microbiome-mediated cancers. Further, it also imparts oncogenic effect by modulation in cytoplasmic and mitochondrial regions of the cell. It hampers DNA replication independent of its kinase domain. Understanding AURKA's diverse roles underscores its potential as a promising drug target, offering therapeutic avenues for various diseases. This comprehensive exploration navigates through complex landscape of AURKA biology, paving way for future investigations and therapeutic interventions.}, }
@article {pmid41907714, year = {2024}, author = {Molinas-Vera, M and Ferreira-Sanabria, G and Peña, P and Sandoval-Espinola, WJ}, title = {The Paraguayan gut microbiome contains high abundance of the phylum Actinobacteriota and reveals the influence of health and lifestyle factors.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2332988}, pmid = {41907714}, issn = {2993-3935}, abstract = {Most gut microbiome studies are focused on populations from developed nations. However, this overlooks the role played by host genetics, lifestyle, and diet, highlighting the need to evaluate under-represented populations. Thus, we performed the first gut microbiome study from a Paraguayan cohort via 16S rRNA sequencing and PICRUSt2 analysis. We evaluated fecal samples from 60 participants from Asunción, while considering categories such as body-mass-index (BMI), sex, age, diet, lifestyle, and clinical history. Firmicutes (76.0 ± 11.6%), Actinobacteriota (10.4 ± 7.9%) and Bacteroidota (9.4 ± 11.4%) were the most abundant phyla. Similarly, the most abundant genera were Blautia (14.1 ± 7.5%), Faecalibacterium (8.07 ± 6.8%), and Bacteroides (6.7 ± 6.8%). Likewise, the most abundant microbial pathways were predicted to be involved with sugar metabolism and fermentation. Interestingly, some categories significantly impacted the gut microbiome composition and function, such as BMI (Moryella, Bifidobacterium), sex (Faecalibacterium), and others. Additionally, dysbiotic indices differed from values previously reported as homeostatic. These observations highlight the need for further studies, considering microbial species and host genetics. Thus, this work expands the knowledge of the gut microbiome from the Collective South, while contrasts found herein reinforce the need for further research with human populations traditionally understudied.}, }
@article {pmid41907715, year = {2024}, author = {Winters, AD and Francescutti, DM and Kracht, DJ and Kuhn, DM and Angoa-Perez, M}, title = {The Effects of Ceftriaxone on Glutamate Transporter Expression and the Gut Microbiome: Implications for a Role of Antibiotic-Induced Dysbiosis in Mediating Drug Seeking and Relapse.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2393727}, pmid = {41907715}, issn = {2993-3935}, abstract = {Ceftriaxone (CTX), a beta-lactam antibiotic, is widely used in drug seeking and relapse studies due to its ability to enhance glutamate transporter (GLT-1) expression in the brain. Since increased synaptic glutamate is believed to drive drug seeking and relapse, CTX's effect on GLT-1 offers potential for treating substance abuse. However, the effect of CTX on the gut microbiome remains unexplored. Mice received CTX at 200 mg/kg per day for 4 d, and its effects on the gut microbiome were assessed. CTX led to increased striatal GLT-1 expression and induced rapid, long-lasting dysbiosis, with females showing a greater response than males. Diversity metrics were significantly altered during the acute phase of CTX treatment. Alpha diversity showed varying recovery levels depending on sex, while beta diversity indicated that CTX-treated mice remained significantly different from controls. CTX caused significant increases in Bacillota and reductions in Bacteroidota. Most taxa were rapidly reduced by CTX, but Enterococcus and Bacillales expanded significantly. Metabolomic analysis revealed significant changes in microbial pathways related to substance use disorders. These findings indicate that CTX causes immediate and persistent alterations in the gut microbiome, highlighting the importance of considering the gut microbiome as a target in substance abuse treatment.}, }
@article {pmid41907718, year = {2024}, author = {Tannock, GW}, title = {Scoring Microbiota Function: A Proposal to Use Features of Evolutionary, Symbiotic Innovation to Recognize a "Healthy" Human Gut Microbiota.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2376543}, pmid = {41907718}, issn = {2993-3935}, abstract = {Research concerning the significance of the bacterial community of the human colon (gut microbiota or microbiome) in the etiology of diseases has depended in large part on molecular and bioinformatic tools to assemble catalogs of bacterial diversity. This article proposes that the gut microbiotas of humans are collectively a metacommunity whose functions are characteristic and consistent across all healthy humans. The pathway of evolutionary innovation in the development of the symbiosis between humans and gut microbiotas is known. Therefore, it is suggested that functional scoring of these long-lasting symbiotic innovations will reap greater benefits in delineating health or disease than can comparative taxonomic analysis. Adoption of a function-scoring approach would offer opportunities for emerging researchers, worldwide, to form multidisciplinary teams to develop essential methodologies to advance this gut microbiota research.}, }
@article {pmid41907719, year = {2024}, author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G}, title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2438621}, pmid = {41907719}, issn = {2993-3935}, abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.}, }
@article {pmid41907720, year = {2024}, author = {Funahashi, K and Lee, CG and Sugitate, K and Kagata, N and Fukuda, N and Song, I and Ishii, C and Hirayama, A and Fukuda, S}, title = {Development of a Specialized Method for Simultaneous Quantification of Functional Intestinal Metabolites by GC/MS-Based Metabolomics.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2429408}, pmid = {41907720}, issn = {2993-3935}, abstract = {Intestinal metabolites produced by gut microbes play a significant role in host health. Due to their different chemical structures, they are often analyzed using multiple analyzers and methods, such as gas chromatography/mass spectrometry (GC/MS) for SCFAs and liquid chromatography/mass spectrometry (LC/MS) for bile acids (BAs), amino acids (AAs), and sugars. In this study, we aimed to develop a specialized method for the simultaneous determination of important intestinal metabolites, specifically addressing the main issue of SCFA volatilization during the dry solidification process. We discovered that these compounds can all be measured in fecal samples by GC/MS after trimethylsilyl (TMS) derivatization despite the expected volatility of SCFAs. Validating the results using SCFA standards suggested that the fecal matrix exerts a stabilizing effect. This method enabled the simultaneous quantification of 65 metabolites. For further validation in a biological context, a mouse study showed that high-MAC and high-fat diets increased SCFAs and BAs in feces, respectively, and showed a negative correlation between Alistipes and sugars, all consistent with previous studies. As a result, we successfully developed a specialized simultaneous quantification method for SCFAs, BAs, AAs, AA derivatives, and sugars in fecal samples using GC/MS-based metabolomics in conjunction with a TMS derivatization pretreatment process.}, }
@article {pmid41907847, year = {2026}, author = {Tng, TJW and Vanan, S and Tan, EK and Zeng, L and Goh, WWB and Wong, SH and Lim, KL}, title = {Examination of shared gut microbiome signatures in aging and Parkinson's disease.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1745455}, pmid = {41907847}, issn = {1663-4365}, abstract = {Parkinson's disease (PD) is a prevalent neurodegenerative disorder that is characterized clinically by a constellation of motoric deficits including resting tremors, bradykinesia, and rigidity. In recent years, there has been increasing interest in the gut-brain axis with several studies examining the relationship between gut microbiome and PD. Although association studies have reported multidimensional microbiome changes in PD, these observed changes may be confounded by various factors, especially age. Notably, existing literature on gut microbiome tends to consider aging and PD separately. This review thus examines the gut microbiome factors associated with both aging and PD. Our comprehensive analysis of the available literature reveals significant overlaps in gut microbes that are associated with aging and PD. For example, the bacterial genera Akkermansia, and Alistipes have shown increased abundance in both conditions, while Faecalibacterium and Blautia conversely show decreased abundance. Our findings were temporally consistent with more recent studies. These shared gut microbiome signatures were identified in patients across the clinical spectrum of PD symptom severity, and may influence aging and disease pathogenesis via depletion of butyrate, a beneficial anti-inflammatory microbial metabolite, since major producers of butyrate (such as Faecalibacterium and Blautia) were constantly decreased with age (across both Asian and Western populations). Given these observations, we wish to highlight the need to consider age-related factors in understanding microbiome changes in PD; the intersection of which could reveal gut microbes and their corresponding microbial metabolites such as butyrate as potential therapeutic targets for PD.}, }
@article {pmid41907858, year = {2026}, author = {Hashim, NT and Babiker, R and Padmanabhan, V and Islam, MS and Priya, SP and Chaitanya, NCSK and Mohammed, R and Dasnadi, SP and Ahmed, A and Gismalla, BG and Rahman, MM}, title = {Oral and cardiometabolic health through the lens of biobanks and large-scale epidemiologic research.}, journal = {Frontiers in oral health}, volume = {7}, number = {}, pages = {1774868}, pmid = {41907858}, issn = {2673-4842}, abstract = {Oral diseases and cardiometabolic disorders are among the most prevalent non-communicable conditions worldwide and share common inflammatory, metabolic, and social determinants. Over the past two decades, growing evidence has linked poor oral health-particularly periodontitis and tooth loss-to cardiometabolic outcomes such as type 2 diabetes and cardiovascular disease. However, progress in this field has long been constrained by fragmented data systems and limited availability of large-scale resources capturing both oral health exposures and cardiometabolic endpoints. Recent advances in biobank infrastructure, population-based cohorts, and electronic health record linkage have transformed this landscape, enabling robust secondary analyses at unprecedented scale. This narrative review synthesizes current evidence from major biobanks and large-scale epidemiologic datasets relevant to oral-cardiometabolic research. We describe how oral health and cardiometabolic outcomes are operationalized across data ecosystems, critically appraise the strengths and limitations of key resources, and integrate epidemiologic findings with established biological mechanisms, including chronic systemic inflammation, microbial dysbiosis, metabolic dysfunction, and vascular impairment. We further highlight the bidirectional nature of the relationship, whereby cardiometabolic disease can also exacerbate oral inflammatory conditions. Methodological challenges-such as exposure misclassification, residual confounding, and reverse causation-are discussed alongside emerging solutions, including data linkage, multi-omics integration, and advanced analytic approaches. Harnessing large-scale data sources offers a powerful opportunity to reposition oral health within cardiometabolic disease research and prevention. Strategic integration of dental and medical data has the potential to inform precision public health approaches and support more holistic models of chronic disease prevention.}, }
@article {pmid41907864, year = {2026}, author = {Taudte, N and Liebe, L and Jänckel, N and Ramsbeck, D and Schilling, S and Potempa, J and Eick, S and Buchholz, M}, title = {Novel small molecule targeting PgQC reduces Porphyromonas gingivalis virulence.}, journal = {Frontiers in oral health}, volume = {7}, number = {}, pages = {1716188}, pmid = {41907864}, issn = {2673-4842}, abstract = {INTRODUCTION: Periodontitis, a chronic inflammatory disease affecting the periodontium, is primarily driven by dysbiosis of the oral microbiome with Porphyromonas gingivalis as a keystone pathogen. Current therapeutic approaches rely on mechanical debridement and antimicrobials, which face limitations including antibiotic resistance and microbiome disruption. Pathoblockers represent a novel therapeutic strategy that selectively targets virulence factors without bactericidal effects, potentially reducing resistance development while preserving beneficial microbiota. Here, we describe the characterization of S-0636, a novel reversible inhibitor of zinc-dependent glutaminyl cyclase (PgQC), as a compound to selectively inhibit the bacterial virulence of P. gingivalis.<br><br>METHODS: The compound's effects were assessed through enzymatic assays, bacterial growth studies, virulence factor activity measurements (gingipain activity, hemagglutination, keratinocyte invasion), selectivity testing against commensal oral bacteria, resistance development analysis over 50 passages, and cytotoxicity evaluation in human cell lines.<br><br>RESULTS: S-0636 demonstrated potent PgQC inhibition with a Ki value of 0.014&#x2005;&#x3bc;M and has successfully reduced the intracellular PgQC activity by 50% at 8&#x2005;&#x3bc;M and had no bactericidal effects. Treatment of P. gingivalis with S-0636 significantly decreased gingipain activity, impaired hemagglutination capacity, and reduced keratinocyte invasion by 76% at 62.5&#x2005;&#x3bc;M. The compound showed high selectivity, with no growth inhibition of ten tested oral commensal species at concentrations up to 0.25&#x2005;mM. Importantly, no resistance development was observed after 50 bacterial passages, and cytotoxicity remained minimal in human cell lines with >80% viability at 0.5&#x2005;mM.<br><br>DISCUSSION: In previous studies, PgQC was suggested as an enzyme responsible for pGlu-modification and stabilization of bacterial virulence factors. The current study now validates PgQC as an attractive target for pathoblocker development, demonstrating that S-0636 effectively attenuates P. gingivalis pathogenicity through selective virulence factor inhibition while preserving bacterial viability and oral microbiome integrity. The absence of resistance development and low cytotoxicity profile support the potential clinical translation of this approach for periodontal disease management, representing a promising alternative to conventional antimicrobial therapies.}, }
@article {pmid41908157, year = {2024}, author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F}, title = {Diversity and composition of gut protist in young rural Zimbabwean children.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1399160}, pmid = {41908157}, issn = {2813-4338}, abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.<br><br>METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.<br><br>RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).<br><br>SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.}, }
@article {pmid41908202, year = {2026}, author = {Awashra, A and Neiroukh, H and AbuBaha, M and Shehadeh, W and Jallad, H and Emara, A and Abu-Khazneh, O and Zahran, A and Elgendy, MS and Fkheideh, T and Sawaftah, Z and Milhem, F and Hajjeh, O and Shubietah, A}, title = {The gut-heart axis in atrial fibrillation: Pathophysiology, evidence, and therapeutic potential.}, journal = {Heart rhythm O2}, volume = {7}, number = {3}, pages = {581-597}, pmid = {41908202}, issn = {2666-5018}, abstract = {BACKGROUND: Recent advances in microbiome research highlight a bidirectional relationship between gut microbiota and atrial fibrillation (AF), the most common sustained arrhythmia worldwide. Gut dysbiosis has been implicated in systemic inflammation, metabolite imbalance, bile acid signaling, and autonomic dysfunction, whereas AF itself alters microbial homeostasis through hemodynamic and neurohormonal changes.<br><br>OBJECTIVE: This review aimed to synthesize current evidence linking gut dysbiosis to AF pathogenesis, identify mechanisms underlying this interaction, and explore the therapeutic potential of microbiota-targeted interventions.<br><br>METHODS: We conducted a narrative review of preclinical, clinical, and epidemiologic studies examining the gut-heart axis in AF. Particular emphasis was placed on microbial metabolites (eg, trimethylamine N-oxide, short-chain fatty acids, indoxyl sulfate), bile acid modulation, and inflammatory signaling. Data on interventions, including diet, probiotics, pharmacologic approaches, and fecal microbiota transplantation, were integrated to assess translational potential.<br><br>RESULTS: Evidence suggests that gut-derived signals contribute to atrial remodeling through activation of the NLRP3 inflammasome, altered calcium handling, and impaired gap junction integrity. Conversely, AF promotes dysbiosis by reducing gut perfusion, altering motility, and exposing patients to polypharmacy. Microbiota-directed strategies, particularly dietary modification and probiotics, demonstrate promise in reducing arrhythmic risk, whereas early data indicate potential biomarker roles for gut microbial signatures in AF stratification. However, causality remains uncertain, given that most studies are observational with limited sample sizes.<br><br>CONCLUSION: The gut-heart axis represents a novel paradigm in AF research. Although preliminary findings support its mechanistic and therapeutic relevance, interventional studies are needed to establish causality and guide clinical application.}, }
@article {pmid41908552, year = {2026}, author = {Yu, N and Pang, S and Li, Y and Diao, H}, title = {Integrated microbiome-metabolome analysis reveals multiorgan toxicity of 1-nitropyrene and the limited efficacy of ferroptosis inhibitor Fer-1 in rats.}, journal = {Frontiers in toxicology}, volume = {8}, number = {}, pages = {1771766}, pmid = {41908552}, issn = {2673-3080}, abstract = {INTRODUCTION: 1-Nitropyrene (1-NP), a prevalent nitro-polycyclic aromatic hydrocarbon, is increasingly recognized as a potential metabolic disruptor, yet its systemic biological effects remain insufficiently characterized.<br><br>METHODS: This study investigated the metabolic, immunological, hepatic, and microbiome alterations induced by chronic 1-NP exposure in rats and assessed whether ferroptosis inhibition via Fer-1 could mitigate these effects.<br><br>RESULTS: Although body weight was not significantly altered overall, high-dose exposure impaired growth from week 4. Exposed groups exhibited progressively elevated fasting blood glucose and impaired glucose tolerance, indicating significant disruption of glucose homeostasis. Serum biochemistry revealed dose-dependent reductions in HDL and total cholesterol, while histopathology confirmed hepatocyte ballooning, inflammation, and steatosis consistent with NAFLD-like progression. Hematological changes, including shifts in neutrophil and lymphocyte populations, suggested chronic inflammatory activation. Untargeted metabolomics identified extensive alterations in pathways related to glycolysis, tryptophan metabolism, glycerophospholipid metabolism, and ABC transporters. Gut microbiota analysis demonstrated reduced richness and significant compositional shifts, with functional predictions linking dysbiosis to xenobiotic degradation, lipid metabolism, and phosphotransferase systems. Integrated microbiome-metabolome analysis revealed coordinated disruptions in host-microbial metabolic networks. Fer-1 intervention modified specific metabolic and microbial signatures but did not substantially alleviate major toxic outcomes.<br><br>CONCLUSION: Overall, chronic 1-NP exposure causes widespread metabolic injury driven by combined effects on host metabolism, immune regulation, hepatic function, and gut microbial ecology. These findings highlight 1-NP as a potent environmental metabolic disruptor and underscore the need for further mechanistic studies to inform mitigation strategies.}, }
@article {pmid41908560, year = {2026}, author = {Anand, S and Shete, O and Srivastava, A and Verma, A and Goswami, S and Aggarwal, S and Luthra, K and Ghosh, TS}, title = {Urinary Microbiome Dysbiosis in Children With Congenital Uropathies at Varying Risk for Urinary Tract Infections.}, journal = {Kidney international reports}, volume = {11}, number = {4}, pages = {103799}, pmid = {41908560}, issn = {2468-0249}, abstract = {INTRODUCTION: Febrile urinary tract infections (UTIs) may occur in 30% to 50% of children with vesicoureteral reflux (VUR) or posterior urethral valves (PUVs), frequently leading to renal scarring despite chemoprophylaxis. Approximately 15% of children with uretero-pelvic junction obstruction (UPJO) may develop UTIs. However, investigations that can identify at-risk children before the first episode of UTI are lacking. In this exploratory study, we investigated the preinfection urinary microbiome in Indian children with congenital anomalies of the kidney and urinary tract (CAKUT) to determine whether microbiome alterations, metabolic potential, and antibiotic resistance profiles precede UTI.<br><br>METHODS: In this prospective cohort study with follow-up, urine samples were collected from 80 children: 36 with newly diagnosed, antibiotic-na&#xef;ve CAKUT (18 UPJO, 12 VUR, 6 PUV) and 44 controls. Patients were stratified a priori into low (n = 19) and high-risk (n = 17) groups using clinically defined UTI-susceptibility criteria. V3-V4 16S ribosomal RNA sequencing was used to define urinary microbial profiles. Alpha- and beta-diversity were compared using Shannon index and permutational multivariate analysis of variance (PERMANOVA), respectively. Sliding-window and network-based analyses were used to map dysbiosis gradients. Patients were followed-up longitudinally to assess UTI incidence. Identified dysbiosis-linked microbial markers at baseline were investigated using Kaplan-Meier and Cox-proportional hazard-based analyses as predictors of UTI-risk. Metabolic functions were inferred from taxonomic data. Antibiotic resistance patterns were characterized using the Comprehensive Antibiotic Resistance Database - Resistance Gene Identifier (CARD-RGI) and the World Health Organization Access, Watch, and Reserve classification.<br><br>RESULTS: Urinary microbial alpha diversity declined significantly from controls to low-risk to high-risk groups (P = 0.002), accompanied by an increase in intragroup variability (P &#x2264; 0.005). PERMANOVA revealed distinct clustering by risk (R [2] = 0.11; P = 0.001). Dysbiosis scores inversely correlated with the first Kendall Principal Coordinates Analysis (PCoA) axis (&#x3c1; = -0.62; P < 0.001). With increasing risk of UTI, the commensal, control-associated genera declined along this axis while the facultative pathogens became dominant. Control-associated microbiomes favored short- and branched-chain fatty acid and spermidine production; high-risk microbiomes overproduced ammonia, putrescine, and cadaverine. Resistance to 18 of 22 routinely tested antibiotics was almost confined to the 31 risk-associated microbiomes (P = 0.001). During the median (interquartile range) follow-up of 564 (518-594) months, 14 of 36 children with CAKUT developed UTIs, and baseline depletion of health-associated microbial consortia correlated with reduced UTI-free survival. A panel of 10 species-level and 12 genus-level taxa were identified as health-associated markers negatively associated with future UTI-risk during follow-up investigation.<br><br>CONCLUSION: Children with CAKUT exhibit urinary microbiome dysbiosis before their first symptomatic UTI, characterized by loss of conserved health-associated taxa, metabolic imbalance, and broad-spectrum antibiotic resistance. These findings support the potential of microbiome-informed, noninvasive risk stratification and microbiome-tailored prophylaxis, while establishing the first Indian pediatric reference set for CAKUT-related UTI prevention.}, }
@article {pmid41908828, year = {2026}, author = {Zhang, Z and Ku, A and Ji, R and Song, B}, title = {Multi-omics analysis reveals the mechanism of Huaganjian in alleviating cholestatic liver fibrosis.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1744312}, pmid = {41908828}, issn = {1663-9812}, abstract = {Huaganjian (HGJ) is a traditional Chinese medicinal formula with liver-protective effects. However, the pharmacological mechanisms of the effects of HGJ on cholestatic liver fibrosis (CLF) are yet to be clarified. To evaluate the effects of HGJ on CLF and elucidate the underlying mechanisms, C57BL/6J mice were fed a 0.1% 3, 5-diethoxycarbonyl-1, 4-dihydrocollidine (DDC) diet to induce CLF. The efficacy of HGJ was evaluated by measuring the biochemical indicators of liver function, fibrosis, and histology. The underlying mechanisms were investigated using an integrated multi-omics approach, including fecal 16S rRNA sequencing, serum metabolomics, and hepatic transcriptomic analysis. The findings were further validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blotting (WB). HGJ significantly alleviated liver injury, cholestasis, and fibrosis. Microbiome analysis revealed that Bifidobacterium, Turicibacter, and Clostridium_sensu_stricto_1 abundances were positively correlated with liver injury and fibrosis marker levels, and these abundances decreased following HGJ treatment. Metabolomic analysis identified 531 differential metabolites, including 299 upregulated and 232 downregulated metabolites, following HGJ intervention. Hepatic transcriptomic analysis revealed 164 differentially expressed genes, including 102 upregulated and 62 downregulated genes. Integrated multi-omics analysis revealed that HGJ alleviated CLF by modulating the glycine/serine/threonine metabolism pathway. RT-qPCR and Western blotting experiments confirmed that in this pathway, aminolevulinic acid synthase 1 levels decreased, whereas serine dehydratase and serine dehydratase-like levels increased after HGJ treatment. Overall, HGJ effectively alleviated CLF, and its mechanisms of action were closely linked to the regulation of the glycine/serine/threonine metabolism pathway.}, }
@article {pmid41908923, year = {2025}, author = {Kurt, &#xd6; and Scanlan, PD and Gentekaki, E and Robertson, LJ and Carmena, D and Dogruman-Al, F and Tsaousis, AD}, title = {The Blastocystis-colorectal cancer hypothesis: correlation is not causation.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {379}, pmid = {41908923}, issn = {2732-5121}, abstract = {Although superficially persuasive, claims suggesting a causal link between Blastocystis and colorectal cancer (CRC) lack robust scientific support. As Blastocystis is the most common gut protist found in human populations globally, its detection in CRC patients is unsurprising and does not imply pathogenicity. Current claims championing a causal role for Blastocystis in CRC are based on speculative correlations, a single poorly controlled animal study, and inconsistent subtype associations. We argue that linking Blastocystis to CRC is premature, misleading, and may give rise to unnecessary concern in patients that are colonised by or test positive for Blastocystis. We emphasise the need for rigorously designed investigations to establish causal roles for any microorganism in disease and the importance of conclusions being based on solid evidence, particularly in matters of public health.}, }
@article {pmid41909054, year = {2025}, author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M}, title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {41909054}, issn = {2673-8007}, support = {R03 HD098482/HD/NICHD NIH HHS/United States ; }, abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.}, }
@article {pmid41909172, year = {2026}, author = {Bao, Y and Xu, K and Du, Y and Feng, M and Li, L and Li, L and Yan, G and Li, X}, title = {PPARγ: a key orchestrator of epidermal barrier, immune responses, and lipid metabolism in atopic dermatitis pathogenesis and therapy.}, journal = {Frontiers in allergy}, volume = {7}, number = {}, pages = {1780908}, pmid = {41909172}, issn = {2673-6101}, abstract = {Atopic dermatitis (AD) is an immune-mediated inflammatory dermatosis characterized by epidermal barrier dysfunction, immune dysregulation, and cutaneous microbial dysbiosis. Existing therapeutic modalities for AD are limited in efficacy and durability, highlighting an unmet clinical need for novel, safe, and effective treatment strategies. Peroxisome proliferator-activated receptor gamma (PPARγ), a pivotal nuclear receptor involved in metabolic and inflammatory regulation, has emerged as a promising therapeutic target for AD. Its pleiotropic mechanisms encompass the restoration of stratum corneum integrity, modulation of aberrant immunoinflammatory signaling, normalization of cutaneous lipid metabolism, and regulation of the cutaneous microbiome and neuroimmune circuitry. This review comprehensively synthesizes the mechanistic evidence linking PPARγ to AD pathogenesis and critically appraises its potential as a novel therapeutic.}, }
@article {pmid41909251, year = {2026}, author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y}, title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1735540}, pmid = {41909251}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.<br><br>METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.<br><br>RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).<br><br>DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.}, }
@article {pmid41909261, year = {2026}, author = {Choi, J and Shim, K and Bae, GS and Jeon, E and Hwang, EH and Kim, G and Baek, SH and Hong, JJ and Kim, DS and Kim, SH and Koo, BS}, title = {Comparative analysis of gut microbiota and host phenotypic characteristics across enterotype-like clusters in cynomolgus and rhesus macaques.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1775757}, pmid = {41909261}, issn = {1664-302X}, abstract = {Microbiome has been increasingly recognized for its close association with host physiology and diseases. Due to their close genetic relatedness to humans and standardized environmental conditions, captive macaque species serve as the most evolutionarily comparable preclinical animal models for studying human microbiome research. However, the characterization of gut microbiota and host phenotypic traits within each enterotype-like cluster of macaque species remains poorly understood. We analyzed microbiome characteristics and host metadata within enterotype-like clusters of cynomolgus and rhesus macaques housed in the same facility but with different origins of birth. At the phylum level, Bacteroidota, Firmicutes, Spirochaetota, and Proteobacteria were predominantly observed in both species. Except for Fibrobacterota at the phylum level, no significant interspecies differences were observed in bacterial composition or alpha diversity across taxonomic levels. Based on a prevalence threshold of 90%, cynomolgus macaques were found to share 12.4% of genera, while rhesus macaques shared 18.2%. Based on the relative abundance patterns of the genera Prevotella 9, Rikenellaceae RC9 gut group, and Treponema, the fecal microbiome of cynomolgus macaques was classified into three enterotype-like clusters (cluster 1, cluster 2, and cluster 3) whereas that of rhesus macaques was classified into two enterotype-like clusters. Using linear mixed-effects models, we identified species-specific associations between enterotype-like clusters and host phenotypes. In cynomolgus macaques, clustering was primarily associated with hematological and selected biochemical parameters, whereas in rhesus macaques, enterotype-like clusters were limited to body weight and hemoglobin. Despite a standardized diet and shared environments, distinct clusters and pronounced microbial individuality associated with birthplace suggest that early-life colonization is a key determinant of long-term gut microbiome structure and host phenotypes in captive primates. Also, identifying enterotype-like clusters in NHPs prior to analysis is essential for accurate and relevant human microbiome modeling, since each cluster may correspond to distinct human enterotypes and phenotypic traits.}, }
@article {pmid41909266, year = {2026}, author = {Zhu, Z and Li, X and Cui, T and Chen, Z and Liu, Y and Chen, X and Tian, Y and Mu, Y and Wu, Y and Ji, Q and Yan, S and Cheng, Y}, title = {Temporal heterogeneity of microbial ecosystems and its formation mechanisms in Moutai-flavor Baijiu fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798174}, pmid = {41909266}, issn = {1664-302X}, abstract = {The influence of workshop age on Moutai-flavor Baijiu fermentation is recognized, but the mechanisms driving microbial community shifts remain unclear. Understanding how the physical environment selects for specific microbiota is crucial for optimizing new workshops. Through 16S/ITS sequencing of pit-entry fermented grains, Daqu, air, and cooling yards in 5-, 10-, 20-, and 30-year-old workshops, Lactobacillus emerged as a key discriminant genus, increasing from 15.02% (5-year) to 35.59% (30-year). SourceTracker analysis revealed the cooling yard as the primary microbial source, contributing 54.2% on average to fermented grains. CO2-TPD analysis showed a 3.6-fold reduction in cooling yard surface basicity (from 0.11 to 0.03 mmol·g[-1]) over 30 years, resulting in high abundances (>10%) of alkalotolerant bacteria (e.g., Alkalibacterium, Nesterenkonia) and low Lactobacillus (2.17%). Nesterenkonia was also a biomarker in 5-year fermented grains. This confirms cooling yard surface basicity drives microecological differences, revealing how long-term production practices domesticate microbial communities and providing a theoretical basis for new workshop adaptation.}, }
@article {pmid41909643, year = {2026}, author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O}, title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.}, journal = {Biofilm}, volume = {11}, number = {}, pages = {100357}, pmid = {41909643}, issn = {2590-2075}, abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.}, }
@article {pmid41909648, year = {2026}, author = {Kumar, V and Das, BK and Roy, S and Bhowal, P and Roy, A and Bruce, TJ and Galindo-Villegas, J}, title = {Exploring the host-pathogen interaction and genome analysis of multidrug-resistant bacterial pathogen Proteus penneri isolated from Labeo rohita.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1733414}, pmid = {41909648}, issn = {1664-3224}, mesh = {Animals ; *Fish Diseases/microbiology/immunology ; *Drug Resistance, Multiple, Bacterial/genetics ; *Host-Pathogen Interactions/genetics ; *Cyprinidae/microbiology/immunology ; Phylogeny ; *Proteus Infections/microbiology/veterinary/immunology ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Multidrug-resistant (MDR) bacterial pathogens represent an escalating challenge to sustainable aquaculture, particularly in high-value freshwater species such as Labeo rohita, a cornerstone of South Asian aquaculture. This study provides the first comprehensive integration of genomic, immunological, and microbiome analyses to characterize Proteus penneri as an emerging MDR pathogen associated with severe disease manifestations in L. rohita, including exophthalmia, ulceration, and hemorrhage. Robust identification through biochemical assays, 16S rRNA sequencing, and phylogenetic analysis confirms the clinical relevance of this isolate. Functional assays demonstrated pronounced virulence, evidenced by hemolysin activity, extensive histopathological damage, and dose-dependent mortality, underscoring its pathogenic capacity in vivo. The observed resistance to multiple frontline antibiotic classes, including tetracyclines, macrolides, and carbapenems, highlights a critical therapeutic limitation in aquaculture settings. Genomic analysis further revealed a diverse repertoire of antimicrobial resistance genes, virulence determinants (notably biofilm formation and secretion systems), and mobile genetic elements, suggesting a strong potential for persistence, adaptability, and horizontal gene transfer. Infection-associated gut microbiome disruption, marked by elevated MAR indices and enrichment of virulence-associated taxa, indicates that P. penneri not only exploits host tissues but also reshapes the microbial ecosystem in ways that may exacerbate disease severity and resistance dissemination. Concurrently, heightened serum cortisol, C3, and Hsp70 levels, along with transcriptional upregulation of key immune and stress-related genes (hsp70, nod, il6, sod, c3, and myd88), reflect an intense pro-inflammatory and physiological stress response. In silico docking analyses implicating myd88-lipopolysaccharide interactions provide mechanistic insight into potential immune-modulatory strategies employed by the pathogen. Collectively, these findings delineate a multifactorial basis for P. penneri virulence and MDR, emphasizing its significance as an emerging aquaculture pathogen. Future research should prioritize functional validation of key virulence and resistance genes, longitudinal surveillance to assess transmission dynamics and AMR spread, and experimental evaluation of alternative disease mitigation strategies, including probiotics, phage therapy, and immune-modulating interventions, to reduce antibiotic reliance and enhance fish health resilience in aquaculture systems.}, }
@article {pmid41909844, year = {2026}, author = {Lin, B and Tong, S and Ba, C and Wang, X}, title = {Precision treatment of gastrointestinal tumours and liver disease interaction mechanisms based on multi-omics data and microbiome hubs.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1791531}, pmid = {41909844}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome ; *Liver Diseases/therapy/microbiology ; *Precision Medicine/methods ; Genomics/methods ; Proteomics/methods ; Metabolomics/methods ; Tumor Microenvironment ; Carcinogenesis ; Multiomics ; }, abstract = {The global prevalence of gastrointestinal tumours and the bottlenecks in their diagnosis and treatment are being systematically overcome by the multi-omics revolution: high-throughput technologies are driving the multidimensional integration of genomics-transcriptomics-proteomics-metabolomics to comprehensively decode the genetic architecture of tumours. Meanwhile, the gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, further facilitating proteome-metabolome multidimensional integration, comprehensively decoding tumour genetic architecture. The gut microbiota, acting as a core regulatory hub, drives carcinogenesis through immune microenvironment remodelling and metabolic pathway hijacking, while mediating a vicious cycle network linking liver disease and tumours via the gut-liver axis. This review examines the application of multi-omics technologies in gastrointestinal tumour research, summarises the role of gut microbiota in tumourigenesis and its interaction with liver disease, and envisions future interventions targeting the gut microbiome for early disease diagnosis and precision treatment.}, }
@article {pmid41909873, year = {2026}, author = {Yu, J and Baek, H and Jaiswal, V and Park, M and Lee, HJ}, title = {Heavy metal accumulation and fecal microbiota response in black soldier fly larvae: identification of Leminorella grimontii as a potential indicator species.}, journal = {Food science and biotechnology}, volume = {35}, number = {5}, pages = {1329-1338}, pmid = {41909873}, issn = {2092-6456}, abstract = {UNLABELLED: With growing environmental concerns about marine pollution from heavy metals, black soldier fly larvae (BSFL) are gaining attention for their potential use in sustainable waste-to-feed systems. In this study, BSFL were raised on diets containing cadmium (Cd), lead (Pb), mercury (Hg), and arsenic (As) to assess their growth, metal accumulation patterns, and changes in microbiota. While Cd mainly accumulated in the larval body, Pb, Hg, and As were primarily excreted through exuviae and feces. This pattern remained consistent even when larvae were fed naturally contaminated mackerel heads. Microbiome analysis of fecal samples showed that Leminorella grimontii had a strong positive correlation with Hg and As concentrations, suggesting its potential as a microbial indicator species for heavy metal exposure. These findings support the use of BSFL in bioconversion systems and suggest L. grimontii as a new biomarker for environmental monitoring.<br><br>GRAPHICAL ABSTRACT: Scheme 1Experimental procedure and fecal microbiome results.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-026-02114-y.}, }
@article {pmid41909880, year = {2025}, author = {Cold, F and Heintz, JE and Ghathian, KSA and Stenbøg, PA and Hansen, LH and Carstens, AB and Petersen, AM and Halkjaer, SI and Bendtsen, F and Ytting, H}, title = {Low incidence of cytolysin-positive E. faecalis and no correlation to survival in Danish patients with alcohol-associated hepatitis: A prospective cohort study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2549729}, pmid = {41909880}, issn = {2993-3935}, abstract = {Alcohol-associated hepatitis (AH) is a severe and life-threatening form of alcohol-associated liver disease with no approved treatments for reducing long-term mortality. Cytolysin-producing E. faecalis in the gut microbiota of AH patients has been reported as highly correlated to mortality. We investigated whether we could reproduce this correlation in a cohort of Danish patients with AH. Fecal samples from 28 hospitalized patients with AH were analyzed for cytolysin-producing E. faecalis and were followed for 1 y after hospital admission. The primary endpoint was comparison of 180-d mortality in AH patients with and without cytolysin-positive fecal samples. Three of twenty-eight (10.7%) fecal samples were identified as cytolysin-positive. There were no significant differences at baseline between cytolysin-positive and -negative patients in terms of age, Glasgow Alcoholic Hepatitis Score, Charlson Comorbidity Index or biochemical variables (INR, bilirubin, albumin). There was no difference in mortality between the groups 180 d after hospital admission; one of the three (33%) cytolysin-positive patients had died compared to 9 of the 25 (36%) cytolysin-negative (p-value for difference = 1.0). We report a low incidence of cytolysin-positive E. faecalis in hospitalized Danish AH patients and no greater risk of mortality compared to cytolysin-negative AH patients.}, }
@article {pmid41909881, year = {2025}, author = {Liu, W and An, M and Wang, Q and Liu, Y and Shang, Y and Dong, X and Ding, H and Fu, S and Han, X and Shang, H}, title = {Gut microbiome-induced metabolites promote the role of Silybin as adjunctive drug in HIV-positive immunological nonresponders.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2569789}, pmid = {41909881}, issn = {2993-3935}, abstract = {HIV-infected immunological nonresponders (INRs) endure persistent T-cell dysfunction and chronic inflammation, facing high risk of various complications and mortality, with no effective therapies available. Silybin, the principal constituent of a plant extract, possesses anti-inflammation and immunomodulatory properties. The gut microbiome has been shown to modulate the efficacy of immune therapies and drugs. We gave 54 INRs oral silybin for three months and used multi-omics to investigate the gut-related factors influencing the efficacy of silybin. Silybin raised CD4[+] T cells counts in 52% of participants and an efficacy classification model based on baseline gut microbiome and metabolites was developed. Favorable gut bacteria produced anti-inflammatory metabolites that downregulated Ras/MAPK/PI3K-Akt signaling pathways also targeted by silybin. Our findings shed light on a novel therapeutic approach for addressing immune dysfunction in HIV-positive INRs and have important implications for personalized medical strategies in the management of HIV infection.}, }
@article {pmid41909883, year = {2025}, author = {Abubakar, D and Abdullahi, H and Ibrahim, I}, title = {Bridging Microbiomes: Exploring Oral and Gut Microbiomes in Autoimmune Thyroid Diseases- New Insights and Therapeutic Frontiers.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2452471}, pmid = {41909883}, issn = {2993-3935}, abstract = {Autoimmune thyroid diseases (AITDs) are the most common organ-specific autoimmune disorders characterized by thyroid dysfunction and immune system deficiencies. In recent decades, the role of the microbiome in autoimmune diseases has gained increasing attention, with emerging research linking gut microbiome alterations to the development of AITDs. This review summarizes current knowledge on the relationship between AITDs and the gut microbiome. Additionally, it emphasizes the role of the oral microbiome in AITDs, an area often overlooked in autoimmune research. Beyond the microbiome, the virome and mycobiome have been recognized as critical but underexplored components of the human microbiome, potentially contributing to immune dysregulation and the pathogenesis of AITDs. The review also explores modulating the microbiome for managing AITDs, including diet adjustment, the potential use of probiotics, postbiotics, symbiotics, and even fecal microbiota transplantation (FMT) to restore a balanced microbiome that may positively influence the immune system and, by extension, the course of AITDs. This review thoroughly explores the intricate relationship between AITDs, the gut, and oral microbiomes, paving the way for precision medicine applications in AITDs. Examining microbiota-thyroid interactions highlights the potential for targeted, personalized treatments and novel therapeutic therapies, guiding future therapeutic strategies for more effective and precisely tailored AITD management approaches.}, }
@article {pmid41909884, year = {2025}, author = {Pateriya, D and Prasoodanan P K, V and Scaria, J and Sharma, VK}, title = {Landscape of flavonoid metabolism in human gut microbiome and its association with health and disease.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2520788}, pmid = {41909884}, issn = {2993-3935}, abstract = {The positive effects of dietary flavonoids on health depend on their bioavailability in the human gut, where the flavonoid-modifying enzymes (FMEs) in gut bacteria play a crucial role in flavonoid metabolism. Thus, to comprehensively examine the role of FMEs in this process, we first constructed a database of potential FMEs containing 6,865 proteins. We identified homologs of these FMEs in gut bacterial genomes and reported species that can potentially modify flavonoids but were not previously known in this context. We examined the differential abundance of FMEs in the gut microbiomes of healthy and diseased individuals from Western and non-Western populations with distinct dietary habits. The differential enrichment of key FMEs between Western and non-Western populations and between disease and healthy samples highlights differences in gut flavonoid metabolism based on diet, population, and health status. This study reveals a comprehensive landscape of flavonoid metabolism in the human gut microbiome.}, }
@article {pmid41909885, year = {2025}, author = {Lau, RI and Wong, MCS and Lau, LHS and Lau, AYL and Mak, IWC and Lo, OSH and Chan, NN and Dai, DLK and Hau, KC}, title = {Role of gut microbiome in pathogenesis and treatment of diseases: Multidisciplinary experts' opinion of the Asian Medical Experts Academy (AMEA).}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2558575}, pmid = {41909885}, issn = {2993-3935}, abstract = {Emerging evidence suggests the role of the gut microbiome in the health and diseases of multiple organs and systems. In the past decade, an increasing trend in the use of microbiome-based therapeutics (e.g., probiotics, prebiotics, synbiotics) has been observed in Asia and globally. However, local and global clinical guidelines on the use of microbiome-based therapeutics are limited. A multidisciplinary working group has been established to foster communication between experts from diverse medical specialties on the clinical application of microbiome-based therapeutics. Through conducting an extensive review on current evidence on the importance of the gut microbiome and the potential use of microbiome-based therapeutics in health and diseases, the experts' working group identified the unmet needs related to the use of microbiome-based therapeutics in the clinical settings in Asia and global contexts. Thirteen position statements were developed, including eight statements focusing on the role of the gut microbiome in health and disease pathogenesis, as well as six statements focusing on the potential clinical applications. A list of potential indications for microbiome-based therapeutics was also proposed based on current evidence and clinical experience. This paper is intended to serve as a reference that assists healthcare professionals in improving care for patients using microbiome-based therapeutics in Asia and globally.}, }
@article {pmid41909889, year = {2025}, author = {Lan, Z and Chen, J and Lan, S and Li, N and Yang, B and Hou, J and Yang, X}, title = {Hydrogen-rich water attenuates radiation-induced oral mucositis in mice via antioxidant and gut microbiota-stabilizing effects: a longitudinal study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2595392}, pmid = {41909889}, issn = {2993-3935}, abstract = {Radiation-induced oral mucositis (RIOM) frequently complicates head and neck radiotherapy, leading to severe pain, compromised nutrition, and often requiring treatment modifications. Although craniofacial-only irradiation is confined to the head and neck region, it can still disrupt gut homeostasis. Mice subjected to head and neck irradiation developed marked epithelial damage in both the oral and intestinal mucosa, as evidenced by pronounced RIOM and diminished barrier integrity. Histological examination revealed substantial mucosal thinning and leukocyte infiltration in the tongue, along with reduced occludin and ZO-1 expression in colonic tissues. Supplementation with hydrogen-rich water (HW) markedly decreased the severity of oral lesions and preserved epithelial thickness, while restoring the expression of tight junction proteins in the colon. Fecal 16S rRNA sequencing showed that radiation alone provoked expansions of Streptococcus and Helicobacter, coupled with a decline in short-chain fatty acid-producing families (Lachnospiraceae, Ruminococcaceae). In contrast, HW supplementation partially reversed these microbial shifts, which correlated with reduced oral inflammatory markers. Collectively, these findings underscore an oral-gut axis whereby HW fosters mucosal healing through microbiome stabilization and decreased inflammatory stress, suggesting that HW as a promising adjunct for managing head and neck irradiation-related complications.}, }
@article {pmid41909890, year = {2025}, author = {Park, G and Oh, S and Kim, M and Jeong, Y and Kim, G}, title = {Common microbial signatures in blood and their amplification in clinical disorders.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2473450}, pmid = {41909890}, issn = {2993-3935}, abstract = {Blood microbiome research has emerged as a significant area of study, exploring microbial signatures within the bloodstream and their potential implications for various clinical disorders. This study aimed to identify common microbial signatures in blood across cohorts and investigate how these signatures are altered in clinical conditions. We conducted a meta-analysis of 15 publicly available studies utilizing amplicon sequencing, including 687 control and 651 case individuals with various disorders from diverse geographic locations to compare their blood microbiome profiles. The results revealed that most microbes detected in the blood originated from the gut, oral cavity, and skin, with several genera such as Corynebacterium, Streptococcus, and Lactobacillus consistently identified across studies. Furthermore, we observed a significant increase in microbial diversity and abundance in individuals with clinical disorders compared to the control group. Notably, microbial genera originating from the gut and oral cavity, including Acinetobacter, Prevotella, and Clostridium sensu stricto-1, were more prevalent in disease cohorts, suggesting a potential link between the translocation of microbial signatures and disease pathology. The study underscores the importance of considering microbial signatures as potential biomarkers in clinical settings and calls for further investigation into the role of circulating microbial DNA in immune response and disease progression.}, }
@article {pmid41909891, year = {2025}, author = {Manzoor, H and Kayani, MUR}, title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2483446}, pmid = {41909891}, issn = {2993-3935}, abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.}, }
@article {pmid41909893, year = {2025}, author = {Jorgensen, JA and Choo-Kang, C and Wang, L and Issa, L and Gilbert, JA and Ecklu-Mensah, G and Luke, A and Bedu-Addo, K and Forrester, T and Bovet, P and Lambert, EV and Rae, D and Argos, M and Kelly, TN and Sargis, RM and Dugas, LR and Dai, Y and Layden, BT}, title = {Toxic metals impact gut microbiota and metabolic risk in five African-origin populations.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2481442}, pmid = {41909893}, issn = {2993-3935}, abstract = {Underlying mechanisms by which exposures to toxic metals/metalloids impact obesity and type 2 diabetes (T2DM) risk remain largely unknown. Gut microbiota have been strongly associated with cardiometabolic risk. To assess relationships between high metal exposures, gut dysbiosis, and metabolic dysregulation, we analyzed associations among gut microbiome taxa, dichotomized metal levels (arsenic, lead, mercury, cadmium), clinical measures (BMI, fasting blood glucose, blood pressure), and diagnoses (hypertension, obesity, diabetes) in 178 African-origin adults (52% female, mean age = 43.0 ± 6.4 years) from Ghana, South Africa, Jamaica, Seychelles, and USA. High vs. low lead and arsenic levels had a significant effect on beta diversity (p < 0.05). Seventy-one taxa were associated with high lead levels: 30 with elevated BMI, 22 with T2DM, and 23 with elevated fasting blood glucose (p < 0.05); 115 taxa were associated with high arsenic levels: 32 with elevated BMI, 33 with T2DM, and 26 with elevated blood glucose (p < 0.05). Porphyrin metabolism was the most enriched metabolic pathway in taxa associated with higher lead and arsenic exposure. These data provide the first findings from African-origin adults that demonstrate the association between the gut microbiome with lead and arsenic exposure and obesity and T2DM risk.}, }
@article {pmid41900768, year = {2026}, author = {Zhou, S and Xu, Z and Shen, J}, title = {Female Reproductive Tract Organ-on-Chips: Modeling Barrier Function and Drug Transport.}, journal = {Pharmaceutics}, volume = {18}, number = {3}, pages = {}, pmid = {41900768}, issn = {1999-4923}, support = {1U01FD007656//United States Food and Drug Administration/ ; 33040//Massachusetts Life Sciences Center/ ; }, abstract = {Female reproductive tract (FRT) disorders such as maternal conditions and gynecological cancers represent a significant global health burden. However, women's health, and particularly locally acting therapies targeting the FRT, has historically been underprioritized in drug development and translational research. Developing safe and effective therapies requires a clear understanding of drug transport across FRT barriers. Conventional in vitro culture systems and animal studies fail to recapitulate the physiological complexity of the human FRT, including stratified mucosal architecture, functional mucus barriers, microbiome interactions, as well as dynamic hormonal regulation. Recently, organ-on-chip (OoC) microfluidic platforms, integrating human cells with precisely controlled perfusion, have emerged as advanced in vitro systems capable of recreating dynamic physiological microenvironments. This review summarizes the major anatomical and physiological barriers of the FRT, including the vagina, cervix, endometrium, and placenta, and discusses critical design considerations for the development of FRT-on-chip models. We highlight the advanced OoC developed to study infection, drug permeation, hormonal responses, and maternal-fetal interface dynamics. Finally, future perspectives are outlined, including the integration of immune components, vascularization strategies, and multi-organ systems to better simulate inter-organ communication. Collectively, these advances underscore the potential of FRT-on-chip models as predictive platforms for preclinical drug screening, toxicity evaluation, and personalized medicine.}, }
@article {pmid41900770, year = {2026}, author = {Vadlapatla, R and Shirazi, AN and Koomer, A and Weng, J and Ghilarducci, ME and Qudus, A and Parang, K}, title = {Microbiome-Responsive Hydrogels: From Biological Cues to Smart Biomaterials.}, journal = {Pharmaceutics}, volume = {18}, number = {3}, pages = {}, pmid = {41900770}, issn = {1999-4923}, abstract = {Background: Stimuli-responsive hydrogels (SRHs) are smart polymeric materials that undergo reversible physicochemical changes in response to abiotic cues and externally applied fields, enabling applications in drug delivery, wound healing, and tissue engineering. However, they exhibit limited biological specificity and do not adequately reflect the dynamic, disease-relevant complexity of native tissue microenvironments. Microbe-colonized tissues display distinctive biochemical features driven, shaped by microbial metabolism, including localized pH gradients, short-chain fatty acid production, secretion of quorum-sensing molecules, biofilm formation, and expression of specialized enzymes. These endogenous, spatiotemporally regulated signals are closely linked to host physiology and pathology but remain underutilized in hydrogel design. This review aims to highlight microbiome-responsive hydrogels (MRHs) as a strategy to address this gap. Methods: This study summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications of MRHs, with emphasis on translational and regulatory challenges. Results: Microbiome-responsive hydrogels (MRHs) address this gap by leveraging microbial metabolic and biochemical cues to induce swelling, degradation, drug release, antibacterial activity, or structural transformation. By directly coupling to microbe-derived stimuli, MRHs offer improved physiological relevance, enhanced local specificity, and new opportunities for precision therapy targeting disease-associated microbial niches. Conclusions: Despite their promise, MRHs remain an early and fragmented field, lacking standardized biological triggers, material design frameworks, and performance evaluation strategies. This review summarizes current engineering approaches, key microbial stimuli, and emerging biomedical applications, with emphasis on translational and regulatory challenges, positioning MRHs as an underexplored platform for next-generation smart biomaterials.}, }
@article {pmid41900857, year = {2026}, author = {Shah, IM and Lebrilla, CB and German, JB and Mills, DA}, title = {Selective Human-Milk-Inspired Antimicrobial Peptides for the Treatment of Bacterial Vaginosis.}, journal = {Pharmaceutics}, volume = {18}, number = {3}, pages = {}, pmid = {41900857}, issn = {1999-4923}, support = {R43AI165105/GF/NIH HHS/United States ; }, abstract = {Background: Antimicrobial resistance (AMR) is a global healthcare threat. Traditional largely non-selective antibiotics produce side effects due to the natural host microbiome being modified creating a loss in homeostasis. In women, AMR is a cause of acute generational impact. For example, bacterial vaginosis (BV), the most common gynecological infection in reproductive-age women, is a serious public health concern due to its high rates of recurrence, secondary infections, and reproductive issues; and two currently prescribed antibiotics for BV do not fully resolve the symptoms. Objective: The strong need for innovative, potent, safe, and selective therapeutics has prompted a search for such bioactive molecules in milk. Resulting from 200 million years of evolutionary pressure, mammalian lactation not only nourishes infants, but it has also been under relentless Darwinian selective pressure to provide protection from a variety of infections. Methods: Computationally designed human-milk-inspired peptides (AMPs) were tested in standard microbicidal assays for activity against BV pathogens, and evaluated for stability and safety. Results: Several AMPs are bactericidal towards Gardnerella vaginalis, a major BV-associated pathogen, and other BV-associated pathogens. Some novel AMPs do not impact the viability of key lactobacilli linked to a healthy vaginal microbiome. These stable, membrane-acting cationic AMPs reduce inflammation during an infection assay and are safe in EpiVag organoid tissues. Conclusions: AMPs can address concerns like non-selectivity and antibiotic resistance-thereby addressing AMR. Lead AMPs from this study offer a promising solution for the development of novel therapeutics for the treatment of BV, which may reduce the burden of AMR.}, }
@article {pmid41900935, year = {2026}, author = {Santaniello, U and Mastorino, L and Pala, V and Rosset, F and Crespi, O and Quaglino, P and Ribero, S}, title = {Pharmacomicrobiomics in Psoriasis: Microbiome-Drug Interactions Across Systemic Treatments.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, pmid = {41900935}, issn = {2075-1729}, abstract = {Psoriasis is a chronic immune-mediated skin disease with highly variable responses to systemic therapies. Emerging evidence highlights the microbiome as a potential modulator of drug efficacy and toxicity. Gut bacteria can enzymatically metabolize drugs, such as methotrexate, altering bioavailability and therapeutic outcomes, while microbial metabolites-including short-chain fatty acids, branched-chain amino acids, and tryptophan derivatives-shape host immunity and barrier integrity, influencing drug action. Baseline microbial signatures have been linked to treatment response, potentially predicting anti-TNF or IL-17 inhibitor efficacy. Systemic therapies themselves reshape microbial communities: IL-17 blockade induces broad shifts in gut and skin microbiota, whereas cyclosporine and anti-TNF agents exert subtler effects. Small molecules such as apremilast and fumarates may reduce fungal overgrowth and influence microbial composition, whereas data on JAK/TYK2 inhibitors remain limited. Notably, current evidence exhibits a literature bias toward the gut microbiota, while the roles of the oral and skin axes remain understudied. Adjunctive microbiome-directed interventions, including probiotics and fecal microbiota transplantation, have demonstrated potential to enhance treatment outcomes by promoting anti-inflammatory taxa and restoring barrier function. Despite these promising findings, current evidence is heterogeneous, often limited by small sample sizes, short follow-up, and variable methodology. Integrating pharmacomicrobiomics data with clinical, genetic, and multi-omics profiling could enable precision medicine approaches in psoriasis, allowing therapy selection tailored to individual microbial and metabolic signatures. Future research should focus on longitudinal, multicenter studies to identify actionable microbial biomarkers, clarify mechanistic interactions between drugs, microbes, and host immunity, and evaluate microbiome-targeted adjuncts in randomized trials. Understanding the bidirectional crosstalk between systemic therapies and the microbiome may transform psoriasis management, improving efficacy, reducing adverse events, and enabling durable, personalized responses.}, }
@article {pmid41901063, year = {2026}, author = {Nunna Sai Venkata, L and Mishra, AK and Mohanta, YK and Rustagi, S and Bahuguna, A and Tomar, A and Baek, KH and Mishra, B}, title = {The Gut Gambit: A Review of How Microbial Imbalance Fuels Metabolic Mayhem.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901063}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology/metabolism ; Oxidative Stress ; *Metabolic Diseases/microbiology/metabolism ; Epigenesis, Genetic ; Probiotics ; Inflammation/microbiology ; Animals ; }, abstract = {BACKGROUND/OBJECTIVES: An imbalance in gut microbiota, known as gut dysbiosis, results in reactive oxygen species overproduction, which can cause inflammatory conditions, damage DNA, trigger immunity, and induce epigenetic modifications of crucial genes that regulate metabolic pathways. Such a condition can also weaken the resilience of the protective gut wall and elevate colon permeability, allowing toxins from the gut to reach the liver and bloodstream, contributing to oxidative damage, autoimmune diseases, and epigenetic changes linked to metabolic disorders.<br><br>METHODS: The Scopus database was exclusively searched for the literature. Relevant articles were identified using predefined keywords, including gut dysbiosis, microbiota, microbiome, oxidative stress, metabolic disorders, inflammation, and epigenetics or combinations. Gut microbiota- and diet-induced metabolic disorders, particularly obesity, insulin resistance, dyslipidemia, and hypertension, may be inherited through epigenetic pathways.<br><br>RESULTS: The evidence analyzed suggests that the gut microbiota serves as a diverse metabolic and immunological organ. Its disruption affects the production of short-chain fatty acids, bile acid metabolism, immune signaling, and the redox balance, which contributes to the development of obesity, insulin resistance, and metabolic syndrome.<br><br>CONCLUSIONS: This review highlights key epigenetic mechanisms underlying metabolic disorders and oxidative stress in the context of gut dysbiosis. Furthermore, therapeutic strategies targeting the gut microbiota, such as dietary interventions, prebiotics, probiotics, postbiotics, and fecal microbiota transplantation, hold promise for mitigating oxidative stress and inflammation associated with metabolic syndrome.}, }
@article {pmid41901066, year = {2026}, author = {Thomas, EG and Ortutu, BF and Watson, JC and Ong, E and Blankley, KE and Meaurio Martin, A and Shankar, S and Zhang, D and Boland, DJ and Wu, CS}, title = {Purified Diets Lacking Fermentable Fiber Reduce Microbial Diversity, Alter Epithelial Transcriptome, and Exacerbate Colitis.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901066}, issn = {2072-6643}, support = {R21ES036683/ES/NIEHS NIH HHS/United States ; RP230204//Texas A&amp;M Health-Center of Excellence in Cancer Research/ ; 58-3091-1-018//Texas A&amp;M AgriLife Institute for Advancing Health Through Agriculture/ ; }, mesh = {Animals ; *Dietary Fiber/administration &amp; dosage ; Mice, Inbred C57BL ; Male ; *Gastrointestinal Microbiome ; *Transcriptome ; *Colitis/microbiology/chemically induced ; Mice ; *Intestinal Mucosa/metabolism/microbiology ; Fermentation ; Fatty Acids, Volatile/metabolism ; Colon/metabolism/microbiology ; Dextran Sulfate ; Feces/microbiology ; *Diet ; Disease Models, Animal ; }, abstract = {Background/Objectives: Dietary fibers play key roles in shaping gut microbiome and intestinal homeostasis. While purified diets offer experimental precision and reproducibility in rodent models, they omit the complex mixture of fermentable and non-fermentable fibers found in grain-based chow diets. We hypothesized that excluding fermentable fiber impairs intestinal homeostasis by reducing microbial metabolites and altering the colonic epithelial transcriptome, thereby increasing susceptibility to inflammation. Methods: Wildtype male C57BL/6 mice were maintained on either a standard grain-based chow diet or a purified low-fat diet (LFD) containing 5% non-fermentable cellulose for ten weeks. Fecal microbiomes, short-chain fatty acid (SCFA) profiles, and colonic epithelial transcriptomes were analyzed. A separate group was challenged with dextran sodium sulfate (DSS) following a five-week dietary intervention to compare colitis severity between the two diet groups. Results: Relative to mice fed the grain-based chow, those consuming the purified LFD (containing only non-fermentable cellulose) showed decreased gut microbial diversity and significantly lower SCFA levels. These changes were accompanied by marked differences in colonic epithelial cell transcriptomes. In LFD-fed mice, the top upregulated gene networks included ribosomal pathways and MHC complex protein binding, suggesting increased growth and gut inflammation. The most downregulated pathways included mineral absorption, actin and tubulin binding, and membrane organelle assembly, indicating major alterations in cellular structure and transport. LFD-fed mice also exhibited increased colonic expression of S100a9, a gut inflammation biomarker, and more severe disease symptoms when challenged with DSS compared to chow-fed mice. Conclusions: Fermentable fibers are one of the factors contributing to intestinal homeostasis and mitigating the severity of ulcerative colitis.}, }
@article {pmid41901079, year = {2026}, author = {Cirio, S and Mantegazza, G and Salerno, C and Guglielmetti, S and Allam, A and Campus, G and Cagetti, MG}, title = {Assessing the Impact of Heyndrickxia coagulans Administered Through Sugar-Free Chewing Gum on Dental Biofilm: A Double-Blind Randomized Controlled Trial.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901079}, issn = {2072-6643}, mesh = {Humans ; *Chewing Gum ; Double-Blind Method ; *Biofilms/drug effects ; Male ; Female ; Adult ; *Dental Plaque/microbiology ; *Probiotics/administration &amp; dosage ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Background:Heyndrickxia coagulans has emerged as a candidate for oral health applications, and chewing gum offers a promising delivery method. This study evaluates whether H. coagulans delivered via sugar-free chewing gum can induce detectable changes in plaque microbial ecology. Methods: A randomized, double-blind, placebo-controlled clinical trial was conducted on 52 healthy adults. Participants consumed probiotic or control gum for 4 weeks. Dental plaque was collected at baseline (T0), mid-intervention (T1), end of intervention (T2), and one week post-intervention (T3). qPCR quantified H. coagulans, while 16S rRNA gene profiling assessed microbial diversity and taxonomic composition. Statistical analyses included rank-based difference-in-differences models, Wilcoxon and Mann-Whitney tests, and differential abundance inference based on negative binomial modeling. Results: Forty-four subjects completed the study. In the Intervention group, the strain was detected in 71.4% of participants at T1 and 61.9% at T2, and it persisted in 9.5% at T3. Differential abundance analysis revealed a broad depletion of taxa linked to oral dysbiosis at T2 with partial persistence at T3, along with selective enrichment of beneficial strains. Conclusions:H. coagulans delivered via chewing gum can reach the dental biofilm and induce modest, transient shifts in microbial composition. However, these biofilm ecology findings should be interpreted in the context of clinical outcomes.}, }
@article {pmid41901112, year = {2026}, author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF}, title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901112}, issn = {2072-6643}, support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; }, mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention &amp; control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; }, abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.}, }
@article {pmid41901128, year = {2026}, author = {Lupu, VV and Nedelcu, AH and Borka-Balas, R and Anton, CR and Tarnita, I and Azoicai, A and Forna, L and Munteanu, D and Anton, SC and Shawais, SK and Badescu, MC and Salaru, DL and Morariu, ID and Anton, E and Petrariu, F and Lupu, A}, title = {The Gut Microbiota: An Essential Component in Understanding Pediatric Obesity: A Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901128}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Pediatric Obesity/microbiology ; Child ; Dysbiosis/microbiology ; Probiotics ; }, abstract = {Background: Childhood obesity has become a major public health concern worldwide. Increasing evidence suggests that alterations in the gut microbiome may play a significant role in the development and progression of pediatric obesity. This narrative review synthesizes and analyzes recent studies investigating microbiome alterations in children with obesity, highlighting emerging insights and their potential implications for disease management. Understanding the relationship between gut microbial composition and obesity may provide new perspectives for prevention and therapeutic strategies in overweight pediatric populations. This narrative review was conducted through a search of major biomedical databases, including PubMed and Web of Science, complemented by manual screening of reference lists of relevant articles. Key findings: Children affected by obesity exhibit significant changes in gut microbiome composition, characterized by reduced microbial diversity and predominance of the Firmicutes and Bacteroidetes phyla. The balance between these two bacterial groups appears critical for maintaining gut homeostasis. Studies consistently report an increased Firmicutes-to-Bacteroidetes ratio in children with elevated body weight, suggesting that disruption of this balance may contribute to metabolic dysregulation and obesity-related pathologies. Given the essential role of the gut microbiota in nutrient metabolism and energy extraction, dysbiosis in obesity is associated with enhanced energy harvest and lipid absorption. Certain bacterial populations may promote increased caloric uptake, thereby contributing to weight gain and adiposity. Multidimensional interventions, including dietary modification and physical activity, have demonstrated the potential to reduce obesogenic microbiota patterns and restore microbial diversity. Additionally, probiotic supplementation is being investigated as a strategy to reestablish microbial homeostasis and potentially support body mass index reduction. Despite promising findings, further research is required to clarify mechanisms, establish causality, and determine the clinical effectiveness of microbiome-targeted therapies before they can be fully integrated into the management of pediatric obesity.}, }
@article {pmid41901151, year = {2026}, author = {Green, GBH and Cox-Holmes, AN and Flowers, JT and Williams, MB and Potier, ACE and Brandom, JL and Watts, SA and Luke, R and Yu, JS and McFarland, BC}, title = {Dietary and Nutritional Strategies for Patients with Glioma: A Narrative Review of Treatment, Recovery, Immune Support, and Microbiota Modulation.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901151}, issn = {2072-6643}, support = {R01CA270750-01A1/CA/NCI NIH HHS/United States ; T32NS121721/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Glioma/therapy/immunology/microbiology/diet therapy ; *Gastrointestinal Microbiome ; *Brain Neoplasms/therapy/immunology/microbiology/diet therapy ; *Nutritional Support/methods ; Quality of Life ; *Diet ; Tumor Microenvironment ; Nutritional Status ; }, abstract = {This narrative review aims to explore the relationship between glioma and nutrition throughout stages of treatment and recovery. Gliomas are aggressive brain tumors that significantly impair quality of life and present treatment challenges. There has been a growing interest regarding the gut-brain axis and the microbiome, particularly their roles in modulating immune function and influencing the response to cancer treatment. This review examines how specific nutritional approaches may assist patients throughout the course of chemotherapy, radiation, immunotherapy, surgical intervention, and the recovery process. It also addresses the potential for integrative nutritional approaches to complement conventional treatment and improve clinical outcomes. Emerging evidence suggests that nutrition may influence immune function, treatment-related side effects, and the tumor microenvironment, in part through effects on the gut microbiota. Nutritional support during therapy has been linked to increased strength, decreased inflammation, and improved treatment tolerance. Dietary patterns may influence gut-brain interactions and systemic immune responses, opening the potential to improve therapeutic outcomes in glioma. In summary, nutrition may represent an important supportive component of glioma care, while microbiota-mediated and metabolic dietary strategies remain areas of active investigation. Further clinical studies are needed to determine whether specific nutritional interventions can improve survival, treatment response, or quality of life in patients with glioma.}, }
@article {pmid41901159, year = {2026}, author = {Brăgaru, MA and Kraft, A and Moldovan, CA and Moldovan, AD and Răzvan, A and Cochior, D and Luca, A and Nica-Badea, D and Chirsanov Capanu, &#x218;E and Rusu, E}, title = {Optimizing Perioperative Nutrition in Elective Gastrointestinal Surgery: An ERAS-Focused Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901159}, issn = {2072-6643}, mesh = {Humans ; *Elective Surgical Procedures/adverse effects ; *Digestive System Surgical Procedures/adverse effects ; *Perioperative Care/methods ; *Malnutrition/prevention &amp; control ; Postoperative Complications/prevention &amp; control ; *Enhanced Recovery After Surgery ; Sarcopenia/prevention &amp; control ; *Nutritional Support/methods ; Nutritional Status ; Dietary Supplements ; }, abstract = {Background/Objectives: Perioperative malnutrition, sarcopenia, and reduced functional reserve are frequent in adults undergoing elective gastrointestinal (GI) surgery and are associated with higher postoperative morbidity and delayed recovery. Enhanced Recovery After Surgery (ERAS) pathways incorporate nutrition-focused elements, but reported effects vary across procedures, protocols, and baseline risk. This review aims to summarize and critically appraise current evidence on perioperative nutritional strategies within ERAS-focused elective GI care, including risk identification, nutritional prehabilitation (oral nutritional supplements and immunonutrition), preoperative carbohydrate loading, early postoperative feeding, and selected microbiome-directed adjuncts. Methods: This narrative literature review was informed by a focused search of PubMed/MEDLINE and Scopus (2010-early 2026), supplemented by targeted screening of relevant clinical practice guidelines and consensus statements (e.g., ESPEN). Evidence was interpreted by hierarchy (guidelines/meta-analyses, randomized trials, observational studies) and discussed with attention to heterogeneity in surgical populations, intervention definitions (composition, timing, duration), and endpoint reporting. Results: Early nutritional risk screening is consistently supported to identify malnutrition and sarcopenia and to trigger tailored optimization plans. Perioperative oral nutritional supplementation, particularly when started preoperatively and continued postoperatively, is frequently associated with improved intake and reduced infectious morbidity in malnourished or at-risk patients, though effect sizes vary. Immunonutrition shows potential benefit in selected high-risk settings but remains formulation- and timing-dependent. Carbohydrate loading is generally endorsed within ERAS and may reduce insulin resistance and improve patient comfort, while impacts on major clinical outcomes are context-dependent. Early oral/enteral feeding is feasible in many elective GI procedures and may accelerate gastrointestinal recovery without increasing major complications when implemented with structured advancement and appropriate patient selection. Probiotics/synbiotics show the most consistent signals in colorectal surgery, with strain-specific effects and important safety boundaries in immunocompromised or critically ill patients. Conclusions: Perioperative nutritional optimization is a core component of elective GI surgical care within ERAS pathways. Benefits are most reproducible in higher-risk patients and when interventions are integrated into high-compliance multidisciplinary programs. Future research should prioritize procedure-specific, risk-stratified trials with standardized interventions and clinically meaningful endpoints.}, }
@article {pmid41901182, year = {2026}, author = {Silverstein, HR and Rizvanov, AA and Haines, DD and Mahmoud, FF and Rose, SC and Solovyeva, VV and Kitaeva, KV and Tosaki, A}, title = {The Simultaneous Prevention of Multiple Diseases: A "One Ring to Rule Them All" Framework for Redox-Driven Health and Longevity.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901182}, issn = {2072-6643}, support = {A.A.R., V.V.S. and K.V.K. were supported by the Kazan Federal University Strategic Academic Leadership Program (PRIORITY-2030)//Ministry of Science and Higher Education of the Russian Federation/ ; This study was also supported by the HUN-REN-DE//Hungarian Research Network/ ; }, mesh = {Humans ; Oxidation-Reduction ; *Longevity ; Oxidative Stress ; Antioxidants ; Dietary Supplements ; *Noncommunicable Diseases/prevention &amp; control ; Cardiovascular Diseases/prevention &amp; control ; Diet ; }, abstract = {Chronic non-communicable diseases rarely occur in isolation; cardiovascular, metabolic, neurodegenerative, malignant, and age-associated disorders share upstream drivers including oxidative stress, chronic inflammation, mitochondrial dysfunction, and metabolic imbalance. This narrative review synthesizes epidemiological, interventional, and mechanistic studies identified through targeted literature searches to examine redox biology as a shared mechanistic hub linking these conditions. We evaluate antioxidant-rich dietary patterns, selected nutraceuticals, myocardial ischemia-reperfusion injury as a clinical exemplar, rare redox-imbalance disorders as mechanistic stress models, and emerging gene-based reinforcement of endogenous antioxidant systems. Rather than proposing clinical targets, we present an integrative, hypothesis-generating framework illustrating how coordinated lifestyle-driven modulation of redox balance may simultaneously influence multiple disease trajectories. Collectively, the evidence supports a unified redox framework for multi-disease prevention for multi-disease prevention and future intervention design.}, }
@article {pmid41901189, year = {2026}, author = {Witt, BL and Singaravelan, N and Tollefsbol, TO}, title = {Combined Effects of Withaferin A and Sodium Butyrate on NF-κB Signaling and Epigenetic Regulation in Breast Cancer Cells.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901189}, issn = {2072-6643}, support = {R01CA178441//Natrional Institutes of Health/ ; }, mesh = {Humans ; *Withanolides/pharmacology ; *Epigenesis, Genetic/drug effects ; *Signal Transduction/drug effects ; Female ; *Butyric Acid/pharmacology ; *NF-kappa B/metabolism/genetics ; Cell Line, Tumor ; *Breast Neoplasms/genetics/drug therapy/metabolism ; Cell Survival/drug effects ; Gene Expression Regulation, Neoplastic/drug effects ; MCF-7 Cells ; Triple Negative Breast Neoplasms/drug therapy/genetics ; }, abstract = {Background/Objectives: There is a clear need for more options to control the progression of breast cancer and prevent the occurrence of breast cancer in minority populations that have a higher rate of mortality due to triple-negative breast cancer (TNBC) subtypes. Prevalent nutraceuticals such as Ashwagandha (also known as the Indian Winter Cherry) have anti-inflammatory and apoptotic capabilities, as well as the ability to inhibit cancer growth. The purpose of this study is to analyze the novel combination of withaferin A (derived from the Indian Winter Cherry and known to have histone deacetylase inhibition capabilities) and sodium butyrate (a short-chain fatty acid produced from the gut microbiome and known to have DNA methyltransferase inhibition capabilities) treatment on breast cancer-derived cell lines. There is a scientific gap of possible causality of decreasing breast cancer progression when treated with sodium butyrate and withaferin A. Methods: Two in vitro cell viability assays were utilized consisting of [MTT (4,5 Dimethylthiazol-2-yl)] and the neutral red assay to analyze the impact of treatment of compounds alone and in combination on breast cancer cells for 72 h. The Highest Single Agent (HSA) combination analysis was utilized to derive combination indexes for our breast cancer cell types. Protein and gene expression was investigated for Class 1 histone deacetylases, de novo DNA methyltransferase, the p65 subunit of NF-κB, and NFκB1. Lastly, DNA methyltransferase enzymatic activity was analyzed via the Epigentek DNMT Activity/Inhibition ELISA Easy Kit. Results: Through the cell viability assay [MTT (4,5 Dimethylthiazol-2-yl)], MCF-7, MDA-MB-231, and MDA-MB-157 cells were found to have a decrease in cell viability due to combinatorial treatment with withaferin A and sodium butyrate. Western blot results depicted a decrease in protein expression levels for DNA methyltransferases due to the administration of 2.5 mM sodium butyrate and 0.2 µM withaferin A alone and in combination for breast cancer cell lines MCF-7, MDA-MB-231, and MDA-MB-157. Additionally, the combination of these two components have successfully inhibited the progression of the NFκB1 gene within analysis through the quantitative polymerase chain reaction (qPCR). Conclusions: The novel combination of withaferin A and sodium butyrate have markedly reduced the progression of breast cancer-derived cell lines for cell viability, epigenetic DNMT gene expression, as well as inhibiting NFκB1 signaling on the gene expression level.}, }
@article {pmid41901191, year = {2026}, author = {Di Maio, G and Tafuri, MG and Casillo, M and Messina, A and Allocca, S and Villano, I and Moscatelli, F and Monda, A and La Marra, M and Monda, V}, title = {Physiological Regulation of Nutritional and Metabolic Biomarkers in Obesity: Implications for Precision Nutrition.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, pmid = {41901191}, issn = {2072-6643}, mesh = {Humans ; *Biomarkers/blood/metabolism ; *Obesity/metabolism/physiopathology ; *Precision Medicine ; *Nutritional Status ; Adipokines/blood ; Gastrointestinal Microbiome ; Insulin Resistance ; }, abstract = {Obesity represents a heterogeneous metabolic disorder characterized by substantial interindividual variation in inflammatory status, insulin sensitivity, and cardiometabolic risk. Traditional anthropometric measures fail to capture this metabolic diversity, limiting risk stratification and personalized intervention strategies. This review critically examines nutritional and metabolic biomarkers that reflect the physiological dysregulation underlying obesity, including adipokines (leptin, adiponectin, resistin), inflammatory markers (C-reactive protein, interleukin-6, TNF-α), insulin resistance indices (HOMA-IR, fasting insulin, HbA1c), and lipid metabolism indicators (LDL cholesterol, triglycerides, HDL cholesterol, and liver enzymes such as ALT and GGT). Among these, elevated CRP, reduced adiponectin, and increased HOMA-IR have demonstrated the strongest clinical utility for early metabolic risk identification. We further evaluate emerging biomarkers-including circulating microRNAs, gut microbiota-derived metabolites (short-chain fatty acids, TMAO, lipopolysaccharides), and bile acid profiles-which offer additional mechanistic insight into diet-microbiome-host interactions. We systematically assess the mechanistic basis, clinical relevance, and nutritional modulation of each biomarker class, emphasizing how dietary composition-particularly fatty acid quality, fiber intake, and overall dietary patterns such as the Mediterranean diet-influences biomarker profiles and metabolic outcomes. Furthermore, we explore how biomarker-based phenotyping enables precision nutrition approaches by identifying individuals most likely to benefit from specific dietary interventions. Integration of multi-biomarker panels with clinical and genetic data holds promise for advancing from population-based dietary guidelines toward individualized nutrition strategies that optimize metabolic health and prevent obesity-related complications. Future research should prioritize validating biomarker-guided intervention frameworks, establishing standardized thresholds across diverse populations, and developing clinically implementable tools for personalized nutritional medicine.}, }
@article {pmid41901195, year = {2026}, author = {Xiong, H and Ji, S and Ding, Q and Zhou, Y and Yao, X and Zhu, Y}, title = {The Impact of Seasonal and Meteorological Factors on Microorganisms Present in Knee Joint Effusions Among Patients with Rheumatoid Arthritis.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {3}, pages = {}, pmid = {41901195}, issn = {1424-8247}, support = {the Macau Science and Technology Development Fund (FDCT (0012/2021/AMJ, 003/2022/ALC,0092/2022/A2, 0144/2022/A3)).The National Natural Science Foundation of China (No. 81973320,No.82160869). Shenzhen-HongKong-Macao Science and Technology Fund (Category C://the Macau Science and Technology Development Fund&#x3001;The National Natural Science Foundation of China&#x3001;Shenzhen-HongKong-Macao Science and Technology Fund&#x3001;University Joint Laboratory of Guangdong Province and Macao Region on Molecular Targets and Intervention/ ; }, abstract = {Background/Objectives: Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovial inflammation and vascular abnormalities. Emerging evidence suggests that dysbiosis of the microbiome contributes to the pathogenesis of this disease, while seasonal and meteorological variations represent significant factors influencing microbial community dynamics. However, the specific pathological mechanisms mediated by microbial populations within knee joint effusions of RA patients remain poorly elucidated. The present study employs 16S rRNA high-throughput sequencing technology to characterize seasonal variation patterns affecting microbial communities in knee joint effusions of RA patients and to investigate the relationship between microbial community structures and climatic lag effects. Methods: Microbial communities in knee joint effusion samples obtained from RA patients were analyzed using 16S rRNA high-throughput sequencing methodologies. A Distributed Lag Non-linear Model (DLNM) was applied to quantify the delayed effects of climatic variables on microbial community composition. The correlation patterns between meteorological parameters and community structure were elucidated through the integration of ridge regression and redundancy analysis (RDA). Preliminary identification of potential biomarkers was conducted using random forest algorithms. Results: According to research findings, the microbial composition of knee joint effusions in RA patients shows seasonal fluctuation patterns that are compatible with those seen in RA patients, even though there is no discernible seasonal change in β-diversity. Compared with samples obtained during other seasons, spring specimens exhibited significantly elevated relative abundances of both beneficial microorganisms and opportunistic pathogenic taxa. Random forest modeling identified Escherichia-Shigella and Curtobacterium as preliminary candidate biomarkers; however, external validation is required to establish their specificity as disease indicators. Further analysis revealed that although short-term meteorological fluctuations exert minimal influence on overall microbial diversity, specific alterations in mean wind speed (MWS) and relative humidity (RH) drive compositional changes in the microbial community, manifested as rapid responses from dominant bacterial taxa and compensatory buffering effects from rare taxa. Conclusions: This study suggests that the synovial cavity microbiota in RA patients may exhibit seasonal variation patterns that are statistically associated with environmental parameters, particularly humidity and temperature. Due to the inherent limitations of the cross-sectional study design, the preliminary candidate biomarkers identified herein require validation through external cohorts. Additional investigations incorporating healthy controls and osteoarthritis (OA) cohorts are necessary to confirm specificity and to elucidate the therapeutic potential of these microbial targets for RA microbiome interventions. Currently, insufficient evidence exists to establish causal relationships among microbial populations, joint pathology, and climatic factors. Longitudinal cohort studies are imperative to validate the temporal dynamics and clinical significance of these associations.}, }
@article {pmid41901248, year = {2026}, author = {Xue, X and Zhang, F and Wang, H and Guo, M and Qin, W and Yang, Y and Huo, Z and Li, X and Han, Q and Li, X}, title = {Si-Wu-Tang Targets Microbiota Homeostasis and Intestinal Mucosal Barriers to Provide Protection Against MASLD by Favoring P. goldsteinii-like Taxa Colonization.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {3}, pages = {}, pmid = {41901248}, issn = {1424-8247}, support = {ZYGXQNJSKYCXNLZCXM-H4//Scientific Research Innovation Capability Support Project for Young Faculty/ ; 2022YFC3502100//National Key Research and Development Program on Modernization of Traditional Chinese Medicine/ ; 2023-JYB-JBZD-046//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Objective: This study examined the pharmacological mechanisms of the therapeutic benefits of SWT to MASLD via regulating the gut-liver axis. Methods: The components of SWT were analyzed by liquid chromatograph mass spectrometer (LC-MS). After establishing an MCD-induced MASLD mice model, we invested the protective mechanism of SWT through 16S rRNA sequencing combined with molecular biological experiments. After eliminating the intestinal microbiota through an antibiotic cocktail experiment, we identified the key microbiota by which SWT improves MASLD. Results: SWT markedly reduced MASLD injury by alleviating intestinal inflammation and restoring the intestinal mucosal barrier, which could be reversed following alcohol exposure. Additionally, SWT altered the intestinal flora of MASLD mice, significantly raising the relative abundance of Parabacteroides goldsteinii-like taxa, while alcohol caused the destruction of P. goldsteinii-like-taxa-centered probiotic habitats and a proliferation of pathogenic bacteria, especially Bacteroides intestinalis-like taxa. After the elimination of intestinal flora, the anti-MASLD effect of SWT was lost. Moreover, the supplement of P. goldsteinii could significantly ameliorate liver damage caused by an MCD diet, functioning similarly to SWT. However, the liver-protective effect of SWT was suppressed following the administration of B. intestinalis. Conclusions: SWT ameliorates MCD diet-induced MASLD via modulating intestinal microbiota homeostasis and restoring intestinal mucosal barriers. Given that P. goldsteinii is effective for treating MASLD, it provides insights into new therapeutic strategies.}, }
@article {pmid41901456, year = {2026}, author = {Tian, S and Zhang, N and Lin, G and Cheng, X and Wang, F and Chang, P and Ahammed, GJ and Shi, Q and Nie, WF and Zhang, Y}, title = {Epigenetic Regulation of Root-Associated Microbiota: Mechanisms and Horticultural Applications.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {41901456}, issn = {2223-7747}, abstract = {The dynamic interaction between plants and their root-associated microbiota represents a sophisticated and profound biological communication that regulates plant development and the formation of adaptation to the surrounding environment. These interactions function as critical regulators of multiple physiological processes, finally influencing soil fertility and agricultural productivity. Plants have evolved epigenetic networks that regulate beneficial plant-microbe interactions through regulating immune responses, gene regulation, and metabolite production to enhance stress tolerance and soil adaptation. These regulations collectively govern microbial colonization patterns while establishing reciprocal feedback loops through root exudate-microbe interactions. This review systematically updates contemporary advances in understanding how epigenetic modifications shape rhizosphere microbiome composition and function, and discusses their potential applications in enhancing the yield and quality of horticultural crops, as well as in mitigating continuous cropping obstacles.}, }
@article {pmid41901493, year = {2026}, author = {Curci, LM and Carrozzo, S and Pecatelli, G and Semeraro, T and Tafuro, C and Lenucci, MS and De Caroli, M}, title = {Environmental and Cultivation Effects on Growth and Phytochemical Profiles of Chicory (Cichorium intybus L.) in Soil, Hydroponics, and Aquaponics.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {41901493}, issn = {2223-7747}, abstract = {The increasing demand for sustainable food production has intensified interest in controlled-environment agriculture and soilless cultivation systems. This study evaluated the performance of local chicory (Cichorium intybus L., cultivar "Otrantina") grown for 45 days in soil, hydroponics, and decoupled aquaponics under two different environments: a fully controlled growth chamber and a naturally variable greenhouse. Morphological, anatomical, biochemical, and physiological traits were analyzed to assess the combined influence of growth environment and cultivation system on plant development and nutritional quality. Across all parameters, the growth environment emerged as the main driver of plant performance. Greenhouse-grown plants exhibited greater leaf expansion, enhanced mesophyll and vascular development, and higher fresh and dry biomass than those cultivated in the growth chamber. Within each environment, hydroponics consistently supported vigorous growth, whereas aquaponics produced smaller leaves and pronounced root elongation, likely reflecting nutrient and pH instability in the decoupled system. Biochemical analyses revealed system-specific adaptive responses. Soilless cultivation promoted higher lipid accumulation and, under growth chamber conditions, increased protein content. Aquaponically grown plants, particularly in the greenhouse, accumulated elevated levels of soluble sugars and phenolic antioxidants, consistent with stress-related metabolic activation. In contrast, soil-grown plants displayed the highest flavonoid concentrations, suggesting a prominent role of rhizosphere-microbiome interactions in modulating secondary metabolism. Overall, these results indicate that, under the tested conditions, environmental control exerts a stronger influence than cultivation systems on chicory growth and metabolism. Hydroponics proved to be the most efficient system for biomass production, whereas aquaponics requires improved nutrient management to ensure stable growth and quality. The distinct metabolic profiles associated with each cultivation system highlight opportunities to tailor chicory nutraceutical traits within sustainable controlled-environment agriculture.}, }
@article {pmid41901497, year = {2026}, author = {Liang, A and Wang, F and Liu, T and Liao, Y and Mu, Z}, title = {Habitat Filtering Shapes Root Endophytic Microbiome Assembly and Its Association with Fruit Quality in Lycium ruthenicum from the Tarim Basin.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, pmid = {41901497}, issn = {2223-7747}, support = {no. 32160390//the National Natural Science Foundation of China/ ; no. 524307001//the Tianchi Talents-Innovative Leaders of Xinjiang/ ; no. TDZKBS202206//the President's Fund of Tarim University/ ; }, abstract = {Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe-host-environment interactions and the quality improvement of desert medicinal plants.}, }
@article {pmid41901529, year = {2026}, author = {Bečić, T and Jukić, I and Prižmić, P&#x160; and Matulić, I and Đogaš, H and Radić, M and Radić, J and Vuković, J and Fabijanić, D}, title = {Heart-Gut Axis in Cardiometabolic Disease: Microbiome-Mediated Pathways Linking Metabolic Syndrome to Cardiovascular Risk.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {3}, pages = {}, pmid = {41901529}, issn = {1648-9144}, mesh = {Humans ; *Metabolic Syndrome/complications/physiopathology/microbiology ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/physiopathology/etiology/microbiology ; Dysbiosis/complications ; Cardiometabolic Risk Factors ; }, abstract = {Background and Objectives: Cardiometabolic disease, a term encompassing metabolic syndrome (MS) and cardiovascular disease (CVD), represents a major and growing global health burden driven by interconnected metabolic and cardiovascular dysfunction. Emerging evidence suggests that the gut microbiota plays a central role in modulating metabolic, inflammatory, and cardiovascular (CV) pathways, giving rise to the concept of the heart-gut axis. However, human evidence integrating microbiome-mediated mechanisms across the cardiometabolic spectrum remains incompletely synthesized. This focused systematic review aimed to synthesize the current human evidence on microbiome-mediated mechanisms linking metabolic syndrome (MS) and related metabolic phenotypes with cardiovascular risk (CVR) and subclinical cardiovascular (CV) outcomes within the conceptual framework of the heart-gut axis. Materials and Methods: A systematic literature search was conducted in PubMed, Scopus, Web of Science, and the Cochrane Library in accordance with PRISMA 2020 guidelines. Human observational and interventional studies evaluating gut microbiota composition, function, or microbiota-derived metabolites in relation to cardiometabolic, and CV outcomes were included. Risk of bias was assessed using the Cochrane RoB 2 and ROBINS-I tools, and findings were synthesized narratively. Results: Ten human studies published between 2016 and 2025 met the inclusion criteria. Across these studies, gut dysbiosis was consistently associated with adverse cardiometabolic risk profiles and subclinical CV outcomes, including insulin resistance, systemic inflammation, subclinical atherosclerosis, and CV prognosis in high-risk populations. Microbiota-derived metabolites, particularly trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs), as well as emerging metabolites such as phenylacetylglutamine (PAGln) and imidazole propionate (ImP), were identified as key mediators linking metabolic syndrome and related metabolic disturbances with CVR and subclinical cardiovascular disease (CVD). Markers of intestinal barrier dysfunction and endotoxemia further supported the role of chronic low-grade inflammation within the heart-gut axis. Conclusions: Current human evidence supports the heart-gut axis as a biologically plausible and clinically relevant contributor to cardiometabolic disease. Gut microbiota-derived metabolites, intestinal barrier dysfunction, and systemic inflammation represent interconnected pathways linking MS with CVR. Advancing our understanding of these mechanisms may inform the development of microbiome-targeted strategies to complement established approaches for cardiometabolic and CV prevention.}, }
@article {pmid41901547, year = {2026}, author = {Theofilis, P and Iliakis, P and Karanikola, AE and Botis, M and Mavromoustakou, K and Xydis, P and Ktenopoulos, N and Karakasis, P and Leontsinis, I and Chrysohoou, C and Tsioufis, K}, title = {Pleiotropic Effects of Cardiac Resynchronization Therapy on Cardiometabolic Modulation in Heart Failure.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {3}, pages = {}, pmid = {41901547}, issn = {1648-9144}, mesh = {Humans ; *Heart Failure/therapy/physiopathology/metabolism ; *Cardiac Resynchronization Therapy/methods/standards ; Energy Metabolism/physiology ; }, abstract = {Cardiac resynchronization therapy (CRT) is a cornerstone intervention for patients with heart failure (HF) and electrical dyssynchrony, improving quality of life, functional capacity, and survival. Beyond mechanical synchrony, mounting evidence suggests CRT exerts systemic and myocardial cardiometabolic benefits. CRT acutely enhances mechanical efficiency and shifts substrate utilization toward greater oxidation of fatty acids and ketones, effects that correlate with long-term reverse remodeling on cardiac magnetic resonance imaging. Earlier metabolomic profiling demonstrated that CRT normalizes circulating energy metabolites, improving Krebs cycle intermediates and substrate balance between glucose and lipids, while baseline metabolite patterns may differentiate responders from non-responders. These metabolic adaptations accompany favorable changes in diastolic performance, right ventricular function, and ventriculo-arterial coupling. In parallel, improved splanchnic perfusion and reduced congestion may ameliorate gut dysbiosis and endotoxemia, mitigating systemic inflammation. Collectively, these findings position CRT as a therapy capable of both mechanical and metabolic restoration in advanced HF. In this review, we discuss the emerging data on how CRT reconditions myocardial energy metabolism, influences ventricular-arterial interactions, and modulates peripheral and gut-derived metabolic pathways.}, }
@article {pmid41901695, year = {2026}, author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P}, title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901695}, issn = {2076-0817}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Aged ; Hospitalization ; Adult ; India ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.}, }
@article {pmid41901728, year = {2026}, author = {Mougiou, D and Gioula, G and Skoura, L and Minti, F and Karampatakis, T and Malandris, D and Pelekoudas, K and Kachrimanidou, M}, title = {Characterization of the Gut Microbiome of Patients with Clostridioides difficile Infection and Healthy Individuals in Greece.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901728}, issn = {2076-0817}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Clostridium Infections/microbiology ; Middle Aged ; Greece ; Aged ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Clostridioides difficile/genetics ; Adult ; Feces/microbiology ; Aged, 80 and over ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND/OBJECTIVES: The gut microbiome plays an important role in the colonization of an individual by Clostridioides difficile and in the development of Clostridioides difficile infection (CDI). The main purpose of this study was to compare the gut microbiomes of patients with CDI and healthy individuals.<br><br>METHODS: We prospectively included 48 individuals: 32 patients with CDI and 16 healthy individuals. Microbiomes were analyzed by sequencing the hypervariable regions of the 16S rRNA gene using an Ion GeneStudio&#x2122; S5 System. Further statistical analysis of microbiome data was performed with the open-source programming language R version 3.5.2.<br><br>RESULTS: Among the CDI patients, Firmicutes and Proteobacteria were the most abundant phyla, while Enterobacteriaceae and Enterococcaceae were the most abundant families. Genus-level analysis showed that Enterococcus was the dominant genus in CDI patients; in contrast, in healthy individuals, Faecalibacterium was the most abundant. The MaAsLin2 tool revealed that members of the family Enterococcaceae and the genus Enterococcus were more abundant in patients with CDI than in healthy individuals. Alpha and beta diversity did not reveal differences between the two study groups.<br><br>CONCLUSIONS: We observed differences in microbiome patterns between healthy individuals and CDI patients that were consistent with the literature. Further studies are needed.}, }
@article {pmid41901740, year = {2026}, author = {Pazmiño-Gomez, B and Rodas-Pazmiño, K and Pazmiño-Pérez, R and Tapia-Guijarro, T and Balcazar-Quimi, W and Valle-Asan, S and Salazar-Vera, S and Villalva-Vera, M and Ochoa-Fajardo, D and Rodas-Neira, E}, title = {Native Bacillus-Based Probiotic Consortia Suppress Vibrio parahaemolyticus and Restructure Hatchery Water Microbiomes in Shrimp Larval Systems.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901740}, issn = {2076-0817}, mesh = {*Probiotics/pharmacology/administration &amp; dosage ; Animals ; *Vibrio parahaemolyticus/drug effects ; *Bacillus/physiology ; *Penaeidae/microbiology/growth &amp; development ; *Microbiota ; Larva/microbiology ; Aquaculture/methods ; Water Microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Shrimp aquaculture is constrained by opportunistic bacterial pathogens, particularly Vibrio parahaemolyticus, whose proliferation in hatchery systems is shaped by microbial community structure. We evaluated the antagonistic activity and microbiome effects of two native Bacillus-based probiotic consortia (CN5, RS3) applied alone or combined (MIX) in shrimp larval culture water over 30 days, relative to a no-probiotic control. Treatments were assessed using standardized in vitro inhibition assays, 16S rRNA gene (V3-V4) amplicon sequencing, functional inference, and integrative multivariate and structural modeling. All probiotic treatments showed consistently high antagonistic activity against V. parahaemolyticus, whereas the control showed no inhibition. Amplicon profiling indicated treatment-associated microbiome restructuring, with increased Bacillus dominance and reduced relative abundance of Vibrio spp. under probiotic conditions. Multivariate analyses separated probiotic and control groups, and PLS-SEM identified Bacillus dominance as a central driver of antagonistic activity mediated by inferred bioactive functional potential, while water-quality variables had limited direct effects. Probiotics were administered directly to the culture water once daily after routine water exchange to 1 × 10[6] CFU mL[-1] (CN5 or RS3); MIX was applied 1:1 (v/v) at the same total dose.}, }
@article {pmid41901742, year = {2026}, author = {Kavvada, A and Gioula, G and Protopapas, A and Protopapas, AA and Christoforidi, M and Minti, F and Savopoulos, C and Chatzidimitriou, M}, title = {Characterization of the Gastric Antrum Microbiome in Helicobacter pylori-Negative Individuals: Insights from a Greek Population Using 16S rRNA Next-Generation Sequencing.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901742}, issn = {2076-0817}, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; Greece ; Female ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Helicobacter pylori ; *Pyloric Antrum/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Helicobacter Infections/microbiology ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Once considered a sterile organ, the human stomach is now known to harbor a diverse microbial community that may influence both gastric homeostasis and disease. While extensive research has been conducted worldwide, regional variation in the gastric microbiome remains insufficiently characterized. This study aimed to describe the gastric antrum microbiome of Helicobacter pylori-negative Greek adults using 16S rRNA next-generation sequencing (NGS).<br><br>METHODS: Samples of gastric biopsies were obtained from patients undergoing gastroscopy at a tertiary hospital in Greece. H. pylori infection was excluded through a combination of bacterial culture and patient medical history. The final study group consisted of 9 subjects. Following DNA extraction, the 16S rRNA gene was sequenced on the Ion Torrent&#x2122; platform. Bioinformatic processing and statistical analyses were performed using the phyloseq, vegan, and ggplot2 R packages. Microbial composition, relative abundance, and alpha diversity (Shannon and Inverse Simpson indices) were evaluated at the genus level.<br><br>RESULTS: The gastric microbiome comprised 19 phyla, 150 families, 213 genera, and 391 species. The predominant phyla were Proteobacteria (36.92%), Firmicutes (34.21%), and Bacteroidetes (12.97%). The most prevalent families were Streptococcaceae, Helicobacteraceae, Prevotellaceae, and Pasteurellaceae. At the genus level, Streptococcus (21.71%), Helicobacter (18.39%), and Prevotella (9.99%) accounted for nearly half of the total relative abundance. Alpha diversity indices indicated moderate richness and evenness across samples.<br><br>CONCLUSIONS: The gastric antrum microbiome of H. pylori-negative Greek individuals exhibits substantial taxonomic diversity dominated by Proteobacteria and Firmicutes. The microbial community structure aligns closely with profiles reported in other global populations. These findings provide a reference baseline for future comparative analyses involving H. pylori-positive individuals to better understand microbiome shifts associated with colonization and gastric disease.}, }
@article {pmid41902183, year = {2026}, author = {Cardoso, MA and Vieira, CSD and Moreira, ICF and Saraiva, FMS and Brito, IAA and Gandara, ACP and Menna-Barreto, RFS and Oliveira, PL and Paes, MC and Pane, A}, title = {Rhodnius prolixus Viruses Interfere with Proliferation and Metacyclogenesis of the Chagas Disease Agent Trypanosoma cruzi.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902183}, issn = {1999-4915}, support = {428100/2018-0//National Council for Scientific and Technological Development (CNPq)/ ; E-26/210.339/2024//the Research Support Foundation of the State of Rio de Janeiro/ ; }, mesh = {*Trypanosoma cruzi/virology/growth &amp; development ; Animals ; *Rhodnius/virology/parasitology ; *Chagas Disease/parasitology/transmission ; Insect Vectors/virology/parasitology ; }, abstract = {The protozoan Trypanosoma cruzi is the etiological agent of Chagas disease, a neglected tropical disease that mostly affects the population of Latin American countries, with an estimated 7 million infected people and more than 10,000 deaths per year worldwide. T. cruzi is typically transmitted by hematophagous triatomine insects, with Rhodnius prolixus being a major insect vector in South America. While the microbiome of triatomine insects has been investigated to a certain extent, the ternary interaction between triatomes insects, T. cruzi, and viruses remains virtually unexplored. In this study, we show by transmission electron microscopy and by RT-PCR that Rhodnius prolixus viruses (RpVs) can infect the intestine of R. prolixus, which places them in close contact with the gut microbiota. These observations suggest that T. cruzi can be infected by the insect viruses while transiting through the gut. Here, we show that the RpVs are capable of infecting the epimastigote forms of T. cruzi in vitro and maintain the viral load stabilized for 3 to 7 days after infection. We also show that, at least in the case of the iFlavirus RpV1, viral genomes are detectable in the T. cruzi cytoplasm. Interestingly, R. prolixus ovarian extracts enriched with RpVs decrease epimastigote proliferation and their capacity for differentiation into the ineffective metacyclic trypomastigotes in vitro. Our results start to shed light on the interaction between RpVs and T. cruzi, suggesting possible routes of infection and unveiling a role for viral infections in the development of this important pathogen.}, }
@article {pmid41902219, year = {2026}, author = {Wang, X and Zhang, J and Chen, J and Huang, Q and Duan, X and Zhu, W}, title = {The Role of Viral Infection and Microbial Dysbiosis in Glaucoma: From Pathogenesis to Therapeutic Strategies.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902219}, issn = {1999-4915}, support = {Grant No. 82471079//the National Natural Science Foundation of China/ ; Grant No. 82501363//the Young Scientists Fund of the National Natural Science Foundation of China/ ; Grant No. 22507154//the Young Scientists Fund of the National Natural Science Foundation of China/ ; Grant No. kq2502222//the Changsha Municipal Natural Science Foundation of China/ ; Grant No. 2025M772429//the Science Foundation for Post Doctorate Research of the Ministry of Science and Technology of China/ ; Grant No. AMF2406D01//the Science and Technology Foundation of Aier Eye Hospital Group of China/ ; }, mesh = {*Dysbiosis/microbiology/complications/therapy ; Humans ; *Glaucoma/microbiology/therapy/virology/etiology ; Animals ; *Virus Diseases/complications ; Gastrointestinal Microbiome ; }, abstract = {Glaucoma is a leading cause of irreversible blindness, yet vision loss often progresses despite effective intraocular pressure (IOP) control, suggesting the involvement of non-hydrodynamic mechanisms. This review explores the potential synergistic interaction between viral persistence and microbial dysbiosis in pathogenesis. While acknowledging that current evidence regarding the microbiome is largely associative and derived from small cohorts or animal models, we analyze how these environmental insults may disrupt autophagic flux and induce immune dysregulation to drive chronic neuroinflammation. Furthermore, we explore theoretical therapeutic strategies targeting this distinct pathological nexus, ranging from metabolic restoration of the gut-eye axis to the repurposing of advanced nanocarriers to overcome ocular barriers. This framework lays the groundwork for next-generation, etiology-based precision management.}, }
@article {pmid41902239, year = {2026}, author = {Whitt, TN and Heath, A and Hill, DJ and Brubaker, DK and Farr Zuend, C}, title = {Risk of HSV-2 Acquisition Among Women with Bacterial Vaginosis: Systematic Review and Meta-Analysis.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902239}, issn = {1999-4915}, support = {Start up funds//Case Western Reserve University/ ; }, mesh = {Humans ; Female ; *Vaginosis, Bacterial/complications/virology/microbiology ; *Herpesvirus 2, Human/physiology ; *Herpes Genitalis/virology/epidemiology ; Vagina/microbiology/virology ; Virus Shedding ; Risk Factors ; Microbiota ; }, abstract = {OBJECTIVE: Bacterial vaginosis is a dysbiosis of the vaginal microbiome, typically characterized by a loss of Lactobacillus. Lactobacillus plays a crucial role in vaginal immunity and protection against sexually transmitted infections. Herpes simplex virus 2, the primary cause of genital herpes, impacts 13% of people worldwide. We undertook this systematic review and meta-analysis to examine the risk of herpes simplex virus 2 acquisition in women with bacterial vaginosis. Secondarily, we examined the impact of bacterial vaginosis on herpes simplex virus 2 shedding, reactivation, and symptoms.<br><br>DATA SOURCES: We searched PubMed, EMBASE, Cochrane, Web of Science, Google Scholar, and ClinicalTrials.gov for articles published before 1 July 2023 for microbiome and herpes simplex virus type 2. Studies were limited to human subjects and the English language. An updated search was performed in January 2026. This study was registered on PROSPERO (CRD42023439139).<br><br>METHODS OF STUDY SELECTION: Studies on non-pregnant, reproductive-aged cisgender women that diagnosed bacterial vaginosis by Amsel Criteria, Nugent Scoring or used molecular techniques, and those that detected herpes simplex virus 2 by serological assay or PCR testing were included. Our search identified 863 results with four publications eligible for inclusion. For our secondary outcomes, 40 results were identified regarding herpes simplex virus 2 shedding, with two publications eligible for inclusion, which did not meet our threshold for meta-analysis. There were 21 results identified for herpes simplex virus 2 reaction and 115 results for herpes simplex virus 2 symptoms, with no articles being eligible for inclusion.<br><br>Quality assessment was performed following data extraction using the quality assessment scales from the Joanna Briggs Institute. Results were extracted, and the pooled hazard ratio was calculated with 95% confidence interval. A total of 1906 women were included in this analysis, and 255 acquired herpes simplex virus 2. The pooled unadjusted hazard ratios produced an effect size of 1.91, (95% confidence interval 1.4649-2.4980), and a p-value of <0.0001, while the pooled adjusted hazard ratios produces an effect size of 1.85, (95% confidence interval of 1.3556-2.5162), and a p-value of 0.0001 indicating that bacterial vaginosis is associated with a increased risk of herpes simplex virus 2 acquisition.<br><br>CONCLUSIONS: This systematic review with meta-analysis indicates that bacterial vaginosis is associated with a significantly increased risk (91% unadjusted, 85% adjusted) of herpes simplex virus 2 acquisition, indicating that bacterial vaginosis treatment may reduce herpes simplex virus 2 acquisition. A notable limitation of these findings is the relatively small number of studies eligible for inclusion in this systematic review and meta-analysis.}, }
@article {pmid41902263, year = {2026}, author = {Shao, H and Deng, Y and Shi, Y and Duan, Y}, title = {Engineered Bacteriophages: A Next-Generation Platform for Precision Antimicrobials and Therapeutics.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902263}, issn = {1999-4915}, support = {2025YFC3408500//the National Key Research and Development Program of China/ ; 32571872//the National Natural Science Foundation of China/ ; QYPY20230033//the Research Funds of Center for Advanced Interdisciplinary Science and Biomedicine of IHM/ ; WK9100000063//the Fundamental Research Funds for the Central Universities/ ; XDB0940000//the Research Funds of Strategic Priority Research Program of the Chinese Academy of Sciences/ ; GZC20232554//the Postdoctoral Fellowship Program of CPSF/ ; 2024M753097//the China Postdoctoral Science Foundation/ ; WK9100000083//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Bacteriophages/genetics ; Humans ; *Phage Therapy/methods ; Animals ; *Precision Medicine/methods ; Genetic Engineering ; Bacterial Infections/therapy ; *Anti-Infective Agents/therapeutic use ; Anti-Bacterial Agents ; }, abstract = {The escalating crisis of antimicrobial resistance (AMR) and the stagnating antibiotic pipeline have renewed interest in bacteriophage therapy. While natural phages offer specificity and low toxicity, their narrow host range, bacterial resistance, and safety concerns limit clinical use. To overcome these hurdles, phages are being engineered using biotechnology. This review outlines the history of phage therapy and systematically summarizes advances in engineered phage preparation, including genetic modification, chemical conjugation, and physical encapsulation. We highlight the application of engineered phages against multidrug-resistant infections, gastrointestinal diseases through gut microbiome modulation, and as targeted delivery vehicles or immune adjuvants in cancer therapy. While significant advances have been made, several critical challenges remain, particularly in regulatory approval, large-scale manufacturing, and ensuring long-term safety. We conclude that engineered phages, as customizable and precise biological tools, are poised to advance precision phage medicine, offering a transformative solution to AMR and fostering convergence across synthetic biology, medicine, and environmental science.}, }
@article {pmid41902328, year = {2026}, author = {Ganamurali, N and Devarajan, M and Sabarathinam, S}, title = {Microbiome Guided Precision Pharmacology in Pregnancy: Organ Crosstalk, Maternal-Fetal Drug Disposition, and PBPK-Informed Dosing.}, journal = {Comprehensive Physiology}, volume = {16}, number = {2}, pages = {e70138}, doi = {10.1002/cph4.70138}, pmid = {41902328}, issn = {2040-4603}, mesh = {Humans ; Pregnancy ; Female ; *Maternal-Fetal Exchange/physiology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/physiology ; Pharmaceutical Preparations/metabolism/administration &amp; dosage ; Animals ; Pharmacokinetics ; }, abstract = {Drug therapy during pregnancy poses unique challenges, requiring a balance between maternal benefit and fetal safety. Profound physiological changes, including altered plasma volume, protein binding, hepatic metabolism, renal clearance, and placental transfer, transform pregnancy pharmacology into a dynamic process. Classical concepts such as initiation, loading, maintenance, tapering, and therapeutic monitoring remain fundamental but demand gestation-specific adaptations. This overview integrates fundamental pharmacological concepts with clinical practices tailored for pregnancy, such as personalized dosing, therapeutic monitoring, and structured tapering. Recent studies further underscore the role of the maternal gut microbiome in shaping drug metabolism, absorption, and overall exposure. Variations in how individuals respond to medication during pregnancy may stem from microbial enzymes and metabolites that interact with the body's pharmacokinetic processes. By merging microbiome data with physiologically based pharmacokinetic modeling and pharmacometric tools, clinicians can enhance drug disposition forecasts and refine precision dosing strategies in obstetric care.}, }
@article {pmid41902480, year = {2026}, author = {Chugh, RM and Bhanja, P and Schueddig, E and Setianegara, J and Lin, Y and Guida, K and Rehman, S and Krepel, S and Koestler, D and Chen, RC and Cook, KL and Saha, S}, title = {Proton FLASH Exposure Preserves Gut Commensal Microbiomes and Spares Intestinal Stem Cells.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e19249}, doi = {10.1002/advs.202519249}, pmid = {41902480}, issn = {2198-3844}, support = {//This work was supported by a sponsored Research Agreement from IBA to perform preclinical research on FLASH Proton Radiotherapy (KUMC-IBA collaborative fund) and KUCC CCSG (P30 CA168524)./ ; }, abstract = {Emerging evidence shows that Proton FLASH radiotherapy can spare normal tissues while maintaining anti-tumor efficacy. However, its impact on intestinal stem cells (ISCs) and the gut microbiome remains unclear. Gut microbiome influences ISC's radiosensitivity. In a mouse model of abdominal irradiation, Proton FLASH exposure exhibited improved survival and less crypt-villus damage compared to Proton Conventional dose rate. Using scRNA-sequencing, we demonstrated that Proton FLASH exposure using pulsed pencil beam scanning spares two distinct ISC populations, Lgr5+ Crypt-based columnar cells (CBCs) and a Ly6a+, Clu+, Areg+, Anxa2+ revival stem cell (revSC) population-by modulating oxidative stress and cell cycle progression. Analysis of α and β-diversity demonstrated that Proton FLASH modulates gut microbiota composition without compromising overall species richness. Notably, Proton FLASH-irradiated mice had higher abundances of Alistipes sp. and Akkermensia sp., both known for protective effects on ISCs and the intestinal mucosa. The role of microbiome in Proton FLASH-mediated sparing effect was further confirmed by fecal microbiota transplantation, where Proton FLASH-donor microbiota demonstrated reduced lethality with protection of crypt villus morphology in recipient mice exposed to Proton Conventional dose rate. Our findings highlight the crucial role of the microbiome in the Proton FLASH-mediated sparing of the mucosal epithelium.}, }
@article {pmid41902532, year = {2026}, author = {Belančić, A and Fajkić, A and Sener, YZ and Jelaković, A and Alić, L and Gkrinia, EMM and Verbanac, D and Jelaković, B}, title = {Gut Dysbiosis as a Shared Mechanism in Obesity and Hypertension: Exploring a Promising Therapeutic Avenue.}, journal = {Endocrinology, diabetes &amp; metabolism}, volume = {9}, number = {3}, pages = {e70159}, doi = {10.1002/edm2.70159}, pmid = {41902532}, issn = {2398-9238}, mesh = {Humans ; *Obesity/microbiology/therapy/complications ; *Dysbiosis/therapy/complications/microbiology ; *Gastrointestinal Microbiome/physiology ; *Hypertension/microbiology/therapy/etiology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Animals ; Prebiotics ; }, abstract = {BACKGROUND: Obesity and hypertension are interrelated global health challenges sharing common pathophysiological mechanisms, including insulin resistance, chronic inflammation and neurohormonal dysregulation. Emerging evidence highlights the gut microbiome as a crucial mediator in this interplay, influencing intestinal barrier integrity, systemic inflammation and metabolic homeostasis.<br><br>METHODS: In this narrative review, we critically examine the interplay between obesity-induced hypertension and the gut microbiome, evaluating current evidence, therapeutic implications and future research priorities.<br><br>RESULTS: Obesity-associated gut dysbiosis disrupts the intestinal epithelial barrier, increasing translocation of bacterial products like lipopolysaccharides into circulation, promoting systemic inflammation that exacerbates insulin resistance, adipose dysfunction and hypertension. Current treatments targeting obesity, from lifestyle modification to bariatric surgery, show beneficial effects on blood pressure, but microbiome-targeted interventions are an evolving therapeutic frontier. Prebiotics, probiotics, synbiotics and faecal microbiota transplantation have demonstrated potential antihypertensive effects in preclinical and clinical studies, although findings are heterogeneous and require confirmation in larger randomised trials. Methodological challenges remain, including the need for advanced microbial sampling techniques beyond faecal analysis to fully capture disease-relevant microbiota alterations.<br><br>CONCLUSION: This review synthesises current knowledge on gut microbiome involvement in obesity-induced hypertension, evaluates microbiome-based therapeutic strategies and identifies critical research gaps to guide future investigations aimed at mitigating the dual pandemics of obesity and hypertension.}, }
@article {pmid41902691, year = {2026}, author = {Lewis, GS and Adejumo, S and Reczek, S and Malas, J and Ramanauskas, K and Walker, JF and Cook, MD and Horswill, CA and Hampton-Marcell, J}, title = {The athlete microbiome project: Integrating deep learning to reveal microbial associations of physical fitness.}, journal = {Physiological genomics}, volume = {}, number = {}, pages = {}, doi = {10.1152/physiolgenomics.00278.2025}, pmid = {41902691}, issn = {1531-2267}, abstract = {Regular physical training improves human fitness and health through direct effects on muscle and metabolism and indirect effects via alterations in gut microbiome composition. To determine whether athletes harbor a distinct gut microbiome and whether microbiome composition associates with established markers of physical fitness, VO2max and percent fat-free mass, we conducted a secondary analysis of amplicon sequencing data and metadata from published human microbiota studies across three continents. Participants were categorized as athletes (n = 656) or non-athletes (n = 199). Using multivariate statistics, random forest models, and a multilayer perceptron neural network, we identified structured differences in gut microbiome composition, associated with fitness metrics and athletic status. Random forest regression models explained up to 63% of the variance in percent fat-free mass and 45% in VO2 max, with taxa such as Faecalibacterium, Megamonas, Bifidobacterium, and Blautia ranking among the most informative predictive features across analyses. Classification models further demonstrated that athletic status could be predicted from microbiome composition: a mixed-effects-informed random forest achieved a balanced accuracy of 71%, while a multilayer perceptron captured coordinated, multivariate microbial patterns and achieved stable performance across stratified five-fold cross-validation and an independent, held-out test set comprising 20% of samples not used during model training (balanced accuracy = 0.91; AUC = 0.97). Together, these findings indicate that athletic status and fitness-related traits are associated with gut microbiome compositional patterns, highlighting candidate taxa for mechanistic validation and demonstrating the utility of integrative machine learning for distinguishing athletes from non-athletes.}, }
@article {pmid41902956, year = {2026}, author = {Christoph, HAM and Kimble, SJA}, title = {Hydroelectric Dam May Impact the Microbiome of an Endangered Northern Map Turtle (Graptemys geographica) Population.}, journal = {Current microbiology}, volume = {83}, number = {5}, pages = {}, pmid = {41902956}, issn = {1432-0991}, support = {529//Maryland Department of Natural Resources/ ; 52008712//Towson University/ ; }, abstract = {UNLABELLED: Classified as state-endangered, Maryland’s population of Northern Map Turtles (NMTs) (Graptemys geographica) faces habitat alteration and fragmentation due to the Conowingo Hydroelectric Dam and other factors. Maryland’s NMTs also reside in an urbanized area with high levels of human activity, which leads to overall disturbance and pollution. The combined impacts of these stressors could be affecting the health of NMTs and may contribute to future decline. The microbiome has been explored as an indicator of organismal health in other species and can be used to inform wildlife management strategies. We collected cloacal (n = 35) and oral (n = 34) microbiome swabs from wild NMTs at four different sites along the Maryland portion of the Susquehanna River in 2022. Using 16 S rRNA sequencing, results suggested that the dam plays a significant role in determining cloacal and oral microbiome structure, with bacteria associated with pollution and disease being significantly more prevalent above the dam. Of note are Acinetobacter spp., which is associated with heavy metal contamination, and Aeromonas spp., which is associated with shell disease in map turtles. Despite the known dietary dimorphism of NMTs, we did not find significant differences in the microbiomes of males and females. The impact that dams have on microbiomes and wildlife is not well understood, and these results may help to enact more specific management strategies in these systems. Our findings will contribute to the conservation of an endangered freshwater turtle population while adding to the limited breadth of knowledge of reptilian health.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00284-026-04846-w.}, }
@article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, }
@article {pmid41903026, year = {2026}, author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S}, title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {2}, pages = {}, pmid = {41903026}, issn = {1573-3890}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diagnosis/blood/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism ; *Metabolomics/methods ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Crohn Disease/diagnosis/blood ; Colitis, Ulcerative/diagnosis/blood/metabolism ; Metabolome ; Mass Spectrometry ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.<br><br>OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.<br><br>METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.<br><br>RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.<br><br>CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.}, }
@article {pmid41903028, year = {2026}, author = {Reytor-González, C and Verde, L and Annunziata, G and Román-Galeano, NM and Horowitz, R and Galasso, M and Muscogiuri, G and Frias-Toral, E and Simancas-Racines, D and Barrea, L}, title = {The Role of Gut Microbiota in Postmenopausal Women: Implications for Lipid Metabolism and Targeted Nutritional Interventions.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {41903028}, issn = {2161-3311}, abstract = {PURPOSE OF REVIEW: This review explores the complex interplay between menopause, estrogen decline, lipid metabolism, and gut microbiota alterations. It highlights the physiological and metabolic changes that predispose postmenopausal women to dyslipidemia and increased cardiovascular disease risk, with particular emphasis on the emerging role of the gut microbiota in modulating lipid homeostasis and inflammatory pathways. In addition, it examines the therapeutic potential of microbiota-targeted nutritional strategies to restore metabolic balance and improve cardiometabolic outcomes in postmenopausal women.<br><br>RECENT FINDINGS: Recent clinical and experimental evidence indicates that menopause-related hormonal changes and aging are associated with gut microbiota dysbiosis, which may contribute to adverse lipid profiles through mechanisms involving bile acid metabolism, short-chain fatty acid production, and low-grade systemic inflammation. Associations between specific microbial taxa and lipid metabolic patterns have been reported; however, findings remain heterogeneous and causal relationships are difficult to establish due to confounding factors such as diet, lifestyle, and medication use. Nutritional interventions aimed at modulating the gut microbiota&#x2014;including Mediterranean, plant-based, and DASH dietary patterns, increased dietary fiber intake, and supplementation with prebiotics, probiotics, polyphenols, phytoestrogens, and omega-3 fatty acids&#x2014;have shown potential to improve lipid profiles and cardiometabolic risk markers.<br><br>SUMMARY: The gut microbiota emerges as a relevant contributor to menopause-associated dyslipidemia and cardiovascular risk. While microbiota-targeted nutritional strategies are promising, further longitudinal and interventional studies are needed to clarify causal pathways and identify clinically actionable microbial signatures. Integrating microbiome-informed nutritional approaches into clinical practice may represent a future strategy to improve cardiometabolic health in postmenopausal women.}, }
@article {pmid41903042, year = {2026}, author = {Lu, GL and Zhao, YH and Ruan, YQ and Ning, J and Wei, L}, title = {Vitamin C modulates Cr(VI)-induced parallel disruptions along the microbiota-gut-brain axis in adult zebrafish: insights from transcriptomic and microbiome analysis.}, journal = {Fish physiology and biochemistry}, volume = {52}, number = {2}, pages = {}, pmid = {41903042}, issn = {1573-5168}, support = {ZDYF2023SHFZ139//Key Research and Development Program of Hainan/ ; 32060169//National Natural Science Foundation of China/ ; KYQD(ZR)21138//Scientific Research Start-up Fund of Hainan University/ ; }, mesh = {Animals ; *Chromium/toxicity ; *Zebrafish/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Ascorbic Acid/pharmacology ; *Brain/drug effects/metabolism ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; RNA, Ribosomal, 16S ; Gene Expression Profiling ; }, abstract = {Hexavalent chromium (Cr(VI)) is a widely present carcinogenic environmental pollutant, has demonstrated well-documented neurotoxic and enterotoxic effects in aquatic organisms, yet limited research exists on mitigating its toxicity through brain-gut-microbiota axis regulation. Vitamin C (VC), a potent antioxidant and immunomodulator, has shown potential in mitigating heavy metal toxicity. Nevertheless, how VC regulates Cr(VI) toxicity via the brain-gut-microbiota axis remains unclear. To investigate VC's potential protective role, adult zebrafish were divided into three groups: control, 2 mg/L Cr(VI), 2 mg/L Cr(VI) + 2 mg/L VC groups, with a 60-day exposure period. Histopathological changes, 16S rRNA, intestinal, and brain RNA-sequencing were examined. The results showed that VC modulated neuropathological lesions and intestinal goblet cell vacuolization caused by Cr(VI). 16S rRNA further confirmed VC partially modulated microbiota homeostasis. Transcriptomic analysis identified 78 differentially expressed genes (DEGs) in the brain; KEGG enrichment analysis showed these DEGs are associated with neurological function and gastrointestinal carcinogenesis pathways. Concurrently, 52 DEGs in intestinal were linked to viral infection and neural signaling pathways. Correlation analyses demonstrated pathogenic Aeromonas was positively correlated with ace, enpep, prss1, asah2, and cd36 in the brain, those are downregulated DEGs, whereas beneficial Pseudomonas was positively correlated with c6ast4 and nfe211b in intestinal, they are upregulated DEGs. This indicates Aeromonas and Pseudomonas could act as key mediators through which VC reduces Cr(VI)-induced neuro- and immunotoxicity. Collectively, these findings provide mechanistic insights into VC's protective role against parallel disruptions along the microbiota-gut-brain axis, suggesting its potential as a waterborne supplement for reducing Cr(VI) toxicity in aquaculture system.}, }
@article {pmid41903043, year = {2026}, author = {Guhanraj, R and Prathiviraj, R}, title = {Bacteriocins as precision antimicrobials: genomic exploration and oral applications of Lactobacillus peptides.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41903043}, issn = {1432-072X}, }
@article {pmid41903083, year = {2026}, author = {Zhang, JR and Li, YW and Chen, HX and Luo, Y and Liu, RM and Wang, JB and Liu, NN and Xiao, JH}, title = {Chronic Excessive Exposure to Fluoride Impairs the Intestinal Mucosal Barrier to Cause Inflammatory Response and Microbiome Dysbiosis in Rats.}, journal = {Biological trace element research}, volume = {}, number = {}, pages = {}, pmid = {41903083}, issn = {1559-0720}, support = {QKHJ-ZK[2021]485//Guizhou Provincial Department of Science and Technology/ ; GKFZ-2018-29//Ministry of Science and Technology of the People's Republic of China/ ; 82260158//National Natural Science Foundation of China/ ; QJJ [2023] 020//Department of Education of Guizhou Province/ ; QKHPT-RC-GCC [2022]001-2; QKHJC-ZK[2025]ZD-031//Guizhou Provincial Department of Science and Technology, China/ ; ZSKH-SYS[2025]-03; ZSKHHZ-[2023]-198//Science and Technology Bureau of Zunyi City/ ; }, }
@article {pmid41903099, year = {2026}, author = {Sumona, AA and Hossen, MB and Hadi, SB and Haque, MA and Haider, MN and Hossain, MT and Alam, MS}, title = {Host-derived Probiotics Enhance Immune Response and Gut Microbiome in the Freshwater Prawn Macrobrachium rosenbergii.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41903099}, issn = {1867-1314}, }
@article {pmid41903138, year = {2026}, author = {Zheng, W and Wu, C and Wang, Y and Yan, X and Han, W and Liu, X and He, C and Chen, X and Zhou, X and Zhang, L and Liu, C and Xu, J and Wang, J and Yuan, X and Song, W and Wang, X and Liang, S and Huang, J and Zhang, Y and Yang, R and Zhang, L and Qin, N and Ma, X and Xu, Q and Li, G}, title = {Mutation elevation and functional alterations in Escherichia coli are pertinent to the onset of gestational diabetes mellitus.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117143}, doi = {10.1016/j.celrep.2026.117143}, pmid = {41903138}, issn = {2211-1247}, abstract = {In the gut microbiome, purifying selection clears deleterious mutations. However, it is unknown whether this selection pressure is modifiable or what its health implications are. Here, we studied metagenomic and metabolic changes linked to gestational diabetes mellitus (GDM), and observed an increase in Escherichia coli (E. coli) mutations during host pregnancy, linking these genetic changes to host physiology. Severe depletion of bacterial genes before GDM onset was mostly traced to E. coli despite its stable abundance-indicating that functional genetic signals outweigh taxonomic shifts. E. coli and related microbes displayed pregnancy-linked single nucleotide polymorphism elevation, enriched at GDM onset in loci encoding membrane and biofilm components. These pangenomic alterations correlated with handicapped intermicrobial interactions of E. coli and with host serum metabolic abnormalities. We propose that pregnancy relaxes purifying selection, permitting mutation elevation in certain gut bacteria. Resulting functional deficits, potentially through altered ecology and metabolism, may subsequently impact host glucose regulation.}, }
@article {pmid41903152, year = {2026}, author = {Li, WK and Liu, B and Xu, SF and Shi, JS and Li, J and Liu, J}, title = {Antiepileptic Effects of Hua-Feng-Dan Against Pentylenetetrazol-Induced Seizures in Mice.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e5336509}, pmid = {41903152}, issn = {2314-6141}, support = {82560832//National Natural Science Foundation of China/ ; U1812403//National Natural Science Foundation of China/ ; 82460879//National Natural Science Foundation of China/ ; 82360859//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Pentylenetetrazole ; Mice ; *Seizures/drug therapy/chemically induced ; *Anticonvulsants/pharmacology/therapeutic use ; Male ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Disease Models, Animal ; Brain/drug effects/metabolism ; Kindling, Neurologic/drug effects ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Hua-Feng-Dan is a Chinese medicine in the treatment of epilepsy and neurodegeneration. The prior studies demonstrated its protection against neuroinflammation, dopaminergic neuron loss, and in the treatment of ischemic stroke, but its anticonvulsive efficacy against epilepsy remains elusive. The aim of this study was to examine antiepileptic effects of Hua-Feng-Dan recipes and the mechanism of protection. Pentylenetetrazol (PTZ)-induced kindling mouse model (35 mg/kg, ip on alternate days × 10) was used to evaluate the antiepileptic effects of Hua-Feng-Dan recipes. Mice were given original, reduced, and nonfermented Hua-Feng-Dan via feed at clinical dose (0.5 g/kg) and diazepam was used as a positive control. The seizure scores were recorded after each PTZ injection. At the end of the experiments, the brain and colon content were collected for RNA-Seq and 16S rRNA-Seq, respectively, followed by bioinformatics and qPCR verification. Hua-Feng-Dan recipes were effective against PTZ-induced seizures, with original the best and half of reduced (0.25 g/kg) ineffective. PTZ-induced aberrant gene expressions in the brain were ameliorated by Hua-Feng-Dan recipes to various extents. Ingenuity Pathway Analysis of differentially expressed genes revealed that PTZ-altered canonical pathways and upstream regulators were attenuated by Hua-Feng-Dan treatments. qPCR verified the expression of early immediate genes, proinflammatory mediators, transporters and apoptosis genes. PTZ-disrupted gut microbiome was also ameliorated by Hua-Feng-Dan recipes, and the modulation of Lachnospiraceae and ASV230 was consistent with the literature. Hua-Feng-Dan recipes were effective against PTZ-induced kindling mice. The mechanisms appeared to be related to the modulation of brain gene expression and gut microbiota. • Hua-Feng-Dan (HFD) recipes were effective against PTZ-induced seizures in mice. • HFD ameliorated abnormal brain gene expressions in PTZ kindling mice via RNA sequencing (RNA-seq). • IPA of DEGs revealed improved canonical pathways and upstream regulators. • 16S rRNA-seq showed microbiome modulation by HFD in PTZ kindling mice. • qPCR verified selected brain genes and bacterial ASVs.}, }
@article {pmid41903180, year = {2026}, author = {Xu, Y and Akinbi, H and Shen, Z and Zhu, J and Shi, L and Du, L and Haslam, DB}, title = {Clinical Care Practices Shape Microbiome-Associated Bloodstream Infection Risk in Geographically Distinct NICUs.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag213}, pmid = {41903180}, issn = {1537-6591}, abstract = {BACKGROUND: Bloodstream infections (BSI) remain a major cause of morbidity and mortality in preterm infants. Although BSI pathogens vary geographically, the role of local microbial colonization patterns and clinical practices in driving these differences is not well understood.<br><br>METHODS: We conducted a prospective cohort study on 127 preterm infants from two geographically distinct NICUs: University of Cincinnati Medical Center (UCMC, USA) and Children's Hospital, Zhejiang University School of Medicine (ZCH, China). Six hundred and sixty-nine longitudinal stool and skin samples collected during the first three weeks of life underwent metagenomic sequencing. Associations between microbiome composition, clinical factors, and BSI epidemiology were evaluated using Generalized Linear Mixed Models and Random Forest.<br><br>RESULTS: Distinct gut and skin microbiome profiles were observed between NICUs and corresponded closely with local BSI patterns. Staphylococcus aureus predominated at UCMC, while Klebsiella pneumoniae and Enterococcus species were more common at ZCH. Skin microbiota showed strong association with BSI isolates, implicating the skin as an underrecognized potential reservoir for pathogen translocation. Linear mixed models and Random Forest machine learning approaches revealed that clinical practices, including intravenous catheter placement and antibiotic exposure had greater influence on microbiome composition than geographic location alone.<br><br>CONCLUSIONS: Our findings demonstrate that modifiable clinical care practices shape the developing microbiome of preterm infants and contribute to geographic differences in BSI epidemiology. The skin microbiome represents a potentially significant risk factor for invasive infection. Further work to clarify how specific clinical practices influence pathogen colonization may inform strategies to reduce BSI incidence in preterm infants.}, }
@article {pmid41903388, year = {2026}, author = {Howell, S and Cumpa, G and Masel, BE}, title = {Altered gut microbiome and post traumatic hypopituitarism in chronic TBI: The need for recognition, evaluation and treatment.}, journal = {Growth hormone &amp; IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society}, volume = {84}, number = {}, pages = {101688}, doi = {10.1016/j.ghir.2026.101688}, pmid = {41903388}, issn = {1532-2238}, abstract = {Post traumatic hypopituitarism (PTHP) occurs in 30-50% of individuals with chronic moderate-severe TBI as well as individuals with mild TBIs who remain symptomatic after a year. Growth hormone deficiency (GHD) occurs in approximately 15-20%, Gonadotropin deficiencies in 10%, as well as Thyroid and Adrenocorticotropin deficiencies in 4-12%. Individuals frequently have more than one deficiency. These numbers cover a wide range and vary based on time of testing, cut-points and methods used. Recent studies have shown hypoaminoacidemia and altered gut microbiome in a subset of individuals with mTBIs with subjective complaints of fatigue and altered cognition: Brain Injury Associated Fatigue and Altered Cognition (BIAFAC). These individuals may become symptomatic months to years after the injury and frequently have a diminished response to growth hormone stimulation testing, although not always below the established cut points for Growth Hormone Deficiency (GHD). Recognition of BIAFAC for its similarities and differences from PTHP by physicians dealing with TBI will lead to more thorough evaluations and may eventually lead to better treatment options for these individuals. This paper will begin with a discussion of the relevance of anatomy to post -TBI changes, and how hypoaminoacidemia may play a role in the symptoms after TBI.}, }
@article {pmid41903508, year = {2026}, author = {Pachinger, L and Stukenbrock, EH}, title = {Antimicrobial effectors of plant-associated fungi: multipurpose proteins with fast-evolving surfaces and structurally conserved cores.}, journal = {Current opinion in microbiology}, volume = {91}, number = {}, pages = {102744}, doi = {10.1016/j.mib.2026.102744}, pmid = {41903508}, issn = {1879-0364}, abstract = {Plants are exposed to a variety of devastating pathogens, causing significant yearly yield losses. In order to facilitate infections, plant pathogens secrete an arsenal of molecules termed effectors, which are known to modulate plant immune responses. Plants, on the other hand, possess receptors allowing them to detect invading pathogens by either recognising conserved molecules associated with invading microbes or by perceiving effector molecules. For decades, molecular phytopathology research has been focused on the bilateral molecular crosstalk between plants and pathogens and has deepened our understanding of virulence and defence mechanisms. In recent years, the impact of the plant microbiome on plant-pathogen interactions has gained interest, given the fact that some microbes can aid protection against invading pathogens, and pathogen invasion substantially modulates microbiome composition. Several antimicrobial effectors have been identified in fungal plant pathogens, pointing to direct mechanisms whereby pathogens can alter their hosts' microbiome to promote host colonisation. These new findings highlight that some effectors may have several functions targeting plant processes and fungi or bacteria associated with the plant. Advances in computational biology have greatly enhanced the analysis of predicted effector proteins and revealed that these often are highly conserved among phylogenetically distant fungi. Comparative analyses of protein structures have also revealed that functional divergence may emerge from changes in surface frustration around conserved protein folds. Further, computational simulations of protein evolution indicate that protein properties associated with (antimicrobial) effectors can emerge rapidly around conserved folds. We here summarise and discuss recent studies based on computational biology methods, providing novel insights into effector origin, evolution, and functional divergence.}, }
@article {pmid41903526, year = {2026}, author = {Bloom, SM and Symul, L and Elsherbini, J and Xu, J and Hussain, S and Shih, J and Sango, A and Mitchell, CM and Hemmerling, A and Parks, TP and Kannan, A and Hussain, FA and Cohen, CR and Holmes, SP and Kwon, DS}, title = {Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.003}, pmid = {41903526}, issn = {1934-6069}, abstract = {Bacterial vaginosis (BV) affects >25% of women worldwide and often recurs after standard-of-care metronidazole (MTZ) treatment. LACTIN-V, a live biotherapeutic product (LBP) containing Lactobacillus crispatus strain CTV-05, significantly reduced recurrent BV in a phase 2b clinical trial, but efficacy was incomplete. Here, we characterize microbiota and immune effects using multi-omics and define correlates of treatment success. By week 12, an L. crispatus-dominant microbiota was achieved in 30% of LBP recipients compared with 9% of placebo recipients (benefit ratio: 3.31; p < 0.005). This is primarily due to CTV-05, but native L. crispatus strains are also present and increase over time. Inflammatory cytokines decrease in both arms after MTZ but return to baseline in placebo recipients. Successful L. crispatus colonization is associated with pre-MTZ microbiota, baseline inflammatory profiles, post-MTZ bacterial load, and clinical and behavioral variables. These findings elucidate LBP microbiota effects and identify predictors of treatment success, informing improved intervention strategies to advance women's health.}, }
@article {pmid41903527, year = {2026}, author = {Salazar, V and Espenschied, ST and Fernandez, AP and Karell, PE and Sangwan, N and Stappenbeck, TS}, title = {The skin microbiota drives cutaneous immune checkpoint inhibitor toxicity in genetically susceptible mice.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.008}, pmid = {41903527}, issn = {1934-6069}, abstract = {Immune checkpoint inhibitors (ICIs) show increasing promise for cancer therapy. However, patients can experience adverse events, particularly those with pre-existing autoimmune disease. We determined that the microbiome can drive ICI-induced systemic toxicity in a mouse model of autoimmune susceptibility. Specifically, ICI treatment of specific pathogen-free (SPF) Act1[-/-] mice, which develop spontaneous autoimmunity due to a deficiency in an immune adaptor, resulted in systemic adverse events that were ameliorated by topical antibiotics. Moreover, germ-free (GF) Act1[-/-] mice failed to develop ICI toxicity. Transfer of gut or skin microbiota from SPF Act1[-/-] mice to GF Act1[-/-] mice showed that only the skin microbiota rendered exGF mice sensitive to ICI toxicity. Notably, therapeutic application of topical antibiotics decoupled ICI-induced toxicity from anti-tumor efficacy in SPF Act1[-/-] mice. This model provides a paradigm for future translational studies in cancer patients to mitigate adverse effects of ICIs and maximize their efficacy by targeting skin microbes.}, }
@article {pmid41903570, year = {2026}, author = {Wang, X and Jia, Y and Wang, C and Li, D and Guo, X and Jiang, S and Zhou, Z and Gao, C and Wang, F}, title = {Decoding serotonin in endometriosis: unveiling its role in disease pathogenesis via the gut-reproductive microbiota axis.}, journal = {Human reproduction (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/humrep/deag047}, pmid = {41903570}, issn = {1460-2350}, support = {20200601011JC//Jilin Provincial Key Laboratory of Precision Infectious Diseases/ ; 3D5200117426//Key Laboratory of Health and Family Planning Commission of Jilin Province/ ; }, abstract = {STUDY QUESTION: How can the potential mechanisms and targets of endometriosis be explored through multi-omics and multi-location approaches?<br><br>SUMMARY ANSWER: This exploration of the gut-reproductive axis in patients with endometriosis found that serotonin is elevated in endometriosis and promotes disease progression through enhanced cell proliferation and inflammation.<br><br>WHAT IS KNOWN ALREADY: Endometriosis is a common inflammatory disease. Recent studies indicate that peripheral serotonin, which is regulated by the gut microbiota, can promote the progression of irritable bowel syndrome and various cancers.<br><br>STUDY DESIGN, SIZE, DURATION: This cross-sectional study enrolled 22 endometriosis patients and 22 control patients with uterine fibroids (surgical cases, October 2022-June 2023). Samples of vaginal secretions, endometrial tissue, peritoneal lavage fluid, feces, and ectopic lesions were collected from both groups. For validation, serum samples were added from 20 additional endometriosis patients and 20 healthy reproductive-age volunteers.<br><br>This study employed 16S rRNA gene sequencing to analyze the microbiota in the vagina, endometrial tissue, peritoneal fluid, and feces of patients with endometriosis and control groups, complemented by untargeted metabolomic analysis of peritoneal fluid. The results identified serotonin as a key metabolite and revealed specific bacterial species, shared between the reproductive and gastrointestinal tracts of endometriosis patients, which were significantly correlated with serotonin levels. Mendelian randomization analysis was conducted to explore the relationship between serotonin, these bacterial species, and endometriosis. Serum serotonin levels in endometriosis patients, BALB/C mouse models, and their respective controls were measured using ELISA. Immunohistochemistry and fluorescence staining were used to detect the expression of serotonin and its receptors in both ectopic and normal endometrium. The effects of serotonin on the biological behavior of various endometriosis cell models, including proliferation, migration, invasion, and apoptosis, were investigated using CCK8 assay, wound healing test, Transwell assay, apoptosis detection, ELISA, transcriptomics, and qPCR. The impact of serotonin on BALB/C mouse models was evaluated using H&amp;E staining, flow cytometry, and ELISA.<br><br>We identified a significant enrichment of Akkermansia muciniphila (a bacterium shared by the gut and reproductive tract) in endometriosis patients, which positively correlated with peritoneal serotonin levels; Mendelian randomization analysis linked both to elevated endometriosis risk. Serotonin levels were elevated in patients' serum (using mouse models) and in ectopic endometrium, in comparison to those of controls. In vitro, serotonin boosted endometriosis cell proliferation, migration, invasion, and inflammation, with upregulated IL-17/NF-&#x3ba;B pathways. In mice, serotonin treatment increased lesion growth, cell proliferation, and inflammation.<br><br>LARGE SCALE DATA: N/A.<br><br>(a) The relatively limited sample size, together with potential imbalance in endometriosis ASRM stage distribution and cesarean section rates, may restrict the generalizability of our findings. In addition, due to the requirement for peritoneal lavage fluid collection, the control group could not consist of entirely healthy women, which may have resulted in a more conservative estimation of group differences. Serum sex hormone levels were not assessed; however, strict inclusion criteria and uniform surgical timing were applied to minimize hormonal confounding. Future studies incorporating cycle-phase-standardized hormone measurements may provide additional insights. (b) Dietary information was not collected in this study, despite the known influence of diet on gut microbiota composition and serotonin metabolism. (c) The direct causal relationship between Akkermansia muciniphila and elevated serotonin levels remains to be established and warrants further validation using germ-free mouse models or fecal microbiota transplantation approaches. (d) The precise mechanisms by which the gut-reproductive tract microbiota axis regulates local and systemic serotonin synthesis remain unclear and require further investigation.<br><br>Our study is the first to utilize a multi-omics approach combined with a joint analysis of the female gut-reproductive tract axis across multiple loci, revealing and validating a significant increase in serotonin levels in patients with endometriosis. This change may be regulated by the gut-reproductive microbiota axis. These findings provide new insights into the pathogenesis of endometriosis and identify potential targets for prevention and treatment.<br><br>This study was funded by the Jilin Provincial Key Laboratory of Precision Infectious Diseases (Grant No. 20200601011JC), Key Laboratory of Health and Family Planning Commission of Jilin Province (Grant No. 3D5200117426). The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.<br><br>TRIAL REGISTRATION NUMBER: ChiCTR2300077490.}, }
@article {pmid41903668, year = {2026}, author = {Brahmachary, P and Keim, EA and Walk, ST and McGee-Lawrence, ME and June, RK}, title = {AhR signaling in joint homeostasis and disease.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2026.03.003}, pmid = {41903668}, issn = {1638-6183}, abstract = {The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that integrates environmental, microbial, and metabolic signals to regulate gene expression across diverse tissues. Recent studies highlight AhR's role in skeletal homeostasis and joint biology, particularly through its interactions with microbiome-derived tryptophan metabolites and the Wnt/β-catenin signaling pathway. This review synthesizes current knowledge on AhR signaling mechanisms, including canonical and non-canonical pathways, and explores the impact of exogenous toxicants and microbiome-derived compounds and endogenous host metabolites that activate AhR. We discuss emerging evidence linking AhR activity to cartilage development, inflammation, and osteoarthritis progression, and highlight the utility of gnotobiotic mouse models in dissecting microbiome-AhR interactions. Finally, we examine the therapeutic potential of AhR modulation in joint disease, emphasizing its relevance as a pharmaceutical target for osteoarthritis and age-related musculoskeletal decline.}, }
@article {pmid41903849, year = {2026}, author = {Ekhlas, D and Verbiest, A and Stas, M and De Meyere, L and Vandermeulen, G and Tóth, J and Geboers, K and Timmermans, L and Verspecht, C and Wauters, L and Vermeersch, P and Jeppesen, PB and Verbeke, K and Joly, F and Derrien, M and Raes, J and Vanuytsel, T}, title = {Early ecological changes in intestinal microbiota with the long-acting GLP-2 analog apraglutide in short bowel syndrome.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {103138}, doi = {10.1016/j.clnesp.2026.103138}, pmid = {41903849}, issn = {2405-4577}, abstract = {BACKGROUND AND AIMS: Short bowel syndrome with intestinal failure (SBS-IF) is a rare, severe organ failure condition requiring long-term parenteral support. In SBS with colon-in-continuity (CiC), rapid transit and increased oxygen reshape gut and microbiota. We aimed to elucidate the effects of apraglutide, a novel long-acting glucagon-like peptide-2 (GLP-2) analogs, on the gut microbiome in SBS-IF-CiC.<br><br>METHODS: We performed a 52-week multicenter, open-label, phase 2 study in adults with SBS-IF-CiC (Leuven n = 7, Paris n = 2) receiving weekly subcutaneous apraglutide. Duodenal, distal small bowel and sigmoid colon biopsies, fecal- and plasma samples were collected over time. Analyses included mucosa-associated and fecal microbiota, fecal parameters, and fermentation metabolites. For baseline comparison, duodenal and sigmoid colonic biopsies from 20 controls (10 per region) were collected.<br><br>RESULTS: Patients exhibited an altered ecosystem characterized by reduced richness, loss of colonic anaerobes and dominance of Lactobacillus and Bifidobacterium with larger inter-subject variability, lower pH, higher moisture, and lower microbial load compared to controls. Apraglutide did not change overall diversity or stool parameters, but reduced inter-subject variability in stool and sigmoid colon. Notably, Bifidobacterium decreased in both stool and sigmoid colon, whereas Prevotella increased in stool from some patients. Still, Lactobacillus remained dominant. Specific taxa correlated with fecal butyrate, propionate, and reduced distal colonic motility, indicating microbial metabolism may support boosted adaptation.<br><br>CONCLUSIONS: This study emphasizes that SBS-IF-CiC features an immature distal gut microbiota and apraglutide promotes early ecological maturation, suggesting that combining GLP-2 analogs therapy with microbiome-targeted strategies may further enhance intestinal and ecosystem adaptation; ClinicalTrials.gov, Number NCT04964986https://www.<br><br>CLINICALTRIALS: gov/study/NCT04964986?term=NCT04964986&amp;rank=1.}, }
@article {pmid41903990, year = {2026}, author = {Gorji, L and Seldomridge, AN and Holder, AM}, title = {Leveraging the Human Microbiome to Improve Immunotherapy Sensitivity.}, journal = {Surgical oncology clinics of North America}, volume = {35}, number = {2}, pages = {285-298}, doi = {10.1016/j.soc.2025.10.007}, pmid = {41903990}, issn = {1558-5042}, mesh = {Humans ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; *Microbiota/immunology ; *Precision Medicine/methods ; Tumor Microenvironment/immunology ; }, abstract = {The human microbiome is composed of distinct microbial communities or ecosystems found throughout the human body, including within unique tumor microenvironments. In this review, we discuss the microbiome's influence on solid tumors, how the microbiome can be modulated to improve response to immunotherapy, and how emerging evidence suggests that microbiome modulation can add to the repertoire of personalized medicine.}, }
@article {pmid41904117, year = {2026}, author = {Chouhan, D and Grossman, AS and Kerns, KA and Stocke, KS and Kim, M and Dong, PT and Kumar, A and Lei, L and Lamont, RJ and McLean, JS and He, X and Bor, B}, title = {Ultrasmall oral Saccharibacteria modulate gingival immunoactivation through type IV pili and TLR2-dependent endocytosis.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70546-5}, pmid = {41904117}, issn = {2041-1723}, support = {1R01DE031274//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; T90 DE026110-07//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; 1S10OD034405-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; T90 DE026110-07//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, abstract = {Saccharibacteria are ultrasmall episymbionts that require host-bacteria to grow. They are positively associated with inflammatory diseases within the human microbiome, yet their mechanisms for interacting with the human host and contributing to diseases remain unknown. This study investigated the tripartite interactions between Saccharibacteria (Nanosynbacter lyticus strain TM7x and other strains), their host/non-host-bacteria, and human oral gingival epithelial cells. Both host and non-host-bacteria strongly induce proinflammatory cytokines in epithelial cells, while Saccharibacteria alone elicits limited immune activation. Remarkably, Saccharibacteria dampened proinflammatory cytokine responses to host/non-host-bacteria during coinfection. Mechanistically, this effect results from Saccharibacteria-mediated clustering and endocytosis of surface TLR2 receptor, ultimately leading to reduce TLR2-mediated cytokine signalling. Sacchribacteria type IV pili appendages facilitate epithelial cell binding and subsequent immune dampening via direct interaction between pili adhesins and TLR2. High resolution imaging shows that Saccharibacteria are internalized by epithelial cells through caveolin-mediated endocytosis, subsequently colocalize with endosome markers, and eventually are trafficked to lysosomes for degradation. Moreover, a subset of the Saccharibacteria survives lysosomal degradation and retains the ability to reinfect host-bacteria, highlighting a mechanism for transient persistence in the oral microbiome and a vital role in human immune and microbiome modulation.}, }
@article {pmid41904277, year = {2026}, author = {M Davidson, I and Nikbakht, E and M O'Neill, H and Haupt, LM and Dunn, PJ}, title = {Shaping the Female Microbiome: A Review of Lifestyle Factors Influencing the Vaginal, Gut, Oral, and Skin Microenvironments.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02747-w}, pmid = {41904277}, issn = {1432-184X}, abstract = {The female microbiome, spanning the vaginal, gut, oral, and skin sites, harbours distinct microbial communities. Although the diversity and function of microbial communities across these sites are becoming increasingly understood, the extent to which modifiable lifestyle and environmental factors such as smoking, diet, alcohol intake, obesity, physical activity, stress, hygiene, and sexual behaviours shape these microbiomes remains underexplored. This review is restricted to modifiable lifestyle and environmental factors and does not comprehensively assess pharmaceutical exposures (e.g., antibiotics or hormonal therapies) or hormonal influence. To date, no review has comprehensively assessed and compiled evidence across the four microbial sites in females, despite their unique hormonal, physiological, and reproductive characteristics that distinctly influence microbial composition and function. This review provides a comprehensive examination of how such factors influence the dynamics of microbial composition and function along with site-specificity while also assessing cross-site microbial interactions. We focus exclusively on females to address a critical knowledge gap to provide a foundation from which future research and interventions can be tailored to women's health. This review discusses the underlying mechanisms driving microbial shifts and their impact on host health, highlighting critical gaps in our current knowledge. The integration of findings from multi-site microbiome research, highlights the potential to inform targeted, preventative, and therapeutic strategies that utilise the inherent dynamic nature of the microbiome to improve health outcomes across the female lifespan.}, }
@article {pmid41904418, year = {2026}, author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S}, title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01413-x}, pmid = {41904418}, issn = {2730-6844}, }
@article {pmid41904606, year = {2026}, author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H}, title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649435}, doi = {10.1080/19490976.2026.2649435}, pmid = {41904606}, issn = {1949-0984}, mesh = {Animals ; *Dietary Fiber/metabolism/administration &amp; dosage ; *Gastrointestinal Microbiome ; Mice ; *Colitis/prevention &amp; control/microbiology/chemically induced ; Feces/microbiology ; Dextran Sulfate ; Colon/microbiology/pathology ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Male ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology ; }, abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.}, }
@article {pmid41904644, year = {2026}, author = {Wang, W and Wen, Y}, title = {The role of systemic inflammation in hepatic encephalopathy: advances in inflammatory mechanisms, prevention and treatment research.}, journal = {Annals of medicine}, volume = {58}, number = {1}, pages = {2650232}, doi = {10.1080/07853890.2026.2650232}, pmid = {41904644}, issn = {1365-2060}, mesh = {*Hepatic Encephalopathy/therapy/etiology/prevention &amp; control/immunology ; Humans ; Gastrointestinal Microbiome/immunology ; *Inflammation/complications/therapy/immunology ; Ammonia/metabolism ; Animals ; Dysbiosis/complications ; Fecal Microbiota Transplantation/methods ; Liver Cirrhosis/complications ; Hyperammonemia ; Rifaximin/therapeutic use ; Blood-Brain Barrier ; }, abstract = {OBJECTIVES: This review synthesizes current evidence establishing systemic inflammation as a key pathogenic driver in hepatic encephalopathy (HE) beyond hyperammonemia. It does not replace the ammonia hypothesis but rather acts as a critical synergistic factor, modulating and amplifying ammonia neurotoxicity. It further evaluates the mechanisms linking inflammation to HE and the therapeutic advances in inflammation-targeted prevention and treatment strategies.<br><br>METHODS: A comprehensive narrative literature review was conducted, analyzing relevant preclinical models and clinical studies. The search and synthesis focused on inflammatory mechanisms in chronic liver disease, gut-liver-brain axis dysfunction, cirrhosis-associated immune dysfunction (CAID), and resulting neuroinflammatory pathways.<br><br>RESULTS: Systemic inflammation, driven by gut dysbiosis, barrier failure, and CAID, amplifies ammonia neurotoxicity and independently contributes to neuroinflammation, blood-brain barrier disruption, and cerebral metabolic dysfunction in HE. Key inflammatory markers, such as IL-6, correlate with disease severity. Therapies targeting inflammation - particularly gut microbiota modulation with rifaximin and fecal microbiota transplantation (FMT) - demonstrate significant efficacy in reducing HE recurrence, lowering systemic inflammation, and improving cognitive outcomes. Other approaches, including albumin infusion, also show promise.<br><br>CONCLUSIONS: Systemic inflammation is a pivotal and synergistic factor in HE pathogenesis. Combining anti-inflammatory strategies that target the gut-liver-brain axis with traditional ammonia-lowering therapies offers a more comprehensive and effective treatment paradigm. Future research should prioritize protocol optimization, long-term safety assessment, and the development of personalized treatment approaches.}, }
@article {pmid41904966, year = {2026}, author = {Sun, H and Longdon, B and Raymond, B}, title = {Effect of the microbiome on pathogen susceptibility across four Drosophilidae species.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70275}, pmid = {41904966}, issn = {1744-7917}, support = {NE/V012053/1//Natural Environment Research Council/ ; BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S002928//BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 109356/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; //China Scholarship Council and University of Exeter PhD Scholarships/ ; }, abstract = {Microbiome have been shown to play an important role in host susceptibility to infections in some hosts. However, less is known about whether microbiota-mediated effects are consistent across host species, as our understanding of such interactions may be affected by publication bias. Following on from a large study of 36 species of Drosophilidae challenged with four bacterial pathogens, we identified two candidate host species that might have protective microbiomes based on low susceptibility and high abundance of culturable microbiota; we selected two other host species for comparison. We tested whether germ-reduced flies, and flies with natural or re-constituted microbiomes varied in their susceptibility to systemic infection with two bacterial pathogens (Providencia rettgeri and Staphylococcus aureus) and one viral pathogen (Drosophila C Virus). The composition and abundance of the bacterial microbiota varied between host species and microbiome treatments. We found an overall interaction between host species and pathogen type, confirming previous work that host species vary in their susceptibility in a pathogen specific manner. Similarly, we found that microbiome treatments had differing effects on host survival among host species, although some effect sizes tended to be small. In D. putrida individuals with manipulated microbiomes showed increased susceptibility to all pathogens tested; in other hosts altered susceptibility was pathogen dependent. While there are always challenges to manipulating microbiomes, especially across multiple host species, our results indicate that host microbiota play limited roles on survival in systemic infection in these four species. This work demonstrates that caution is required when generalizing about potential beneficial impact of microbiomes.}, }
@article {pmid41905017, year = {2026}, author = {Gao, D and Hu, D and Xu, H and Li, X}, title = {A phage cocktail targeting multiple receptors reduces Salmonella Enteritidis colonization in chicks and modulates the cecal microbiome.}, journal = {Veterinary microbiology}, volume = {316}, number = {}, pages = {110999}, doi = {10.1016/j.vetmic.2026.110999}, pmid = {41905017}, issn = {1873-2542}, abstract = {Salmonella Enteritidis is a major pathogen responsible for foodborne illnesses, frequently causing public health issues through the contamination of poultry products and posing a serious threat to the poultry industry. In recent years, phages have emerged as a promising alternative to antibiotics for prevention and control strategies. In this study, a rationally designed phage cocktail from previous research was used, consisting of four phages targeting different receptors: GSP162, GSP193, GSP001, and GSP032. An infection model of chicks infected with S. Enteritidis strain SE006 was established to systematically assess the in vivo protective effects of the phage cocktail. The results demonstrated that the phage cocktail reached high concentrations in the chick ceca and showed a trend toward reduction in the ceca load of S. Enteritidis. In the phage-treated group, the cecal S. Enteritidis load was reduced by an average of 0.75 ± 0.34 log10 CFU/g on day 1 and 1.01 ± 0.33 log10 CFU/g on day 4 post-treatment, respectively. Gut microbiota analysis revealed that the phage cocktail modulated the dysbiosis induced by S. Enteritidis SE006 infection and facilitated the establishment of the early cecal microbial community in chicks. This study provides preliminary experimental evidence supporting the potential of phage-based biocontrol of Salmonella in poultry, laying a foundation for further field validation in commercial settings before practical application.}, }
@article {pmid41905051, year = {2026}, author = {Nguyen, TD and Huang, YC and Zhang, S and Itayama, T and Mo, J and Liu, X and Liu, W and Wang, Z}, title = {Sex-specific gut microbiota dysbiosis and intergenerational effects of florfenicol in Tigriopus japonicus: Maternal-only or biparental contributions?.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141871}, doi = {10.1016/j.jhazmat.2026.141871}, pmid = {41905051}, issn = {1873-3336}, abstract = {Florfenicol, an antibiotic widely used in mariculture, raises concerns about long‑term impacts on non‑target marine organisms. However, its intergenerational effects and underlying mechanisms remain poorly understood. We exposed marine copepods (Tigriopus japonicus) to florfenicol in acute assays and chronically exposed the parental generation (F0) to environmentally detected concentrations, followed by a cross‑mating design to evaluate effects in unexposed offspring (F1). Acute exposure caused no naupliar mortality after 96 h, although copepodite swimming activity declined significantly at ≥ 25 mg/L, indicating limited direct toxicity under short‑term exposure. In contrast, chronic F0 exposure delayed metamorphosis, skewed sex ratios toward females, and unexpectedly increased fertility. In F1, developmental delay persisted when either both parents or only mothers were exposed, suggesting a trade‑off between reproductive output and developmental pace. The female‑based sex ratio also carried over, with contributions from both maternal and paternal exposure. Gut microbiome dysbiosis occurred in both sexes but was sex‑specific, characterized by reduced beneficial taxa (e.g., Lactobacillus) and enrichment of opportunistic, antibiotic‑resistant Acinetobacter, particularly following maternal exposure. This study provides the first evidence that parental, sex‑specific microbiome disruption mediates intergenerational antibiotic effects, highlighting dominant maternal influences while also implicating paternal roles. Validation across taxa, broader antibiotic assessments, and targeted molecular investigations are needed to confirm these patterns and elucidate further underlying pathways. Overall, our findings underscore the ecological risks of florfenicol contamination in mariculture zones and emphasize the importance of incorporating parental and intergenerational responses into ecotoxicological assessments.}, }
@article {pmid41905316, year = {2026}, author = {Young-Yusty, S and Prescilla-Ledezma, A and Acosta-de Patiño, H}, title = {Diversity and antibiotic resistance profiles of bacteria isolated from the oral cavity of captive snakes.}, journal = {Revista Argentina de microbiologia}, volume = {58}, number = {3}, pages = {100711}, doi = {10.1016/j.ram.2026.100711}, pmid = {41905316}, issn = {0325-7541}, abstract = {Venomous snake bites are a global public health issue, causing between 81000 and 138000 annual deaths and 400000 permanent disabilities. This study investigated the oral bacterial diversity and antibiotic resistance profiles in captive Viperidae snakes. Oral swabs from 48 specimens across four species (Porthidium lansbergii, Bothriechis nigroviridis, Cerrophidion sasai, and Bothrops asper) were analyzed using culture-dependent methods. Bacterial isolation and identification using the VITEK 2 automated system revealed 41 strains from 12 genera, predominantly Gram-negative bacteria, including Morganella morganii (11 isolates) and Providencia rettgeri (10 isolates). Antibiotic susceptibility testing demonstrated significant resistance patterns, with 100% resistance to cephalothin and cefazolin in M. morganii, and emerging extended-spectrum β-lactamase (ESBL) production in Enterobacter cloacae and Sphingomonas paucimobilis. The comparative analysis showed that P. lansbergii exhibited the highest bacterial diversity. These findings highlight the complex oral microbiota of venomous snakes and underscore the need for evidence-based antibiotic strategies in snakebite management, particularly given the global rise in antimicrobial resistance.}, }
@article {pmid41905324, year = {2026}, author = {Chalif, J and Moruzzi, C and Velasquez, J and O'Connor, R and Fulton, J and Mehra, Y and Cohn, DE and Copeland, LJ and Cosgrove, CM and Nagel, CI and O'Malley, DM and Monovich, L and Spakowicz, DJ and Chambers, LM}, title = {Implementing non-invasive biospecimen collection in gynecologic oncology: Insights from a prospective gut microbiome feasibility study.}, journal = {Gynecologic oncology}, volume = {208}, number = {}, pages = {63-68}, doi = {10.1016/j.ygyno.2026.03.008}, pmid = {41905324}, issn = {1095-6859}, abstract = {OBJECTIVE(S): The gut microbiome is increasingly recognized as an important modulator of treatment response and other outcomes in gynecologic cancers, but data are limited regarding the logistics of incorporating stool sample collection into clinical practice. We evaluated the feasibility of integrating non-invasive stool biospecimen collection into routine gynecologic oncology care, described recruitment and compliance, and identified factors associated with participation.<br><br>METHODS: This prospective, single-institution study was conducted from March 2023 to April 2024. Eligible gynecologic oncology patients were approached for Total Cancer Care&#xae; enrollment and offered participation in an optional linked stool biospecimen substudy. Patients who consented received an at-home stool collection kit. Clinical and demographic data were abstracted from the electronic medical record, and multivariable logistic regression identified predictors of Total Cancer Care enrollment, stool kit acceptance, and stool kit return.<br><br>RESULTS: A total of 666 patients were approached, of whom 407 (61%) enrolled in Total Cancer Care. Among enrollees, 234 (58%) accepted a stool kit, and 100 (43%) of those who accepted returned a completed sample. On multivariable analysis, prior clinical trial participation (p&#xa0;<&#xa0;0.01) and provider (p&#xa0;<&#xa0;0.05) were independently associated with Total Cancer Care enrollment. Stool kit acceptance was most strongly predicted by treating provider (p&#xa0;<&#xa0;0.0001). No demographic or clinical variables were significantly associated with kit return.<br><br>CONCLUSION(S): Implementation of an at-home stool collection program in gynecologic oncology is feasible. Provider engagement was the strongest determinant of acceptance. These findings provide real-world benchmarks for recruitment and compliance and establish a foundation for future microbiome-focused translational studies.}, }
@article {pmid41905328, year = {2026}, author = {Matheoud, D and Akbar, I and Hercun, J and Stratton, JA}, title = {A liver-mitochondria-immune axis in Parkinson's disease: emerging perspectives on a hepatic origin for mitochondrial autoimmunity as a driver of Parkinson's disease.}, journal = {Current opinion in immunology}, volume = {100}, number = {}, pages = {102761}, doi = {10.1016/j.coi.2026.102761}, pmid = {41905328}, issn = {1879-0372}, abstract = {Parkinson's disease (PD) is increasingly understood as a systemic disorder with early manifestations outside the central nervous system. Converging clinical, metabolic, and immunological observations highlight overlaps between PD and primary biliary cholangitis (PBC), a prototypic autoimmune cholestatic liver disease. A shared hallmark of both conditions is mitochondrial dysfunction and immune dysregulation, particularly in the context of bile acid (BA) metabolism. In this Current Opinion-style perspective, we integrate recent advances in microbiome biology, BA signaling, and mitochondrial antigen presentation to propose that hepatic stress may contribute to PD pathogenesis by promoting immune exposure to mitochondrial antigens, a proautoimmune cytokine environment, and the generation of mitochondrial‑reactive cytotoxic T cell responses. We discuss how alterations in BA and the promotion of dysbiosis - documented in both PBC and PD - can induce ductular reaction, immunogenic apoptosis, and MitAP, thereby providing a mechanistic bridge between liver inflammation and adaptive immunity. Despite divergent clinical presentations, PBC and PD may share critical upstream pathways linking hepatic metabolism, mitochondrial antigenicity, and immune tolerance. We argue that further investigation of a liver-mitochondria-immune axis may yield new insights into PD initiation and progression.}, }
@article {pmid41905375, year = {2026}, author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS}, title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101294}, doi = {10.1016/j.lanmic.2025.101294}, pmid = {41905375}, issn = {2666-5247}, abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.<br><br>METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.<br><br>FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26&#xb7;1 years [SD 3&#xb7;8]) and 12 to the placebo group (27&#xb7;3 years [4&#xb7;8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0&#xb7;65; 95% CI 0&#xb7;20-2&#xb7;16, p=0&#xb7;49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.<br><br>INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.<br><br>FUNDING: Freya Biosciences.}, }
@article {pmid41905409, year = {2026}, author = {Kim, YJ and Park, N and Cheng, X and Lee, Y}, title = {Advanced engineering of microbiome-related therapeutics for targeted treatment of inflammatory bowel diseases.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {114872}, doi = {10.1016/j.jconrel.2026.114872}, pmid = {41905409}, issn = {1873-4995}, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the intestine arising from complex interactions among genetic and environmental factors, intestinal barrier dysfunction, immune dysregulation, and gut microbiota dysbiosis. Current therapies for IBD-including anti-inflammatory agents, immunosuppressants, and targeted biologics-remain challenging, as they often cause long-term adverse effects and fail to address the underlying pathological mechanisms. Given these challenges, nano- and bioengineering of microbiome-related therapeutics-including microbial-derived metabolites, probiotics, and prebiotic natural products-has emerged as a promising strategy, offering high biocompatibility and the ability to modulate key disease drivers such as immune responses, barrier restoration, redox balance, and microbiota composition. In this review, we examine the major pathological features of IBD and present engineered microbiome-related platforms designed to overcome the limitations of conventional compounds-such as poor solubility, low bioavailability, rapid degradation or absorption, low probiotic viability, and insufficient accumulation at target sites-while highlighting their therapeutic efficacy in IBD management. Finally, we outline future directions for developing these advanced delivery systems toward more effective and potentially disease-modifying treatments.}, }
@article {pmid41905430, year = {2026}, author = {Rokkas, T and Graham, DY}, title = {The Unfinished Agenda in Helicobacter pylori Treatment: Resistance, Microbiome Effects, and Future Directions.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.02.041}, pmid = {41905430}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Helicobacter pylori (H. pylori) infection is the principal cause of peptic ulcer disease, MALT lymphoma and non-cardia gastric cancer. The major advances in diagnostics and treatment, eradication success are threatened by rising antimicrobial resistance and concerns about disruption of the normal microbiome. This review summarizes current unresolved issues in H. pylori treatment, with a focus on resistance, optimal regimens, ecological impact, and emerging therapies.<br><br>METHODS: Extensive review of randomized controlled trials, meta-analyses, international consensus guidelines, molecular epidemiology studies, microbiome analyses, and translational research related to H. pylori eradication, resistance, microbiome effects, and novel therapies.<br><br>RESULTS: Global resistance to clarithromycin, metronidazole, and fluoroquinolones significantly undermines the performance of traditionally effective antimicrobial therapies. The corner stone of successful antimicrobial therapy is susceptibility-guided therapy but remains of limited use with H. pylori because of lack of infrastructure. Eradication regimens potentially induce substantial alterations in gut and gastric microbiota and expand the antimicrobial resistome. Probiotics and N-acetylcysteine offer at best very modest improvements in eradication and tolerability. Novel and still experimental platforms, including engineered phage therapy, antimicrobial peptides, nanoparticle-delivered urease inhibitors, biofilm-targeting agents and vaccines show promise. Implementation gaps, persistent use of suboptimal regimens, and global inequities constrain the impact of available therapies.<br><br>CONCLUSIONS: Optimizing H. pylori treatment requires evidence-based regimen selection, precision-guided strategies, antimicrobial stewardship and equitable access to essential medications. Advances in molecular diagnostics, antimicrobial development, and implementation science are all critical to reducing the global burden of H. pylori-associated disease and gastric cancer.}, }
@article {pmid41905743, year = {2026}, author = {Zhang, Z and Guo, S and Li, X and Wang, Z and Han, X and Li, J and Li, Z and Zhao, J and Stephenson, SL and Gmoshinskiy, VI and Kurakov, AV and Li, Y and Liu, P}, title = {Divergent edaphic filters drive ecosystem-specific microbiome assembly and metabolic strategies in Northern China's transitional zone.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124371}, doi = {10.1016/j.envres.2026.124371}, pmid = {41905743}, issn = {1096-0953}, abstract = {Soil microbial communities are pivotal drivers of ecosystem processes; however, their responses to pedogenic settings and vertical stratification across ecological gradients remain inadequately characterized. In this study, we integrated soil physicochemical analyses, high-throughput 16S rRNA gene sequencing, and microbial metabolic profiling across seven soil subtypes from forest (SSL) to grassland (SCD) ecosystems in the transitional ecoregions of Northern China. Soil subtypes were sampled at three depths (0-5, 5-10, and 10-15 cm). Our results demonstrated that soil type and depth exerted strong filtering effects on the microbial assembly. Within the surface soil layer (0-15 cm) examined in this study, SSL soils exhibited higher microbial metabolic activity (AWCD) and functional diversity than SCD soils. Carbon metabolism peaked in the surface layers. Bacterial species richness was greater in SCD soils, but the structure of the community present diverged significantly between ecosystems. The Proteobacteria and Acidobacteriota dominated in SSL, whereas the Proteobacteria and Actinobacteriota prevailed in SCD. Soil depth exerted a stronger diversity-reducing effect in SCD than in SSL. Redundancy and Mantel tests identified soil water content, pH, and available phosphorus as key determinants of community variation. Functional potential prediction revealed enhanced aerobic chemoheterotrophy and nitrate reduction in SCD, while SSL was enriched in nitrogen fixation and pathogen-related taxa. These findings demonstrated that ecosystem-specific edaphic properties govern both taxonomic composition and functional attributes, highlighting the prevalence of niche-based assembly processes for soil microbiomes in transitional ecoregions.}, }
@article {pmid41905755, year = {2026}, author = {Milleman, K and Bosma, ML and Saito, A and Gorecki, P and Ding, Y and Lanka, U and DelSasso, A and Wills, K and Milleman, J}, title = {Changes in Salivary Flow and Oral pH Following Use of Different Mouthrinse Formulations in Addition to Brushing Versus Brushing Only.}, journal = {Journal of dental hygiene : JDH}, volume = {100}, number = {2}, pages = {9-19}, pmid = {41905755}, issn = {1553-0205}, mesh = {Humans ; *Mouthwashes/pharmacology ; Hydrogen-Ion Concentration ; Male ; Female ; Adult ; *Saliva/drug effects/metabolism/chemistry ; *Toothbrushing/methods ; Middle Aged ; Single-Blind Method ; *Oils, Volatile/pharmacology ; Young Adult ; Ethanol ; }, abstract = {Purpose Mouthrinses contain inactive ingredients (e.g., solvents, such as alcohol) and active ingredients (e.g., antimicrobials, such as essential oils [EOs]) that work in combination to control gingival inflammation and regulate the oral microbiome. The purpose of this one-day, examiner-blind, randomized, parallel-group-controlled clinical trial was to understand the effect of different EO-containing mouthrinses, with and without alcohol, on salivary flow and pH.Methods Subjects aged ≥18 years were recruited to participate in a one-day trial conducted at an independent research center. Salivary flow and pH were measured following a regimen of brushing and rinsing with an EO-containing mouthrinse versus brushing and rinsing with a water rinse control (BW). Eligible participants were assigned 1:1:1:1 to the BW group or one of three EO-containing mouthrinse groups. Change in salivary flow and pH after a single use of an EO-containing mouthrinse compared to the BW group was assessed at 0 (salivary flow only), then at 2.5, 5, 10, 15, and 30 minutes.Results A total of 159 subjects completed the clinical trial. At 30 minutes following the intervention, the mean salivary flow was similar across all groups. The mean salivary pH increased in all groups through 15 minutes before returning to near-baseline levels by 30 minutes (all of which were within the normal oral pH range of 6.2-7.6). No adverse events were reported.Conclusion The inclusion of alcohol in the tested mouthrinse formulations did not affect salivary flow or pH compared with the alcohol-free mouthrinses, indicating that a single use of either an alcohol-containing or alcohol-free EO-containing mouthrinse does not contribute to oral dryness. Future trials investigating the long-term use of mouthrinses and their effect on salivary flow and pH will help to build on the current evidence base and inform clinical decision-making.}, }
@article {pmid41905820, year = {2026}, author = {Tsuji, S and Gonchigsuren, U and Akagawa, S and Yamanouchi, S and Kato, S and Unishi, G and Okano, M and Okuda, K and Kino, J and Araki, A and Takaya, J and Teraguchi, M and Nakamura, A and Kaneko, K}, title = {Response to Letter to the Editor re: "Age-related changes in the urinary microbiome of healthy Japanese children".}, journal = {Journal of pediatric urology}, volume = {}, number = {}, pages = {105883}, doi = {10.1016/j.jpurol.2026.105883}, pmid = {41905820}, issn = {1873-4898}, }
@article {pmid41905975, year = {2026}, author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC}, title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45955-7}, pmid = {41905975}, issn = {2045-2322}, }
@article {pmid41906342, year = {2026}, author = {Wu, J and Tian, J and Zhang, X and Kong, Z}, title = {Metagenomic Analysis of Soybean Rhizosphere Microbiome in Black Soil: Community Composition and Functional Insights.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70505}, pmid = {41906342}, issn = {1365-3040}, support = {XDA28030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32241045//National Natural Science Foundation of China/ ; }, }
@article {pmid41906693, year = {2026}, author = {Sarkar, SK and Ekwudo, MN and Lu, D and Masson, B and Kiridena, P and van de Garde, N and Renoir, T and Vince, JE and Deepagan, VG and Hannan, AJ and Gubert, C}, title = {Inhibition of the NLRP3 Inflammasome With MCC950 Improves Gut Health in Huntington's Disease Mice.}, journal = {Journal of neurochemistry}, volume = {170}, number = {4}, pages = {e70419}, doi = {10.1111/jnc.70419}, pmid = {41906693}, issn = {1471-4159}, support = {//Bethlehem Griffiths Research Foundation/ ; //National Health and Medical Research Council/ ; //EU-JPND/ ; //ERA-NET NEURON/ ; //Flicker of Hope Foundation/ ; //DHB Foundation (Equity Trustees)/ ; //Margaret Friend Trust/ ; //University of Melbourne/ ; //Science and Technology Fellowship/ ; }, mesh = {Animals ; *NLR Family, Pyrin Domain-Containing 3 Protein/antagonists &amp; inhibitors/metabolism ; *Huntington Disease/drug therapy/metabolism/genetics ; Mice ; Indenes/pharmacology ; *Inflammasomes/antagonists &amp; inhibitors/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Sulfones/pharmacology ; Male ; Mice, Transgenic ; Sulfonamides/pharmacology ; *Furans/pharmacology ; Cyclopropanes ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; }, abstract = {Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder featuring abnormal cognition, psychiatric symptoms, movement, and gastrointestinal function. It is caused by a tandem-repeat gene mutation encoding an expanded polyglutamine tract in the huntingtin protein. Our group was the first to demonstrate gut microbial disruption in both clinical HD cohorts and validated preclinical models, supporting a role for microbiota-gut-brain axis dysfunction in HD. The NLRP3 inflammasome, a key innate immune sensor that integrates microbial, metabolic, and host-derived danger signals, has been implicated in HD pathology. However, its contribution to gut health and microbiota-linked cognitive deficits in HD remains unknown. This study addressed this critical gap by investigating whether targeting NLRP3 can restore gut and brain health in HD through modulation of the microbiota-gut-brain axis. We aimed to investigate the role of the NLRP3 inflammasome in microbiota-gut-brain axis dysfunction by targeting its inhibition. Here, we assessed whether inhibiting NLRP3 can ameliorate cognitive deficits, gut abnormalities, gut microbial alteration, and associated molecular and behavioural disturbances in HD. NLRP3 inflammasome inhibitor MCC950 was administered to R6/1 transgenic HD mice and their wild-type (WT) littermate controls from 6 to 20 weeks of age. Cognitive and behavioural performance was evaluated using validated tests, alongside assessments of general health and gut function. HD mice exhibited reduced body and brain weight, increased fluid consumption, memory impairments, motor deficits, exacerbated gastrointestinal phenotype, and altered gut microbiota. Treatment with MCC950 did not affect body or brain weight, cognitive and motor performance, and it also did not affect the gut microbial profile of HD mice. However, MCC950 significantly rescued gut health, as evidenced by increased faecal output (in females) and water content (in both males and females), improved stool consistency (in both sexes), and ameliorated macroscopic gut abnormalities. Our findings highlight a promising therapeutic avenue for addressing the significant gastrointestinal anomalies observed in HD. By targeting the NLRP3 inflammasome in R6/1 HD mice, we have identified a novel strategy to improve gut health. These results support further investigation of inflammasome inhibition as a means to alleviate central and peripheral symptoms in HD and improve overall disease management.}, }
@article {pmid41906784, year = {2026}, author = {Cho, J and Do, S and Kim, K and Chang, HK and Chung, HH}, title = {The impact of cervicovaginal microbiome on HPV infection in vaccinated young Korean women.}, journal = {Journal of gynecologic oncology}, volume = {}, number = {}, pages = {}, doi = {10.3802/jgo.2026.37.e88}, pmid = {41906784}, issn = {2005-0399}, support = {2021R1G1A1095216/NRF/National Research Foundation of Korea/Korea ; }, abstract = {OBJECTIVE: To investigate the prevalence of high-risk human papillomavirus (hrHPV) infection and its association with cervicovaginal microbiome (CVM) diversity among young Korean women who received human papillomavirus (HPV) vaccination.<br><br>METHODS: Seventy-two Korean women aged 20-35 years were enrolled in Seoul, South Korea. Cervicovaginal samples were analyzed using liquid-based cytology, HPV genotyping, and 16S rRNA sequencing. Alpha diversity and microbial compositions were compared according to HPV infection and cytology results.<br><br>RESULTS: The prevalence of hrHPV infection was 44.4% (n=32), with HPV 39 and 52 being the most common types. Women with abnormal cytology or hrHPV positivity exhibited significantly higher microbial alpha diversity (Shannon index, p<0.05). bacterial vaginosis-associated bacteria (BVAB) such as Gardnerella leopoldii, G. vaginalis, and Megasphaera lornae were significantly associated with hrHPV positivity, along with Lactobacillus iners showed a strong positive correlation with microbial diversity, abnormal cytology, and hrHPV infection (p<0.001).<br><br>CONCLUSION: Despite national HPV vaccination, hrHPV infection remains common among young Korean women, primarily driven by non-vaccine types. The dominance of L. iners and enrichment of BVAB were key microbial features associated with hrHPV infection and abnormal cytology, suggesting that ecological imbalance in the CVM may contribute to viral persistence. These findings highlight the potential role of microbiome modulation as a complementary approach in post-vaccination HPV management and prevention.}, }
@article {pmid41907053, year = {2026}, author = {Lynn, ID and Wenzel, MA}, title = {Ephemeral signatures of phylosymbiosis in dermal microbiomes within the requiem shark family (Carcharhinidae).}, journal = {Access microbiology}, volume = {8}, number = {3}, pages = {}, pmid = {41907053}, issn = {2516-8290}, abstract = {The elasmobranch dermal microbiome may be important for buffering effects of environmental stress on host health and population viability via functional metabolic interactions. Dermal microbiomes among elasmobranch orders co-vary with host phylogeny (phylosymbiosis), indicating functional co-evolution with their hosts at deep phylogenetic splits. However, the extent of phylosymbiosis and potential for functional co-evolution within particularly species-rich elasmobranch families remains unknown. Here, we re-analyse Illumina amplicon sequence data from the 16S rRNA gene from eight Carcharhinid shark species (plus one Ginglymostomatid outgroup) across six independent studies and explicitly examine the extent of phylosymbiosis in dermal microbiomes within this family. We found extensive divergence in operational taxonomic unit (OTU) abundance and functional metabolic capacity between studies, driven by disparity in OTU sharing and probably reflecting geographical and seasonal factors. Total microbiome structure was incongruent with shark phylogeny, providing no evidence for phylosymbiosis when considering all species and OTUs. However, using bootstrapping and subsampling methods, we identified several subsets of OTUs where Bray-Curtis dissimilarity supported perfect topological congruence with shark phylogeny or strong associations with phylogenetic distances, but not both. Partial Mantel tests identified ten candidate OTUs that supported a moderately strong signal of phylosymbiosis across all shark species and included the immunostimulant skin symbiont genera Lactiplantibacillus and Alcaligenes. Overall, this provides provisional evidence for phylosymbiosis in a minority fraction of the elasmobranch dermal microbiome within the Carcharhinidae family and will necessitate coordinated large-scale studies to establish the generality of these findings.}, }
@article {pmid41907094, year = {2026}, author = {Abo Qoura, L and Kostyushev, D and Parodi, A and Boyarintsev, DI and Chulanov, V and Pokrovsky, VS}, title = {Nanoparticle-Host Interactions: The Impact of Physiological and Pathological Factors on Biodistribution, Immune Processes, and Translational Challenges.}, journal = {Cellular and molecular bioengineering}, volume = {19}, number = {1}, pages = {1-27}, pmid = {41907094}, issn = {1865-5025}, abstract = {BACKGROUND: The clinical translation of nanoparticles (NPs) for therapeutic applications is hindered significantly by unpredictable biodistribution in diseased patients, which results from the complex interplay between engineered physicochemical properties of NPs and specific changes in the function of biological barriers.<br><br>METHODS: This review delves into the multifaceted factors that govern NP biodistribution, highlighting the critical roles of intrinsic NP design, including size, shape, and surface chemistry, along with host-specific physiological and pathological conditions. We overview how these properties can change systemic circulation, organ-specific accumulation, and clearance pathways. The role of surface functionalization in targeted delivery is examined through the lens of altered serum composition, which affects protein corona formation. Particular attention is given to immune response, whether pathogen/antigen-primed, macrophage-monocyte-mediated clearance, compromised biological barriers, and host-specific factors such as sex, age, drug exposure, and gut microbiome. Disease contexts, including cancer and viral infections, are considered to evaluate translational challenges.<br><br>RESULTS: NP biodistribution is shaped by the interplay between engineered physicochemical properties and disease-associated biological changes. Intrinsic NP characteristics influence systemic circulation, organ-specific accumulation, and clearance pathways. Altered serum composition affects protein corona formation and immune responses, including overactivated or suppressed immune states. Compromised biological barriers, including increased permeability of the blood-brain barrier, enhanced renal excretion, and reduced liver retention, further modify pharmacokinetic profiles. Host-specific variability and pathological conditions introduce additional complexity, creating unique barriers that passive targeting strategies often fail to overcome.<br><br>CONCLUSION: Developing a comprehensive grasp of these interrelated mechanisms is crucial for engineering NPs that can translate preclinical results into expected clinical outcomes, ultimately closing the gap between research innovation and patient care.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-026-00888-z.}, }
@article {pmid41907166, year = {2026}, author = {Qingyang, J and Qiming, L and Ruixia, G}, title = {How are kefir microbial communities and product characteristics maintained in industrial production?.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100579}, pmid = {41907166}, issn = {2666-5174}, abstract = {Kefir, a millennia-old symbiotic fermented dairy product, has emerged as a focal point of research in the global functional foods sector owing to its distinctive organoleptic properties and extensive health-promoting effects. Kefir grains, serving as the natural starter culture for traditional kefir, constitute a complex symbiotic consortium comprising lactic acid bacteria, acetic acid bacteria, and yeasts, whose stratified spatial distribution and metabolic synergistic interactions determine the characteristic flavor profile and probiotic functionality of kefir. Nevertheless, contemporary kefir production faces fundamental challenges stemming from the incompatibility between traditional fermentation methodologies and modern industrial manufacturing processes, resulting in commercial kefir products exhibiting deficiencies in core functional microbial populations, flavor homogenization, and suboptimal functional efficacy claims. This review analyzes the current research landscape concerning kefir grains and kefir microbial communities, while providing a comprehensive overview of the organoleptic characteristics, nutritional composition, and functional properties of kefir. Through a systematic examination of three distinct fermentation production methodologies and principal challenges confronting commercial development, this study proposes synthetic microbial communities and kefir grain-like starter cultures as innovative production strategies for advancing kefir manufacturing.}, }
@article {pmid41907402, year = {2026}, author = {Xia, J and Chen, S and Qian, P and Gan, M and Wu, J and Wang, H and Zhang, F and Mo, Y and Yin, L and Gu, L and Zhang, D}, title = {Dietary capsaicin attenuates type 2 diabetes via gut microbiota and bile acid metabolic pathways.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115298}, pmid = {41907402}, issn = {2589-0042}, abstract = {Diabetes is a serious global health concern. Notably, individuals who prefer spicy food exhibit a lower diabetes risk, making the exploration of capsaicin-the pungent compound in chili peppers-highly relevant. The gut microbiota and its metabolites are key targets in diabetes management. This study demonstrates that dietary capsaicin alleviates type 2 diabetes (T2D) in mice. It reduces intestinal levels of conjugated bile acids (e.g., TDCA, GCA, and TCA) and normalizes the abundance of bile acid-related bacteria, Parabacteroides and Lactobacillus. Capsaicin also lowers the compensatory increase of intestinal bile salt hydrolase and regulates the function of bile acid-stimulated receptors. Bioinformatics analysis of ileum gene profiles indicated that regulated genes are primarily linked to immunity. This was confirmed by measuring inflammatory cytokines in serum and pancreas and by assessing immune-related gene expression in the ileum. In conclusion, capsaicin can prevent and treat T2D by modulating gut microbiota, bile acid metabolism, and inflammatory responses.}, }
@article {pmid41907436, year = {2026}, author = {Laing, E and Boldt, L and Ganguillet, S and Slack, E and Maier, L and Beziere, N}, title = {8-azido-3,8-dideoxy-D-manno-octulosonic acid-mediated metabolic oligosaccharide engineering for specific labeling of diverse Enterobacterales.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115255}, pmid = {41907436}, issn = {2589-0042}, abstract = {Current microbiome studies lack real-time or spatial information, often requiring large cohorts for longitudinal investigations. Real-time, in vivo molecular imaging would alleviate these shortcomings but is hampered by the limited labeling performance of current strategies. Here, we use the azido-modified sugar 8-Azido-3,8-dideoxy-D-manno-octulosonic acid (Kdo-N3) to metabolically engineer the core oligosaccharide of Gram negative lipopolysaccharide, enabling conjugation with DBCO-fluorophores. We extend this approach by systematically screening multiple Enterobacteriaceae strains, optimizing labeling conditions, validating core-oligosaccharide-specific labeling using LPS knockout mutants, and demonstrating in vivo species-specific MOE-BCC labeling with Kdo-N3 inside the murine gastrointestinal tract and subsequent in vivo imaging. Beyond Salmonella Typhimurium and Escherichia coli Nissle 1917, a broad range of Enterobacterales species were amenable to Kdo-N3 sugar incorporation, potentially unlocking species-specific studies of bacterial interaction in vitro and in vivo.}, }
@article {pmid41907460, year = {2026}, author = {Jacry, C and Bertoni Mann, M and Abadie, M and Borges-Martins, M and Frazzon, J and Kothe, CI and Guedes Frazzon, AP}, title = {The oral eukaryotic microbiome of Melanophryniscus admirabilis, a microendemic and critically endangered toad.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20831}, pmid = {41907460}, issn = {2167-8359}, mesh = {Animals ; *Microbiota ; *Endangered Species ; Brazil ; *Mouth/microbiology ; *Bufonidae/microbiology ; *Anura/microbiology ; RNA, Ribosomal, 18S/genetics ; }, abstract = {BACKGROUND: The oral eukaryotic microbiome of amphibians remains largely unexplored, despite its potential importance for host health and resistance to fungal pathogens such as Batrachochytrium dendrobatidis (Bd). Melanophryniscus admirabilis, a critically endangered red-belly toad species endemic to Brazil and restricted to a 700-m stretch of the Forqueta River, offers unique insights into host-microbiome interactions within highly specialized and threatened neotropical environments. While its narrow distribution limits broader applications, the genus Melanophryniscus is widely distributed across South America, potentially serving as a broader model for comparative microbiome research across varied ecological contexts.<br><br>METHODS: We analyzed the oral eukaryotic microbiota of ten wild M. admirabilis using 18S rRNA gene amplicon sequencing, with the Illumina MiSeq platform. Taxonomic assignments were performed at the phylum, class, and genus levels. Microbial community structure was assessed via hierarchical clustering and non-metric multidimensional scaling (NMDS) method based on Bray-Curtis dissimilarity. In addition, functional profiles were inferred from taxonomic data using PICRUSt2 to explore the potential ecological roles of the detected taxa.<br><br>RESULTS: Excluding host-derived reads, the predominant fungal phyla identified were Ascomycota and Basidiomycota. Among them, the genus Malassezia was present across all samples, suggesting a potentially host-adapted association. Given its known adaptation to mucosal environments and consistent abundance in our dataset, we hypothesize that Malassezia may compete with the fungal pathogen Bd, potentially acting as a natural microbial protector. Other fungal genera, including Phlebia, Microdochium, Fusarium, and Rhodotorula, were detected at lower abundance and may reflect a mixture of commensal, environmental, or opportunistic fungi. Functional prediction analyses revealed signatures of saprotrophic activity and suggested potential metabolic contributions to host-associated niches. The high proportion of unclassified and multi-affiliated sequences highlights the current limitations of reference databases for amphibian-associated eukaryotes, and underscores the value of this study in providing a novel community-level description of oral fungi in a neotropical anuran species.<br><br>CONCLUSION: This study provides the first characterization of the oral eukaryotic microbiome of M. admirabilis, revealing a diverse and structured fungal community dominated by Malassezia, with predicted functions related to environmental adaptation and fungal competition. These findings suggest that the oral cavity of amphibians harbors functionally active microbial communities that may play a role in pathogen resistance and host-microbe symbiosis.}, }
@article {pmid41907517, year = {2026}, author = {Patoine, C and Sheffler, J and Sims, T and Gutierrez, V and Park, G and Mayonu, M and Wang, B and Nagpal, R}, title = {Obesity-associated gut microbiome influences diet-induced metabolic and cognitive outcomes in older adults.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2605879}, pmid = {41907517}, issn = {2993-3935}, abstract = {Obesity in older adults is a known risk factor for Alzheimer's disease and related dementias, potentially driven by metabolic dysfunction, inflammation and gut dysbiosis. The gut-brain axis, influenced by diet and the gut microbiome, is increasingly recognized as a contributor to neurodegeneration. In this sub-analysis of a 10-week randomized dietary education intervention (NCT06121986), we examined how obesity modulates gut microbiome, metabolome, and cognitive responses in 31 adults aged 55-85, with or without mild cognitive impairment. Participants received education on either a Mediterranean Diet or a Modified Mediterranean-Ketogenic Diet. Analyses were stratified by baseline obesity (BMI ≥30 kg/m[2]). Individuals with obesity exhibited lower microbial alpha-diversity, higher Bacteroides, and lower Akkermansia and Christensenellaceae_R-7_group, along with poorer memory and executive function. Only in the obese group did fat loss correlate with improvements in episodic memory and cognitive flexibility. In contrast, increased fat mass was associated with improved memory in non-obese participants. Gains in skeletal muscle mass predicted cognitive improvement in adults aged ≥73. Changes in gut (acetate, propionate, lactate) and plasma (acetate, pyruvate, citric acid) metabolites were linked to cognitive and body composition outcomes. These exploratory findings highlight the gut-muscle-brain axis as a modifiable target to enhance cognitive health in aging populations.}, }
@article {pmid41907518, year = {2026}, author = {Jiang, Q and Li, J and Wu, S and Zhang, L and Dong, L and Weng, S and Tang, W and Chen, S}, title = {Enterococcus faecalis impairs IGSF9-dependent C1q degradation to accelerate MAFLD-HCC progression.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2600896}, pmid = {41907518}, issn = {2993-3935}, abstract = {The global increase in metabolic associated fatty liver disease (MAFLD)-related hepatocellular carcinoma (HCC) necessitates urgent investigation of its underlying mechanisms. Our study reveals that high fat diet (HFD)-induced gut dysbiosis enriches Enterococcus faecalis, a potential carcinogenic bacterium. Mechanistically, which suppresses hepatic IGSF9 expression, exacerbating liver injury (elevated ALT/AST/ALP), steatosis, fibrosis, and HCC susceptibility. Clinically, reduced hepatic IGSF9 correlates with poor prognosis, particularly in MAFLD-HCC patients. Mechanistically, IGSF9 binds C1QC and E3 ubiquitin ligases (NEDD4/UBE3A) to promote C1QC ubiquitination and degradation; IGSF9 deficiency leads to pathogenic C1q accumulation, accelerating MAFLD progression. Importantly, early interventions targeting this axis - including Bifidobacterium pseudolongum supplementation, overexpressing IGSF9, and C1q neutralization - effectively prevented MAFLD-HCC progression in preclinical models. These findings provide preliminary evidence that the E. faecalis/IGSF9/C1q axis could be involved in MAFLD-HCC, with IGSF9 may serve as both a prognostic biomarker and therapeutic target, which worth further exploration in future studies.}, }
@article {pmid41715057, year = {2026}, author = {Duncan, R and Gargari, G and Mantegazza, G and Russo, R and Guglielmetti, S}, title = {In vitro assessment of the impact of astragalus, pineapple stem and bergamot extracts on human fecal bacteria.}, journal = {BMC complementary medicine and therapies}, volume = {26}, number = {1}, pages = {}, pmid = {41715057}, issn = {2662-7671}, abstract = {BACKGROUND: Botanical extracts are increasingly incorporated into functional foods and dietary supplements due to their purported health benefits; however, their impact on the healthy adult gut microbiota remains insufficiently characterized. This study aimed to assess the microbiota-modulating potential of three commercially relevant botanicals (Astragalus membranaceus root extract, pineapple stem extract, and bergamot extract) in both native and digested forms, simulating gastrointestinal passage via the standardized INFOGEST protocol.<br><br>METHODS: Antimicrobial activity was first evaluated in monocultures of nine gut-associated bacterial strains representative of the healthy adult intestinal microbiota, including Lactobacillus acidophilus LA14, Lacticaseibacillus paracasei DG, Hafnia alvei HA4597, Bifidobacterium longum BB536, and B. animalis subsp. lactis BL-04. Botanicals were tested up to a supraphysiological concentration (100&#xa0;mg/mL, worst-case exposure). Subsequently, each extract (native and digested) was incubated for 48&#xa0;h under anaerobic conditions with a complex bacterial consortium derived from multiple fecal aliquots obtained from a single healthy adult donor. Microbial composition was assessed using 16&#xa0;S rRNA gene profiling. &#x3b1;-diversity (Shannon index) and &#x3b2;-diversity (Bray-Curtis distances) were computed, and differential abundance was analyzed.<br><br>RESULTS: In monoculture, botanical extracts exhibited minimal and strain-specific antimicrobial activity at 100&#xa0;mg/mL, with inhibition observed primarily for Akkermansia muciniphila, Bacteroides fragilis, and Collinsella aerofaciens. In the fecal consortium model, none of the botanical treatments, regardless of digestion status, produced significant alterations in &#x3b1;- or &#x3b2;-diversity. Modest taxonomic changes were detected, including a reproducible decrease in Collinsella spp. following treatment with digested Astragalus extract. Notably, core beneficial taxa such as Faecalibacterium prausnitzii and A. muciniphila remained unaffected.<br><br>CONCLUSIONS: At physiologically relevant concentrations, Astragalus membranaceus, pineapple stem, and bergamot extracts, in both native and digested forms, do not induce disruptive effects on the structure of the human gut microbial community, supporting their microbiome compatibility under the conditions tested.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12906-026-05284-8.}, }
@article {pmid41898793, year = {2026}, author = {Zagorianakou, N and Makrydimas, S and Moustakli, E and Mitrogiannis, I and Makrydimas, G}, title = {Miscarriage and the Microbiome: Host Genetics, Immunity, and the Reproductive Tract Ecosystem.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898793}, issn = {2073-4425}, mesh = {Humans ; Female ; *Abortion, Spontaneous/microbiology/genetics/immunology ; Pregnancy ; *Microbiota/immunology/genetics ; Placenta/microbiology/immunology ; Endometrium/microbiology/immunology ; }, abstract = {Background/Objectives: Pregnancy loss is a common and multifactorial complication of human reproduction, traditionally attributed to fetal chromosomal abnormalities, maternal anatomical and endocrine disorders, and immune dysfunction. Growing evidence now indicates that the maternal microbiome, particularly within the reproductive tract, plays a critical role in implantation, placental development, and the maintenance of immune tolerance during early pregnancy. Importantly, the influence of the microbiome on miscarriage appears to be strongly modulated by host genetic background and immune regulation. Methods: This narrative review summarizes current evidence linking alterations in the vaginal, endometrial, placental, and gut microbiomes to miscarriage, with a specific focus on host genetics and immune-microbial interactions. Results: We discuss how genetic variation in innate and adaptive immune pathways, inflammatory signaling, and mucosal barrier function may shape host responses to microbial communities, thereby influencing susceptibility to PL. In addition, we highlight emerging data on microbiome-driven regulation of gene expression and epigenetic modifications in the endometrium and decidua, emphasizing the role of microbial metabolites in immune tolerance and placental function. Conclusions: By integrating findings from microbiome research, host genomics, immunology, and epigenetics, this review proposes a framework in which miscarriage is viewed as a consequence of disrupted host-microbe crosstalk rather than isolated pathology. Finally, we address key methodological challenges and outline future research directions aimed at advancing mechanistic understanding and translational applications.}, }
@article {pmid41898797, year = {2026}, author = {Li, H and Yu, Z and Wu, Z and Lin, Y and Liu, T and Liu, Y and An, J and Zhao, J and Liu, Y and Ma, X and Wang, H}, title = {High-Resolution Microbial Fingerprinting for Forensic Individual Identification: A Proof-of-Concept Study Integrating 2bRAD-M and Hierarchical Attention Network.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898797}, issn = {2073-4425}, support = {32260187 to H.W.//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Saliva/microbiology ; *Skin/microbiology ; Proof of Concept Study ; *Microbiota/genetics ; *Forensic Genetics/methods ; *DNA Fingerprinting/methods ; Biomarkers ; }, abstract = {Background: Human skin and saliva microbial communities have emerged as promising forensic biomarkers due to their individual specificity. However, existing studies are limited by small sample sizes and methodological inconsistencies. This proof-of-concept study aims to develop a novel framework integrating 2bRAD-M sequencing with a hierarchical attention network (HAN) for forensic individual identification, addressing these limitations through large-scale public data integration and controlled validation. Methods: We utilized 2263 skin and saliva samples from public databases (Qiita, HMP, NCBI SRA) for model development. These public data included longitudinal samples collected over periods up to 180 days. A contemporary validation cohort of 6 volunteers, providing 26 forensic-relevant samples (including simulated touch evidence), was sequenced using 2bRAD-M for validation. Data integration involved batch effect correction (ComBat), normalization (CSS), and cross-database harmonization using GTDB for taxonomic assignment. The HAN model was optimized with triplet margin loss for metric learning. Results: The HAN model achieved 98.7% Rank-1 accuracy for pristine samples, outperforming random forest (70.2%) and CNN (75.8%). Microbial signatures showed high temporal stability (ICC = 0.86 over 180 days) and robustness in mixed samples (87.4% accuracy). Discriminatory biomarkers included Cutibacterium (skin) and Prevotella (saliva). Particulate matter exposure significantly influenced microbial composition (PERMANOVA R[2] = 0.32, p < 0.001). Conclusions: This study establishes a proof-of-concept pipeline for microbial forensics, demonstrating high accuracy under controlled conditions. Future work must address antibiotic exposure, sample diversity, and cross-laboratory validation before forensic implementation.}, }
@article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, pmid = {41898837}, issn = {2073-4425}, mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, }
@article {pmid41898896, year = {2026}, author = {Rodriguez-Pereira, A and Hawkes, FM and Emami, SN}, title = {Crop: The Black Box of Mosquito Vector Fitness.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898896}, issn = {2075-4450}, support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; VR/2024-02921//Swedish Research Council/ ; APP44269/MRC_/Medical Research Council/United Kingdom ; }, abstract = {In mosquitoes, digestion involves the foregut (including the crop), midgut, and hindgut, with the midgut and crop playing important roles in processing sugar and blood meals. The well-studied midgut is a known major pathogen entry point; however, the less-explored crop may affect vector fitness and immunity. This review provides an overview of the anatomy and function of the crop, before drawing together the current state of knowledge of (I) the crop's role in digestion, (II) its immune function, and (III) the importance of the crop microbiome and its potential role in mosquito fitness. After decades of chemical control, vector management must move beyond immediate disease prevention toward a global approach that considers mosquito biology and the crop's diverse roles. This may make it a suitable target for new innovations by providing insights into detoxification mechanisms, microbiome-mediated functions, and their potential combined effects on vectorial capacity. Future research is needed to better understand crop function.}, }
@article {pmid41898937, year = {2026}, author = {Al Darwish, H and Cacao, M and Hart, T and Patel, D and Russo, S and Salama, S and Tariq, M and Ananda, AT and Sun, JS}, title = {Escherichia coli Mono-Association Modulates Ionotropic Receptor-Dependent Behaviors in Drosophila melanogaster.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898937}, issn = {2075-4450}, support = {Presidential Postdoctoral Research Fellowship//Rutgers, The State University of New Jersey/ ; Goyette Family Endowment//Rutgers, The State University of New Jersey/ ; }, abstract = {Chemosensory systems are crucial for insect survival, enabling host-seeking, food acquisition, and oviposition site selection. While insect-associated microbes are known to influence host development and immunity, their role in modulating chemosensory behavior remains poorly understood. Here, we show that mono-association with Escherichia coli alters sensory-driven behaviors in both larval and adult axenic Drosophila melanogaster. In larvae, E. coli mono-association altered phototaxis and mechanosensory responses across genotypes, while changes in tunneling and thermosensory behaviors were reduced or absent in ionotropic receptor (IR) co-receptor mutants. In adults, E. coli mono-association increased attraction to fermentation cues (apple cider vinegar, ethanol) and enhanced sucrose consumption in wild-type and Orco-deficient flies, whereas these effects were reduced or absent in IR co-receptor mutants (IR25a[-] and IR76b[-]). Together, these findings indicate that under defined gnotobiotic conditions, E. coli exposure alters sensory-driven behavioral outputs relative to axenic controls. Effects are reduced or absent in IR co-receptor mutants, consistent with a role for IR pathways in mediating these behavioral shifts. These findings support a role for microbial cues in shaping insect sensory-driven behaviors and highlight the importance of microbial status in interpreting behavioral phenotypes. This work provides a framework for future studies investigating how microbial signals interact with conserved sensory pathways.}, }
@article {pmid41898972, year = {2026}, author = {Derguini, A and Basher, NS}, title = {Cockroaches as Vectors of Pathogens and Antimicrobial Resistance: Evidence from Healthcare, Community, and Agricultural Settings.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898972}, issn = {2075-4450}, support = {IMSIU-DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)./ ; }, abstract = {Synanthropic cockroaches, especially Blattella germanica and Periplaneta americana, are persistent pests of human dwellings, healthcare facilities, food establishments, farms, and transport infrastructure. Accumulating field and laboratory studies indicate that synanthropic cockroaches carry clinically important bacteria, fungi, and parasites, including multidrug-resistant strains harbouring extended-spectrum β-lactamase, carbapenemase, and other antimicrobial-resistant determinants. Cockroaches acquire these organisms from sewage, waste, food residues, animal excreta, and contaminated clinical environments, and retain them on the cuticle and within a complex gut microbiota. Dissemination is predominantly mechanical, via contact transfer and deposition of regurgitate and faeces on food, equipment, and surfaces, but may be amplified by gut colonisation, microbial interactions, and horizontal gene transfer within the cockroach microbiome. In hospitals, cockroaches can connect high-burden reservoirs (drains, waste areas, kitchens) with vulnerable units, including intensive care units (ICUs), neonatal intensive care units (NICUs), burn units, and haemato-oncology wards. In food and livestock systems, they may contaminate housing, ingredients, and finished products, enabling spillover along supply chains and at ports. This review synthesises current evidence and highlights the following priorities: integrate cockroaches into infection prevention, food safety, and biosecurity; incorporate cockroach sampling into antimicrobial resistance (AMR) and genomic surveillance; and advance mechanistic research on cockroach-microbiota-pathogen interactions to improve pest management and safely explore cockroach-derived antimicrobial compounds. In this review, we distinguish external mechanical carriage (cuticular contamination) from internal gut carriage; we use "gut colonisation" only when persistence/replication or prolonged shedding is demonstrated.}, }
@article {pmid41898993, year = {2026}, author = {Tanachaiwiwat, P and Sanscrainte, ND and Okech, BA and Estep, AS}, title = {Insecticide Resistance Mutations, Enzymatic Activity, and Pathogen Infection in Culex quinquefasciatus from Haiti.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898993}, issn = {2075-4450}, support = {P0138_22_HS//Armed Forces Health Surveillance Directorate, Global Emerging Infection Surveillance Program/ ; 6036-10400-002-000-D//United States Department of Agriculture/ ; }, abstract = {Haiti is a Caribbean country of about 11 million people with a high burden of mosquito-transmitted disease and limited vector control, thereby making effective operational mosquito control of high importance. Previous studies have examined vector-borne disease burden and insecticide resistance markers in Haitian Aedes and Anopheles mosquitoes, but not Culex species. In this study, we examined collections of Culex quinquefasciatus from 12 locations in northern and southern Haiti for the presence of markers of insecticide resistance (using a variety of target-site mutations and biochemical assays) and pathogens (using a deep-sequencing microbiome workflow). The metagenomic analysis identified Wolbachia, Rhabdoviridae, and Plasmodium infections in all sample pools at relatively high levels, along with less frequent detections of other potential pathogens. Insecticide resistance marker examination identified variable frequencies of knockdown resistance and acetylcholinesterase resistance mutations, as well as variation in resistance-associated enzymatic activities in these populations. These findings indicate that insecticide resistance to pyrethroid and organophosphate insecticides is likely. Although there was variation among Culex mosquito populations and no clear activity pattern, enzymatic activity was significantly higher at the southern sites than at the northern sites. Similar findings in Cx. quinquefasciatus populations in other locations in the Americas strongly suggest that vector control with pyrethroid and organophosphate adulticides may be of limited efficacy.}, }
@article {pmid41898998, year = {2026}, author = {Al Naggar, Y and Ghramh, HA and Elfarnawany, A and Mohamed, A}, title = {How Environmental and Ecological Stressors Reprogram Honey Bee Chemistry Through the Microbiome-Metabolome Axis.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, pmid = {41898998}, issn = {2075-4450}, abstract = {Honey bees are exposed to a wide range of environmental and ecological stressors that threaten individual health and colony sustainability. Growing evidence suggests that many of these stressors converge on a common target: the gut microbiome and its metabolic functions. The honey bee microbiome-metabolome axis represents a central regulatory system linking microbial symbionts with host nutrition, detoxification, immune competence, neural signaling, and social behavior. This review synthesizes current knowledge on how major stressors-including pesticides, antibiotics, pathogens, nutritional imbalance, thermal stress, habitat change, and environmental contaminants-reprogram honey bee chemistry by disrupting microbial community structure and, importantly, microbial and host metabolic pathways. We highlight recurring patterns consistent with functional dysbiosis, characterized by impaired energy metabolism, reduced production of short-chain fatty acids, altered amino acid and lipid metabolism, compromised antioxidant and detoxification capacity, and weakened immune regulation. However, much of the current evidence is correlative and derived from short-term or laboratory-focused studies; longitudinal and multi-site field validation of causal links remains limited. Importantly, emerging multi-omics studies suggest that profound metabolic disturbances can occur even when taxonomic changes in the microbiome are modest, emphasizing the need to move beyond descriptive community profiling toward functional and mechanistic assessments. We further discuss how stress-induced metabolic reprogramming at the individual level scales up to influence behavior, division of labor, and colony-level resilience. Finally, we propose a conceptual model illustrating how diverse stressors converge to disrupt the microbiome-metabolome axis, potentially leading to functional dysbiosis and host impairment.}, }
@article {pmid41899109, year = {2026}, author = {Sokolovs-Karijs, O and Brīvība, M and Gudrā, D and Saksis, R and Zodāne, AA and Rozenberga, M and Bunka, L and Frigotto, A and Osīte, J and Reinis, A and Segliņa, G and Krūmiņa, A}, title = {The Clinical Role of the Adenoid Microbiome in the Development of Adenoid Hypertrophy and Otitis Media with Effusion.}, journal = {Journal of clinical medicine}, volume = {15}, number = {6}, pages = {}, pmid = {41899109}, issn = {2077-0383}, support = {No.8.2.2.0/20/I/006//University of Latvia/ ; Nr. 6-DN-20/2/2025//Riga Stradi&#x146;&#x161; University/ ; }, abstract = {Background: The adenoid surface serves as a potential bacterial reservoir for upper respiratory tract pathologies, including Adenoid Hypertrophy (AH) and Otitis Media with Effusion (OME). While dysbiosis is implicated in the pathogenesis of these conditions, it remains unclear whether the microbiome of children with otitis media differs significantly from those with simple hypertrophy when compared against a healthy baseline. This study aimed to characterize the adenoid microbiome in children with adenoid hypertrophy with and without middle ear effusion, contrasting them with a healthy control group. Methods: We conducted a cross-sectional case-control study involving 58 pediatric participants divided into three groups: adenoid hypertrophy, adenoid hypertrophy and otitis media with effusion and healthy controls. Nasopharyngeal swabs were collected, and bacterial community composition was analyzed using 16S rRNA gene V4 sequencing. Alpha and beta diversity metrics, taxonomic composition, and differential abundance were evaluated. Results: Alpha diversity was significantly reduced in both disease groups compared to healthy controls (p < 0.001), indicating a collapse of microbial richness and evenness. Beta diversity analysis revealed a distinct separation between healthy and diseased cohorts; however, the microbial profiles of the AH and AH with OME groups were nearly identical. Taxonomic analysis demonstrated that disease was characterized by the depletion of health-associated commensals, specifically Veillonella, Actinomyces, and Gemella, and a concomitant expansion of Fusobacterium, Haemophilus, and Streptococcus. Conclusions: Adenoid hypertrophy is associated with a profound dysbiotic shift characterized by the loss of protective commensal flora and the dominance of pathobionts. The lack of significant microbial differentiation between the AH and AH with OME groups suggests that the adenoid surface acts as a centralized reservoir of dysbiosis, the composition of which is conserved regardless of the presence of middle ear effusion. These findings highlight the importance of restoring the commensal microbiome in the management of chronic adenoid disease.}, }
@article {pmid41899514, year = {2026}, author = {Loaiza-Bonilla, A and Leyfman, Y and Cortiana, V and Crawford, R and Modi, S}, title = {Defining a Multi-Omic, AI-Enabled Stool Screening Paradigm for Colorectal Cancer: A Consensus Framework for Clinical Translation.}, journal = {Cancers}, volume = {18}, number = {6}, pages = {}, pmid = {41899514}, issn = {2072-6694}, abstract = {Colorectal cancer (CRC) develops through both conventional adenoma-carcinoma and serrated neoplasia pathways, yet noninvasive screening still under-detects the advanced precursor lesions that enable true cancer prevention. Stool-based screening reduces CRC mortality, but its preventive impact remains constrained by limited detection of advanced precancerous lesions (APLs), including advanced adenomas and sessile serrated lesions. Next-generation multitarget stool DNA assays (mt-sDNA; e.g., Cologuard Plus) have established high sensitivity for CRC and specificity approaching 94%, leaving improved APL detection as the principal opportunity for innovation. This review presents a consensus framework for a multi-omic stool screening paradigm that integrates host epigenetic markers (DNA methylation) with gut microbiome features using artificial intelligence (AI). Multi-omics capture complementary layers of early tumor biology: epithelial shedding and field effects reflected in host methylation signals together with luminal ecological and inflammatory changes represented by microbial features. Evidence from cross-cohort microbiome studies indicates that microbial signatures provide an additive-rather than standalone-axis of information for CRC and its precursor lesions. Because microbiome-based models are highly susceptible to batch effects arising from collection devices, extraction chemistry, sequencing platforms, and bioinformatic pipelines, practical mitigation strategies are outlined, including harmonized pre-analytics, batch-aware study design, leakage-resistant validation, and computational harmonization. A translational roadmap linking analytical validity, locked-model development, and prospective colonoscopy-verified clinical validation is proposed, aligned with TRIPOD + AI, STARD, PROBAST-AI, SPIRIT-AI, CONSORT-AI, and DECIDE-AI reporting standards. Scenario modeling using BLUE-C prevalence estimates suggests that improving APL sensitivity from approximately 43% to 55-65% at ~94% specificity could translate to detecting roughly 13-23 additional advanced precancerous lesions per 1000 individuals screened, highlighting the potential prevention impact of a multi-omic approach. This framework aims to guide developers and clinical investigators toward next-generation stool tests capable of materially improving precursor-lesion detection while maintaining clinically acceptable specificity.}, }
@article {pmid41899578, year = {2026}, author = {He, L and Yu, X and Xiao, DH and Zhang, HY and Xing, LJ and Liu, ZD}, title = {The Oral-Gastric Microbial Axis in Gastric Cancer: Mechanisms Underlying Development and Progression.}, journal = {Cancers}, volume = {18}, number = {6}, pages = {}, pmid = {41899578}, issn = {2072-6694}, support = {82174240//National Natural Science Foundation of China/ ; PW2024E-03//Shanghai Pudong New District Health Industry Special/ ; PY2026010//Longhua Hospital Talent Program/ ; }, abstract = {The etiology of gastric cancer (GC) is increasingly defined by the complex interplay within the oral-gastric microbial axis. This conceptual shift extends beyond the classical Helicobacter pylori (H. pylori) model. Instead, it encompasses a broader polymicrobial network. Mechanisms underlying ectopic colonization of oral pathobionts are examined alongside their synergistic contributions to mucosal dysbiosis. Remodeling of the tumor microenvironment is discussed through the analysis of critical functional modules, including biofilm formation, metabolic reprogramming, and immune dysregulation. Carcinogenesis is reportedly promoted by specific genotoxic metabolites and perpetuation of chronic inflammation. Diagnostic capabilities are evaluated with a focus on noninvasive biomarkers, where integration of artificial intelligence for risk stratification is identified as a transformative tool for early detection. Furthermore, therapeutic perspectives are expanded by evidence linking microbial composition to the efficacy of immune checkpoint inhibitors and chemotherapy. Strategies for prevention and treatment are proposed based on restoration of microbial homeostasis. Collectively, a roadmap for translating microbiome research into personalized clinical practice for gastrointestinal malignancies is provided by this review.}, }
@article {pmid41899581, year = {2026}, author = {Ou, Y and Wei, H and Peng, C and Li, J and Wei, K and Zhan, C and Zhang, Z}, title = {Overcoming MDSC-Mediated Immunosuppression in Hepatocellular Carcinoma: From Mechanisms to Novel Immunotherapeutic Approaches.}, journal = {Cancers}, volume = {18}, number = {6}, pages = {}, pmid = {41899581}, issn = {2072-6694}, support = {82073373//the National Natural Science Foundation of China/ ; AA24263028//the Guangxi Science and Technology Major Program/ ; }, abstract = {Background: Myeloid-derived suppressor cells (MDSCs) drive immunosuppression in the hepatocellular carcinoma (HCC) tumor microenvironment (TME), contributing to immune checkpoint blockade (ICB) resistance. This review explores underlying mechanisms and therapeutic strategies. Methods: We synthesize the recent literature on MDSC biology in HCC, focusing on signaling pathways, metabolic/epigenetic reprogramming, and novel interventions, including AI-driven analyses. Results: Key mechanisms include JAK-STAT3 activation for MDSC expansion, CXCL12-CXCR4 for recruitment, enhanced glycolysis/lipid metabolism for suppressive function, and epigenetic changes sustaining immunosuppression. Therapeutic approaches encompass inhibitors, differentiation promoters, metabolic modulators, transcriptional reprogramming, microbiome modulation, and combinations with ICB/locoregional therapies or standard chemoimmunotherapy, yielding improved outcomes in trials. Conclusions: Targeting MDSC redundancies via multi-modal strategies offers a roadmap for overcoming resistance, with AI enhancing biomarker-guided precision immunotherapy in HCC.}, }
@article {pmid41899599, year = {2026}, author = {Huang, J and Zhu, XH and Trotman, LC and Tsao, CK}, title = {The Role of Gut Microbiome in Prostate Cancer: Current Evidence and Emerging Opportunities.}, journal = {Cancers}, volume = {18}, number = {6}, pages = {}, pmid = {41899599}, issn = {2072-6694}, abstract = {Prostate cancer (PCa) is one of the most common malignancies in men, and growing evidence implicates the gut microbiome as a significant, modifiable contributor to disease evolution and management. Dysbiosis influences PCa biology through effects on inflammation, immune regulation, metabolism, and hormone signaling. Microbial imbalance can promote systemic inflammation and increase intestinal permeability, activating immune signaling pathways such as NF-κB-IL-6-STAT3. In parallel, microbiome-driven metabolic effects, including IGF-1 signaling and microbial androgen synthesis or recycling, may contribute to resistance to androgen deprivation therapy (ADT). Microbial metabolites, notably short-chain fatty acids (SCFAs) and trimethylamine N-oxide (TMAO), exert context-dependent effects on tumor growth, treatment resistance, and progression. Conversely, beneficial microbes have been associated with improved treatment sensitivity and immune regulation. Together, these insights support the gut microbiome as a potential biomarker and emerging therapeutic target in PCa. Modulation strategies, including diet, probiotics, antibiotics, and fecal microbiota transplantation (FMT), are being explored to improve treatment response and address resistance. As mechanistic evidence continues to grow, ongoing monitoring of the gut microbiome may help inform risk stratification and treatment optimization in prostate cancer.}, }
@article {pmid41899742, year = {2026}, author = {Keith, R and Willis, S and Christian, N and Khayat, F and Gallagher, J and Gunter, WS and Kachanova, J and Mehring, A and Pigg, R and Proctor, D and Smith, AE and Stopforth, CK and Piuma, P and Smith, T and Bhatnagar, A}, title = {Evaluating Microclimate Modification and Acute Cardiovascular Stress Responses to a Dense Urban Microforest: The Green Oasis (GRO) Protocol.}, journal = {International journal of environmental research and public health}, volume = {23}, number = {3}, pages = {}, pmid = {41899742}, issn = {1660-4601}, mesh = {Humans ; *Microclimate ; Male ; *Stress, Physiological ; Cross-Over Studies ; Adult ; Female ; Heart Rate ; Middle Aged ; Trees ; *Conservation of Natural Resources ; Vascular Stiffness ; Cities ; }, abstract = {The Green Oasis (GRO) Project is a targeted urban greening intervention designed to evaluate the environmental and health impacts of compact, high-density plantings in dense built environments. Initiated in downtown Louisville, the project transformed Founders Square, a 0.64-acre sparsely planted park, into a microforest ("Trager Microforest"), a multilayered planting of 119 trees and more than 200 shrubs. The impact of this intervention is being assessed through a randomized crossover study in which participants walk in the microforest and a nearby impervious parking lot. Physiological outcomes include heart rate, heart rate variability, arterial stiffness, and stress biomarkers measured in saliva, urine, and sweat. Environmental conditions are continuously monitored by fixed and mobile weather stations, air pollution sensors, and biodiversity surveys. Baseline assessments were conducted in 2023 and 2024, with post-planting evaluations now underway (2025-). Power calculations indicate adequate sensitivity (n ≈ 40-50) to detect changes in cardiovascular stress responses in participants. Complementary ecological measurements include soil microbiome composition, greenhouse gas fluxes, and avian diversity. This study addresses critical gaps in understanding how small-scale, high-density greening interventions affect cardiovascular resilience, stress physiology, and microclimatic regulation. By integrating environmental, biological, and human health data, GRO establishes a comprehensive framework for evaluating the efficacy of urban microforests as nature-based solutions. The results are expected to inform urban planning, public health strategies, and climate adaptation policies, demonstrating how compact greening interventions can simultaneously mitigate heat, reduce pollution, enhance biodiversity, and promote human wellbeing in dense urban cores.}, }
@article {pmid41900279, year = {2026}, author = {De Luca, L and Menna, F and Lupo, S and Vingolo, EM and Carlà, MM and Mancini, M and Oliverio, GW and Minutoli, L and Baldascino, A and Mazzotta, C and Aragona, P and Meduri, A}, title = {The Ocular Surface Bacterial Microbiome and the Impact of Contact Lens Use: A Literature Review.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900279}, issn = {2076-2607}, abstract = {The ocular surface microbiome plays a critical role in maintaining ocular health, preventing infections, and regulating immune responses. Contact lens (CL) wear has been linked to alterations in microbial composition, potentially leading to dysbiosis and increased susceptibility to ocular infections. This review aims to summarize current evidence on the effects of CL use on the ocular microbiome and to discuss strategies to preserve microbial homeostasis. A literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar for English-language human studies published between January 2005 and January 2025. We included original studies and systematic reviews evaluating the ocular surface bacterial community in contact lens (CL) wearers using either sequencing-based approaches (microbiome; e.g., 16S rRNA gene sequencing/metagenomics) or culture-based methods (microbiota). Two authors screened titles/abstracts and full texts. Overall, 12 studies met the inclusion criteria and were qualitatively synthesized. Across included studies, CL wear was associated with reproducible changes in the ocular surface bacterial community, most commonly a shift toward a skin-like profile and increased detection/relative abundance of opportunistic taxa (e.g., Pseudomonas, Acinetobacter, and Staphylococcus aureus) together with reduced representation of typical ocular commensals in several sequencing-based datasets. Culture-based studies reported increased recovery of opportunistic bacteria from lenses and storage cases, supporting contamination/biofilm-related mechanisms. Lens care solutions and preservatives were reported to modulate bacterial profiles and may contribute to dysbiosis, although evidence remains heterogeneous across study designs and analytic pipelines. CL use is associated with significant alterations in the ocular microbiome, increasing the risk of microbial keratitis and corneal inflammatory events. Strategies to maintain microbial balance, including careful selection of lens care products and development of antimicrobial lenses, may improve ocular surface health in CL wearers. Future longitudinal studies with standardized sampling and analytic workflows are needed to clarify causal links between CL-associated microbial changes and clinical outcomes.}, }
@article {pmid41900304, year = {2026}, author = {Yamada, H and Ono, Y and Ota, H and Kobayashi, Y and Fukushi, Y and Wada, S and Arase, H}, title = {Anti-β2GPI/HLA-DR Antibody, Chronic Endometritis, and Uterine Endometrial Microbiome in Women with Recurrent Pregnancy Loss: A Prospective Cohort Study.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900304}, issn = {2076-2607}, support = {JP21gk0110047, JP22gk0110061, JP23fk0108682, and JP25gn0110094//Japan Agency for Medical Research and Development/ ; 20K09642, 23K08888, and 24K02691//Japan Society for the Promotion of Science/ ; }, abstract = {Anti-β2GPI/HLA-DR antibody, chronic endometritis (CE), and endometrial dysbiosis are likely to be associated with the etiologies of recurrent pregnancy loss (RPL). This prospective cohort study aimed to investigate these new risk factors together with conventional causes for RPL, and to evaluate pregnancy outcomes in women individually treated. A total of 87 women with RPL underwent conventional assessment together with anti-β2GPI/HLA-DR antibody measurements, CD138 immunohistochemistry for CE, and 16S rRNA sequence analysis for endometrial microbiome. Women with anti-β2GPI/HLA-DR antibody, CE, and endometrial dysbiosis received low-dose aspirin and heparin, antibiotics, and probiotics, respectively. Pregnancy outcomes of the participants were assessed. Anti-β2GPI/HLA-DR antibody, CE, non-Lactobacillus-dominant microbiome (NLDM)-1 (Lactobacillus + Bifidobacterium < 80%), and NLDM-2 (Lactobacillus without iners + Bifidobacterium < 80%) were detected in 16 (18.4%), 22 (25.3%), 27 (31.0%), and 46 (52.8%) women, respectively. Based on conventional assessment, 65.5% of women with RPL were classified as unexplained etiology; however, the percentage reduced to 16.1% when these new tests were assessed together. All 9 pregnancies with anti-β2GPI/HLA-DR antibody, 13 (92.9%) of 14 pregnancies with CE, and 24 (92.3%) of 26 pregnancies with NLDM-2 resulted in live birth. Assessment of these new tests may be clinically useful for reducing the proportion of unexplained RPL, and for providing high live birth rates if women receive relevant treatments.}, }
@article {pmid41900306, year = {2026}, author = {Liu, W and Zhai, W and Wan, X and Wang, J and Ren, Y and Deng, W}, title = {Dynamic Alterations of Extracellular Polymeric Substances and Their Associations with Microbial Communities in the Soil Plastisphere.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900306}, issn = {2076-2607}, support = {42407532 and 42577565//National Natural Science Foundation of China/ ; 202303021211013//Fundamental Research Program of Shanxi Province/ ; S202510108078 and S202510108080//Funding Project of Shanxi University Undergraduate Innovation Training Program/ ; }, abstract = {Extracellular polymeric substances (EPS) facilitate microbiome adhesion on microplastic surfaces and ensure matrix cohesion, playing a crucial role in establishing the structure and function of the plastisphere. Nevertheless, the dynamic alterations in the composition and features of plastisphere EPS and their relationships with biotic and abiotic factors remain poorly understood, especially in soil ecosystems. The study investigated the variations in the EPS secretion behavior of the plastisphere using three types of microplastics across three representative soils with three incubation durations. Results showed that plastisphere EPS had a more complex composition and lower aromaticity, apparent molecular weight, and polarity than natural soil dissolved organic matter did. Continuous changes in EPS composition and features were detected during incubation. The bacterial plastisphere community played a central role in regulating EPS secretion, and other factors (such as soil properties, incubation time and microplastic types) influenced EPS secretion via the bacterial composition of the plastisphere. A decrease in the number of microbial OTUs was significantly correlated with EPS components that governed the dynamics of the EPS composition and features of the plastisphere during incubation, a pattern that was particularly evident for bacteriomes. This study advances our insight into microbiome-EPS interactions within the soil plastisphere and deepens our understanding of its formation mechanisms.}, }
@article {pmid41900307, year = {2026}, author = {Huang, F and Wu, X and Zou, L and Li, T and Qu, T}, title = {Underlying Mechanisms for Growth Promotion by Low-Concentration Single Salt and Alkali Stresses and Growth Inhibition by Combined Salt-Alkali Stress in Quercus mongolica.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900307}, issn = {2076-2607}, support = {20260402003ZP//Jilin Provincial Science and Technology Department/ ; }, abstract = {Soil salinization is a global ecological issue that severely constrains forest tree growth and ecological restoration. The salt-alkali stress response mechanisms of Quercus mongolica, a key temperate forest species in China, remain unclear. A two-factor pot experiment was conducted using NaCl (0, 50, 100, 200 mmol·L[-1]) and NaHCO3:Na2CO3 (1:1; 0, 50, 100, 150 mmol·L[-1]). Plant traits, soil properties, and enzyme activities were measured. Furthermore, high-throughput sequencing revealed that microbial responses enhanced network cooperation under 100 mmol·L[-1] salt stress and improved network stability under 50 mmol·L[-1] alkali stress. These responses also upregulated resistance genes and increased soil enzyme activities. This activation of seedling antioxidant and osmotic adjustment systems was directly associated with an increase in growth parameters. Under combined stress, however, soil environment deterioration and microbial network disruption, along with reduced key soil enzyme activities, resulted in an insufficient defense system to counteract reactive oxygen species (ROS) accumulation, thereby reducing growth parameters. The study found that low-concentration individual salt or alkali stress promoted Quercus mongolica seedling growth, while combined stress was associated with significant inhibition. This study refines the theoretical framework for non-salt-tolerant trees and establishes a basis for determining their survival thresholds in saline-alkali soils.}, }
@article {pmid41900312, year = {2026}, author = {Ussowicz, M and Rosa, M and Gajek, K and Brzoza, A and Jarmoliński, T and Panasiuk, A and Wawrzyniak-Dzierżek, E and Łaczmański, &#x141;}, title = {Between the Sponge and the Tap-Bacterial Communities at Overlooked Hospital Hygiene Hotspots.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900312}, issn = {2076-2607}, support = {FNRD.C200.20.002//Wroclaw Medical University/ ; SUBZ.C200.26.031//Wroclaw Medical University/ ; }, abstract = {Hospital environments host diverse microbial communities that may contribute to nosocomial infections. Moisture-retaining surfaces such as cleaning sponges and faucet edges represent high-contact, under-investigated hygiene hotspots, particularly in wards caring for immunocompromised patients. Environmental samples were collected from cleaning sponges (n = 14) and faucet edges (n = 4) across multiple hospital rooms of a paediatric haematology-oncology unit, with domestic physician sponges as controls (n = 3). DNA was extracted and sequenced targeting the V3-V4 and V7-V9 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. Taxonomic composition and alpha/beta diversity were assessed using QIIME 2 and R. Sponge samples were dominated by Moraxellaceae, particularly Acinetobacter and Enhydrobacter, and showed significantly lower alpha diversity than faucet samples (Shannon index: Kruskal-Wallis H = 8.4, p = 0.01; Faith's phylogenetic diversity: H = 9.17, p = 0.01). Faucet samples were enriched in human-associated genera including Staphylococcus, Streptococcus, and Chryseobacterium. Statistically significant beta-diversity differences were detected between sponge and faucet communities by PERMANOVA based on Bray-Curtis dissimilarity (p = 0.01), whereas no significant clustering by room or floor location was observed (p = 0.29). Potentially pathogenic taxa including Aeromonas, Pseudomonas, and Enterobacteriaceae were identified across both surface types. Domestic control sponges showed distinct microbiome profiles from hospital samples. Microbial communities differ significantly between hospital sponges and faucets, with surface type rather than location as the primary determinant of community structure. The presence of opportunistic pathogens on both surface types highlights the importance of enhanced hygiene protocols, inclusion of faucet edges and sink drains in routine decontamination schedules, and regular microbiological surveillance in clinical settings caring for immunocompromised patients.}, }
@article {pmid41900320, year = {2026}, author = {Cheng, H and Han, J and Liu, K and Wang, L and Meng, Q and Liu, C and Liu, X and Wang, M and Yang, F and Li, X}, title = {Integrated Metagenomic and Metabolomic Profiling of Boar Semen During Ambient-Temperature Storage.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900320}, issn = {2076-2607}, support = {2022020101//Agricultural Breeds Research Project of Henan Province/ ; HAAS2023RCQD01//the Key Technology Research and Development Program for Precision and Efficient Breeding of Local Pigs in Hainan Province/ ; }, abstract = {The reproductive efficiency of breeding boars substantially influences swine industry productivity. Sperm viability during ambient-temperature storage is critically affected by environmental factors, including microbial activity. This study aimed to elucidate the dynamics and interactions between the seminal microbiome and metabolome during boar semen storage at 17 °C. Using integrated 16S rRNA sequencing and untargeted metabolomics, we analyzed semen samples from six healthy boars (31-33 months old) collected at day 0 (control), 2, 4, and 6 of storage. Our results demonstrate that storage leads to a marked decline in microbial diversity, progressive enrichment of the opportunistic genus Proteus, depletion of key antioxidant and cofactor metabolites such as vitamin B6, and extensive metabolic reprogramming-including alterations in short-chain fatty acid, purine, and lipid oxidation pathways. Multi-omics correlation analysis further revealed strong associations between microbial succession and metabolic shifts, highlighting their combined role in driving sperm functional decline. These findings provide a mechanistic basis for improving semen preservation strategies through microbiome and metabolite-targeted interventions.}, }
@article {pmid41900329, year = {2026}, author = {Qin, H and Liu, Y and Yin, S and Zhai, Z and Xiao, B}, title = {Regulatory Effects of Lactobacillus crispatus and Lactobacillus rhamnosus on the Formation and Composition of Gardnerella Biofilms.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900329}, issn = {2076-2607}, support = {82471664//National Natural Science Foundation of China/ ; 81971342//National Natural Science Foundation of China/ ; 2022CR46//Peking University First Hospital/ ; }, abstract = {Bacterial vaginosis (BV), the most common lower genital tract infection among women of childbearing age, is characterized by a decline in Lactobacillus populations and the excessive proliferation of anaerobic bacteria. Clinically, metronidazole remains the first-line therapeutic agent. However, the increasing recurrence rate has become an urgent clinical challenge. An important factor of BV recurrence is the persistent presence of Gardnerella biofilms, which enhances pathogenic resistance to antibiotics. In contrast, a healthy vaginal microbiome, predominated by Lactobacillus, exerts protective effects by producing antimicrobial compounds that inhibit BV pathogen colonization and restore microbial homeostasis. Given this, Lactobacillus preparations have gained widespread attention for their adjunctive therapeutic potential in BV management. Accordingly, in this study, we selected two extensively investigated Lactobacillus species, Lactobacillus crispatus and Lactobacillus rhamnosus, to evaluate their inhibitory capacity against Gardnerella biofilms. Our findings suggest that hydrogen peroxide and D-lactic acid are prominent bioactive components involved in the inhibition of Gardnerella biofilm formation by these Lactobacillus species, though the potential contribution of bacteriocins and other uncharacterized factors cannot be excluded. Notably, this inhibitory activity is not accompanied by alterations to the composition of pre-formed biofilms. This study clarifies the anti-biofilm mechanism of specific Lactobacillus, providing a valuable reference for future research on probiotic-based strategies for the treatment of BV.}, }
@article {pmid41900338, year = {2026}, author = {Song, P and Deng, Y and Yu, Y and Zhang, L and Liu, Y}, title = {Plant Growth-Promoting Microorganisms Mediate Plant Metabolic Reprogramming to Manage the Rhizospheric Microbiome.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900338}, issn = {2076-2607}, support = {SCCXTD-2025-03//Sichuan Rape Innovation Team Project of the Modern Agricultural Industry Technology System/ ; NKYRCZX2024014//Talent Research Fund of Sichuan Academy of Agricultural Sciences/ ; 1 + 9KjGG006//Science and Technology Project of Sichuan Academy of Agricultural Sciences/ ; 5+1QYGG004//Science and Technology Project of Sichuan Academy of Agricultural Sciences/ ; 2026NSFSC1044//the Natural Science Foundation of sichuan province/ ; }, abstract = {The microbial community surrounding plant roots plays a vital role in plant growth, nutrient uptake, stress resilience and other potential functions. This review synthesizes available evidence that plant growth-promoting microorganisms (PGPMs) not only directly benefit the plant but also modulate the rhizospheric microbiome by mediating metabolic reprogramming of the host plant. PGPMs modify the composition of root exudates through the regulation of phytohormone signaling and transcriptional networks, thereby promoting beneficial microbes and suppressing disease. Key mechanisms involve the jasmonate, ethylene, and strigolactones signaling pathways. Transcription factors MYB72, ERF1 regulate biosynthesis and secretion of metabolites like organic acids and coumarins. The exudates serve as specific signals for microbial community assembly and as enhancers of feedback loops that reinforce plant-microbe mutualism. We examine the ecological and agricultural significance of PGPM-induced metabolic reprogramming of the host due to PGPMs that enhances disease suppression, abiotic stress tolerance, and nutrient use efficiency. Lastly, we address advanced methods and strategies for transferring these biological pathways to the agricultural realm and on to a more sustainable agricultural practice with emphasis on the need to integrate multi-omics (whole genomics, transcriptomics, and metabolomics), synthetic microbial communities and plant genetic engineering for microbiome-assisted agriculture. This synthesis reveals that PGPM-induced metabolic reprogramming operates through an integrated cross-scale framework linking microbial perception, phytohormone signaling, transcriptional regulators, and transporter-mediated exudate efflux, with root exudates functioning as plant-controlled ecological filters that selectively shape the rhizosphere microbiome. We further identify key translational challenges, including context-dependent efficacy and the lab-to-field gap, and propose a roadmap combining multi-omics, synthetic communities, and genome editing to realize the potential of microbiome-assisted sustainable agriculture.}, }
@article {pmid41900341, year = {2026}, author = {Albanese, G and Giurgiu, AI and Urcan, AC and Pașca, C and Ternar, TN and Bonta, V and Di Criscio, D and Iorizzo, M and De Cristofaro, A and Dezmirean, DS}, title = {Probiotic Assessment of Lactic Acid Bacteria Strains and Consortia for Enhancing Honey Bee Health and Nutrition.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900341}, issn = {2076-2607}, abstract = {The decline of honey bee health has intensified interest in microbiome-based strategies to support colony resilience and reduce reliance on chemical interventions. In this study, we performed an in vitro probiotic screening of five lactic acid bacteria (LAB) strains of honey bee origin and two multi-strain consortia for prospective application in apiculture. Two formulations were evaluated: LAB Mix 1 (Apilactobacillus kunkeei and Lactobacillus apis) and LAB Mix 2 (Lactiplantibacillus plantarum, Fructobacillus fructosus, and A. kunkeei). Functional and safety-related traits were investigated, including auto-aggregation, cell-surface hydrophobicity, inter-strain compatibility, organic acid production, oxidative detoxification capacity, antibiotic susceptibility, haemolytic activity, and growth dynamics in sugar-based feeding syrups. All strains exhibited time-dependent increases in aggregation and hydrophobicity, with A. kunkeei and F. fructosus showing particularly strong surface-associated properties. No mutual antagonism or haemolytic activity was observed. Organic acid profiling revealed strain-specific metabolic signatures, with high lactic and citric acid production by L. plantarum and LAB consortia. Several strains displayed peroxidase activity, suggesting a role in oxidative stress mitigation. Growth assays demonstrated that high sugar concentrations severely limited bacterial growth, whereas moderate dilution significantly improved growth. Under osmotic stress conditions, mixed cultures generally achieved higher optical density values than individual strains. Collectively, these findings support bee-associated LAB and multi-strain formulations as promising candidates for further probiotic development.}, }
@article {pmid41900349, year = {2026}, author = {Li, S and Wu, MJ and Yang, Q and Yang, J and Yang, H and Zhao, Z and Yin, H}, title = {Aeribacillus pallidus Inoculant Orchestrates Functional Microbial Succession for Enhanced Nitrogen Transformation in High-Protein Waste Composting.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900349}, issn = {2076-2607}, support = {202302AE090009//Yunnan Province Science and Technology Department/ ; 202404BI09004//Yunnan Province Science and Technology Department/ ; }, abstract = {The valorization of protein-rich meat and bone meal (MBM) via composting is hampered by significant nitrogen loss. Genomic analysis of Aeribacillus pallidus (A. pallidus) strain 60 revealed a genetic repertoire encoding potent proteolysis and nitrogen assimilation. We hypothesized that this strain could function as a microbial catalyst to redirect nitrogen flux during MBM composting. In a laboratory-scale trial, inoculation with A. pallidus triggered a rapid thermal surge (reaching 70 °C) and proteolytic cascade, significantly accelerating maturation. Crucially, this process enhanced relative nitrogen retention, increasing final total Kjeldahl nitrogen (TKN) concentration by 10.87-13.33% and nitrate by 13.75-18.65% compared to controls. Physicochemical and microbial profiling revealed that these improvements were driven by an inoculant-induced environmental modification rather than sustained inoculant dominance. The created thermal niche facilitated a distinct two-stage succession: an initial enrichment of proteolytic genera (Thermoactinomyces, Ammoniibacillus) followed by the establishment of a putative nitrifying community dominated by Pseudoxanthomonas. This study illustrates how a pioneer inoculant can drive functional microbiome assembly through niche modulation, providing a targeted strategy for optimizing nitrogen recovery in protein-dense waste valorization.}, }
@article {pmid41900352, year = {2026}, author = {Khitrov, AA and Burakova, IY and Smirnova, YD and Pogorelova, SV and Chirkin, EA and Morozova, PD and Garmonov, DA and Ozhimkova, EV and Syromyatnikov, MY and Korneeva, OS}, title = {Effect of a Combination of Prebiotic Supplements Based on Fucus and Kelp on the Gut Microbiome of Mice with Induced Inflammation.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900352}, issn = {2076-2607}, support = {project FZGW-2024-0003//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Gut microbiota imbalances can lead to the development of various inflammatory diseases in the body. The development of drugs aimed at maintaining intestinal health is a key area of biotechnology. Algae-based prebiotics are one such drug. The aim of this study was to conduct a comparative analysis of the fecal microbiota of Mus musculus with and without a prebiotic supplement. We studied the effects of enzymatically processed Laminaria digitata and Fucus vesiculosus seaweeds on the gut microbiome of mice with induced inflammation using DNBSEQ-G50 sequencing. The results showed that these prebiotic supplements can reduce the impact of inflammation on the intestine. An increase in the relative abundance of Anaerostipes rhamnosivorans, Dysosmobacter welbionis, Akkermansia muciniphila, Flavonifractor plautii, and a decrease in Longicatena caecimuris relative to the LPS group were observed. Furthermore, enzymatically processed algae were found to increase the relative abundance of gut bacterial metabolic pathways responsible for glucose breakdown. Thus, both enzymatically processed and unprocessed algae-based prebiotic supplements restored gut microbiome composition and gut morphology in LPS-exposed mice, as confirmed by microbiome analysis and histological examination.}, }
@article {pmid41900362, year = {2026}, author = {Das, JK and Chia, CW and Tian, Q and Angelova, A and Ferrucci, L and Tanaka, T}, title = {Gut Microbiota Affects Age-Related Plasma Metabolites.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900362}, issn = {2076-2607}, support = {ZIA AG000997-10//Intramural Research Program of the National Institutes of Health/ ; }, abstract = {Older age is a well-established risk factor for many chronic diseases, yet the biological mechanisms underlying this increased risk are not fully understood. Both gut microbiome composition and the plasma metabolome change with age and may help explain how aging influences disease susceptibility. In this study, we examined the associations between age-related gut microbiota and metabolomic biomarkers in participants of the Baltimore Longitudinal Study of Aging (BLSA), covering a broad age range (27-98 years; 55% female). At the phylum level, we identified four age-associated phyla: Firmicutes, which was negatively associated with age, and Proteobacteria, Euryarchaeota, and Verrucomicrobia, which were positively associated with age. At the genus level, six genera-Akkermansia, Escherichia, Klebsiella, Methanobrevibacter, Oscillibacter, and Ruthenibacterium-were positively associated with age, whereas Faecalibacterium and Longibaculum were negatively associated with age. Many of these microbial taxa were found to influence one or more aging-related metabolites, mediating their effects across various metabolite classes, including bile acids, amino acids, triglycerides, cholesteryl esters, and phosphatidylcholines. Notably, three metabolites, Asparagine, Sphingomyelin C26:0, and Dihydroceramide (d18:0/24:1), were associated with a decreased risk of mortality, whereas six metabolites-Glycoursodeoxycholic acid, Triacylglyceride (16:1_34:3), Triacylglyceride (18:0_34:3), Phosphatidylcholine aa C32:1, Phosphatidylcholine aa C32:2, and Cholesteryl ester 16:1-were linked to an increased risk of mortality. This study highlights connections between age-associated gut microbial taxa at both the phylum and genus levels as potential mediators of circulating metabolites that are linked to mortality risk.}, }
@article {pmid41900370, year = {2026}, author = {Shahzaib, Y and Zhong, T and Yang, H and Xin, Y and Liu, S and Wu, K and Zhang, P}, title = {Bacillus velezensis BY6 Controls Armillaria Root Rot in Poplar by Reshaping Rhizosphere-Phyllosphere Microbiomes and Inducing Systemic Resistance.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900370}, issn = {2076-2607}, support = {KC202415501//The Corps Financial Science and Technology Plan Project/ ; KX6282, KX6445//Shihezi University high-level talents research project/ ; CZ007157//Tianchi research project/ ; }, abstract = {Armillaria solidipes, the causal agent of Armillaria root rot, poses a severe and persistent threat to poplar forest plantations. This study evaluated the biocontrol efficacy of the endophytic bacterium Bacillus velezensis BY6 against this pathogen and elucidated its multimodal mechanisms of action. BY6 application significantly reduced disease severity by 37.19% at 30 days post-treatment. 16S rRNA (V3-V4) microbiome analysis revealed that BY6 reshaped both the rhizosphere and phyllosphere bacterial communities, consistently enriching beneficial taxa, including Pantoea ananatis and members of Acidobacteria, while suppressing opportunistic groups. Concurrently, BY6 activated systemic defenses in poplar, evidenced by enhanced activities of key enzymes PAL and POD, and the upregulated expression of SA/JA pathway marker genes (PR1, JAZ, and COI1), coupled with the downregulation of the auxin transporter gene AUX1. These data indicate that the biocontrol efficacy of B. velezensis BY6 was mediated by a dual mechanism: the modulation of both rhizospheric and phyllospheric bacterial communities, direct elicitation of systemic defense pathways in poplar, which synergistically enhanced resistance against A. solidipes.}, }
@article {pmid41900374, year = {2026}, author = {Turpin, V and Kakilla, C and Foote, J and Chen, O and Hooper, W and Ayad, W and Ghassemi, A and Zimmermann, N and Rea, K and Wescott, A}, title = {Limosilactobacillus reuteri 3613-1 Delays Onset of Unconfirmed Urinary Tract Infections in Otherwise Healthy Women.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900374}, issn = {2076-2607}, abstract = {Urinary tract infections (UTIs) impose a substantial burden on women's health, and probiotics have emerged as an alternative strategy to support urogenital wellbeing. This study evaluated the antimicrobial properties of Limosilactobacillus reuteri 3613-1 and its ability to improve UTI outcomes in women with a history of recurrent uncomplicated UTIs. In vitro assays demonstrated that L. reuteri 3613-1 inhibited the growth of Escherichia coli isolates and proved superior inhibition of Gardnerella vaginalis and Candida albicans compared with a comparator L. reuteri strain, supported by confirmed reuterin production and genomic profiling. A randomized, double-blind, placebo-controlled clinical trial (n = 130) assessed daily supplementation with L. reuteri 3613-1 for 24 weeks. While the proportion, frequency, and intensity of confirmed UTIs did not differ significantly between groups, L. reuteri 3613-1 delayed the onset of the first UTI, reaching significance in participants with suspected while unconfirmed UTIs. Vaginal pH and vaginal microbiome composition remained stable and comparable between groups across the intervention. The product was safe and well tolerated. Overall, L. reuteri 3613-1 shows promise as a probiotic candidate with antimicrobial activity and potential to delay symptom onset in women susceptible to recurrent UTIs, warranting further investigation in larger studies.}, }
@article {pmid41900381, year = {2026}, author = {Lemichez, S and Bernard, M and Chable, V}, title = {Bacterial and Fungal Communities in Old Vines and Their Progeny: Insights into Microbial Inheritance Through Mass Selection.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900381}, issn = {2076-2607}, support = {2023/1052//Association Nationale de la Recherche et de la Technologie/ ; }, abstract = {Mass selection is increasingly promoted in viticulture to enhance resilience by restoring intra-varietal diversity, yet its effects on the structure and inheritance of plant-associated microbiomes remain poorly understood. Here, we investigated bacterial and fungal communities associated with old grapevine mother plants and their progeny across four Bordeaux estates practicing mass selection, using a fully in situ experimental design. Root and leaf microbiomes were characterized by metabarcoding and analyzed using multivariate ordination, hierarchical clustering, and assembly-process metrics (βNTI and NST). Microbial community composition and structure were primarily shaped by plant compartment and vineyard origin, whereas generation effects were significant but weak. Microbial resemblance between mother vines and their offspring was limited and highly context-dependent, occurring mainly under comparable environmental conditions. Assembly-process analyses revealed heterogeneous deterministic signals, particularly in root-associated bacterial communities, but did not consistently result in phylogenetic similarity between generations. Although inheritance signals were generally weak, their recurrence across multiple vineyards and contrasted field conditions highlights their ecological relevance. By integrating environmental variability, this in situ approach mitigates the adaptive bias in plant-microbiome interactions and shows that mass selection does not rely on systematic microbial transmission but rather operates within a nuanced framework of environmentally mediated interactions.}, }
@article {pmid41900386, year = {2026}, author = {Yan, C and Zhang, B and Shi, B and Du, Y and Liu, Z and Huang, J and Lian, Q}, title = {Identification of Pathogens and Biological Control of Wheat Fusarium Crown Rot in Xinjiang with Pseudomonas aeruginosa J-7.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900386}, issn = {2076-2607}, abstract = {Wheat Fusarium crown rot (FCR), predominantly caused by Fusarium species, is a devastating fungal disease that severely threatens global wheat production. In this study, we combined phytopathological assays, molecular techniques, and bioinformatic analyses to systematically identify the causal agents of FCR in Xinjiang and to screen for potential biocontrol bacteria. A total of 296 fungal isolates were obtained from 195 FCR samples, collected from Yumin County and Xinhe County. Morphological and phylogenetic analyses revealed that Fusarium culmorum was the predominant pathogen, accounting for 73.6% of the total isolates. To evaluate the resistance of local wheat cultivars, F. culmorum XN22-1, a highly virulent strain from Xinhe County, was inoculated to 30 wheat varieties. The results demonstrated that most cultivars lacked resistance to FCR, with the exception of three varieties-Xinchun 19, Xinchun 50, and Youpi 23, which showed a mid-resistance. Given the scarcity of resistant cultivars, we focused on biological control. To control FCR, Pseudomonas aeruginosa J-7, exhibiting broad-spectrum antagonistic activity, was successfully isolated from rhizosphere soil based on the analysis of healthy rhizosphere soil microbial diversity. Subsequently, pot experiments showed that P. aeruginosa J-7 could significantly reduce the disease incidence and lower the disease index of wheat FCR. Furthermore, whole-genome sequencing, in-plate metabolite analysis, and observation on inhibition of spores and mycelium revealed that P. aeruginosa J-7 mediates its biocontrol activity primarily through the production of phenazine and siderophores, which collectively inhibit conidial germination and cause structural damage to the mycelium. This study not only clarifies the composition of FCR pathogens in Xinjiang but also provides a promising biocontrol agent and new strategic insights for the management of wheat crown rot.}, }
@article {pmid41900394, year = {2026}, author = {Wang, R and Hu, J and Li, J and Chen, Z and Ayala, B and Liu, X and Kang, P and Pan, Y}, title = {Halophyte-Specific Rhizosphere Effects Drive the Differentiation of Microbial Community Assembly in a Desert-Grassland Salt Marsh.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900394}, issn = {2076-2607}, support = {2025D01B69//Xinjiang Natural Science Foundation Project/ ; XJNUZBS2532//Doctoral Scientific Research Foundation of Xinjiang Normal University/ ; }, abstract = {Arid salt marsh ecosystems endure chronic water scarcity and high salinity stress, with the stability of their functions inextricably linked to the pivotal role of the rhizosphere microenvironment of halophytes. This study focused on three typical halophytes (Kalidium cuspidatum, Nitraria tangutorum, Reaumuria soongarica) in the Jiantan wetland, and deeply explore how these halophytes differently regulate the soil microenvironment through the rhizosphere effect. The results showed that the rhizosphere soil of Kalidium cuspidatum had higher pH, Na[+], and K[+] contents, while the rhizosphere soil of R. soongarica had higher total carbon, soil organic carbon, alkali-hydrolyzable nitrogen, and microbial biomass. Microbial community analysis revealed that rhizosphere soil of fungal diversity was significantly higher in K. cuspidatum than in R. soongarica, with distinct differences in bacterial and fungal community structures. These differences were closely associated with factors such as Na[+], Olsen phosphorus, microbial biomass carbon and alkali-hydrolyzable nitrogen. Among the dominant phyla, Proteobacteria and Ascomycota predominate, with Desulfobacterota and Mortierellomycota exhibiting the highest explanatory power (>48%) for physicochemical property variations. The microbial network of rhizosphere soil of R. soongarica has the highest complexity (with 633 nodes and 3300 edges), but the proportion of positive correlation edges was the lowest (21.58%). Structural equation modeling indicates that soil physical properties indirectly influence network complexity by negatively regulating chemical properties and microbial biomass, while microbial diversity had a direct positive effect on dominant phylum composition and network complexity. This study elucidated the differentiated adaptive strategies of rhizosphere microenvironment-microbe interactions in halophytes, providing a theoretical basis for wetland ecological restoration.}, }
@article {pmid41900430, year = {2026}, author = {Ma, Y and Ding, J and Nie, Z and Qian, H and Zheng, J and Wang, H}, title = {Microbial Inoculants Alleviate Continuous Cropping Obstacles in Eggplant Through Soil Properties and Rhizosphere Microbiota.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900430}, issn = {2076-2607}, support = {2025ZDXT06//Major Agricultural Technology Collaborative Extension Project of Zhejiang Province/ ; 2021C02065//Grand Science and Technology Special Project of Zhejiang Province/ ; 2025HNCT-02//the Technology Project of the Hangzhou Academy of Agricultural Sciences/ ; }, abstract = {Eggplant cultivation faces major challenges from continuous cropping obstacles, which degrade soil health and limit sustainable production. Microbial inoculants offer a promising strategy for addressing such issues by modifying the soil environment and rhizosphere ecology. In this study, a field experiment was conducted to evaluate the effects of three bacterial inoculants, including Bacillus zhangzhouensis (BF1), Bacillus mobilis (BF2), and Zhihengliuella halotolerans (BF3), on soil properties, microbial community structure, and crop performance in a continuously cropped eggplant system. The results showed that three inoculants exerted strain-specific effects: BF1 significantly promoted eggplant vegetative growth and yield, increasing plant height by 32.1%, stem diameter by 28.7%, and total yield by 142.4% relative to the control; BF3 selectively improved fruit quality and soil nutrient status, elevating eggplant fruit total amino acid, soluble protein, and soluble sugar contents by 68.9%, 52.3%, and 41.2%, respectively, and increasing soil organic carbon (SOC), total nitrogen (TN), and available nitrogen (AN) by 13.73%, 18.03%, and 84.92% compared with the control. BF2 showed limited efficacy relative to the control. All inoculants enhanced the abundance of beneficial bacteria and reshaped the rhizosphere microbial community structure. The findings demonstrate the potential of strain-specific microbial inoculants to alleviate continuous cropping obstacles and promote sustainable eggplant production.}, }
@article {pmid41900433, year = {2026}, author = {Zhang, Y and Zhang, T and Zhang, M and Jia, Y and Huang, X}, title = {Dietary Changes Are Associated with Seasonal Restructuring of the Gut Microbiome in Cervus nippon kopschi.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900433}, issn = {2076-2607}, support = {20232BAB215018//Natural Science Foundation of Jiangxi Province/ ; 2023521603//Basic Research and Talents Special Project of Jiangxi Academy of Forestry/ ; 2023521606//Basic Research and Talents Special Project of Jiangxi Academy of Forestry/ ; }, abstract = {Seasonal dietary shifts are associated with significant alterations in the gut microbiome of herbivores, yet the specific impacts of these shifts on microbial metabolic functions have not been fully elucidated. To address this gap, we employed DNA metabarcoding of fecal samples and 16S rRNA gene sequencing to explore the relationship between seasonal diet and gut microbiome composition in a population of sika deer (Cervus nippon kopschi). Our findings indicate pronounced seasonal variations in both dietary composition and gut microbial community structure. Notably, during the winter months, the gut microbiome exhibited a significant enrichment of predicted pathways (predicted using PICRUSt2) related to fatty acid and lipid biosynthesis and degradation, amino acid degradation, and the TCA cycle. Conversely, the active growing seasons (spring and summer) were characterized by enhanced glycolysis and amino acid biosynthesis pathways. These functional shifts showed significant correlations with seasonal changes in dietary nutrients, such as crude protein and fiber, and climatic factors. Our results suggest that seasonal dietary changes are associated with a restructuring of the gut microbiome's metabolic potential, which may assist sika deer in adapting to fluctuating physiological demands and environmental challenges across different seasons.}, }
@article {pmid41900457, year = {2026}, author = {Williams, NW and Ali, T and Boudreau, PD}, title = {Novel Genomes of Sphingomonadales Strains Isolated from Diverse Environments.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900457}, issn = {2076-2607}, support = {P20GM130460/GM/NIGMS NIH HHS/United States ; }, abstract = {Glycosphingolipids are amphiphilic compounds that feature sugar or glycan moieties installed onto a ceramide lipid. The synthesis of glycosphingolipids by members of the human gut microbiome, and their known immune stimulating activity, have made them of interest for potential pharmaceutical roles. However, the known diversity of glycosphingolipid glycans in bacteria remains limited, highlighting the need to isolate novel glycosphingolipid-producing organisms as a source of these compounds. The order Sphingomonadales, one of the major clades of sphingolipid producing bacteria, conserves a serine palmitoyltransferase (SPT) enzyme needed for the initial biosynthetic step in sphingolipid production which can be targeted as part of isolation efforts. With these bacteria known to live in diverse environments such as soil microbiomes, soap scum biofilms, and cyanobacterial microbiomes, there are many environments to target for the isolation of these bacteria. In this work, we designed a set of polymerase chain reaction (PCR) primers for the isolation of diverse Sphingomonadales strains by targeting the SPT gene (spt), which we used to isolate strains from the genera Sphingomonas and Novosphingobium in soil, soap scum biofilms, and xenic cyanobacterial cultures. In these efforts, streptomycin improved the encounter rate, as represented by the SPT assay true-positive rate. Our isolates represent novel genomic space: with genomes from both genera that have low similarity to known genomes, suggestive of novel species, while several novel plasmids were also missing known marker sequences.}, }
@article {pmid41900467, year = {2026}, author = {Lanara, M and Asimakis, E and Bel Mokhtar, N and Koutsodima, P and Batargias, C and Toskas, K and Stathopoulou, P and Tsiamis, G}, title = {Comparative Analysis of the Intestinal Microbiota in Wild and Aquaculture Populations of Sparus aurata.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900467}, issn = {2076-2607}, abstract = {Fish host complex intestinal bacterial communities that contribute to a wide range of functions, from nutrient assimilation to modulation of the immune system. Understanding how environmental and host-related factors shape the fish gut microbiota is essential for advancing sustainable aquaculture practices. This study compared the intestinal microbiota of gilthead sea bream (Sparus aurata) between wild and aquaculture populations in western Greece using 16S rRNA gene amplicon sequencing targeting the V3-V4 region, combined with culture-based methods. The analysis was based on a 97% similarity threshold and included 141 gastrointestinal samples of fish collected at two aquaculture facilities and two wild fisheries, representing two different growth phases (150 g and 300 g body weight). High-throughput sequencing data revealed a clear separation of gut microbial communities according to origin (wild vs. aquaculture), geographic location, and body growth phase, with most wild fish groups exhibiting higher microbial diversity than their farmed counterparts, except for group MES_150 which showed similar or lower values. The gut microbiota was dominated by Pseudomonadota (53%), Bacillota (29%), Actinomycetota (7%), Deinococcota (5%), and Bacteroidota (4%). A shared core microbiome, comprising Psychrobacter, Staphylococcus, Geobacillus, Aeromonas, Enterobacter, Pantoea, Bacillus, and Acinetobacter, was detected across all populations. Wild fish were enriched in Psychrobacter, Aeromonas, and Photobacterium, while aquaculture fish displayed higher abundances of Vibrio, Allomeiothermus, and Staphylococcus. Network analysis revealed mostly mutually exclusive interactions in both groups but distinct patterns of co-occurrence, driven mainly by Paenibacillus, Enterobacter, and Staphylococcus in wild samples, and by Vibrio, Aeromonas, and Pseudomonas in farmed fish. Culture-based assays demonstrated greater diversity in wild fish, dominated by Pseudomonas, Staphylococcus, and Vibrio strains, in contrast to the frequent occurrence of Staphylococcus and Psychrobacter in aquaculture samples. The findings suggest that aquaculture practices significantly alter gut microbial community structure and reduce diversity, with potential implications for fish health and disease resistance. The identified core and differentially abundant taxa provide candidates for probiotic development to improve aquaculture sustainability.}, }
@article {pmid41900478, year = {2026}, author = {Trofin, F and Badescu, AC and Iancu, LS and Buzila, ER and Anton-Păduraru, DT and Sima, CM and Temneanu, OR and Matei, A and Bilha, SC and Benea, IA and Dorneanu, OS}, title = {Seeding the Future: How Feeding Mode Shapes the Infant Gut Microbiota.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900478}, issn = {2076-2607}, abstract = {Early life represents a critical developmental programming window during which nutrition and microbial exposures shape long-term physiological function. Feeding mode is a major determinant of infant gut microbiota assembly and metabolic activity. This narrative review synthesizes current evidence comparing breastfeeding (BF) and formula feeding in relation to microbial composition, functional capacity, and immune programming during the preweaning and early postweaning periods. BF may support a relatively stable, bifidobacteria-dominated microbiota enriched in pathways involved in carbohydrate utilization, vitamin biosynthesis, and immune modulation. Human milk oligosaccharides, secretory IgA, lactoferrin, and milk-associated microbes collectively guide microbial succession, enhance barrier integrity, and support immune tolerance. In contrast, formula-fed infants typically exhibit greater microbial diversity, earlier transition toward adult-like profiles, and increased abundance of facultative anaerobes, alongside the enrichment of pathways related to bile acid and amino acid metabolism. Microbiota patterns in formula-fed infants are further influenced by formula composition, including protein load, lipid structure, and supplementation with prebiotics, probiotics, and human milk oligosaccharide analogues. Although advances in formula design have reduced compositional gaps, functional differences in microbial stability and immune programming persist. Recognizing early infancy as a sensitive programming window underscores the need for microbiome-informed nutritional strategies and longitudinal, multi-omics research to clarify causal mechanisms and optimize early-life interventions.}, }
@article {pmid41900479, year = {2026}, author = {Park, H and Kim, JS and Kim, DJ and Suk, KT}, title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900479}, issn = {2076-2607}, support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; }, abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.}, }
@article {pmid41889817, year = {2026}, author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL}, title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.16.712136}, pmid = {41889817}, issn = {2692-8205}, abstract = {UNLABELLED: Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.<br><br>IMPORTANCE: Laboratory mice are foundational models for immunology, yet their specific pathogen-free rearing and housing environments impose ecological constraints that reshape the gut microbiome and immune tone. This study introduces a scalable, pathogen-monitored Eco-tank system that restores environmental microbial complexity while preserving experimental control. By demonstrating that housing ecology reshapes microbiome functional potential and modulates baseline immune resistance without compromising vaccine responsiveness, this work highlights environmental context as a critical experimental variable in preclinical immunology and offers a tractable framework for improving translational relevance.}, }
@article {pmid41889844, year = {2026}, author = {Brache-Smith, DM and Sogin, EM and Badillo, J and Maeda, S}, title = {Identification of bacterial candidates that promote the growth of the seagrass Zostera marina.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.19.712741}, pmid = {41889844}, issn = {2692-8205}, abstract = {BACKGROUND: Globally, seagrass ecosystems are threatened by anthropogenic activities that are leading to increased levels of eutrophication, coastal pollution and thermal conditions. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates.<br><br>RESULTS: Our cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, which reflected 18% of the total microbial diversity of the starting inoculum. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51%), dissimilatory nitrate reduction to ammonia (71%), and C-N bond cleavage (83%). Six of the isolates, which represent new lineages of Agarivorans, coded for the nitrogenase gene cassette. Additionally, 52% of the genomes had genes for sulfur and/or thiosulfate oxidation, 88.5% for phosphorus solubilization, and 60.5% for IAA production. Genomic analysis also revealed that some pathways, including denitrification and dissimilatory nitrite to ammonia DNRA, required cross-species cooperation as no one taxa contained all the genes needed to complete these metabolic pathways. Based on draft genome models and results from phenotypic assays, isolates Streptomyces sp. (Iso23 and Iso384), Mesobacillus sp (Iso127), Roseibuim sp. (Iso195), Peribacillus sp. (Iso49), and Agarivorans sp. (Iso311) represent a minimal microbial community that is likely to promote seagrass growth and enhance restoration efforts.<br><br>CONCLUSION: Our work provides a detailed genomic and phenotypic analysis of bacteria isolated from Zostera marina and identifies a minimal microbial community with complementary PGP traits. Isolating, identifying and characterizing bacteria that promote seagrass growth is critical towards enhancing restoration efforts of seagrass meadows.}, }
@article {pmid41889866, year = {2026}, author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Garipcan, A and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S}, title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.17.708620}, pmid = {41889866}, issn = {2692-8205}, abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii , consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.}, }
@article {pmid41889867, year = {2026}, author = {Barua, A and Cong, F and Bao, H and Deng, WM}, title = {Tumor-induced species-specific dysbiosis drives renal innate immunity and nephrogenic ascites.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.10.710910}, pmid = {41889867}, issn = {2692-8205}, abstract = {Ascites is a life-threatening complication of advanced malignancies, yet how tumors disrupt systemic fluid homeostasis remains poorly understood. Here, using a Drosophila tumor allograft model that recapitulates key features of cancer-associated ascites, we identify a tumor-microbiome-renal axis that controls host fluid balance. Tumor-bearing hosts develop severe abdominal fluid accumulation accompanied by marked expansion and systemic dissemination of the gut commensal Acetobacter aceti . Tumor-induced bacterial dissemination activates innate immune signaling in the Malpighian tubules, the insect renal tubules, leading to uric acid accumulation, nephrolithiasis, and progressive ascites. Selective elimination of A. aceti , or renal-tubule-specific suppression of IMD/NF-κB signaling, abolishes these pathological changes. Conversely, mono-association of axenic hosts with A. aceti is sufficient to recapitulate the ascites phenotype through IMD pathway activation. Together, these findings demonstrate that tumors can remotely induce nephrogenic pathology through species-specific microbiome-dependent immune activation, establishing a mechanistic link between cancer progression and systemic fluid imbalance.}, }
@article {pmid41889965, year = {2026}, author = {Landau, LJB and Jain, S and Griffin, N and Saikia, A and Kramer, JM and Knox, S and Ruhl, S and Gokcumen, O}, title = {Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.18.712472}, pmid = {41889965}, issn = {2692-8205}, abstract = {Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies across species and sexes. The evolutionary mechanisms underlying this molecular diversity remain poorly understood. Here, we compared mouse and human salivary gland secretomes at genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. We performed RNA-seq analysis of the major mouse salivary glands (parotid, submandibular, and sublingual), liver and pancreas from both sexes, compared them with reanalyzed previously published human salivary gland transcriptomes, and integrated them with proteome data of mouse and human whole saliva. We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, respectively, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, five times higher than in the liver, a classic model of sex-biased expression. These genes cluster in regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ∼16.4% of male-biased submandibular expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Our results reveal how lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian salivary gland secretome.}, }
@article {pmid41890109, year = {2026}, author = {Stincone, P and Braun, LM and Bağcı, C and Navarro-Diaz, M and Pérez-Lorente, AI and Farrell, SP and Gómez-Pérez, D and Bode, J and Steuer-Lodd, K and Mahmoudi, M and Chaudhry, V and Romero, D and Aron, AT and Ziemert, N and Molina-Santiago, C and Kemen, EM and Petras, D}, title = {Cooperative siderophore use stabilizes a protective leaf microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.18.712463}, pmid = {41890109}, issn = {2692-8205}, abstract = {Plant-associated microbial communities provide crucial protection against pathogens. Specialized metabolites play key roles in plant-microbe and microbe-microbe interactions and, ultimately, in plant health; however, the molecular mechanisms underlying their plant-protecting properties remain largely unknown. Nutrient deficiency (e.g., iron) on leaf surfaces creates intense competition among microbes, driving both antagonism and cooperation. Using a gnotobiotic Arabidopsis thaliana model and a synthetic leaf microbial community, we show that community stability and plant protection depend on cooperative siderophore exchange between the basidiomycete yeast Rhodotorula kratochvilovae and commensal Pseudomonas species. Removal of Pseudomonas caused a strong shift in the community metabolome and accumulation of the yeast siderophore rhodotorulic acid (RA). RA selectively promoted the growth of commensal Pseudomonas via TonB-dependent transporters, which are absent in pathogenic Pseudomonas strains. Inactivation of these transporter genes abolished RA uptake, destabilized the synthetic community, and eliminated protection against Pseudomonas syringae infection. RA and Rhodotorula also induced host iron-deficiency and jasmonate-related defense metabolites, linking microbial cooperation to plant stress responses. These findings reveal that microbial siderophore exchange acts as a key mechanism that maintains stability in the phyllosphere microbiome. Rather than solely promoting competition, iron-binding compounds can serve as cooperative currencies that align microbial fitness with host protection.}, }
@article {pmid41890193, year = {2026}, author = {Zhu, B and Qu, S and Li, J and Deng, W and Shen, WJ and Chen, J}, title = {The mechanisms underlying COVID-19 induced insulin resistance: a narrative review.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1781679}, pmid = {41890193}, issn = {1664-2392}, mesh = {Humans ; *Insulin Resistance/physiology ; *COVID-19/complications/metabolism ; SARS-CoV-2 ; Gastrointestinal Microbiome ; Diabetes Mellitus/etiology/metabolism ; }, abstract = {The COVID-19 pandemic, caused by SARS-CoV-2, has resulted in a significant increase in insulin resistance and new-onset diabetes among recovered individuals. This review examines the multifactorial mechanisms underlying these metabolic complications, including activation of the immune system and inflammatory cascades, lifestyle changes, nutritional deficiencies, imbalances in amino acid metabolism, alterations in ketogenesis, disruptions in the gut microbiome, psychological impacts, and COVID-19 vaccines. We discuss how these factors collectively contribute to insulin resistance, particularly in the context of COVID-19, and highlight potential therapeutic strategies, such as dietary interventions and ACE2 activators, that may mitigate these effects. Our analysis underscores the need for targeted approaches to prevent and treat insulin resistance in post-COVID-19 patients, emphasizing the importance of understanding the pandemic's long-term metabolic consequences.}, }
@article {pmid41890637, year = {2026}, author = {Fujita-Jimbo, E and Kawahara, G and Momoi, T}, title = {Foxp2 mutations and abnormal brain and gastrointestinal development: insights from animal models of speech-language and autism spectrum disorders.}, journal = {Frontiers in neuroanatomy}, volume = {20}, number = {}, pages = {1783101}, pmid = {41890637}, issn = {1662-5129}, abstract = {Autism spectrum disorder (ASD) and speech and language disorder (SLD) are distinct neurodevelopmental conditions, yet both share overlapping communication impairments. Forkhead box P2 (FOXP2), a key transcription factor involved in speech and language development, harbors pathogenic mutations such as R553H, which cause SLD and have been suggested to contribute to aspects of ASD-related phenotypes. This review synthesizes insights from animal models to explore the molecular mechanisms by which Foxp2 mutations disrupt the development of the cerebral cortex, thalamus, and enteric nervous system. We highlight findings from heterozygous Foxp2 mutants and discuss severe phenotypes observed in homozygous Foxp2 mutants (Foxp2[R552H/R552H] and Foxp2[R552H/R552H]/mCherry-Tg mice), including profound ultrasonic vocalization deficits, brain malformations, and early lethality. Notably, these mice exhibit gastrointestinal abnormalities involving the epithelium, smooth muscle, and enteric nervous system, which are linked to impaired autoregulation and interference with Wnt signaling during development. Such observations underscore the relevance of the brain-gut-microbiome axis and Hirschsprung-like pathology in neurodevelopmental disorders. Finally, this review discusses future directions using gene-editing approaches in non-mammalian models-zebra finches, zebrafish, and Drosophila-to dissect neural networks underlying intellectual disability and communication deficits. Collectively, these studies provide a framework for understanding FOXP2-related molecular mechanisms in the pathogenesis of ASD and SLD.}, }
@article {pmid41890703, year = {2026}, author = {Li, X and Liu, F and Zhu, Y and Shi, H}, title = {Gut Microbiota, Insulin Resistance, and Alzheimer's Disease: A Narrative Review of Mechanistic Links and Therapeutic Perspectives.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {593664}, pmid = {41890703}, issn = {1178-7074}, abstract = {Alzheimer's disease (AD) is increasingly regarded as a "neurometabolic syndrome" wherein systemic insulin resistance exacerbates cerebral glucose hypometabolism, tau hyperphosphorylation, and neuroinflammation. We hypothesize that gut microbiota dysbiosis produces metabolites that are associated with peripheral insulin sensitivity, potentially contributing to disruptions in cerebral insulin signaling and an increased risk of AD. We conducted integrated search of PubMed, Web of Science, and Scopus to synthesize evidence showing: (i) consistent taxonomic shifts in AD, highlighting reduced Firmicutes and increased Proteobacteria and Bacteroidetes, depletion of Ruminococcaceae and enrichment of Blautia and Bilophila; (ii) functional consequences of dysbiosis, leading to lower short-chain fatty acids, altered secondary bile‑acid signaling, elevated lipopolysaccharide and trimethylamine‑N‑oxide, and perturbed tryptophan catabolism; (iii) these microbial metabolites compromising gut and blood-brain barrier integrity, thereby triggering chronic inflammation, potentially modulating the PI3K‑Akt‑GSK‑3β pathway, and linking peripheral insulin resistance to cerebral dysfunction; and (iv) a translational discussion of therapeutic strategies that target both microbiota and insulin pathways, including dietary modulation, probiotics and prebiotics, fecal microbiota transplantation, intranasal insulin, metformin, and metabolite-based agents, show promise. This review uniquely integrates taxonomic, functional, and therapeutic literature to propose a mechanistic microbiota-insulin resistance-AD axis and highlights the need for longitudinal and interventional trials.}, }
@article {pmid41890730, year = {2026}, author = {Yanamadala, Y and Gokulan, K and Karn, K and Sutherland, V and Cunny, H and Santos, JH and Davis, K and Khare, S}, title = {Gestational and lactational exposure to HIV tri-combination therapy induces sex- and dose-dependent changes in inflammatory cytokine profiles, intestinal permeability, and villi morphology in adult rat offspring.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1668334}, pmid = {41890730}, issn = {1664-3224}, mesh = {Animals ; Female ; Pregnancy ; *Cytokines/metabolism ; Male ; Rats ; Permeability ; *Intestinal Mucosa/drug effects/metabolism/pathology/immunology ; *Prenatal Exposure Delayed Effects/immunology ; Lactation ; *HIV Infections/drug therapy/immunology ; *Anti-HIV Agents/adverse effects ; Lamivudine/adverse effects ; Sex Factors ; Piperazines ; Inflammation Mediators/metabolism ; Intestinal Barrier Function ; }, abstract = {INTRODUCTION: Gestational antiretroviral therapy (ART) has significantly reduced the risk of vertical transmission of HIV, but concerns linger about its long-term effects on the fetal immune system and intestinal health. Our previous work has demonstrated dose-dependent changes in the fecal and mucosa-associated microbiome of adult rat offspring perinatally exposed to TC-ART (tri-combination ART: dolutegravir, abacavir, and lamivudine). These changes may either be driven by alterations in immune system and intestinal barrier integrity or potentially impact them.<br><br>METHODS: In this study, we further investigated the long-term effects of perinatal TC-ART exposure on intestinal permeability, cytokine profiles, and intestinal mucosa morphology.<br><br>RESULTS: We observed statistically significant sex-dependent differences, with male offspring exhibiting reduced weight gain, a dichotomous response between low and high dose for inflammatory cytokines [interleukin-5 (IL-5), IL-7, and IL-12], differential regulation for the mRNA expression of intestinal permeability-related genes (21 downregulated), and disrupted villous architecture, while females showed dose-dependent decreases in inflammatory cytokines [IL-17, IL-5, and macrophage colony-stimulating factor (M-CSF)]. In females, while some intestinal permeability genes were downregulated, the upregulation of other permeability genes suggests a compensatory mechanism to maintain the intestinal barrier function, indicating an overall milder response to TC-ART.<br><br>DISCUSSION: These findings suggest that perinatal exposure to TC-ART may have differential impacts on intestinal health, with females exhibiting a more adaptive response compared to males, highlighting the need for sex-specific considerations in evaluating long-term effects of ART.}, }
@article {pmid41890754, year = {2026}, author = {Song, Z and Han, X and Zhou, Z and Hua, H and Wang, F and Zhang, X and Wen, S}, title = {Comprehensive management of hematopoietic stem cell transplantation complications: from infection prevention to immune microenvironment reconstruction.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1740067}, pmid = {41890754}, issn = {1664-3224}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology/prevention &amp; control/therapy/immunology ; *Hepatic Veno-Occlusive Disease/etiology/prevention &amp; control/therapy ; *Infections/etiology/therapy ; Gastrointestinal Microbiome ; Disease Management ; Transplantation Conditioning/adverse effects/methods ; Animals ; }, abstract = {This article systematically reviews the management of key complications in hematopoietic stem cell transplantation (HSCT), including infections, graft-versus-host disease (GVHD), and hepatic sinusoidal obstruction syndrome (VOD/SOS). It highlights the importance of optimizing conditioning regimens to reduce infection risk and discusses the role of novel antiviral agents like letermovir in transforming infection control. For GVHD, the pathogenesis involving effector and regulatory T-cell imbalances is analyzed, together with prevention strategies such as post-transplant cyclophosphamide with antithymocyte globulin and TCRαβ/CD19 depletion. Ruxolitinib is emphasized for steroid-refractory GVHD, and gut microbiota modulation is noted as a promising intervention. For VOD/SOS, early biomarker detection and defibrotide treatment are critical. The review also explores the impact of immune reconstitution on infection control, GVHD development, and relapse, and examines how emerging approaches, including single-cell sequencing, microbiome analysis, and artificial intelligence, can be applied in building whole-course risk management models. Future directions include developing intelligent platforms and personalized strategies to enhance long-term patient outcomes.}, }
@article {pmid41890921, year = {2026}, author = {Calafate, C and Alpuim Costa, D and Campos, T and Ribeiro, PC and Martinho, F and Freitas, C and Botelho de Sousa, C and Negreiros, I and Canastra, A and Borralho, P and Pereira, AG and Marçal, C and Ribeiro, R and Sousa, JG and Dinis, C and Chaleira, R and Calha, R and Rocha, JC and Calhau, C and Moreira-Rosário, A and Faria, A}, title = {Assessing mental health, cognitive function and quality of life of breast cancer patients: exploring associations with gut microbiota in an observational and preliminary study.}, journal = {Frontiers in psychology}, volume = {17}, number = {}, pages = {1437697}, pmid = {41890921}, issn = {1664-1078}, abstract = {INTRODUCTION: Breast cancer patients face several physical and psychological problems, such as anxiety, depression, and cognitive dysfunction. The disease and treatments can also impact the microbiota, which is associated with cognitive and psychological issues and, consequently, affected quality-of-life (QoL). This study aimed to correlate the initial gut microbiota of newly diagnosed HR+ (Hormone Receptor)/HER2- breast cancer patients with their mental health, cognitive function, and QoL at baseline and after 3 months of neoadjuvant chemotherapy.<br><br>MATERIALS AND METHODS: This is a prospective, longitudinal, observational, exploratory study. Newly diagnosed HR+/HER2- breast cancer patients undergoing neoadjuvant chemotherapy were recruited upon diagnosis. At baseline (before neoadjuvant chemotherapy), general and lifestyle information, adherence to the Mediterranean diet, biochemical analysis, gut microbiota profile, the European Organization for Research and Treatment of Cancer Quality-of-Life Questionnaire Core-30 (EORTC QLQ-C30), the Montreal Cognitive Assessment (MoCA) and the Hospital Anxiety and Depression Scale (HADS), were collected. The EORTC QLQ-C30, MoCA, and HADS were repeated 3 months later.<br><br>RESULTS: From the 11 participants, most showed mild cognitive impairment at baseline, and there was no clear trend of improvement or deterioration at 3 months. Participants had borderline anxiety at baseline, which improved to a normal range, while depression remained stable. QoL declined for most women, with over 70% experiencing problems at 3 months. The association of these parameters with microbiota profile suggested that women with poorer cognitive function over time had lower Shannon index and microbial richness. Women with improved scores in the depression subscale of the HADS appear to have higher Shannon index and lower richness. Contrarily, Shannon index was lower and richness was higher for improved anxiety and global QoL scores. The results also suggest that changes in the abundance of various genera and phyla may be linked to the evolution of scores for the 3 questionnaires.<br><br>CONCLUSION: Our study suggests a link between the microbiota profile at diagnosis and the psychological symptoms that develop at 3 months of breast cancer treatment. These findings shed light on potential strategies for positively modulating the microbiota to help enhance the body's resilience, particularly mental health, throughout the disease and treatments.}, }
@article {pmid41890980, year = {2026}, author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W}, title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101384}, pmid = {41890980}, issn = {2352-7714}, abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.}, }
@article {pmid41891018, year = {2026}, author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K}, title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.18.26348688}, pmid = {41891018}, abstract = {Background Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom. Results Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in alpha and beta diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis-relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus gnavus and Flavonifractor plautii and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation. Conclusions These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions aimed at reducing anxiety.}, }
@article {pmid41891123, year = {2026}, author = {Jara, J and Alba, C and Fernández, L and Orozco Fernández, R and López Carrasco, A and Brunel García, I and Vilches Jiménez, JC and Buño-Soto, A and Regidor, PA and Gutiérrez, R and Lázcoz, B and Rodríguez, JM and Orgaz, B}, title = {Probiotic supplementation improves quality of life and modulates oestradiol in women with endometriosis: a randomised double-blind pilot trial.}, journal = {The European journal of contraception &amp; reproductive health care : the official journal of the European Society of Contraception}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/13625187.2026.2644896}, pmid = {41891123}, issn = {1473-0782}, abstract = {OBJECTIVE: Endometriosis is a chronic, oestrogen-dependent inflammatory disorder affecting up to 10% of reproductive-age women, associated with pelvic pain, infertility, and reduced quality of life. Emerging evidence implicates the vaginal microbiome and oestrogen metabolism in its pathogenesis. This study aimed to evaluate the potential therapeutic role of the oral administration of Ligilactobacillus salivarius CECT 30632, a probiotic with demonstrated ability to metabolise oestrogens in vitro, to improve the quality of life in women with endometriosis.<br><br>MATERIAL AND METHODS: We conducted a pilot, randomised, double-blind, placebo-controlled clinical trial assessing its effects, alongside standard dienogest treatment, in 37 women with endometriosis. Outcomes included changes in the vaginal microbiota composition (16S rRNA sequencing), in the immunological markers, in serum oestradiol levels, and in the quality-of-life of participants assessed with the EHP-30 questionnaire.<br><br>RESULTS: Vaginal microbial diversity remained unchanged between groups; however, &#x223c;20% of participants exhibited individualised microbiota shifts, including transitions to Lactobacillus-dominated profiles. In the immunological markers, the IL-10 levels decreased in 65% of probiotic supplemented participants (p&#x2009;=&#x2009;0.042). Serum oestradiol levels were significantly reduced (&#x223c;50%) in the probiotic group (p&#x2009;=&#x2009;0.013). The probiotic supplementation was associated with significant improvements in pain, emotional well-being, and perceived self-control (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Daily oral intake of L. salivarius CECT 30632 was associated with changes in circulating oestradiol levels and improvements in the quality of life in women with endometriosis. These preliminary findings support further powered trials to confirm efficacy and clarify underlying mechanisms.}, }
@article {pmid41891189, year = {2026}, author = {Jiménez-Padilla, Y and Sinclair, BJ}, title = {Gut yeasts accelerate chill coma recovery in Drosophila melanogaster.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.251533}, pmid = {41891189}, issn = {1477-9145}, support = {//Queen Elizabeth Scholars/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {The role of microbial symbionts in host stress tolerance remains underexplored. Gut microbiome studies in Drosophila melanogaster have largely focused on bacteria, whereas yeasts have been assumed to provide nutrition rather than engage in true symbiosis. We explored the effect of gut yeasts on chill coma recovery time (CCRT, a proxy for cold tolerance) and its yeast species-specificity and dependence on live yeast cells. We generated flies with distinct gut microbiota conditions: axenic (microbe-free), with their native microbiota (derived from the microbes associated with flies conventionally reared in our colony), or gnotobiotic flies mono-associated with either live or heat-killed yeasts (Saccharomyces cerevisiae - not normally associated with Drosophila guts, and three species previously isolated from wild flies - Lachancea kluyveri, Pichia kluyveri, or P. nakasei). We quantified yeast abundance, sex differences in yeast ingestion, and measured CCRT after exposure to 0 °C for 8 hours. Female axenic flies recovered 42% more slowly than those with their native microbiota, but this delay was fully rescued by live L. kluyveri, P. kluyveri, or P. nakasei, not by S. cerevisiae or dead yeasts. The effect was rapid (occurs within 48 h), sex-specific (restricted to females), and appeared to be dose-dependent. We also confirmed that yeasts in the gut are alive, facilitating a true (albeit transient) symbiotic interaction. Our findings show that yeast symbionts may contribute to natural variation in thermal tolerance and may broadly impact host phenotypes. Excluding yeasts or assuming a solely nutritional role risks overlooking key symbiotic interactions that have profound functional consequences.}, }
@article {pmid41891399, year = {2026}, author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK}, title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71738}, doi = {10.1002/cam4.71738}, pmid = {41891399}, issn = {2045-7634}, support = {R21CA293626/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; }, abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.}, }
@article {pmid41891724, year = {2026}, author = {Goerlich, K and Mitchell, AP}, title = {Impact of Candida albicans NDT80 and UME6 on biofilm formation and fluconazole susceptibility.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0001426}, doi = {10.1128/msphere.00014-26}, pmid = {41891724}, issn = {2379-5042}, abstract = {The microbiome-associated fungus Candida albicans is an opportunistic pathogen. Virulence traits include its ability to produce biofilm, a surface-associated growth form that persists on mucosae and implanted medical devices. C. albicans clinical isolates vary in ability to produce biofilm and the constituent filamentous cell types. Here, we focus on two transcription factors that promote filamentation and biofilm formation, Ndt80 and Ume6. We address two questions. First, how variable is the impact of Ndt80 among C. albicans strains? Second, what is the genetic interaction between NDT80 and UME6? We find that Ndt80 is required for filamentation and biofilm formation in five clinical isolates in addition to the reference strain SC5314, where Ndt80 function has been well established. RNA-sequencing (RNA-seq) data indicate that UME6 RNA levels are reduced in an ndt80Δ/Δ mutant, possibly a result of altered RME1 and WOR1 expression, both of which control UME6. Increased expression of UME6 in ndt80Δ/Δ mutants of three strain backgrounds restores filamentation and biofilm formation, though RNA-seq assays indicate that it does not suppress the overall ndt80Δ/Δ gene expression defect. Ndt80 has an additional role in promoting tolerance to the antifungal drug fluconazole, an inhibitor of ergosterol synthesis. This ndt80Δ/Δ phenotype varies considerably among clinical isolates. In three strains tested, increased expression of UME6 in ndt80Δ/Δ mutants enhances their susceptibility to fluconazole. Therefore, our results show an unexpected relationship between Ume6 expression and azole drug sensitivity. To our knowledge, Ume6 has previously been understood to function only in filamentation, biofilm formation, and related processes.IMPORTANCEOur focus is the fungal pathogen Candida albicans. Two traits, biofilm/hypha formation and azole resistance, are major drivers of its infection ability. We examine the roles of two biofilm transcriptional regulators, Ndt80 and Ume6, in several C. albicans clinical isolates. Prior studies in one strain background (SC5314) indicated that Ndt80 controls both biofilm/hypha formation and azole drug susceptibility and that Ume6 controls biofilm/hypha formation. The four new findings here are that (i) Ndt80 effects on fluconazole sensitivity vary considerably with strain background; (ii) Ndt80 is required for filamentation and biofilm formation in multiple clinical isolates; (iii) the Ndt80 target Ume6 contributes to Ndt80 control of filamentation and biofilm formation in multiple clinical isolates; and (iv) Ume6 influences fluconazole vulnerability, the first Ume6 function to our knowledge that is unrelated to filamentation.}, }
@article {pmid41891974, year = {2026}, author = {Zhang, H and Li, D and Zhu, L and Yan, H and Yang, L and Yang, X and Zhou, Y}, title = {Multi‑omics and their integration in psoriasis research (Review).}, journal = {Molecular medicine reports}, volume = {33}, number = {5}, pages = {}, doi = {10.3892/mmr.2026.13852}, pmid = {41891974}, issn = {1791-3004}, mesh = {Humans ; *Psoriasis/genetics/metabolism/microbiology/pathology ; *Genomics/methods ; Metabolomics/methods ; Epigenomics/methods ; Proteomics/methods ; Biomarkers ; Epigenesis, Genetic ; Genome-Wide Association Study ; Genetic Predisposition to Disease ; Transcriptome ; Animals ; Microbiota ; Multiomics ; }, abstract = {Psoriasis is a chronic, immune‑mediated skin disorder characterized by keratinocyte hyperproliferation, inflammatory infiltrates and systemic comorbidities. While genetic predisposition and immune dysregulation are established contributors, recent advancements in high‑throughput omics technologies have provided deeper insights into the molecular complexity of psoriasis. The present review synthesized findings from various omics layers, genomics, epigenomics, transcriptomics, proteomics, metabolomics and microbiomics, to elucidate their roles in psoriasis pathogenesis. Large‑scale genome‑wide association studies have identified both common and region‑specific susceptibility loci. Epigenetic factors and transcription factors regulate psoriasis‑related genes by modulating chromatin accessibility, DNA methylation, non‑coding RNAs and direct gene activation/inactivation, thereby reshaping the transcriptome. Genetic and epigenetic influences also drive significant alterations in the proteome and metabolome, both in the skin and plasma, shedding light on disease mechanisms and offering potential for biomarker discovery. While microbiome research in psoriasis remains in its early stages, shifts in skin and gut microbial communities have been observed, suggesting their involvement in disease pathogenesis. Together, the multi‑layered insights underscore the future potential of integrated systems approaches to unravel disease mechanisms and support the discovery of clinically actionable biomarkers and therapeutic targets, paving the way for more precise diagnosis and targeted therapeutic development in psoriasis.}, }
@article {pmid41892210, year = {2026}, author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D}, title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.}, journal = {Biology}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/biology15060450}, pmid = {41892210}, issn = {2079-7737}, support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; }, abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.}, }
@article {pmid41892267, year = {2026}, author = {Tomuța, RA and Caltea, A and Ghitea, MC and Ghitea, EC and Gîtea, MF and Ghitea, TC and Banica, F}, title = {Physical Activity Is Associated with Gut Microbiome Features and Organic Acid Patterns in Adults Consuming Plant-Rich Diets: An Exploratory Cross-Sectional Study.}, journal = {Biology}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/biology15060507}, pmid = {41892267}, issn = {2079-7737}, support = {410072//University of Oradea/ ; }, abstract = {BACKGROUND: Plant-rich dietary patterns are widely associated with metabolic and gastrointestinal health benefits. However, individuals consuming predominantly plant-based foods may also experience chronic low-dose exposure to dietary pesticide residues. At the same time, physical activity is recognized as an important lifestyle factor influencing metabolic health and gut microbiome composition. How microbiome features and microbiome-related metabolic profiles vary according to physical activity level in adults consuming plant-rich diets and reporting gastrointestinal symptoms remains insufficiently characterized.<br><br>OBJECTIVE: To explore associations between physical activity level, gut microbiome characteristics, and urinary organic acid patterns in adults consuming predominantly plant-rich diets and experiencing gastrointestinal symptoms, within a cohort characterized by comparable estimated dietary pesticide exposure used as a contextual dietary background variable.<br><br>METHODS: This cross-sectional observational study included 93 adults consuming &#x2265;50% plant-based foods for at least six months and reporting persistent gastrointestinal symptoms. Participants were stratified according to physical activity level using WHO-based thresholds (<150 vs. &#x2265;150 min/week of moderate-intensity activity). Stool microbiota were assessed using a targeted quantitative PCR panel, and microbial diversity was summarized using a laboratory-derived Shannon index. A voluntary subgroup (n = 50) underwent targeted urinary organic acid analysis (LC-MS/MS). Dietary pesticide exposure was indirectly estimated using national surveillance data combined with individual dietary records and was applied uniformly across groups. Analyses were primarily descriptive and exploratory; results are presented as associations.<br><br>RESULTS: Estimated dietary pesticide exposure did not differ between physical activity groups. Participants with lower physical activity were older and exhibited lower microbial diversity and a higher prevalence of reduced abundance in selected commensal taxa. Differences were observed in selected intermediary organic acid markers, while no statistically significant difference was found for the bile acid-related indicator. Several cross-domain correlations were identified between microbial features and metabolite patterns. However, given the cross-sectional design, age imbalance between groups, and subgroup-based metabolomic analyses, the findings should be interpreted as hypothesis-generating rather than indicative of independent effects of physical activity.<br><br>CONCLUSIONS: In adults consuming plant-rich diets and reporting gastrointestinal symptoms, physical activity level was associated with distinct microbiome and microbiome-related metabolic patterns under comparable estimated dietary pesticide exposure. These findings highlight the potential contribution of lifestyle factors to interindividual variability in gut microbial and metabolic profiles, while underscoring the need for age-adjusted, longitudinal, and biomarker-based studies to clarify directionality and mechanisms.}, }
@article {pmid41892298, year = {2026}, author = {Prud'homme, GJ and Wang, Q}, title = {Antiaging Properties of the Klotho Protein.}, journal = {Cells}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/cells15060507}, pmid = {41892298}, issn = {2073-4409}, support = {2-SRA-2018-497-A-B//Juvenile Diabetes Research Foundation International/ ; OG-3-13-4066//Diabetes Canada/ ; 81570518, 81630020, 82370814//National Science Foundation of China/ ; N/A//St. Michael's Hospital Foundation, Toronto, Canada/ ; N/A//Keenan Research Centre for Biomedical Science, Toronto, Canada/ ; }, mesh = {*Klotho Proteins/metabolism ; Humans ; *Aging/metabolism/genetics ; Animals ; *Glucuronidase/metabolism ; Inflammation/metabolism ; Cellular Senescence ; }, abstract = {Mice genetically deficient in α-Klotho (henceforth Klotho) display accelerated aging. The mechanisms are only partially understood. Here, we examine how these relate to the 12 hallmarks of aging consisting of chronic inflammation (inflammaging), as well as damaging changes to the genome (DNA damage), telomeres, epigenetic regulation, proteostasis, nutrient sensing, mitochondria, stem cells, intercellular communication, macroautophagy, microbiome and cell replication (senescence). Inflammation aggravates the other hallmarks. We report that Klotho counters the majority of these hallmarks. It ameliorates mitochondrial function and reduces reactive oxygen species (ROS), telomere attrition and cellular senescence. It protects against inflammation by inhibiting NF-κB and the NLRP3 inflammasome. This applies to inflammaging, several chronic inflammatory diseases, atherosclerosis, diabetes, and Alzheimer's disease. Klotho also counters some aging factors outside of these hallmarks. Low Klotho (often due to kidney disease) produces hyperphosphatemia, which injures cells (especially endothelial cells) and promotes aging. Another key action of Klotho is the mitigation of fibrosis in major organs (kidneys, heart, lungs and other), mainly through the inhibition of TGF-β and Wnt. Klotho also protects against muscle atrophy (sarcopenia)-a common feature of aging-and exhibits anti-cancer activity. We describe several factors that increase Klotho, and are potentially amenable to clinical therapy.}, }
@article {pmid41892413, year = {2026}, author = {Šuran, J and Pavlović, N and Božić, J and Kumrić, M and Vukojević, K and Filipović, N and Radić, B}, title = {IBS and SIBO: Gut Microbiota, Pathophysiology, and Non-Pharmacological Interventions.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030251}, pmid = {41892413}, issn = {2079-6382}, abstract = {Irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO) share symptoms such as abdominal pain, bloating, and altered bowel habits. Both are linked to dysbiosis and gut-brain axis dysfunction. IBS is a multifactorial disorder characterized by abnormal motility, visceral hypersensitivity, low-grade inflammation, and alterations in the microbiota. In contrast, SIBO is defined by excessive bacterial colonization of the small intestine that can mimic or worsen IBS symptoms. Gut microbes and their metabolites influence motility, immune activation, barrier integrity, and gas production; methanogen overgrowth is associated with constipation-predominant presentations, while hydrogen- and hydrogen sulfide-related pathways may contribute to diarrhea and bloating. Because recurrent or empiric antibiotic use is common-particularly in suspected SIBO-yet carries risks of resistance, microbiome disruption, and relapse, there is a strong rationale to prioritize effective non-antibiotic strategies. Accordingly, this review synthesizes current evidence on IBS/SIBO pathophysiology and microbiota interactions. It evaluates non-pharmacological interventions including dietary approaches, probiotics/prebiotics, herbal therapies, and mind-body treatments (e.g., cognitive behavioral therapy and gut-directed hypnotherapy). We emphasize an integrative framework that supports symptom control and quality of life while helping reduce unnecessary antibiotic exposure.}, }
@article {pmid41892439, year = {2026}, author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR}, title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030277}, pmid = {41892439}, issn = {2079-6382}, support = {PRR-C05-i03-I-000190//RumiRes project-"Vigil&#xe2;ncia epidemiol&#xf3;gica de resist&#xea;ncias antimicrobianas e res&#xed;duos medicamentosos em Pequenos ruminantes da Regi&#xe3;o Centro"/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.<br><br>METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.<br><br>RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.<br><br>CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.}, }
@article {pmid41892455, year = {2026}, author = {Dashti, AA and Vali, L and Walsh, F}, title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030294}, pmid = {41892455}, issn = {2079-6382}, support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; }, abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.}, }
@article {pmid41892571, year = {2026}, author = {Munteanu, C and Prifti, E and Achim, L and Silaghi, CN and Mârza, SM}, title = {Next-Generation Hydrogels Integrating Natural Antioxidants and Microbiome Modulators for Improved Cancer Management.}, journal = {Gels (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/gels12030249}, pmid = {41892571}, issn = {2310-2861}, abstract = {Cancer remains a leading cause of death worldwide, and current treatments are often limited by toxicity and resistance. Emerging research highlights the crucial roles played by gut microbiome dysbiosis and oxidative stress in cancer development and treatment response. Through their antioxidant, anti-inflammatory, and immunomodulatory properties, natural antioxidants such as resveratrol, along with microbiome modulators like probiotics, prebiotics, and synbiotics, offer promising therapeutic benefits. However, issues such as low bioavailability, instability, and challenges related to targeted delivery hinder the clinical translation of these bioactive compounds. Next-generation hydrogels have emerged as adaptable platforms capable of delivering and protecting these agents in a site-specific and controlled manner. This review summarizes the design and synthesis of multifunctional hydrogels incorporating natural antioxidants and microbiome modulators for cancer therapy.}, }
@article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag069}, pmid = {41892593}, issn = {1751-7370}, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, }
@article {pmid41892598, year = {2026}, author = {Shah, RK and Lin, JJ and Makkapati, T and Berkowitz, AA and Greenwald, BD}, title = {The Effect of Traumatic Brain Injury on the Gastrointestinal System: A Comprehensive Review.}, journal = {Brain sciences}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/brainsci16030254}, pmid = {41892598}, issn = {2076-3425}, abstract = {BACKGROUND/OBJECTIVES: Traumatic brain injury (TBI) is a significant public health concern resulting in physical, cognitive, and behavioral impairments. Emerging evidence highlights a bidirectional relationship between brain injury and gut health, known as the brain-gut axis. This paper provides a comprehensive review of current literature exploring the relationship between TBI and various gastrointestinal (GI) pathologies, examining how brain injuries contribute to GI dysfunction and how gut health influences neurorecovery.<br><br>METHODS: A comprehensive search of peer-reviewed articles was conducted between March and June 2025 using databases including PubMed, Scopus, and Cochrane. Studies from 2010 onwards involving human subjects were screened. Search terms included combinations of "traumatic brain injury," "TBI," and "[gastrointestinal pathology]." Data regarding study design, population, GI outcomes, and proposed mechanisms were analyzed.<br><br>RESULTS: TBI triggers secondary injury cascades, including neuroinflammation, dysautonomia, and gut microbiome dysbiosis. The review identifies a wide spectrum of TBI-associated GI disorders, including dysphagia, esophageal disorders, gastric disorders, and intestinal disorders. Bowel dysfunction, manifesting as constipation or incontinence, is prevalent due to neurogenic factors and cognitive impairments. Additionally, metabolic dysregulation following TBI leads to malnutrition, hyperglycemia, and hypoglycemia, all of which impact morbidity.<br><br>CONCLUSIONS: The GI system is integrally connected to TBI recovery through immune modulation and nutrient absorption. Dysfunction within the brain-gut axis, specifically altered motility, permeability, and inflammation, contributes to secondary brain injury and impedes neurological outcomes. Clinical assessment of GI dysfunction should be integrated into routine TBI care. Therapeutic strategies, including early enteral nutrition, are essential to optimize recovery and reduce systemic inflammation.}, }
@article {pmid41892682, year = {2026}, author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A}, title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.}, journal = {Brain sciences}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/brainsci16030340}, pmid = {41892682}, issn = {2076-3425}, support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; }, abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.}, }
@article {pmid41892691, year = {2026}, author = {Li, L and Smardz, M and Soh, D and Marsh, PD and Hoare, A and Diaz, PI}, title = {Nutritional Pressure from Serum Amplifies Dysbiotic Features in an Oral Microbiome Synthetic Community.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag070}, pmid = {41892691}, issn = {1751-7370}, abstract = {Despite rapid advances in characterizing the human microbiome, the ecological pressures shaping its transitions from healthy to diseased states remain poorly resolved. This is particularly true for periodontitis, a slow-progressing chronic inflammatory disease associated with well-defined shifts in the subgingival microbiome. Here, we report the development of a complex synthetic community model of the subgingival microbiome, designed for systematic interrogation of ecological factors that drive community restructuring. The model includes 22 prevalent and abundant subgingival species maintained in mucin-rich medium under microaerophilic, continuous culture conditions, in a chemostat. Using this system, we interrogated the impact of serum, as a surrogate for the inflammatory exudate produced by the host in response to biofilm accumulation, on community structure and function. Through integrated 16S rRNA gene sequencing, metatranscriptomics, and metabolomics, we found that serum was not required for a community with a periodontitis-like configuration to establish, but its presence intensified features of dysbiosis. Serum increased total biomass, promoted polymicrobial aggregate formation, promoted nitrogen and protein metabolism thereby modifying the environmental pH towards alkalinity, and introduced nitrosative stress. Serum also modified the community metatranscriptome in ways that paralleled microbiome activities in human periodontitis. Serum, however, decreased community diversity by disproportionally conferring a competitive advantage to the pathogen Porphyromonas gingivalis. This synthetic community model has revealed serum as a key nutritional pressure that modulates subgingival microbiome ecology and may perpetuate dysbiosis.}, }
@article {pmid41892780, year = {2026}, author = {Safi, S and Berro, D and Amram, J and Burden, D and Palazzolo, D and Cuadra, GA}, title = {Influence of E-Liquids and Oral Commensal Bacteria on the Growth of Porphyromonas gingivalis Planktonically and in Biofilms.}, journal = {Dentistry journal}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/dj14030172}, pmid = {41892780}, issn = {2304-6767}, abstract = {Background: The increasing use of electronic cigarettes (ECIGs), especially among youth, has raised concerns about the impact of vaping on oral health. While ECIGs are often marketed as a safer alternative, the existing literature suggests that their use may have detrimental effects on the pulmonary and cardiovascular systems. The oral cavity is the first point of contact for ECIG aerosol, and new reports link vaping to the onset of periodontal disease. It is critical to understand the potential effects of vaping on the oral microbiome, which affects systemic health. This study investigates how flavored E-liquids and commensal bacteria influence the growth of Porphyromonas gingivalis, a periodontal pathobiont, under planktonic and biofilm conditions. Methods: P. gingivalis was grown planktonically in the presence of the supernatants of four streptococcal species (Streptococcus gordonii, Streptococcus intermedius, Streptococcus mitis, and Streptococcus oralis) and flavored E-liquids (tobacco, menthol, cinnamon, strawberry, and blueberry) under anaerobic conditions. Multispecies biofilms, including all the species mentioned above and Fusobacterium nucleatum, were also grown anaerobically and quantified by crystal violet assays, qPCR, and CFU counts. Results: Although E-liquids inhibit P. gingivalis growth under planktonic conditions, the presence of commensal supernatants partially mitigates this effect. However, P. gingivalis growth in multispecies biofilms is increased by E-liquid treatments. Conclusions: This study highlights the enhanced growth of P. gingivalis as part of an oral microbial community in the presence of E-liquids. These results suggest that E-liquid-induced alterations in multispecies biofilms may contribute to the observed dysbiosis in vapers and the associated risk of oral diseases.}, }
@article {pmid41892792, year = {2026}, author = {Skutnik-Radziszewska, A and Lis, VE and Skutnik, A and Szulimowska, J and Zalewska, A}, title = {Changes in Salivary Biomarkers and Oral Immune Parameters in Patients with Psoriasis: A Systematic Review.}, journal = {Dentistry journal}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/dj14030184}, pmid = {41892792}, issn = {2304-6767}, abstract = {Background: Psoriasis is a chronic immune-mediated inflammatory disease characterized by systemic inflammation and complex immune dysregulation that extends beyond the skin and may affect the oral environment. Increasing evidence suggests that saliva may serve as a non-invasive diagnostic medium reflecting both local and systemic pathological processes. This systematic review aimed to critically evaluate current evidence on salivary biomarkers in psoriasis, focusing on inflammatory mediators, oxidative stress parameters, immune-related factors, and oral microbiota alterations, and to assess their potential clinical and diagnostic relevance. Methods: A systematic literature search was performed according to PRISMA guidelines using PubMed, Scopus, and Web of Science databases, covering studies published between 1994 and October 2024. Original human studies evaluating salivary biomarkers in patients with psoriasis were included based on predefined PECOS criteria. Studies involving confounding inflammatory oral diseases without separate analysis were excluded. Eleven eligible studies were included in a qualitative synthesis. Results: The analyzed studies consistently demonstrated multidimensional alterations in salivary composition in psoriasis patients compared with healthy controls. Increased levels of pro-inflammatory cytokines (TNF-α, IFN-γ, IL-2) and reduced anti-inflammatory IL-10 indicated persistent immune activation. Elevated oxidative stress markers, including total oxidant status and oxidative stress index, supported the role of redox imbalance in disease pathogenesis. Alterations in innate immune components, such as salivary α-amylase, immunoglobulin A, and lysozyme, suggested impaired oral immune regulation. Moreover, emerging microbiome data revealed shifts toward pro-inflammatory bacterial taxa, including Prevotella and Porphyromonas. Some studies indicated that biologic therapy may modulate salivary biomarker profiles. Conclusions: Salivary biomarkers reflect systemic inflammatory and immunological alterations associated with psoriasis and represent promising non-invasive tools for disease monitoring and clinical assessment. Nevertheless, substantial methodological heterogeneity and limited sample sizes highlight the need for large-scale, standardized, and longitudinal studies to validate their diagnostic applicability.}, }
@article {pmid41892839, year = {2026}, author = {Lista, AR and Ayala Mosqueda, CV and Palacios, R and García Mansilla, MJ and Rodríguez Sojo, MJ and Ho Plágaro, A and Garcia Garcia, J and Gálvez, J and Rodríguez Nogales, A and Ruiz Malagón, AJ and Rodríguez Sánchez, MJ}, title = {Modulation of Microbiome-Mitochondria Axis as a Novel Approach for Treatment of Obesity: A Scoping Review.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/medsci14010124}, pmid = {41892839}, issn = {2076-3271}, support = {PI18/00826, PY20-01157, PI20/01447, B-CTS-664-UGR20, PI19/01058, PI24/02089 and JDC2022-049478-I, CD23/00117, IFI21/00030//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Obesity/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Mitochondria/metabolism ; Animals ; Probiotics/therapeutic use ; Energy Metabolism ; Fecal Microbiota Transplantation ; Prebiotics ; }, abstract = {Background: Obesity is a multifactorial, chronic disease characterised by excessive fat accumulation, low-grade inflammation, and metabolic dysfunction. Emerging evidence suggests that the gut microbiome-mitochondria axis may play a significant role in the pathophysiology of obesity, particularly in regulating energy metabolism, inflammatory responses, and mitochondrial function. However, most mechanistic insights into this axis derive from preclinical animal studies, while human evidence remains limited and largely associative. Mitochondrial dysfunction disrupts cellular energy balance, increases reactive oxygen species production, and may exacerbate gut dysbiosis, further contributing to metabolic disturbances. In addition, factors such as micronutrient deficiencies also play a relevant role in obesity development and progression. Objectives: This review aims to examine the bidirectional interactions between the gut microbiome and mitochondrial systems in obesity, with a focus on the underlying molecular mechanisms and their potential as therapeutic targets. Methods: Evidence from experimental models and clinical studies was analysed to evaluate how modulation of the microbiome-mitochondria axis through probiotics, prebiotics, dietary strategies, and faecal microbiota transplantation influences mitochondrial function, inflammation, and metabolic regulation. Results: Preclinical studies indicate that the gut microbiome modulates mitochondrial activity through the production of bioactive metabolites, including short-chain fatty acids, secondary bile acids, and tryptophan-derived compounds, which influence mitochondrial efficiency, lipid metabolism, and glucose regulation. Dysbiosis reduces these beneficial metabolites, impairing mitochondrial signalling and promoting adiposity and insulin resistance. Interventions targeting this axis have shown potential in restoring metabolic balance, improving mitochondrial function, and mitigating obesity-related complications such as hyperlipidaemia and glucose intolerance. Conclusions: Targeting the microbiome-mitochondria axis represents a promising therapeutic strategy for obesity, with the evidence based largely on preclinical findings. However, further well-designed human studies are required to clarify causality, optimise interventions, assess long-term safety and efficacy, and establish standardised clinical protocols for implementation.}, }
@article {pmid41893096, year = {2026}, author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N}, title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/jof12030163}, pmid = {41893096}, issn = {2309-608X}, support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; }, abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.}, }
@article {pmid41893120, year = {2026}, author = {Wu, XH and Gu, QY and Ma, CY and Zhang, W and Dai, CC}, title = {Research Progress in Plant Beneficial Fungi-Mediated Alleviation of Drought Stress in Crops.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/jof12030188}, pmid = {41893120}, issn = {2309-608X}, abstract = {Climate change has emerged as a major global concern and has substantially intensified the occurrence of abiotic stresses in plants. Among the abiotic constraints limiting crop production, drought stress is regarded as one of the most severe and pervasive challenges. To this end, developing efficient and sustainable strategies to mitigate drought has become an urgent priority in agricultural research. Current approaches to improving drought tolerance mainly include optimizing irrigation management, applying chemical regulators, and breeding drought-resistant cultivars. However, these strategies often suffer from high input costs, limited durability of effects, potential environmental risks, or restricted regional applicability, making it difficult to achieve long-term and stable drought mitigation. In recent years, a growing body of evidence has indicated that rhizosphere microorganisms play pivotal regulatory roles in plant drought adaptation, with beneficial fungi being particularly important. Nonetheless, the key processes and mechanisms by which microbiomes mediate crop adaptation to drought need to be elucidated systematically. In this review, we synthesize recent advances in the field and, against the backdrop of increasingly severe global drought, summarize the major impacts of drought stress on crop growth and physiological processes. We further systematically synthesize the key mechanisms by which beneficial fungi alleviate drought stress in crops. Finally, we outline future research directions to deepen our understanding of rhizosphere-crop-microbe interaction networks and to provide a theoretical basis for developing beneficial fungus-centered microbial biofertilizers and microbiome-mediated strategies to enhance crop drought resilience.}, }
@article {pmid41893137, year = {2026}, author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS}, title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/jof12030205}, pmid = {41893137}, issn = {2309-608X}, support = {21R097//ARIFSID/ ; }, abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.}, }
@article {pmid41893303, year = {2026}, author = {Wang, Y and Guo, X and Lu, J and Li, L and Tang, Y and Xiao, H and Li, S and Liu, W}, title = {Enhancement of Disease Resistance in Pengze Crucian Carp (Carassius auratus var. Pengze) by Carvacrol Through Modulation of Intestinal Microbiota and Serum Metabolism.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030151}, pmid = {41893303}, issn = {2218-1989}, support = {JXSNKYJCRC202305//Jiangxi Academy of Agricultural Sciences/ ; 3246210059//National Natural Science Foundation of China/ ; CARS-45-42//China Agriculture Research System/ ; }, abstract = {Objectives: This study aimed to investigate the regulatory effects of dietary carvacrol on intestinal micro biota composition, serum metabolic profiles, and their association with increased resistance to Aeromonas hydrophila in Pengze crucian carp. Methods: Juvenile fish (5.63 ± 0.35 g) were randomly allocated into two experimental groups: a control group (CK) fed a basal diet and a treatment group (CA) supplemented with 600 mg/kg microencapsulated carvacrol. Following an 8-week feeding trial, nine specimens per group were sampled for venous blood and intestinal tract collection. Remaining individuals were subjected to a 12-h A. hydrophila challenge prior to identical sample collection. Results: Key findings revealed that carvacrol supplementation induced significant microbial modulations, notably reducing Firmicutes abundance while enhancing Cetobacterium populations by 33.25% compared to controls. Post-challenge analysis demonstrated marked declines in intestinal microbial diversity indices (Observed ASV, Chao1, ACE, and PD whole tree) in the CK group, whereas the CA group maintained stable microbial diversity. Pathogenic genera including Aeromonas, Shewanella, and Vibrio showed significant proliferation in challenged controls, contrasting with maintained microbial homeostasis in carvacrol-fed specimens. Serum metabolomic profiling identified the most significantly altered metabolic pathways associated with carvacrol administration: glycerophospholipid metabolism, linoleic acid metabolism, arachidonic acid metabolism, α-linolenic acid metabolism, GPI-anchor biosynthesis, and autophagy-animal pathways. Conclusions: Our results demonstrate that dietary carvacrol may reinforce intestinal microbial barrier function by optimizing beneficial microbial composition and reducing the proportion of pathogens, and modulate immune-related metabolic pathways critical for host defense, which might be involved in enhanced disease resistance.}, }
@article {pmid41893315, year = {2026}, author = {Chen, Z and Jiang, S}, title = {Chemical Signaling and Metabolomic Crosstalk in Endophytic Fungi-Medicinal Plant Symbioses for Natural Product Discovery and Sustainable Bioproduction.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030164}, pmid = {41893315}, issn = {2218-1989}, support = {K2025-001//Guiyang Kangyang University/ ; }, abstract = {Background: Medicinal plants function as complex holobionts, with their therapeutic potential significantly shaped by the associated microbiome, particularly endophytic fungi. These symbionts engage in a sophisticated "chemical signaling" with their hosts, acting as biotic elicitors that modulate plant secondary metabolism while simultaneously responding to host cues to activate their own cryptic biosynthetic gene clusters (BGCs). This review aims to critically summarize the multi-layered mechanisms driving this metabolic crosstalk and evaluate strategies to harness this symbiotic intelligence for natural product discovery. Methods: A systematic literature survey spanning the last decade was conducted across major databases. The search specifically targeted studies investigating endophytic fungi in medicinal plants, focusing on experimental designs for BGC activation, applications of spatial metabolomics (matrix-assisted laser desorption/ionization mass spectrometry imaging, MALDI-MSI), and the structural elucidation of novel bioactive natural products through co-culture or in planta models. Results: Our analysis reveals that host-derived chemical cues, such as specific root exudates and oxylipins, act as primary triggers to awaken silent fungal BGCs. We collated numerous recently discovered bioactive metabolites-including novel polyketides, highly rearranged terpenoids, and unique alkaloids-demonstrating their potent antimicrobial and cytotoxic properties. Furthermore, a critical evaluation of spatial metabolomics studies demonstrates that metabolic exchange is highly localized at the plant-fungus interface, providing contextual insights that traditional bulk tissue extraction fails to capture. Conclusions: This review bridges the gap between ecological understanding and synthetic biology applications. We conclude that translating the mechanisms of this "chemical signaling" into biotechnological strategies offers a sustainable pathway for the bioproduction of high-value pharmaceuticals, thereby reducing reliance on the wild harvesting of medicinal plants.}, }
@article {pmid41893325, year = {2026}, author = {Han, G and Yuan, S and Yu, W}, title = {Obesity and Cancer: From Systemic Metabolic Reprogramming to Immunotherapy Paradox.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030174}, pmid = {41893325}, issn = {2218-1989}, support = {2023YZ02//Yangtze University/ ; }, abstract = {With the global rise in overweight and obesity, excess adiposity has emerged as a modifiable carcinogenic exposure. Beyond energy surplus, obesity establishes a durable pro-tumorigenic baseline through endocrine-metabolic rewiring, chronic low-grade inflammation, and structural/mechanical remodeling of tissues, thereby shaping organ-specific microenvironments that favor malignant transformation and progression. This review integrates systemic metabolic and endocrine alterations with tumor microenvironmental physical barriers, immune reprogramming, and neuroimmune regulation to explain heterogeneity in cancer risk, progression, and treatment response. We propose a stratified assessment framework based on measurable indicators-body composition, inflammatory status, and treatment exposure-to support risk prediction, mechanistic validation, and the design of actionable experimental and clinical strategies.}, }
@article {pmid41893329, year = {2026}, author = {Casadevall, C and Enríquez-Rodríguez, CJ and Eliassaf, A and Castro-Acosta, A and Faner, R and López-Campos, JL and Monsó, E and Pascual-Guàrdia, S and Camps-Ubach, R and Cosío, BG and Agustí, A and Shalev, O and Gea, J and On Behalf Of The Biomepoc Group, }, title = {Sex-Specific Plasma Metabolomic Signatures in COPD Reveal Creatine, Purine/Urate, and Bile-Acid Axes.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030178}, pmid = {41893329}, issn = {2218-1989}, support = {PI21/00785//Instituto de Salud Carlos III (ISCIII) and the European Union/ ; PI25/01093//Instituto de Salud Carlos III (ISCIII) and the European Union/ ; M-BAE BA22/00009)//Instituto de Salud Carlos III (ISCIII) and the European Union/ ; PFIS, ref. FI22/00003//Instituto de Salud Carlos III (ISCIII) and the European Union/ ; Research Grant 2020//SEPAR/ ; Research Grant 2024//FUCAP/ ; }, abstract = {Metabolomic studies in COPD reveal systemic metabolic perturbations, yet sex is often treated as a covariate rather than a biological driver. We aimed to identify plasma metabolites differentiating COPD from controls and to define sex-specific metabolic signatures in both groups. Methods: In this controlled observational study (BIOMEPOC cohort), untargeted plasma metabolomics was performed by LC-MS/MS. Differential abundance was tested across four contrasts (COPD vs. controls; men vs. women within controls; men vs. women within COPD; sex-by-disease interaction) with a false discovery rate (FDR) correction. Because smoking history differed between COPD and controls, a post hoc ever-smokers analysis was conducted. Results: COPD differed from controls in nine metabolites (all decreased): DL-stachydrine, 3-methyl-L-histidine, fructose, pipecolinic and nipecotic acids, 5-nitro-o-toluidine, conjugated linoleic acid, aminoadipate, and creatinine. This pattern is compatible with metabolic depletion, remodeling, and/or altered flux across multiple compartments rather than simple substrate deficiency, spanning muscle-related pools, amino acid handling, carbohydrate-associated metabolism, and exposome-linked inputs. In ever-smokers, results were directionally consistent, with five metabolites remaining nominally significant. Among controls, five metabolites were higher in men after FDR correction (PABA, cis-4-hydroxy-D-proline, N-acetylasparagine, deoxycarnitine, and creatinine), consistent with physiological sex dimorphism in energy pathways, connective-tissue remodeling, and diet/microbiome-related metabolism. Within COPD, six metabolites differed by sex after FDR correction, defining three axes: creatine energy buffering (men: higher GAA/creatinine, lower creatine), purine/urate handling (men: higher urate), and conjugated bile acids (men: higher GCDCA), implicating muscle bioenergetics, redox/inflammatory tone, and gut-liver crosstalk. Conclusions: Plasma metabolomics identifies a pattern compatible with systemic remodeling in COPD and sex-associated divergences in creatine, purine/urate, and bile-acid pathways, supporting a sex-influenced view of systemic COPD heterogeneity and highlighting targets for mechanistic validation.}, }
@article {pmid41893350, year = {2026}, author = {Muroya, S and Ojima, K and Banno, A and Nagai, H and Kakibuchi, K and Higuchi, T and Sakamoto, S and Matsukawa, K}, title = {Dietary Citrus Peel Supplementation Enhances Hepatic Energy Metabolism, Muscle 9-HODE Generation and Isoleucine Catabolism in Beef Cattle.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030201}, pmid = {41893350}, issn = {2218-1989}, support = {2021-21//Japan Racing Association/ ; 25K02159//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Citrus components potentially suppress adipogenic differentiation and lipid accumulation, and exhibit anti-inflammatory and antioxidant effects. We hypothesized that the bioactive compounds in Citrus junos Sieb ex Tanaka (yuzu) fruit peel can alter the systemic metabolism and productivity of beef cattle.<br><br>METHODS: Japanese Brown (JBR) steers were fed with a diet supplemented with 2.5% yuzu peel during the last month of the finishing period. To investigate the effect of dietary yuzu supplementation (DYS) on beef and liver metabolism, we explored the metabolomic profiles of longissimus thoracis (LT, loin) muscle at 14 d postmortem using capillary electrophoresis (CE-TOF/MS) and high-performance liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS).<br><br>RESULTS: The DYS treatment enhanced the beef fat score compared to that recorded in beef in the no-DYS (None) group (p = 0.050); however, the other carcass quality traits were not significantly different between the DYS and None groups. CE-TOF/MS and LC-TOF/MS revealed 242 and 107 annotated peaks, respectively, for the LT muscle. DYS significantly increased 9(S)-hydroxyoctadecadienoic acid (9-HODE, a beef flavor precursor), cyclo(-Leu-Pro), spermidine, asymmetric dimethylarginine, and 7&#x3b1;-hydroxycholesterol levels and reduced 2-ethylhydracrylic acid (2-EHAA), &#x3b3;-tocopherol, coenzyme Q10 (CoQ10), sphingomyelin(d18:1/16:0), Cys-Gly, Tyr-Arg, and palmitoylcarnitine levels in postmortem LT muscle (p < 0.050). Concomitantly, in the fresh liver, DYS increased acetyl-CoA, 6-phosphogluconic acid, S-methylglutathione, ATP, ribulose 5-phosphate, and ADP levels and suppressed the content of thiamine, Ala-Ala, riboflavin, and ascorbate 2-sulfate (p < 0.050).<br><br>CONCLUSION: Collectively, yuzu ingredients activated ATP production in the liver through the elevation of hepatic energy metabolism primarily in the citrate cycle and &#x3b2;-oxidation, and potentially altered muscle metabolism, including linoleic acid oxidation, FAD-mediated electron transport chain, and isoleucine catabolism, as demonstrated in the reduced accumulation of 2-EHAA and CoQ10 in DYS beef. Moreover, DYS likely affects the gut microbiome by enhancing the production of cyclo(-Leu-Pro), an antimicrobial dipeptide.}, }
@article {pmid41893361, year = {2026}, author = {Zhang, Q and Jin, Z}, title = {Gut Microbiota-Bile Acid Axis in Type 2 Diabetes-Associated Gallbladder Diseases: Mechanisms and Therapeutic Potential.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030212}, pmid = {41893361}, issn = {2218-1989}, support = {No. SH2025042//Zhenjiang Key R&amp;D Program-Social Development Track/ ; }, abstract = {Gallbladder diseases spanning cholelithiasis, cholecystitis, and gallbladder cancer represent a clinically heterogeneous continuum in which type 2 diabetes mellitus (T2DM) acts as a key metabolic modifier. Conventional models centered on bile supersaturation alone do not sufficiently account for the persistent inflammation and inter-individual variability frequently observed in practice. Here, we synthesize emerging evidence implicating the gut microbiota-bile acid (BA) axis as an integrative mechanism linking metabolic dysregulation, barrier dysfunction, and biliary pathobiology in the diabetic host. Hyperglycemia and insulin resistance, together with impaired mucosal resilience, are associated with shifts in microbial community structure and BA-transforming functions (e.g., bile salt hydrolase and 7α-dehydroxylation), favoring a more hydrophobic BA pool. These changes may disrupt BA receptor signaling, including FXR-FGF15/19 and TGR5-related pathways, thereby amplifying metabolic inflammation, promoting lithogenic bile formation, and impairing gallbladder motility. In parallel, barrier vulnerability may facilitate microbial translocation and LPS-driven immune activation, reinforcing a feed-forward loop that supports the gallstone-inflammation-carcinogenesis trajectory. Translationally, microbiome- and BA-oriented strategies (dietary patterns, bile acid therapeutics, and targeted microbiome modulation) are promising adjuncts, yet precision management should explicitly consider medication- and weight loss-related confounding-particularly with incretin-based therapies-to optimize biliary outcomes across disease stages.}, }
@article {pmid41893403, year = {2026}, author = {Westerström, P and Bivand, JM and Kommedal, &#xd8; and Ehrnström, B and Andreassen, JS and Afset, JE}, title = {Odontogenic Brain Abscess in a Hereditary Haemorrhagic Telangiectasia (HHT) Patient: Case Report with a Comprehensive Literature Review.}, journal = {Tropical medicine and infectious disease}, volume = {11}, number = {3}, pages = {}, pmid = {41893403}, issn = {2414-6366}, abstract = {BACKGROUND: Recent diagnostic methods have enabled the detection of often culture-negative pathogens, including anaerobic bacteria from the oral cavity. Characterising the microbial diversity and co-occurrence of bacteria in such infections is important for understanding the molecular pathophysiology in odontogenic brain abscesses.<br><br>CASE PRESENTATION: We describe a case of polymicrobial odontogenic brain abscess in a 59-year-old man of Vietnamese ethnicity with a documented increased risk of brain abscess due to Hereditary Haemorrhagic Telangiectasia (HHT). The microbiological diagnostic work-up included conventional culture, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), targeted 16S rDNA analysis using three broad-range group-specific PCR (polymerase chain reaction) assays and next-generation sequencing (NGS). A literature review was conducted, including database searches for each identified microorganism. Twelve anaerobic bacterial species were detected, among which Treponema medium, Capnocytophaga HMT-323 and Candidatus Saccharibacteria oral taxon 488 have not previously been reported in brain abscesses. In addition, we identified the extremely rare pathogens Arachnia propionica and Capnocytophaga ochracea.<br><br>CONCLUSION: This is the first report of Ca. Saccharibacteria oral taxon 488 in a clinical sample and the first detection of any species from this phylum in a brain abscess, co-detected with A. propionica, consistent with its obligate epibiotic lifestyle. Our findings broaden the known microbial diversity associated with odontogenic brain abscesses and underscore the value of 16S rDNA NGS in characterising polymicrobial infections, particularly when fastidious or uncultivable organisms are involved.}, }
@article {pmid41893554, year = {2026}, author = {Lin, Q and Wu, X and Li, L and Peng, T and Zou, X and Li, G and Wang, J and Tang, X and Yue, X and Guo, C and Li, P}, title = {Impact of Aspergillus flavus Infection on the Rhizosphere Bacterial Microbiota of Peanut (Arachis hypogaea L.).}, journal = {Toxins}, volume = {18}, number = {3}, pages = {}, pmid = {41893554}, issn = {2072-6651}, support = {2024JH2/102600162; 2025JH2/101800102;2023JH1/10200002//Liaoning Provincial Department of Science and Technology/ ; 2023BS0803;2025JCX1002;2025QN2614;2025XKJS8531//Liaoning Academy of Agricultural Sciences/ ; 2023BBA002//Hubei Province Major Science and Technology Special Project/ ; SWDSJC2023002//Key Laboratory of Oilseeds Processing&#xff0c;Ministry of Agriculture and Rural Affairs, China/ ; 20254032//Agricultural Product Quality and Safety Risk Assessment Project of the Ministry of Agriculture and Rural Affairs/ ; }, mesh = {*Arachis/microbiology/growth &amp; development ; *Aspergillus flavus ; *Rhizosphere ; *Microbiota ; *Bacteria/genetics/classification/growth &amp; development ; Soil Microbiology ; Plant Roots/microbiology/growth &amp; development ; *Plant Diseases/microbiology ; Phylogeny ; }, abstract = {This study investigated the effects of inoculating peanuts with two Aspergillus flavus strains (Aspergillus flavus CGMCC 3.4408 and A. flavus LNZW 23) on plant growth and the rhizosphere bacterial community. Infection significantly inhibited peanut growth. By 60 days post-inoculation (dpi), plant height in inoculated groups (CGMCC 3.4408, 26.4 cm; LNZW 23, 25.5 cm) was significantly lower than in the non-inoculated control (CK, 32.3 cm), with concomitant significant reductions in shoot and root biomass. Analysis of rhizosphere microbiota revealed that early infection (7 dpi) reduced bacterial species richness and phylogenetic diversity. Beta diversity analysis (PCoA) confirmed a significant divergence in microbial community structure between inoculated and control groups over time, with a statistically significant difference also observed between the two inoculated strains (p = 0.016). In terms of community composition, Proteobacteria, Acidobacteriota, and Actinobacteria were the three dominant phyla. At the genus level, infection altered the relative abundance of key taxa; genera such as KD4-96, Vicinamibacteraceae, and RB41 decreased at 7 dpi, while Sphingomonas remained relatively stable. By 60 dpi, community dominance increased, marked by rising abundances of Actinobacteria and Proteobacteria. In conclusion, A. flavus infection not only suppresses peanut growth but also persistently alters its rhizosphere microbial community, with effects demonstrating both time-dependency and strain-specificity.}, }
@article {pmid41893658, year = {2026}, author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N}, title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893658}, issn = {2306-7381}, support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&amp;M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; }, abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.}, }
@article {pmid41893724, year = {2026}, author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W}, title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, pmid = {41893724}, issn = {2306-7381}, support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; }, abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.}, }
@article {pmid41894063, year = {2026}, author = {Romero, JDJR and Barko, P and Suchodolski, JS and Williams, DA and Ganz, HH and Gal, A}, title = {Serum metabolomics of diabetic dogs treated with daily administration of a commercially available lyophilized feces preparation.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41894063}, issn = {1573-7446}, support = {Vera Arvilla Traxler Fund//University of Illinois at Urbana-Champaign Companion Animal Research Grant Program/ ; }, }
@article {pmid41894083, year = {2026}, author = {Li, Y and Jiang, M and Pang, J and Ma, C and Zhang, H and Yin, F and Jia, Y and Zou, X and Zuo, T and Zhang, H}, title = {High-altitude exposure remodels the gut microbiota: health and disease.}, journal = {MedScience}, volume = {}, number = {}, pages = {}, pmid = {41894083}, issn = {3091-4981}, abstract = {With the increasing number of individuals travelling to or residing in high-altitude regions, understanding the physiological and pathological consequences of such environments has become increasingly important. High-altitude exposure poses significant challenges to human health, primarily due to hypobaric hypoxia, which triggers a cascade of responses, including energy deficiency, oxidative stress, and inflammation. One of the critical consequences is the disruption of the gut barrier, which facilitates the translocation of the gut microbiota and further exacerbates local and systemic inflammation. Notably, the gut microbiota, a dynamic environmental sensor, undergoes significant remodelling in high-altitude environments. The modified production of microbial metabolites such as bile acids influences gut homeostasis as well as glucose and lipid metabolism, and ultimately contributes to individual variability in high-altitude acclimatization. These changes have been implicated in the pathogenesis of altitude-related illnesses such as acute and chronic mountain sickness, as well as in metabolic and gastrointestinal disorders such as diabetes, obesity, irritable bowel syndrome, colorectal cancer, cholelithiasis, and osteoporosis. Preliminary explorations have demonstrated the therapeutic potential of microbiome-based interventions such as faecal microbiota transplantation in acute and chronic mountain sickness. Further research into gut microbiota modulation may provide applicable options for promoting high-altitude acclimatization and preventing high-altitude illness.}, }
@article {pmid41894116, year = {2026}, author = {Luo, S and Dang, Y and Chen, HD and Peng, J and Li, L}, title = {Community heterogeneity scaling of gut microbiomes across Chinese ethnicities and lifestyles appears invariant.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41894116}, issn = {1618-1905}, }
@article {pmid41894142, year = {2026}, author = {Sun, B and Zhao, C and Chen, X and Yang, B and Cui, W and Zhang, J and Hou, X and Yan, X and Ni, Q and Cheng, P and Chen, K}, title = {Fucoxanthin: A Comprehensive Review on Digestion, Biotransformation, Microbiome Interaction, and Targeted Delivery.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c12697}, pmid = {41894142}, issn = {1520-5118}, abstract = {Fucoxanthin, a marine carotenoid with diverse bioactivities, has attracted increasing attention for its health-promoting potential. However, its gastrointestinal fate and targeted delivery remain insufficiently understood, limiting its translation into effective applications. This review summarizes current knowledge on fucoxanthin's digestion, biotransformation, tissue distribution, interactions with the gut microbiota, and different delivery systems. In vivo, fucoxanthin is hydrolyzed to fucoxanthinol in the intestine and further converted to amarouciaxanthin A in the liver, undergoing subsequent dehydrogenation, isomerization, and esterification before distribution into plasma, liver, adipose tissue, and heart. Additionally, fucoxanthin modulates gut microbial composition through a duplibiotic effect, linking its metabolism to host-microbiota interactions. Lipid-, polysaccharide-, and protein-based delivery systems have been developed due to low oral bioavailability; these are also compared and summarized. Together, this review provides a theoretical framework for the rational design of functional foods and therapeutic applications of fucoxanthin.}, }
@article {pmid41894324, year = {2026}, author = {Thompson, J and Connors, BM and Zavala, VM and Venturelli, OS}, title = {Physics-constrained neural ordinary differential equation models to discover and predict microbial community dynamics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2517661123}, doi = {10.1073/pnas.2517661123}, pmid = {41894324}, issn = {1091-6490}, support = {HR00112530072//DOD | ARPA | Defense Sciences Office, DARPA (DSO)/ ; R01EB030340//HHS | National Institutes of Health (NIH)/ ; HR00112320001//DOD | ARPA | Defense Sciences Office, DARPA (DSO)/ ; CBET-2315963//National Science Foundation (NSF)/ ; }, mesh = {Machine Learning ; *Microbiota/physiology ; *Neural Networks, Computer ; *Models, Biological ; Ecosystem ; }, abstract = {Microbial communities play essential roles in shaping ecosystem functions and predictive modeling frameworks are crucial for understanding, controlling, and harnessing their properties. Competition and cross-feeding of metabolites drives microbiome dynamics and functions. Existing mechanistic models that capture metabolite-mediated interactions in microbial communities have limited flexibility due to rigid assumptions. While machine learning models provide flexibility, they require large datasets, are challenging to interpret, and can overfit to experimental noise. To overcome these limitations, we develop a physics-constrained machine learning model, which we call the neural species mediator (NSM), that combines a mechanistic model of metabolite dynamics with a machine learning component. The NSM outperforms mechanistic or machine learning components on in vitro experimental datasets and provides insights into direct biological interactions. In summary, carefully embedding a neural network into a mechanistic model of microbial community dynamics improves prediction performance and interpretability compared to its constituent mechanistic or machine learning components.}, }
@article {pmid41894325, year = {2026}, author = {Russ, D and Saha, C and Paul, K and Zheng, Z and Law, TF and Anguita-Maeso, M and Lundberg, DS and Fitzpatrick, CR and Dangl, JL}, title = {Specialization of independently acquired flagellar FliC proteins in plant-associated Sphingomonas balances swimming and immunogenicity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2535583123}, doi = {10.1073/pnas.2535583123}, pmid = {41894325}, issn = {1091-6490}, support = {ALTF 743-2019//European Molecular Biology Organization (EMBO)/ ; 2021.0102//Knut och Alice Wallenbergs Stiftelse (kawforskning)/ ; 532852-2019//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; IOS-2416244//NSF (NSF)/ ; }, mesh = {*Flagellin/genetics/immunology/metabolism ; *Sphingomonas/genetics/immunology/physiology ; *Flagella/immunology/genetics/metabolism ; *Bacterial Proteins/genetics/immunology/metabolism ; }, abstract = {Plants monitor their environment for microbial invaders using pattern-recognition receptors that detect microbe-associated molecular patterns (MAMPs). Flagellin, the main component of bacterial flagellum, contains the flg22 epitope recognized by the plant immune receptor FLS2. Immune recognition can create an evolutionary conflict, requiring bacteria to balance flagellar function and immune evasion. Here, we show that plant-associated Sphingomonas resolve this constraint by partitioning two flagellar functions, motility and colonization, across two divergent and independently acquired flagellin genes. Comparative genomics revealed widespread coexistence of FliC proteins expressing either an immunogenic variant (FliC-H) or a nonimmunogenic variant (FliC-L). The nonimmunogenic FliC-L is necessary and sufficient for full directional swimming, whereas FliC-H is dispensable for swimming, but sufficient for full attachment and colonization. Flagellin expression patterns mirror these functions. Thus, FLS2 recognizes the flagellar variant required for colonization rather than motility, potentially restricting colonizing bacteria from entering internal leaf and root tissues.}, }
@article {pmid41894949, year = {2026}, author = {Brem, AK and Khan, Z and Radermacher, J and Georgiadis, K and Lazarou, I and Grammatikopoulou, M and Pickering, E and Mitterreiter, J and Aakre, JA and Ashton, NJ and Baquero, M and Beser-Robles, M and Braboszcz, C and Brandt, S and Brown, J and Cacciamani, F and Campill, S and Collins, C and Deshpande, P and Diaz, A and Durrleman, S and Engelborghs, S and Ferré-González, L and Frisoni, GB and Gjestsen, MT and Gove, D and Honigberg, L and Huang, B and Hudak, A and Kaushik, S and Letoha, T and Marquardt, G and Mendes, AJ and Müllenborn, M and Paletta, L and de Barros, NP and Pszeida, M and Vik-Mo, AO and Rostamipour, H and Perneczky, R and Rauchmann, BS and Russegger, S and Schirmer, T and Shadmaan, A and Solana, AB and Soria-Frisch, A and Tegethoff, P and Ribbens, A and De Witte, S and van der Giezen, M and Nikolopoulos, S and Corbett, A and Fröhlich, H and Aarsland, D and , }, title = {Screening for Alzheimer's disease in the community using an AI-driven screening platform: design of the PREDICTOM study.}, journal = {The journal of prevention of Alzheimer's disease}, volume = {13}, number = {5}, pages = {100545}, doi = {10.1016/j.tjpad.2026.100545}, pmid = {41894949}, issn = {2426-0266}, abstract = {BACKGROUND: Recent developments in physiological, imaging and digital biomarkers combined with the approval of new disease-modifying drugs against Alzheimer's disease (AD) and diagnostic blood tests provide an opportunity to shift the first diagnostic steps to the home-setting. While these novel biomarkers enable scalable screening and earlier detection and treatment of AD, they require an evaluation of their accuracy, feasibility, and safety in primary care and the community setting.<br><br>OBJECTIVES: The aim of PREDICTOM is to develop and test the accuracy of an artificial intelligence (AI) driven screening platform for the risk assessment and early detection of AD to extend the clinical pathway to home-based screening using established and novel biomarkers.<br><br>DESIGN/SETTING: PREDICTOM is a European (Norway, UK, Belgium, France, Switzerland, Germany, Spain) observational, prospective cohort study using a cloud-based platform that stores a digitalised journey for each participant and provides a collection of artificial-intelligence (AI) algorithms and tools for risk assessment and early diagnosis and prognosis.<br><br>PARTICIPANTS: Cohort 1 consists of 4000 adults aged 50 years or older at risk of developing AD. Cohort 2 consists of 615 participants selected from Cohort 1 based on estimates indicating high (N = 415) or low (N = 200) risk of AD. Data from existing cohorts will guide the analytic strategy of the study.<br><br>MEASUREMENTS: Cohort 1 will undergo home-based assessments (Level 1), Cohort 2 will undergo in-clinic assessments (Levels 2 and 3). Level 1 includes at-home screening, collecting digital and physiological data (questionnaires, cognition, hearing, eye-tracking) and biofluids (capillary blood via finger-stick and saliva) for biomarker analysis. Level 2 comprises a more complex biomarker collection, most of which can be completed in primary care, including EEG, MRI, venous blood, microbiome from stool, cognition, hearing, and eye-tracking. Level 3 includes a diagnostic evaluation to confirm or rule out AD pathology using established biomarkers (cerebrospinal fluid, or amyloid PET).<br><br>CONCLUSIONS: PREDICTOM will develop AI-driven algorithms for the early detection of AD using biomarkers that can be collected at home or in the community care setting, and evaluate their integration into a well-defined and comprehensive clinical pathway.}, }
@article {pmid41895098, year = {2026}, author = {Ninham, B and Battye, M and Carlin, M}, title = {Gut, brain and the Glycocalyx: A portrait of Parkinsons disease.}, journal = {Advances in colloid and interface science}, volume = {353}, number = {}, pages = {103880}, doi = {10.1016/j.cis.2026.103880}, pmid = {41895098}, issn = {1873-3727}, abstract = {Parkinson's disease (PD) has generated extensive data without a unifying mechanism. Although growing evidence implicates the gut microbiome in PD pathogenesis, the gut-brain connection remains unresolved. While the nature of such interactions remains elusive, increasingly it is the glycocalyx, a nanoscale structural network lining endothelial surfaces that is emerging as a key linkage to disease mechanisms. We propose the endothelial surface layer-glycocalyx (ESL-GC) complex as the missing mechanistic interface. Within this framework, microbiome dysbiosis, disruption of ESL-GC structure and function, potassium dysregulation, other specific ion effects, and reactive gas nanobubbles act together as foundational contributors to PD pathology. This model reframes PD from a primarily dopamine-centred neurodegenerative disorder to an interface-based systems disorder and offers a coherent basis for integrating previously conflicting findings.}, }
@article {pmid41895157, year = {2026}, author = {Žukauskaitė, K and Rauduvytė, K and Baušys, A and Horvath, A and Poškus, T and Stadlbauer, V}, title = {Surgery and the Gastrointestinal Microbiome in Cancer: Bidirectional Impacts and Therapeutic Opportunities - a Narrative Review.}, journal = {Surgical oncology}, volume = {66}, number = {}, pages = {102411}, doi = {10.1016/j.suronc.2026.102411}, pmid = {41895157}, issn = {1879-3320}, abstract = {Gastrointestinal cancers rank among the most common malignancies globally, and although surgical resection remains the cornerstone of curative therapy, it is associated with considerable postoperative morbidity and mortality. Emerging evidence suggests that the gut microbiome is a critical determinant in the pathogenesis of postoperative complications, including surgical site infections, anastomotic leakage, and postoperative ileus. Microbiome-targeted interventions - including probiotics, prebiotics, and synbiotics - have shown promise in modulating microbial communities and supporting postoperative recovery; however, clinical efficacy remains inconsistent, and standardized perioperative protocols are yet to be established. This review summarizes current evidence on the interactions between gastrointestinal cancer surgery and the perioperative gut microbiome, emphasizing opportunities to harness microbiome-targeted interventions to reduce complications and enhance recovery.}, }
@article {pmid41895258, year = {2026}, author = {Reilly, ER and Charron-Lamoureux, V and Mannochio-Russo, H and Morgan, EW and Boyle, NR and Koo, I and Coudriet, E and Hao, F and Mohanty, I and Perdew, GH and Dorrestein, PC and Patterson, AD}, title = {Systemic rhythmicity of host and bacterial bile acid amidates in the mouse.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101541}, doi = {10.1016/j.cels.2026.101541}, pmid = {41895258}, issn = {2405-4720}, abstract = {Bacterial bile acid amidates (BBAAs) represent an emerging class of host-microbe co-metabolites formed when gut bacteria conjugate bile acids with amino acids beyond taurine and glycine. Although these conjugates have been shown to modulate immune signaling and epithelial integrity, their spatial and temporal distribution across host tissues remains poorly understood. Here, we profiled 690 samples from time-restricted-fed mice, spanning 14 organs, digestive tract contents, and biofluids, to map the temporal dynamics of BBAAs. We identified widespread and tissue-specific oscillations of BBAAs, with the greatest temporal synchronization observed in the ileal contents and progressively diminished rhythmicity in the periphery. Amidates with hydrophilic or hydrophobic side chains remained relatively constant, while aromatic conjugates exhibited the most substantial variation. These findings reveal that BBAAs are temporally and spatially distributed throughout the body, supporting a model in which microbes encode systemic signals through the timing and structure of their metabolites.}, }
@article {pmid41895287, year = {2026}, author = {Gubatan, J and Sojwal, RS and Ye, J and Boye, TL and Hoang, JN and Fardeen, T and Temby, M and Rubin, SJS and Spencer, SP and Kotagiri, P and Rogalla, S and Rosen, MJ and Nielsen, OH and Boyd, S and Sonnenburg, J and Sinha, SR}, title = {Multi-omics reveal vitamin D regulation of immune-gut microbiome interactions and tolerogenic pathways in inflammatory bowel disease.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102703}, doi = {10.1016/j.xcrm.2026.102703}, pmid = {41895287}, issn = {2666-3791}, abstract = {Loss of immune tolerance to the gut microbiome plays a pathogenic role in inflammatory bowel disease (IBD). How dietary factors alter host immune-gut microbiome interactions in IBD is unclear. Here, we apply multi-omics (immunoglobulin A or G and 16S rRNA sequencing [IgA-seq, IgG-seq], blood single-cell RNA sequencing [scRNA-seq], and immune repertoire sequencing) to investigate the effects of 12 weeks of vitamin D on host immune microbe interactions in patients with IBD. Vitamin D treatment associates with decreased disease activity and inflammatory markers and increased IgA-bound and decreased IgG-bound gut microbiota. Vitamin D alters the profiles of IgA-bound (increased Lachnospiraceae, Blautia) and IgG-bound (decreased Proteobacteria, Enterococcaceae) gut bacteria. Vitamin D increases B cell activating factor (BAFF) signaling between plasmacytoid dendritic cells and B cells, alters BCR and TCR clonotypes that associate with Ig-bound gut microbiota, and increases α4β7+ B and T regulatory cells. Our results demonstrate that vitamin D promotes immune tolerance to gut microbiota in patients with IBD. Clinical trial is registered under NCT04828031.}, }
@article {pmid41895322, year = {2026}, author = {Sykes, BE and Lutzoni, F and Renwick, A and Oita, S and Skarha, SM and Arnold, AE}, title = {Fungal endophytes of an endangered tree vary with stress and microenvironment in an ex situ conservation nursery.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70181}, doi = {10.1002/ajb2.70181}, pmid = {41895322}, issn = {1537-2197}, support = {DEB-1541496//National Science Foundation/ ; }, abstract = {PREMISE: Plants in ex situ conservation nurseries acquire diverse fungal associates that may be moved among nurseries or into the wild during outplanting, including fungal endophytes that contribute to a broad range of functions and occur in leaves, sometimes alongside pathogens. To improve understanding of fungal symbionts in a plant of high conservation concern, we characterized foliar fungal endophytes of Torreya taxifolia, one of the world's most threatened conifers, in an ex situ conservation nursery.<br><br>METHODS: We used culture-based and culture-free approaches to characterize fungal endophytes in leaves of T. taxifolia over 2 years and evaluated how endophytes varied spatially and as a function of environmental, plant-specific, and edaphic factors. We also contrasted them with fungi in other plants (local species and species cultivated at a regional scale) and with soil fungi.<br><br>RESULTS: Culture-free methods revealed species-rich and phylogenetically diverse foliar fungal endophytes of T. taxifolia that vary spatially, reflecting symbiont acquisition from nearby plants, environmental factors, and plant stress. Endophyte community composition is subject to both stochasticity and temporal turnover and differs markedly from fungal communities in soils and other plants in the area.<br><br>CONCLUSIONS: Our study provides novel insights into factors that can shape fungal endophyte communities for a critically endangered tree species. In addition to identifying local determinants of endophytic symbioses, our work illustrates that plants in conservation nurseries host rich foliar fungal communities of potential importance in plant germplasm protection.}, }
@article {pmid41895330, year = {2026}, author = {Siddiqui, R and Khan, NA}, title = {Towards Digital Periodontology in Space Medicine.}, journal = {Aerospace medicine and human performance}, volume = {97}, number = {4}, pages = {300-302}, doi = {10.3357/AMHP.6830.2026}, pmid = {41895330}, issn = {2375-6322}, mesh = {Humans ; *Aerospace Medicine ; *Space Flight ; Astronauts ; Microbiota ; *Periodontics ; Computer Simulation ; Weightlessness ; Periodontal Diseases ; }, abstract = {During spaceflight, microgravity, radiation, and altered immune function can disrupt balance, increasing susceptibility to both oral and systemic inflammation. We propose a periodontal digital twin, a computational model that integrates oral microbiome, immune, and metabolic data to simulate individual health in real time. The proposed framework conceptualizes a data-driven model linking multiomic and physiological inputs from astronauts to personalized simulations of oral ecosystem dynamics. By continuously updating with new biological and environmental data, the digital twin can predict early deviations from homeostasis. A periodontal digital twin could function as an early warning system for immune dysregulation and microbial imbalance during long-duration missions, supporting targeted preventive or therapeutic interventions. Beyond its application to astronaut health, this approach provides a new lens to study host-microbe coadaptation and establishes a foundation for precision and predictive healthcare in both terrestrial and extraterrestrial contexts. Siddiqui R, Khan NA. Towards digital periodontology in space medicine. Aerosp Med Hum Perform. 2026; 97(4):300-302.}, }
@article {pmid41895350, year = {2026}, author = {S, SK and Jadhav, P and Paul, A and Kumar, R and Paul, D and Bose, S}, title = {Understanding gut microbiota dysbiosis as a plausible link between Obstructive Sleep Apnea (OSA), viral infections, and lifestyle diseases.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108466}, doi = {10.1016/j.micpath.2026.108466}, pmid = {41895350}, issn = {1096-1208}, abstract = {Obstructive sleep apnea (OSA) is a multifactorial disorder which is influenced by intermittent hypoxia, sleep fragmentation, and systemic inflammation. Recent evidence suggests that lifestyle diseases and viral infections further exacerbate OSA severity through common inflammatory and metabolic pathways. Parallelly, gut dysbiosis has gained recognition as a key mediator which links respiratory, metabolic, and infectious disease processes via the gut-lung axis. This review explores the convergent role of gut microbial dysbiosis across OSA, lifestyle-associated comorbidities such as obesity, diabetes, and cardiovascular disease and viral infections including respiratory syncytial virus (RSV), influenza, dengue, Human Immunodeficiency Virus (HIV), and SARS-CoV-2. Across these conditions, a recurring pattern of reduced beneficial commensals (e.g., Bifidobacterium, Faecalibacterium prausnitzii, Roseburia, Akkermansia muciniphila) and a noted increase of pro-inflammatory taxa (e.g., Escherichia, Streptococcus, Enterobacteriaceae) has been observed. It contributes to epithelial barrier breakdown, endotoxemia, metabolic dysfunction, and immune dysregulation. In OSA patients, intermittent hypoxia is observed that causes gut barrier impairment and microbial translocation, thus amplifying systemic inflammation. Similarly, viral infections reshape the gut ecology, bringing adverse effects to host immunity and respiratory outcomes. The review highlights upon the therapeutic potentials of prebiotics and probiotics supplementation for modulating gut dysbiosis. It discusses the role of these therapeutic interventions in improving metabolic homeostasis, reducing inflammation, and potentially mitigating OSA-related complications. Collectively, this analysis highlights gut dysbiosis as a plausible unifying mechanism connecting lifestyle diseases, viral infections, and OSA, presenting a compelling avenue for integrated, microbiome-targeted interventions.}, }
@article {pmid41895366, year = {2026}, author = {Fehér, B and Amorim das Vírgens, IP and Bakony, M and Tóth, E and Solymosi, O and Ütő, E and Kói, T and Hegyi, P and Váncsa, S and Ács, N and Can, G and Gupta, N and Biju, J and Melczer, Z}, title = {Cervicovaginal detection of genital mycoplasmas is associated with preterm birth and low birth weight: a systematic review and multivariate meta-analysis of adverse pregnancy outcomes.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2026.03.008}, pmid = {41895366}, issn = {1097-6868}, abstract = {OBJECTIVE: Genital mycoplasmas (Mycoplasma genitalium, Mycoplasma hominis and Ureaplasma species) are highly prevalent in women of reproductive age worldwide. The relevance of cervicovaginal detection in pregnancy remains controversial. This study aimed to assess their associations with adverse pregnancy outcomes.<br><br>DATA SOURCES: We conducted a systematic review and meta-analysis of observational studies published up to February 1, 2026, in Medline, Embase, and the Cochrane Library.<br><br>STUDY ELIGIBILITY CRITERIA: Eligible studies reported the presence of any genital mycoplasmas and at least one adverse pregnancy outcome.<br><br>Four reviewers independently selected studies and extracted data. Pooled odds ratios and mean differences with 95% confidence intervals were calculated. Univariate and subgroup analyses were performed for primary and secondary outcomes, and multivariate analysis for preterm birth. Sensitivity analyses restricted to cohort studies and cervicovaginal sampling were conducted.<br><br>RESULTS: Of 11,957 records, 156 studies were included in meta-analysis. In sensitivity analyses excluding amniotic fluid and placental specimens, significant associations with spontaneous preterm birth and low birth weight remained for cervicovaginal samples. Cervicovaginal detection of Ureaplasma parvum was significantly associated with preterm birth (OR 1.63; CI: 1.36-1.96). For Ureaplasma species, first-trimester detection showed stronger associations compared to second-trimester positivity (p = 0.044). Cervicovaginal Ureaplasma detection was also associated with low birth weight (OR 1.56; CI: 1.33-1.83) and small for gestational age (OR 1.47; CI: 1.19-1.80). Mycoplasma hominis showed significant associations with both preterm birth (aOR 1.75; CI: 1.21-2.53) and low birth weight (OR 1.81; CI: 1.51-2.16) when detected in cervicovaginal samples.<br><br>CONCLUSION: Associations between genital mycoplasmas and adverse pregnancy outcomes are not limited to intraamniotic presence but are also observed with cervicovaginal detection. Given the observational nature of the available data and residual confounding, these associations should be interpreted cautiously and do not support routine screening or treatment. Cervicovaginal detection should be interpreted within the broader context of the vaginal microbial environment rather than as evidence of an isolated pathogenic effect.}, }
@article {pmid41895406, year = {2026}, author = {Tain, YL and Hsu, CN}, title = {Developmental Origins and Environmental Determinants of Cardiovascular-Kidney-Metabolic Syndrome: A Pediatric Precision Prevention Perspective.}, journal = {Biomedical journal}, volume = {}, number = {}, pages = {100970}, doi = {10.1016/j.bj.2026.100970}, pmid = {41895406}, issn = {2320-2890}, abstract = {Cardiovascular-Kidney-Metabolic Syndrome (CKMS), formally defined by the American Heart Association in 2023, emphasizes the interconnections among chronic kidney disease, cardiovascular disease, obesity, and diabetes. Although CKMS typically manifests in adulthood, accumulating evidence indicates that vulnerability is established early in life through developmental programming shaped by maternal, perinatal, and early-childhood exposures. This review summarizes the developmental origins, environmental determinants, and mechanistic pathways of CKMS, with a particular emphasis on kidney programming and pediatric precision prevention. Recent nationally representative data indicate that CKMS risk-stage (stage ≥1) affects approximately 90% of U.S. adults and 40% of adolescents, highlighting the extensive population burden long before overt clinical disease develops, yet kidney health remains underrecognized within cardiometabolic risk assessment. In children, early metabolic disruption, excess adiposity, and subclinical cardiovascular dysfunction interact with structural or developmental renal vulnerability to accelerate CKD progression and amplify lifelong risk. Evidence from the Developmental Origins of Health and Disease framework demonstrates that maternal malnutrition, metabolic disease, toxicant exposures, preterm birth, and perinatal complications permanently alter nephron endowment, vascular function, and metabolic regulation. Animal studies reveal convergent mechanisms-including oxidative stress, aberrant renin-angiotensin activity, epigenetic modifications, gut microbiota dysbiosis, and sex-specific responses-that predispose offspring to CKMS and highlight targets for early-life reprogramming. Prevention should begin with maternal health and the first 1000 days, incorporating nutritional and lifestyle interventions, early screening for obesity, hypertension, and dyslipidemia, and emerging microbiome- or antioxidant-targeted therapies. Advances in multi-omics, digital health, and AI-enabled monitoring facilitate early risk stratification and precision prevention, although pediatric-specific guidelines remain limited. Viewed through a life-course lens, CKMS represents a gradual, self-reinforcing process rooted in developmental programming and environmental exposures. Integrating maternal and pediatric interventions within a life-course precision prevention framework provides a roadmap to disrupt disease trajectories, reduce intergenerational risk, and promote lifelong cardiovascular, kidney, and metabolic health.}, }
@article {pmid41895437, year = {2026}, author = {Rinanda, T and Riani, C and Artarini, A and Sasongko, L}, title = {Exploring the role of gut methanogenic archaea in childhood stunting in Aceh Province, Indonesia.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {103040}, doi = {10.1016/j.anaerobe.2026.103040}, pmid = {41895437}, issn = {1095-8274}, abstract = {BACKGROUND: Emerging evidence highlights the critical role of gut microbiota in childhood growth; however, the contribution of methanogenic archaea remains underexplored. In this study, we investigated the involvement of gut methanogens in linear growth impairment by analyzing their abundance, diversity, methanogenesis, and interactions with bacterial short-chain fatty acids (SCFAs) and glucagon-like peptide-1 (GLP-1) levels in stunted versus normal children.<br><br>METHODS: This case-control study included 42 children aged 24-59 months from Pidie, Aceh, Indonesia. Gut archaea were profiled through 16S rDNA amplicon sequencing, and mcrA gene expression was measured using quantitative Polymerase Chain Reaction. SCFAs were analyzed using gas chromatography-mass spectrometry, and GLP-1 levels were quantified using immunoassay. The microbial co-occurrence networks were also assessed.<br><br>RESULTS: Archaeal 16S rDNA amplicon sequencing revealed a lower abundance of Methanobacteriaceae, particularly Methanobrevibacter, in stunted children, although their presence contributed to greater microbial diversity. Reduced mcrA gene expression in stunted children indicates a decrease in methanogenesis. Although not statistically significant, mcrA gene expression positively correlated with height, SCFA concentrations, and GLP-1 levels. Microbial network analysis revealed a lower density of microbial networks, indicating reduced stability and resilience in stunted children, with Methanobrevibacter playing a substantial role. Notably, Methanobrevibacter exhibited a positive association with Elusimicrobium, a rare human-associated microbe, and a negative correlation with Lachnospiraceae in normal children, indicating unique microbial interactions that may influence metabolic health.<br><br>CONCLUSION: Methanogens, particularly Methanobrevibacter, may play a crucial role in shaping gut microbial ecology and supporting metabolic pathways relevant to linear growth during early childhood.}, }
@article {pmid41895499, year = {2026}, author = {Kim, DH and Byeon, E and Jeong, H and Kim, MS and Yoon, C and Maszczyk, P and Hu, M and Wang, M and Wang, Y and Yang, Z and Lee, JS}, title = {Gut microbiome disruption impairs arsenic biotransformation and exacerbates toxicity in the water flea Daphnia magna.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {}, number = {}, pages = {110522}, doi = {10.1016/j.cbpc.2026.110522}, pmid = {41895499}, issn = {1532-0456}, abstract = {Arsenic risk in waters depends on chemical speciation, yet studies on host-associated microbiota to the in vivo detoxification mechanisms remain unclear. We exposed Daphnia magna for 21 days to inorganic arsenic at 2 mg/L with/without a broad-spectrum antibiotic cocktail that disrupts the gut microbiome. We assessed life-history traits, whole-body arsenic species by HPLC coupled to ICP-MS, and gut community composition by 16S rRNA gene sequencing with LEfSe and PICRUSt2 analyses. Both Arsenic and antibiotics alone impaired growth and reproduction, while co-exposure produced the strongest effects. Microbiome disruption increased total arsenic burden (~14%) and shifted speciation away from detoxified end-products. Formation of arsenobetaine decreased by an order of magnitude, whereas dimethylarsinic acid approximately doubled. Under arsenic exposure alone, core taxa such as Aeromonas proliferated, accompanied by enrichment of predicted arsenic reductases and methyltransferases. Antibiotic treatment eliminated these taxa, favored Streptococcus, Methylophilus, and Veillonella, and suppressed predicted arsenic-processing functions. These results demonstrate that an intact Daphnia gut microbiome facilitates conversion of inorganic arsenic to less toxic organoarsenicals and mitigates toxicity. Microbiome integrity emerges as a practical control on arsenic fate and hazard in freshwater zooplankton, relevant to risk assessment under antibiotic co-contamination.}, }
@article {pmid41895971, year = {2026}, author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M}, title = {Microbiota of foods: a comprehensive review of diversity and potential implications.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118899}, doi = {10.1016/j.foodres.2026.118899}, pmid = {41895971}, issn = {1873-7145}, mesh = {*Food Microbiology ; *Fermented Foods/microbiology ; *Microbiota ; Fermentation ; Metagenomics ; Humans ; Metabolomics ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.}, }
@article {pmid41895972, year = {2026}, author = {Yu, J and Qiang, H and Hoffmann, TG and Mahajan, P and Chaiwong, S and An, X}, title = {From bruise to breakdown: Multi-omics of transport-induced deterioration in apples.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118900}, doi = {10.1016/j.foodres.2026.118900}, pmid = {41895972}, issn = {1873-7145}, mesh = {*Malus/microbiology/metabolism/chemistry ; *Fruit/microbiology/chemistry/metabolism ; Cell Wall/metabolism ; *Metabolomics/methods ; *Stress, Mechanical ; Lipid Peroxidation ; Polysaccharides/metabolism ; Pectins/metabolism ; Microbiota ; Multiomics ; }, abstract = {Mechanical damage during express transportation is a major driver of postharvest quality deterioration in fresh produce. In this study, we integrated physiological and biochemical assays with microscopic observations and multi-omics approaches to comprehensively characterize the consequences of transportation-induced mechanical stress in Fuji apples. Structural analyses revealed that mechanical injury caused immediate disruption of cell wall architecture, including polysaccharide depolymerization and increased exposure of functional groups. Microscopic and FTIR analyses confirmed that mechanical stress caused cell wall collapse, polysaccharide network depolymerization, and increased exposure of functional groups. Biochemical assays further demonstrated that damage markedly accelerated cell wall disassembly, as reflected by a 140.91% increase in pectin solubilization and a 91.24% rise in cellulase activity, while also intensifying lipid peroxidation (52.71% increase in MDA content) and enzymatic browning (93.20% increase in PPO activity). Non-targeted metabolomics revealed extensive metabolic reprogramming, including the accumulation of stress-related phenolics, inhibition of tryptophan metabolism, and disruption of lipid-derived signaling pathways. Moreover, mechanical stress profoundly reshaped the apple fruit's epiphytic microbiome, shifting the community structure from protective Bacillus-dominated populations to spoilage-associated Metchnikowia yeasts with strong pectinolytic capacity. By linking macroscopic phenotypes with molecular and microbial signatures, this work provides mechanistic insight into how postharvest mechanical impact accelerates deterioration in apples and offers a scientific foundation for developing targeted intervention strategies in transport-intensive supply chains.}, }
@article {pmid41895994, year = {2026}, author = {Çelik, MN and Dazıroğlu, ME&#xc7; and Pınar, BA and Nanì, MF and Romano, B and Ağagündüz, D and Capasso, R}, title = {Microbiome crosstalk and nutrition: the interplay between gut microbiota-organ axis and dietary factors.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118945}, doi = {10.1016/j.foodres.2026.118945}, pmid = {41895994}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet ; Probiotics ; Animals ; Prebiotics ; *Nutritional Status ; Gastrointestinal Tract/microbiology ; }, abstract = {The gut microbiota (GM) is referred to as the central organ due to its dynamic and adaptable contact network with other organs through humoral, immunological, metabolic, endocrine, and neurological pathways. Recent studies have emphasized the concept of the "gut-organ axis", which shows that the effects of GM go beyond the gastrointestinal system (GIS) and encompass the reciprocal interactions between other organs. Communication along these axis occurs mainly through mediators such as short-chain fatty acids (SCFAs), microbial metabolites, neurotransmitters, cytokines, and hormonal signals. Therefore, imbalances in GM may surpass gut problems and be linked to diseases affecting the brain, liver, lungs, heart, mouth, skin, and many other organs. Understanding these reciprocal interactions can inform strategies for disease prevention and treatment. Emerging evidence suggests that interactions between the GM and other organ-specific metabolites it secretes are dynamic and influenced by various environmental and lifestyle factors, particularly diet. The gut and other organ microbiomes are maintained in balance with the help of nutritional supplements like probiotics, prebiotics, symbiotic, vitamins, omega-3 fatty acids, and dietary fiber. Consuming processed or red meat, high-fat, high-sugar, high-glycemic index foods, and excessive salt can upset this balance and raise the risk of systemic inflammation and disease. The purpose of this review is to examine the interactions between various organ-specific microbiomes in the human body, to elucidate the effects of these interactions on health, and to highlight how microbiome-targeted nutritional interventions can modulate these interactions, potentially affecting disease risk and overall metabolic homeostasis.}, }
@article {pmid41896037, year = {2026}, author = {Shi, S and Bastías, DA and Wang, H and Faville, M and O'Callaghan, M}, title = {A roadmap for plant-microbiome breeding to enhance plant stress tolerance.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.02.012}, pmid = {41896037}, issn = {1878-4380}, abstract = {Plants constantly form associations with microorganisms, and some are vital for plant performance, especially under stress conditions. Although some microorganisms have been developed into commercial bioinoculant products, their associations with plants can be transient, and their efficacy is often inconsistent in the field. Here, we propose a framework and key research steps needed for plant breeders and microbiologists to work together to match plant genetics with compatible microbial inoculants. Recent studies have successfully identified plant genetic factors that play a role in the recruitment of beneficial microorganisms, and many associated technologies are ready for implementation towards this goal. This innovative and collaborative approach could provide novel, enduring plant-microbiome associations for environmental sustainability and food security under a changing climate.}, }
@article {pmid41896075, year = {2026}, author = {Waymouth, VJ and Keynton, ACW and Brumley, DR and Ebert, B and Watt, M}, title = {Cell walls and their role in the plant root microbiome.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2026.02.005}, pmid = {41896075}, issn = {1878-4372}, abstract = {Plant roots form a microbiome that interacts at the cell wall extracellular matrix before entering the cell. The root primary and accessory walls present a dynamic, cell-type-dependent scaffold that microbes must navigate, using shared cellulose or contrasting chitin motifs and influencing plant gene responses that encode enzymes for cell wall biosynthesis and degradation. We propose that an interface evolves as microbes reach the root tip and interact with host polymers, potentially driving concurrent degradation of root and microbial cells. Knowledge gaps span diffusion, fluid flow, nutrient exchange, and the physics of microbial motion within the wall boundary. Advances in in situ imaging and mathematical modelling can help understand the dynamics of cell walls to design root microbiomes to function in agroecosystems.}, }
@article {pmid41896210, year = {2026}, author = {Zhang, X and Cheng, HS and Zhan, X and Li, X and Huang, J and Liu, H and Chua, D and Wang, G and Li, X and Shi, Y and Wang, F and Xu, Z and Qu, J and Pethe, K and Li, G and Tan, NS and Mac Aogáin, M and Chotirmall, SH and Li, L}, title = {Single-bacterial cell insights into mechanisms of ceftriaxone resistance in Neisseria subflava.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-68621-y}, pmid = {41896210}, issn = {2041-1723}, support = {Grant No. 32470194//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The contribution of airway pathobionts to chronic respiratory disease is increasingly recognized, yet the evolutionary processes that shift commensals to pathogens remain poorly understood. Here we investigate how antibiotic pressure drives adaptation in Neisseria subflava, a common airway commensal associated with bronchiectasis. Using serial passage under ceftriaxone exposure, we observe a >300-fold increase in resistance, accompanied by enhanced biofilm formation and genetic reprogramming. Whole-genome sequencing reveals recurrent mutations in the adhesin gene ataA, while single-cell transcriptomics identifies six functionally distinct clusters indicating adaptive programs in growth, metal homeostasis, oxidative stress, and cell-wall remodeling. Notably, biofilm integrity is maintained through compensatory upregulation of comP and bamE, which promotes phagocytic evasion and resistance in experimentally evolved strains and clinical isolates. Iron availability further stabilizes biofilm and modulates antibiotic tolerance, underscoring metal homeostasis as a contributory adaptive axis. Together, these findings reveal a multifaceted strategy by which N. subflava exploits antibiotic selection to transition towards pathogenicity. By integrating experimental evolution with single-cell resolution, we establish a framework for understanding the commensal-to-pathobiont transition, with broad implications for the airway microbiome and antimicrobial resistance in chronic respiratory disease.}, }
@article {pmid41896243, year = {2026}, author = {He, Y and Peng, H and Li, L and Sheng, S and Wang, Q and Li, W and Lin, F and Yi, J}, title = {Valeric acid from oral microbiome suppresses esophageal cancer growth by disrupting eEF1A1 -mediated translational output.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71209-1}, pmid = {41896243}, issn = {2041-1723}, abstract = {Dysbiosis of the oral microbiome has been associated with esophageal squamous cell carcinoma (ESCC), but how it impacts ESCC remains largely unknown. Surprisingly, we find that the oral microbiota derived from ESCC patients-not that from healthy controls-exhibits potent inhibitory and cytotoxic effects on ESCC cells. This anti-tumor effect is attributable to Veillonella, which is enriched in the ESCC-associated microbiota. Mechanistically, Veillonella produces valeric acid, which is transported into cells via MCT1 and inhibits the GTPase activity of eEF1A1, thereby suppressing protein translation. These findings identify valeric acid as a potential postbiotic for ESCC treatment and underscore the necessity of functional validation beyond observational and correlative studies.}, }
@article {pmid41896298, year = {2026}, author = {Byonanebye, A and Khamis, FM and Mwangi, M and Namikoye, ES and Ajene, IJ and Akutse, KS}, title = {Temperature dependent immunological responses of Spoladea recurvalis exposed to entomopathogenic fungi.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45475-4}, pmid = {41896298}, issn = {2045-2322}, support = {DPP-020/2022-2024//Biovision Foundation for Ecological Development/ ; }, }
@article {pmid41896360, year = {2026}, author = {Yang, X and Tang, J and Lai, Z and Dong, Z and Liao, J and Guo, Y and Wang, Z}, title = {Comparative Analysis of Nasal and Cloacal Bacterial Communities in Three Sea Turtle Species under Rescue Center Conditions.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02751-0}, pmid = {41896360}, issn = {1432-184X}, support = {No. 2021B1212110005//Science and Technology Infrastructure Project of Department of Science and Technology of Guangdong Province/ ; }, }
@article {pmid41896437, year = {2026}, author = {Jin, H and Zhou, W and Ying, R}, title = {Impact of ileostomy reversal on gut microbiome and metabolome in rectal cancer: a review of mechanisms and clinical consequences.}, journal = {Langenbeck's archives of surgery}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00423-026-04031-4}, pmid = {41896437}, issn = {1435-2451}, support = {2024S00023//the Social Development Science and Technology Project of Wenling City, Zhejiang Province/ ; }, }
@article {pmid41896632, year = {2026}, author = {Lei, J and Qi, J and Zhai, J and Chen, Z and Li, N and Zhang, Y and Yuan, Y and Sun, C}, title = {Dynamic gut responses to sepsis uncovered by multi-omics profiling in a rodent model.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09940-0}, pmid = {41896632}, issn = {2399-3642}, support = {82470617//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Sepsis reflects an immune dysregulation in response to infection, and the intestine functions as the largest immune organ in the human body. However, the multidimensional dynamic changes within the gut environment during the progression of sepsis remain incompletely understood. Here, we show the alterations in the gut over the course of pneumonia-induced sepsis through the analysis of cellular, microbial, metabolic, and protein profiles over time. We demonstrate that subsets of immune cells, including mononuclear phagocytes and T cells, undergo compositional and transcriptional shifts. Simultaneously, specific structural cells and mucus-producing cells exhibit adapted roles in antigen presentation and the regulation of intestinal homeostasis. Furthermore, we detail alterations in the gut microbiome composition, metabolite levels, and colonic protein expression, identifying shared fluctuation patterns across these biological dimensions. These findings outline the interactions among the gut microbiome, cellular activity, and immune responses, providing potential therapeutic targets for future sepsis management.}, }
@article {pmid41896639, year = {2026}, author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP}, title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41896639}, issn = {2399-3642}, support = {NIH R35 GM144276//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Behavior, Animal ; *Foxes/microbiology/physiology ; Phenotype ; Domestication ; Male ; }, abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.}, }
@article {pmid41896698, year = {2026}, author = {Jung, S and Militsi, E and Huck, O}, title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70215}, pmid = {41896698}, issn = {1601-0825}, abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.<br><br>METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).<br><br>RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sj&#xf6;gren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct &#x3b2;-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.<br><br>CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.}, }
@article {pmid41896724, year = {2026}, author = {Connell, E and Sami, S and Khondoker, M and Minihane, AM and Pontifex, MG and Müller, M and McArthur, S and Le Gall, G and Vauzour, D}, title = {Circulatory dietary and gut-derived metabolites predict early cognitive decline.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649487}, doi = {10.1080/19490976.2026.2649487}, pmid = {41896724}, issn = {1949-0984}, mesh = {Humans ; *Cognitive Dysfunction/microbiology/blood/metabolism/diagnosis ; Male ; *Gastrointestinal Microbiome ; Female ; Aged ; Middle Aged ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Biomarkers/blood ; Dysbiosis/microbiology ; Diet ; Bile Acids and Salts/blood ; Methylamines/blood ; Aged, 80 and over ; Tryptophan/blood ; }, abstract = {INTRODUCTION: A key component of disease prevention is the identification of at-risk individuals. Microbial dysbiosis in the early stages of cognitive decline and Alzheimer's disease (AD) and can modulate the levels of microbe-derived metabolites (MDM), thought to contribute to neuroinflammation, blood‒brain barrier dysfunction, and neuronal degeneration. However, the precise role of MDM in this process, as well as their potential value as risk factors, remains poorly understood.<br><br>METHODS: Mass spectrometry platforms determined the serum concentration of 33 metabolites (13 tryptophan-related compounds, 15 bile acid compounds, 3 TMAO-related metabolites and 2 cresol metabolites) from cognitively healthy subjects, subjective cognitive impairment (SCI) participants and mild cognitive impairment (MCI) participants (n&#x2009;=&#x2009;50 per group, matched for age, BMI and sex). Multiple linear regression and machine learning techniques were applied to identify a metabolite panel capable of classifying early cognitive decline. 16S rRNA amplicon sequencing was employed to identify bacterial taxa associated with these metabolic changes.<br><br>RESULTS: Multiple linear regression modelling, adjusted for sex, BMI, age, albumin (for its role in metabolite transport), liver and kidney function, and background diet, identified key neuroprotective metabolites, namely choline, 5-hydroxyindole acetic acid, and indole propionic acid (IPA), as lower in SCI and MCI individuals compared to healthy controls. In contrast, the cytotoxic metabolite, indoxyl sulfate, and kynurenic acid were elevated. A random forest algorithm with multiclass classification further validated these findings, highlighting six metabolites (indoxyl sulfate, choline, 5-hydroxyindole acetic acid, IPA, kynurenic acid, and kynurenine) as classifiers of early cognitive decline, achieving an area under the curve (AUC) of 0.79.<br><br>CONCLUSION: These findings suggest that MDM may serve as putative composite biomarkers of early cognitive decline, offering potential clinical relevance for metabolic risk stratification and supporting the future development of minimally invasive screening tools.}, }
@article {pmid41896753, year = {2026}, author = {Lin, D and Li, Q and Suleiman, M and An, M and Zhu, Y}, title = {Microbiome and metabolomics analysis of different bryophytes under cadmium stress.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08651-2}, pmid = {41896753}, issn = {1471-2229}, support = {2022D01C678//Natural Science Foundation of Xinjiang/ ; }, }
@article {pmid41897048, year = {2026}, author = {Pignataro, E and Brindisi, G and Gori, A and Colletti, G and Moraca, P and Cinicola, BL and Spalice, A and Anania, C and Zicari, AM}, title = {Pediatric Vernal Keratoconjunctivitis (VKC): Current State and Future Directions-A Narrative Review of Clinical Features, Diagnostic Strategies, and Emerging Therapies.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/children13030335}, pmid = {41897048}, issn = {2227-9067}, abstract = {Vernal keratoconjunctivitis (VKC) represents far more than a typical allergic eye disease. It is a distinct and often underestimated chronic inflammatory condition that primarily affects children during critical stages of physical and emotional development. Though frequently grouped with seasonal allergic conjunctivitis, VKC differs significantly in its immunopathology, clinical presentation, and long-term implications. Its intense ocular symptoms and its potential for corneal damage and substantial psychosocial burden require, rather than symptom control, coordinated and multidisciplinary management. This narrative review explores VKC from every angle, with a particular focus on its implications for pediatric care. VKC, in fact, represents a genuine clinical challenge: as its symptoms can mimic milder forms of conjunctivitis, its course is often unpredictable, and its treatment requires balancing efficacy and safety in vulnerable age groups. We examined the immunological mechanisms that make it a model of localized Th2 inflammation, the diagnostic pitfalls that delay recognition, and the evolving treatment landscape, from conventional therapies like cyclosporine A and tacrolimus to innovative agents such as omalizumab and dupilumab. We also highlighted the role of emerging biomarkers, the influence of environmental and microbiome factors, and the urgent need for standardized care pathways. As research continues to expand our understanding, VKC is emerging as a prime example of how personalized medicine and translational science can intersect to address complex immune-mediated diseases in children. For the ones treating pediatric allergic disorders, VKC is no longer a rare curiosity: it is a clinical challenge worth understanding deeply.}, }
@article {pmid41897098, year = {2026}, author = {Baghdadi, ZD}, title = {Equity or Two-Tier Care? Guardrails for Silver Diamine Fluoride and Delegated Early Childhood Caries Pathways.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/children13030386}, pmid = {41897098}, issn = {2227-9067}, abstract = {Early childhood caries (ECC) is a complex, multifactorial disease shaped by biofilm ecology, host susceptibility, diet and behaviors, and structural determinants of health. Silver diamine fluoride (SDF) is an effective non-restorative option for arresting cavitated lesions in many settings and can support access when definitive care is delayed. However, translating short-horizon "arrest" outcomes into broad policy claims-that SDF-first, delegated pathways can substitute for dentist-led diagnosis and comprehensive rehabilitation-risks institutionalizing a two-tier standard of care for children facing the greatest access barriers. This perspective critically appraises evidence-to-implementation pathways for SDF and delegated ECC management, using risk-of-bias and reporting guidance as interpretive tools and drawing on pragmatic regimen trials, microbiome substudies, oral health-related quality of life (OHRQoL) analyses, and implementation work including the Canadian Caries Risk Assessment Tool (CCRAT) in primary care. We explicitly distinguish what studies demonstrate (e.g., feasibility and short-term arrest differences by reapplication interval) from what they do not establish (e.g., long-term tooth survival, pulpal outcomes, definitive treatment completion, and equity impacts). We propose practical guardrails that position SDF as interim management within a continuum of care: dentist-led diagnosis and escalation when pulpal risk is suspected; time-bound referral pathways with completion tracking; protocolized follow-up aligned with lesion/risk status; outcome sets that extend beyond "arrest" to include pain, function, OHRQoL, tooth survival, and equity stratification; and lesion-site sampling plus preregistered analyses when mechanistic claims are advanced.}, }
@article {pmid41897337, year = {2026}, author = {Nawaz, S and Sugiura, T and Yusuf, I and Sultany, A}, title = {Gut-Heart Axis in HFpEF: The Emerging Role of Microbiome-Driven Inflammation and Endothelial Dysfunction.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/biom16030401}, pmid = {41897337}, issn = {2218-273X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammation/microbiology/metabolism ; *Heart Failure/microbiology/physiopathology/metabolism ; Animals ; Dysbiosis/microbiology ; Stroke Volume ; *Endothelium, Vascular/physiopathology ; }, abstract = {Heart failure with preserved ejection fraction (HFpEF) represents the predominant form of heart failure, affecting over 50% of all heart failure patients with increasing prevalence in aging populations. Despite significant advances in cardiovascular medicine, HFpEF remains a complex clinical syndrome with poorly understood pathophysiology and limited treatment options. While most studies have traditionally focused on the renin-angiotensin-aldosterone system (RAAS) and other related mechanisms, emerging evidence has unveiled a critical bidirectional relationship between dysregulation of gut microbiota and HFpEF development. This phenomenon, mediated through microbiome-driven inflammation and endothelial dysfunction, introduces a novel concept and potential emerging conceptual framework in understanding HFpEF. This comprehensive review explores this novel gut-heart axis by synthesizing the latest evidence from original studies and clinical trials. We discuss novel mechanisms involving bacterial metabolites, including short-chain fatty acids (SCFAs), trimethylamine N-oxide (TMAO), bile acids, and amino acid derivatives. We also examine how gut dysbiosis may contribute to systemic inflammation through lipopolysaccharide translocation, NLRP3 inflammasome activation, and endothelial dysfunction. Furthermore, clinical trials investigating microbiome-targeted interventions, including probiotics, fecal microbiota transplantation, metabolite supplementation, and precision medicine approaches, are critically evaluated for their therapeutic potential. This review provides a framework for hypothesis generation and future research directions about therapeutic strategies targeting the gut-heart axis in HFpEF management.}, }
@article {pmid41897363, year = {2026}, author = {Nuncio, ASP and Motovilov, K and Weed, M and Shah, S and Bazzi, S and Idnani, E and Lime, T and Sauceda, DC and Mangieri, RA and Maguire, C and Melamed, E}, title = {High-Dose Ethanol-Induced Immunosuppression Modulates Sex-Specific Disease Outcomes in a Murine Model of Multiple Sclerosis.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/biom16030427}, pmid = {41897363}, issn = {2218-273X}, support = {K08 T26-1616-11/AA/NIAAA NIH HHS/United States ; NA//Homer Lindsey Bruce &amp; Fred Murphy Jones Endowed Fellowship/ ; F31 AA032720/AA/NIAAA NIH HHS/United States ; 5T32 DA018926-18/DA/NIDA NIH HHS/United States ; NA//The University of Texas at Austin Graduate Continuing Fellowship/ ; U01 AA016651/AA/NIAAA NIH HHS/United States ; T32 AA007471/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; *Ethanol/pharmacology/administration &amp; dosage ; Male ; *Encephalomyelitis, Autoimmune, Experimental/immunology/drug therapy/pathology ; Mice ; *Multiple Sclerosis/immunology/drug therapy/pathology ; Female ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; T-Lymphocytes/immunology/drug effects ; Immunosuppression Therapy ; }, abstract = {Both epidemiological studies and prior work in animal models suggest that moderate-dose alcohol reduces disease severity across several autoimmune conditions, including multiple sclerosis (MS). However, the mechanisms underlying the potentially beneficial effects of alcohol and how these effects may change with alcohol dose in autoimmunity remain underexplored. In this study, we characterize the effects of chronic, high-dose ethanol consumption in experimental autoimmune encephalomyelitis (EAE), a murine model of MS, by examining EAE disease severity, gut microbial composition, and peripheral cell immunophenotypes. We found that high-dose ethanol-fed males exhibited a significant amelioration in peak EAE disease severity, in association with decreased T cell activation and B cell proportions. Concurrently, we observed proinflammatory shifts in gut microbiota and hepatic lipid accumulation. Our results suggest that high dose ethanol may benefit autoimmune neuroinflammation in EAE through immunosuppressive effects on adaptive immunity, however its toxic systemic effects preclude the use of alcohol as an immunomodulator in MS. Overall, our findings reveal a mechanistic basis for alcohol's beneficial properties in autoimmunity and could inform the development of more targeted disease modifying therapies that recapitulate these benefits without alcohol-associated toxicity.}, }
@article {pmid41897366, year = {2026}, author = {van Steensel, MAM}, title = {The Evolving Microbial Paradigm in Acne.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/biom16030430}, pmid = {41897366}, issn = {2218-273X}, support = {nil//ArrowBiome pte ltd/ ; }, mesh = {*Acne Vulgaris/microbiology/drug therapy/pathology ; Humans ; *Propionibacterium acnes/pathogenicity/drug effects ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Sebum/metabolism ; Biofilms/drug effects/growth &amp; development ; }, abstract = {This review discusses the microbiology of acne vulgaris, a chronic inflammatory condition of the pilosebaceous unit that affects most adolescents and can persist into adulthood. The current standard of care consists largely of antibacterial interventions, based on the traditional view of Cutibacterium acnes as a pathogen. Alternative treatments are suggested by the "comedo switch" hypothesis, which attributes acne to aberrant differentiation of LRIG1+ sebaceous progenitor cells. While there is strong evidence to support this idea, it does not explain the efficacy of antibacterial interventions. We propose a unified mechanism wherein C. acnes phylotype IA1 can act as a trigger for the comedo switch. Unlike commensal strains, phylotype IA1 has high lipase activity, hydrolyzing sebum triglycerides into free fatty acids, specifically palmitic acid. This metabolite stimulates LRIG1+ progenitors, inducing inflammation and initial comedo formation. The review discusses C. acnes phylotypes, emphasizing known virulence factors of IA1, such as enhanced biofilm formation. We evaluate the efficacy and limitations of both old and new antibacterials, noting how newer materials that selectively remove C. acnes IA1 can reduce non-inflammatory acne lesions, supporting a key role for this phylotype in the pathogenesis of acne.}, }
@article {pmid41897395, year = {2026}, author = {Micke, B and Novotny, J}, title = {Longitudinal Analysis of Rat Gut Microbiome Composition and Fecal Metabolism Markers Following Prolonged Morphine Exposure.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/biom16030460}, pmid = {41897395}, issn = {2218-273X}, support = {SVV-260790//Charles University/ ; }, mesh = {Animals ; *Morphine/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology/chemistry ; Rats ; Rats, Wistar ; Male ; Metabolome/drug effects ; RNA, Ribosomal, 16S/genetics ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Biomarkers/metabolism ; Bacteria/genetics/classification ; Longitudinal Studies ; }, abstract = {This study investigated temporal group-level changes in gut microbiome composition and fecal metabolic markers in Wistar rats following a 10-day administration of morphine. Fecal samples were collected at predefined post-discontinuation time points and analyzed using 16S rRNA gene sequencing and GC×GC-TOF/MS-based metabolomics, with a focus on short-chain fatty acids (SCFAs). Morphine exposure was associated with transient alterations in gut microbiome structure at early post-treatment time points, including changes in alpha diversity and shifts in the relative abundance of major bacterial taxa. Unsupervised multivariate analysis of fecal metabolomic profiles revealed substantial inter-individual variability without persistent global separation between control and morphine-treated groups. Targeted analysis identified transient reductions in the relative signal intensities of selected SCFAs shortly after morphine withdrawal, while no significant differences were observed at later time points. These findings suggest that morphine-associated perturbations of the gut microbiome and fecal metabolome are predominantly time-dependent and tend to diminish during extended post-discontinuation phases.}, }
@article {pmid41897480, year = {2026}, author = {Jang, NY and Jaiswal, V and Park, M and Lee, HJ}, title = {Immune-Enhancement Effects of 6-Methoxykaempferol on Cyclophosphamide-Induced Immunosuppression via Improving Antioxidant Enzyme Expression, NF-κB and MAPK Signaling, and Modulating Gut Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antiox15030334}, pmid = {41897480}, issn = {2076-3921}, support = {Project No. RS-2022-RD010230//Cooperative Research Program for Agriculture, Science and Technology Development of the Rural Development Administration, Republic of Korea./ ; }, abstract = {The immune system maintains homeostasis through coordinated innate and adaptive responses, and its imbalance increases disease susceptibility. The immunomodulatory effects of 6-methoxykaempferol (6MK), a methoxylated flavonoid found in sweet cherries, were studied in a mouse model of cyclophosphamide (CPA)-induced immunosuppression. The expression of key signaling proteins in the NF-κB and MAPK pathways was studied to explore the underlying molecular mechanisms. The Toll-like receptor-4/myeloid differentiation factor-2 receptor complex (TLR4/MD2), which can stimulate the immune response by activating these pathways, was used to study possible interactions with 6MK using docking analysis. 6MK administration significantly restored immune organ integrity (spleen up to 15.1% and thymus up to 16.8%), enhanced NK cell function (up to 43.8%), promoted T (up to 24.5%) and B cell proliferation (up to 26.4%), increased pro- and anti-inflammatory cytokine (IL-1β, IL-6, TNF-α, IL-4, IL-10, and TGF-β) levels, and elevated NO (up to 25.6%) and immunoglobulin (IgG, IgA, and IgM) concentrations. Additionally, 6MK upregulated antioxidant enzymes (CAT, HO-1, and SOD) and reactivated suppressed NF-κB and MAPK pathways. The docking-supported hypothesis, based on putative interactions and the estimated free energy of binding, suggests that 6MK possesses agonistic potential for the TLR4/MD2. Changes in the gut microbiome due to 6MK treatment, such as an increase in alpha diversity, abundance of Dorea longicatena, and the upregulation of formaldehyde-consuming pathways, may also contribute to immune enhancement. These findings show that 6MK may alleviate immunosuppression, suggesting its potential for future studies targeting immune-related diseases and conditions.}, }
@article {pmid41897542, year = {2026}, author = {Ferreira, IM and Martins, SA and Gonçalves, L and Jesus, M and Brandão, E and Soares, S}, title = {Beyond Sensory Properties: Molecular Interactions of Antioxidant Flavour-Active Polyphenols Across the Food-Oral-Gut Axis.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antiox15030397}, pmid = {41897542}, issn = {2076-3921}, support = {GA 101040462/ERC_/European Research Council/International ; CA22161//European Cooperation in Science and Technology/ ; project UID/50006/2025//Laborat&#xf3;rio Associado para a Qu&#xed;mica Verde/ ; CEECIND/01598/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2023.00959.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; COMPETE2030-FEDER-00914400 (project 15462)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Dietary antioxidants are widely valued for their potential health benefits, but incorporating them into functional foods is not straightforward. Polyphenols are among the most abundant and important antioxidants in foods, and this review focuses on them because the same structural features linked to their health-promoting effects can also cause pronounced bitterness and astringency, ultimately limiting consumer acceptance. This review examines how these challenges are interconnected across three levels: food matrix interactions, bioavailability, and consumer psychobiology. We describe how non-covalent interactions between polyphenols, proteins, and polysaccharides can have both positive and negative effects. While these interactions may alter oral lubrication and flavour release, they also protect highly reactive bioactive compounds from gastric degradation. Furthermore, we broaden the concept of bioavailability by exploring the microbiota-mediated "colonic rescue" of polyphenols that are not released during earlier digestion. We also highlight the role of extraoral bitter taste receptors (TAS2Rs) along the gastrointestinal (GI) tract. Activation of these receptors during digestion can trigger relevant metabolic and endocrine responses, indicating that systemic absorption is not the only pathway to bioactivity. Finally, we connect these mechanisms to individual differences in food acceptance, showing that genetic factors (e.g., TAS2R38 and the salivary proteome) and psychological traits (such as neophobia and reward sensitivity) can shape rejection or flavour-nutrient learning. Overall, the successful development of functional foods will require a "sensory-by-design" approach. This strategy utilises matrix interactions strategically to improve both consumer acceptance and physiological efficacy.}, }
@article {pmid41897732, year = {2026}, author = {Lee, H and Na, W and Sohn, C}, title = {Comparative Microbiome Profiles of Korean Fermented Foods Based on Production Type and Additive Use.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/foods15061010}, pmid = {41897732}, issn = {2304-8158}, support = {NRF-RS-2024-00463020//National Research Foundation of Korea/ ; }, abstract = {Fermented foods are produced through controlled microbial activity and are valued for their extended shelf life, sensory attributes, and potential health benefits. This study examined the effects of production methods on microbial ecology by comparing microbial community structure, Shannon diversity, and pH changes in traditional and commercially produced Korean fermented foods. Cabbage and radish kimchi were fermented for four weeks to assess microbial succession and physicochemical changes, and additional fermented foods, including soy sauce, soybean paste, pepper paste, fruit vinegar, yogurt, and aged kimchi, were compared according to production method. Microbial communities were analyzed using amplicon sequencing targeting the V3-V4 regions of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region. Traditionally produced cabbage kimchi exhibited high microbial diversity at the early fermentation stage, initially dominated by Weissella and Leuconostoc, followed by a gradual shift toward lactic acid bacteria dominance at later stages. In contrast, commercially produced cabbage kimchi maintained a simplified microbial community dominated by a limited number of lactic acid bacteria throughout fermentation. Radish kimchi showed production-method-dependent patterns, with the rapid dominance of lactic acid bacteria during traditional fermentation and partial recovery of microbial diversity during commercial fermentation. Shannon diversity was consistently higher in traditionally produced kimchi during fermentation. In contrast, commercially produced kimchi exhibited more rapid acidification. Across other fermented foods, traditionally produced soy-based products exhibited complex microbial communities dominated by Bacillus spp., whereas commercially produced products were characterized by yeast-dominant profiles. Fruit vinegar and yogurt showed low microbial diversity regardless of the production method. These findings demonstrate the importance of production strategies in shaping microbial ecology, fermentation dynamics, and resulting product characteristics across various Korean fermented foods.}, }
@article {pmid41897851, year = {2026}, author = {Fragomeni, B and Hird, SM and Zezeski, AL and Geary, TW and McCoski, SR and Hay, EH}, title = {Vaginal Microbiome Is Associated with Breed and Pregnancy Status in Beef Cattle.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060874}, pmid = {41897851}, issn = {2076-2615}, support = {3030-31000-019-000D//USDA-ARS CRIS/ ; }, abstract = {Reproductive performance is a key determinant of overall livestock productivity. In both beef and dairy systems, reproductive failure represents a leading cause of cow culling. Reproductive traits are complex in nature and present a low heritability in general. Additionally, the collection of such phenotypes usually relies on indirect measures of fertility, such as conception success. Therefore, further investigation into genetic and non-genetic factors of reproductive traits in cattle is necessary. The hosts' microbiome plays a crucial role in vertebrate biology, including reproduction. We, therefore, hypothesize that microbiome indicators may serve as a biomarker of fertility. This study explored the relationship between vaginal microbiome profiles and pregnancy among three beef cattle genetic groups using field data. Vaginal swabs were collected from 74 cows at Fort Keogh, MT, including 23 Angus, 23 Hereford Line 1, and 28 crossbreds, and DNA was extracted and analyzed via 16S rRNA gene amplification. Significant differences in alpha diversity (p < 0.05) were found among Line 1 cows compared to Angus and crossbreds in many indicators of alpha diversity. Pregnancy status did not influence alpha diversity of samples significantly, but trends toward significance were observed. PERMANOVA analysis indicated that genetic groups and pregnancy status affected microbial composition (p < 0.05), but their interaction was not significant. Each genetic group showed unique compositions of operational taxonomic units (OTUs), with higher proportions of Ureaplasma and Mycoplasma families in Line 1. Additionally, variations in microbial communities were observed between pregnant and non-pregnant cows, with certain uncultured bacteria more prevalent in non-pregnant cows. While field data are useful for such studies and represent a real production system, better-designed experiments are necessary to validate findings and test hypotheses. These results suggest variation in vaginal microbiomes across breeds and pregnancy status, emphasizing the need for further research to identify factors affecting these changes.}, }
@article {pmid41897857, year = {2026}, author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L}, title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060880}, pmid = {41897857}, issn = {2076-2615}, support = {42367014//The National Natural Science Foundation of China/ ; }, abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.}, }
@article {pmid41897872, year = {2026}, author = {Yang, X and Liu, K and Yang, W and Jin, T and Li, J and Wang, Z and Li, F}, title = {Reciprocal Hybridization Between Herbivorous and Carnivorous Sub-Cold-Water Fish Reveals Divergent Intestinal Characteristics and Microbiome Assembly.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060895}, pmid = {41897872}, issn = {2076-2615}, support = {CSTB2023TIAD-KPX0023//Zhijian Wang/ ; }, abstract = {Hybridization is pivotal for germplasm innovation, yet how reciprocal crossing regulates digestive characteristics in sub-cold-water fish remains unclear. This study systematically compared differences in intestinal morphology, physiological function, and microbial community assembly among herbivorous Schizothorax prenanti, carnivorous S. davidi, and their reciprocal hybrids using histological analysis, digestive enzyme assays, and 16S rRNA sequencing. Results indicated that parental intestinal characteristics were highly consistent with their feeding habits. Orthogonal hybrids exhibited a mosaic phenotype, combining the maternal muscular gut structure with high paternal-like lipase activity, and were characterized by an enrichment of the potential probiotic Lactococcus. In contrast, reciprocal hybrids presented a mismatch between morphology and function: despite developed hindgut folds, key digestive enzyme activities were low, and the gut microbiota was dominated by environmental bacteria such as Methylobacterium. Our findings indicate a spatially dependent assembly dynamic: the host genetic background strongly drives microbiome divergence in the anterior segments (foregut and midgut), whereas the long-term administration of a standardized diet ultimately promotes structural convergence in the hindgut. The orthogonal cross yielded a phenotype characterized by an apparent co-occurrence of specific host enzymes and distinct microbiota, suggesting an inferred physiological potential for lipid digestion that requires further multi-omics validation. These findings provide preliminary insights into the associations between genetic background and intestinal traits, providing a theoretical basis for the targeted breeding of Schizothorax species.}, }
@article {pmid41897913, year = {2026}, author = {An, Q and Chen, S and Ma, S and Bai, R and Lu, Z and Liu, Y and Wang, F and Wang, Q and Song, Y and Zhang, G and Lyu, Y and Wang, L and Wang, Y and Xia, Z}, title = {Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060936}, pmid = {41897913}, issn = {2076-2615}, support = {1051-2225006//General Program of the 2025 Talent Fund, Veterinary Teaching Hospital, China Agricultural University/ ; }, abstract = {Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.}, }
@article {pmid41897927, year = {2026}, author = {Fukuda, EP and Lu, Y and Fowler, E and Jessup, RW and Drewery, ML}, title = {Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060950}, pmid = {41897927}, issn = {2076-2615}, support = {2021-77040-34881//National Institute of Food and Agriculture/ ; 2020-38422-32250//National Institute of Food and Agriculture/ ; N/a//Translational Health Research Center/ ; }, abstract = {While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity.}, }
@article {pmid41897949, year = {2026}, author = {Wang, Z and Lin, Z and Lin, B and Peng, S and Xu, Y and Wang, X and Wu, H and Xie, B and Chen, B and Zhao, M and Lin, F and Sun, T and Li, Z}, title = {Composite Probiotic Fermented Feed Enhances Growth Performance and Intestinal Health in Weaned Piglets by Modulating the Gut Microbiome and Metabolome.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060972}, pmid = {41897949}, issn = {2076-2615}, support = {2023N0044//Fujian Provincial Agricultural Guidance (key) Project/ ; 2024S0033 and 2022S0027//Fujian Provincial Department of Science and Technology Spark Program/ ; }, abstract = {This study investigated the effects of compound microbial fermented feed on the growth performance, intestinal architecture, microbiota composition, and metabolic profiles of weaned piglets. Fifty-four weaned piglets were randomly allocated to three dietary treatment groups: a control group (basal diet), a 50% fermented feed group (T1), and a 100% fermented feed group (T2), for a 33-day feeding period. The results indicated that both T1 and T2 diets significantly improved final body weight and average daily gain (ADG), while decreasing the feed-to-gain ratio (F/G) compared with the control (p < 0.05). Morphological assessment revealed that the T1 group significantly elevated the villus height-to-crypt depth ratio in the jejunum and increased the density of goblet cells in the cecum and colon (p < 0.05). Multi-omics analysis indicated that fermented feed significantly reshaped the gut microbiota structure (p < 0.05), characterized by the enrichment of beneficial taxa, including Oscillospiraceae and Lachnospiraceae (p < 0.05), and the modulation of nucleotide and bile acid metabolism. Furthermore, correlation analysis identified significant linkages between the abundance of jejunal Oscillospiraceae and colonic/cecal Lactobacillus with growth performance, intestinal morphology, and key metabolites. This finding systematically elucidates the mechanisms by which compound microbial fermented feed promotes growth and intestinal health in weaned piglets via microbiota-mediated pathways, offering a robust scientific framework for the development of antibiotic-free nutritional strategies.}, }
@article {pmid41897953, year = {2026}, author = {Fan, J and Xue, X and Zhang, H and Wang, F and Chao, Z and Wei, L and Liu, H and Ren, Y and Sun, R}, title = {Intestinal Development in Wuzhishan Pigs at Different Growth Phases: Insights from Microbiome and Metabolomics.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060976}, pmid = {41897953}, issn = {2076-2615}, support = {2021YFF0702804//The National Key R&amp;D Program of China/ ; U22A20508//National Natural Science Foundation of China/ ; 202002011//The 2020 Research Program of Sanya Yazhou Bay Science and Technology City/ ; HNARS-02-Z01//Hainan Local Pig Agricultural Research System/ ; }, abstract = {Wuzhishan pigs are a typical Chinese indigenous miniature pig breed, with thin skin and high amino acid content in muscle; slow weight gain and long feeding phases limit their value. As the primary digestive and absorptive organ, the intestine is crucial for growth, yet current studies on its development are limited. This study aimed to investigate intestinal physiological differences in Wuzhishan pigs across four phases (pre-weaning: 7, 14 days; weaning: 35, 38, 45 days; fattening: 70, 100 days; maturity: 180, 240 days) by evaluating intestinal morphology, digestive enzyme activity, gut microbiota diversity via 16S rRNA gene sequencing, and metabolite characteristics via metabolomic analysis. Results showed poor intestinal morphology and enzyme activity during weaning, significant ileal and colonic microbial diversity differences across phases, increased beneficial bacteria with age, and enriched opportunistic pathogens (Streptococcus, Romboutsia, Terrisporobacter) during weaning; weaning also had lower lipid metabolites, correlated with decreased Fusobacterium, Lactobacillus, and Muribaculaceae. Fattening enhanced amino acid metabolism, with increased Lactobacillus correlated with higher amino acids and muscle-related metabolites, while maturity increased immune-related metabolites (e.g., pyridoxine) in the vitamin B6 pathway. These results explain delayed rapid weight gain in Wuzhishan pigs and provide a theoretical basis for maintaining intestinal stability and production performance.}, }
@article {pmid41897963, year = {2026}, author = {Del Treste, A and Sacchettino, L and Costanza, D and Trapanese, L and Salzano, A and Napolitano, F and Cortese, L and d'Angelo, D and Campanile, G and Greco, A}, title = {Intestinal Dysbiosis Relating to Gut-Brain Axis and Behavior in Dogs: A Systematic Review with Text Mining Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060986}, pmid = {41897963}, issn = {2076-2615}, abstract = {The intestinal microbiome plays a fundamental role in canine health and well-being, regulating functions, including digestion, immunity, metabolism, and behavior. Dysbiosis refers to the disruption of the balanced composition of resident commensal communities, and gut bacteria can influence behavior via neurological, metabolic, endocrine, and immune-mediated pathways. Growing evidence supports the existence of a bidirectional communication between the gut and the central nervous system, known as the gut-brain axis, through which intestinal microorganisms may influence behavior via neurological, metabolic, endocrine, and immune-mediated pathways. Despite the expanding interest in this field, the contribution of intestinal dysbiosis to the development and severity of behavioral and neurological disorders in companion dogs remains poorly understood. This review aims to critically analyze the literature from 2011 to 18 September 2025 concerning the association between dysbiosis, the gut-brain axis, and both gastrointestinal and non-gastrointestinal illnesses in dogs. To our knowledge, this review represents the first application of Text Mining (TM) in this domain: TM facilitates the identification and analysis of valuable information from extensive datasets, converting unstructured content into structured data, thereby enabling quantitative analysis. We used the following search terms on three bibliographic databases (PubMed, Scopus, and Web of Science): "dysbiosis" AND "canine" OR "dog" AND "gut-brain axis" AND "behavior". Of the 1176 records retrieved, 35 studies were checked following the PRISMA guidelines, and they met the predefined inclusion criteria in the final analysis.}, }
@article {pmid41898245, year = {2026}, author = {Bernstein, C and Bernstein, H}, title = {The Causal Role of Bile Acids in Cancers of the Digestive System.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030598}, pmid = {41898245}, issn = {2227-9059}, abstract = {Bile acids are widely distributed in the human gastrointestinal tract. A literature review indicates that bile acids may have a role in initiating cancers in every organ of the digestive system. The estimated number of new digestive system cancers world-wide in 2022 was about 5 million. In the particular case of colon cancer, secondary bile acids produced in response to a high fat diet disrupt colonic epithelial cell mitochondrial membranes. This disruption leads to the release of oxidative free radicals that damage DNA, potentially leading to carcinogenic mutations. High levels of colonic bile acids may also alter the gut microbiome, with some bacteria causing inflammation and increased reactive oxygen species leading to DNA damage. Also, bile acids taken up by receptors on the surface of gastrointestinal tract cells can activate NF-kB. In turn, NF-kB may activate a super-enhancer at an oncogene. Bile acid reflux also plays a significant role in esophageal adenocarcinoma, stomach cancer and small intestine carcinogenesis. In addition, cancers of the pancreas, liver, and biliary tract can be caused by the constriction of the common bile duct leading to reflux of bile acids back into these organs. Gastroesophageal reflux involving bile acids may also contribute to hypopharyngeal squamous cell carcinogenesis. Thus, bile acids are a likely major contributory cause of cancer throughout the digestive tract.}, }
@article {pmid41898284, year = {2026}, author = {Rosas-Sánchez, GU and Germán-Ponciano, LJ and Pérez-Vega, MI and Gutiérrez-Coronado, O and Muñoz-Carrillo, JL and Soriano-Hernández, AD and Barrientos-Bonilla, AA and Rosales-Muñoz, CG and Soria-Fregozo, C}, title = {Probiotics as Modulators of Adult Neurogenesis and Synaptic Plasticity: New Perspectives in the Pathophysiology and Treatment of Affective Disorders.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030637}, pmid = {41898284}, issn = {2227-9059}, abstract = {Affective disorders, such as major depressive disorder and anxiety disorders, represent a major global health burden, with current treatments proving inadequate for a substantial proportion of patients. Emerging research highlights the microbiota-gut-brain (MGB) axis as a crucial bidirectional communication system influencing brain function and neuroplasticity through neural, endocrine, immune, and metabolic pathways. This narrative review examines probiotics-live beneficial microorganisms-as modulators of adult neurogenesis and synaptic plasticity, two processes fundamentally implicated in the pathophysiology of affective disorders. Preclinical evidence demonstrates that specific strains, particularly from the Lactobacillus and Bifidobacterium genera, promote hippocampal neurogenesis and synaptic function through epigenetic regulation via short-chain fatty acids (SCFAs), notably butyrate-mediated histone deacetylase inhibition, modulation of neuroinflammatory pathways, regulation of neurotransmitter receptor expression across glutamatergic, GABAergic, and monoaminergic systems, and production of neuroactive peptides. Clinical evidence from randomized controlled trials and recent meta-analyses indicates that probiotic supplementation produces significant reductions in depressive and anxiety symptoms, with effects correlating to changes in gut microbiota composition and peripheral neuroplasticity biomarkers, particularly brain-derived neurotrophic factor (BDNF). However, significant methodological limitations persist, including small sample sizes, lack of standardization in probiotic strains and dosages, inconsistent outcome measures, and considerable interindividual variability. While the mechanistic and clinical evidence is biologically plausible and directionally promising, it is not yet sufficient to support definitive therapeutic recommendations. Future research must prioritize adequately powered clinical trials with standardized consortia, comprehensive multi-omics biomarker panels, and precision psychobiotic strategies guided by microbiome-defined patient stratification.}, }
@article {pmid41898327, year = {2026}, author = {Belosic Halle, Z and Tomasic, V and Biscanin, A and Cacic, P and Saric, I and Mustapic, S and Stojic, J and Luetic, K and Bekic, D and Paic, M and Micetic, D and Krznaric Zrnic, I and Olic, I and Razov Radas, M and Skocilic, I and Golčic, M and Rados, L and Radic, J and Prejac, J and Mikolasevic, I}, title = {Immune-Mediated Colitis Induced by Immune Checkpoint Inhibitors: Pathophysiology, Clinical Management, and the Emerging Role of Fecal Microbiota Transplantation.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030683}, pmid = {41898327}, issn = {2227-9059}, abstract = {BACKGROUND/OBJECTIVES: Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of various malignancies, but their use is frequently accompanied by immune-related adverse events, among which immune-mediated colitis (IMC) represents one of the most common and clinically significant gastrointestinal toxicities. IMC may lead to treatment interruption, increased morbidity, and compromised quality of life. This review aims to provide a comprehensive overview of the pathophysiology, risk factors, diagnosis, management, and emerging therapeutic strategies with particular emphasis on the role of the gut microbiota and fecal microbiota transplantation (FMT).<br><br>METHODS: This review integrates current international guidelines, meta-analyses, clinical trials, and recent translational studies addressing IMC. The available evidence on immunological mechanisms, predictive biomarkers, clinical presentation, diagnostic algorithms, and treatment options was critically synthesized to outline a structured and multidisciplinary management approach.<br><br>RESULTS: IMC is driven by dysregulated immune activation, cytokine release, and alterations in gut microbiota. Incidence and severity vary according to ICI class, combination regimens, tumor type, and patient-related factors. Diagnosis requires exclusion of infectious causes, laboratory assessment, and endoscopic and histologic evaluation with CTCAE-based severity grading. Corticosteroids remain the cornerstone of first-line therapy, while infliximab and vedolizumab are effective in steroid-refractory cases. Emerging therapies, including JAK inhibitors and FMT, have shown promising results in refractory disease.<br><br>CONCLUSIONS: IMC is a complex and potentially severe complication of ICI therapy that necessitates early recognition, accurate grading, and individualized, multidisciplinary management. Severity-guided treatment, timely escalation to biologics, and careful balancing of immunosuppression with antitumor efficacy are essential for optimal outcomes. Future research should focus on biomarker validation, microbiome-targeted therapies, and prospective trials to refine therapeutic algorithms and define the optimal role and timing of FMT in clinical practice.}, }
@article {pmid41898341, year = {2026}, author = {Prince, Y and Davison, GM and Matsha, T and Raghubeer, S}, title = {The Role of Fusobacterium in Periodontal Disease and Its Implications for Cardiovascular Health.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030697}, pmid = {41898341}, issn = {2227-9059}, support = {MRC-RFA-UFSP-01-2013/ VMH Study//South African Medical Research Council/ ; Grant number: 115450//National Research Foundation/ ; }, abstract = {Fusobacterium species, particularly Fusobacterium nucleatum, is known as a key adhesive bridging microorganism in the development of periodontal disease, inducing microbial imbalances and chronic inflammation within the oral cavity. Their role is to provide a bridge between both early colonisers (such as Streptococcus and Actinomyces) and late colonisers (such as Porphyromonas gingivalis and Treponema denticola), which results in multispecies biofilm formation. This triggers an immune reaction which may provide both a protective and destructive effect on the periodontal ligament and alveolar bone. Recent studies have discovered their significance beyond oral pathology. Therefore, Fusobacterium have been implicated in several systemic diseases, including cardiovascular disease (CVD). Virulent mechanisms, such as adhesion, invasion, modulation of host immunity, and pro-inflammatory signalling, contributes to periodontal tissue bone loss and entry into the circulation. Circulating bacteria interact with vascular endothelium and promote atherosclerotic plaque formation. The role of Fusobacterium nucleatum as a microbial link between periodontal disease and cardiovascular disease is highlighted and discussed. Overall, current evidence is mostly observational and preclinical, supporting an associative link between F. nucleatum-mediated periodontal disease and CVD. The literature highlights key mechanistic pathways while underscoring the important need for longitudinal studies to clarify causality and identify target therapeutic interventions.}, }
@article {pmid41898386, year = {2026}, author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y}, title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062521}, pmid = {41898386}, issn = {1422-0067}, mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; }, abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.}, }
@article {pmid41898402, year = {2026}, author = {Antohi, AL and Gheorghiță, AD and Andronic, O and Gradisteanu Pircalabioru, G and Treteanu, AR}, title = {Across the Social Network of the Gut: Bacterial, Fungal, and Viral Determinants of Checkpoint Inhibitor Efficacy and Toxicity.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062538}, pmid = {41898402}, issn = {1422-0067}, support = {PN-IV-P8-8.1-PRE-HE-ORG-2023-0054 - Contract no 17PHE/2023//Unitatea Executiva Pentru Finantarea Invatamantului Superior Si A Cercetarii Stiintifice Universitare/ ; grant agreement - 101087007 - eBio-hub//HORIZON-WIDERA-2022-TALENTS-01/ ; ROGEN 324809//Development of genomic research in Romania-ROGEN/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use/pharmacology ; Animals ; *Neoplasms/drug therapy/immunology/microbiology ; Fungi/immunology ; Bacteria ; Dysbiosis/microbiology ; Viruses ; Mycobiome ; }, abstract = {Recent findings suggest that the gut microbiome significantly influences cancer outcomes, including responses to immune checkpoint inhibitor (ICI) treatments. Although early research focused on gut bacteria, it is now understood that the microbiome includes a bacteriome, virome, and mycobiome, all of which can modulate host immunity. Some commensal bacteria enhance anti-tumor immune responses and improve ICI efficacy, as demonstrated in both mice and patients. Fecal microbiota transplants (FMT) from patients responding to ICI have successfully reversed resistance in certain non-responders. In addition to bacteria, gut fungi and viruses are gaining attention as further factors influencing ICI effectiveness and toxicity. Recent multi-omics studies across cancer cohorts show that fungal and viral populations in the gut vary between ICI responders and non-responders. Commensal fungi may shape anti-cancer immunity by inducing inflammatory or tolerogenic pathways, while viral components can stimulate innate immune sensors that promote tumor surveillance. On the other hand, gut dysbiosis marked by expansion of pathobionts (including opportunistic fungi) and reduction in beneficial microbes is linked to serious immune-related adverse events (irAEs) such as ICI-induced colitis. This review discusses the multi-kingdom gut microbiome-bacteria, fungi, and viruses-and their interactions with the immune system in cancer therapy. We emphasize known mechanisms linking these microbes to anti-tumor immunity, overview human studies associating gut microbiome profiles with ICI outcomes and explore strategies to modulate the microbiome to enhance ICI efficacy while reducing toxicity. Understanding and utilizing the gut mycobiome and virome in conjunction with the bacteriome could pave the way for new biomarkers and therapeutic adjuvants in cancer immunotherapy.}, }
@article {pmid41898403, year = {2026}, author = {Nicze, M and Borówka, M and Dec, A and Bułdak, &#x141; and Bołdys, A and Okopień, B}, title = {Resistant and Refractory Obesity: The Complexity of Anti-Obesity Therapy Failure.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062539}, pmid = {41898403}, issn = {1422-0067}, mesh = {Humans ; *Obesity/drug therapy ; *Anti-Obesity Agents/therapeutic use/pharmacology ; Treatment Failure ; *Drug Resistance ; }, abstract = {Pharmacotherapy is a key component of obesity management, yet treatment failure remains a prevalent challenge in clinical practice. Such failure may present as insufficient pharmacological response, early discontinuation, or post-treatment weight regain, underscoring the discrepancy between clinical trial efficacy and real-world outcomes. The effectiveness of anti-obesity medications (AOMs) is influenced by psychiatric comorbidities, including depression, anxiety, and disordered eating patterns, as well as environmental and socioeconomic factors such as limited healthcare access, weight-related stigma, and high medication costs. Individual characteristics, including physical activity, body composition, visceral adiposity, and microbiome profile, further modulate treatment outcomes. Pharmacokinetic and pharmacotherapeutic limitations such as drug-phenotype mismatch, route of administration, suboptimal formulations, and exposure to counterfeit products also compromise efficacy. No less important are genetic and immunological factors, comprising pharmacogenomic variants of both incretin and melanocortin receptors along with antidrug antibodies (ADAs), which may constitute therapy resistance. Concomitant medications and comorbid endocrine disorders can additionally attenuate weight-loss effects. The objective of this review is to characterize the multifactorial nature of resistance and refractoriness to anti-obesity therapy, and the importance of identifying pretreatment predictive factors for recognizing individuals at risk of inadequate or lack of response, thereby enabling personalized management strategies and improving long-term clinical outcomes, particularly in "difficult-to-treat" patients.}, }
@article {pmid41898417, year = {2026}, author = {Li, SWL and Au, OTH and Lau, EYT and Lu, RY and Zaleski, AL and Liang, JQ}, title = {Interplay Between Gut Microbiota and Cholesterol Metabolism in Colorectal Cancer.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062553}, pmid = {41898417}, issn = {1422-0067}, support = {14104523//University Grants Committee/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Colorectal Neoplasms/metabolism/microbiology ; *Cholesterol/metabolism ; Animals ; Dysbiosis/metabolism/microbiology ; Bile Acids and Salts/metabolism ; Lipid Metabolism ; }, abstract = {Both gut microbiota dysbiosis and disrupted cholesterol metabolism are associated with colorectal cancer (CRC). While the interactions between these two factors have been well explored in diseases such as cardiovascular disease and atherosclerosis, their interactions and underlying mechanisms in CRC pathogenesis remain insufficiently explored, constituting a critical area for further investigation. This review examines the complex relationship between gut microbiota and cholesterol metabolism in CRC development from 2 perspectives: how specific gut microbial species can increase CRC risk by modulating cholesterol metabolism, particularly through bile acids and oxysterols, and how disrupted cholesterol metabolism can exacerbate microbial dysbiosis and promote CRC. The bidirectional relationship between gut dysbiosis and cholesterol dysregulation creates a vicious cycle that drives CRC development. Moreover, the potential of targeting the gut microbiome and cholesterol metabolism to develop new strategies for preventing and treating CRC is discussed, highlighting the promise of certain bacterial strains that exert protective effects via cholesterol-lowering mechanisms. By elucidating the intricate connections between gut microbiota, cholesterol metabolism, and CRC, this review paves the way for innovative approaches in CRC prevention and therapy.}, }
@article {pmid41898420, year = {2026}, author = {Kowalczyk, P and Kurylczyk, A and Węglarz, A and Makulska, J}, title = {Diet-Microbiome-Redox Interactions and Oxidative Stress Biomarkers in Livestock: Computational and Spatial Perspectives for Translational Health and Production.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062556}, pmid = {41898420}, issn = {1422-0067}, mesh = {Animals ; *Livestock/metabolism/microbiology ; *Oxidative Stress ; *Biomarkers/metabolism ; Oxidation-Reduction ; *Diet ; *Microbiota ; }, abstract = {Oxidative stress (OS) is a central regulator of health and productivity in livestock, emerging from complex interactions between dietary inputs, microbiome composition, environmental stressors, and host metabolism. This narrative review synthesizes current knowledge on OS in cattle, pigs, sheep, and poultry, emphasizing mechanistic pathways, tissue-specific responses, and translational applications. We highlight the central role of redox-inflammatory signaling hubs, including nuclear factor kappa B (NF-κB), nuclear factor erythroid 2-related factor 2 (Nrf2)/Kelch-like ECH-associated protein 1 (Keap1), and inflammasomes, as integrators of metabolic and immune stress. Microbiome-metabolome interactions modulate systemic oxidative responses, influencing liver, mammary gland, gastrointestinal tract, adipose tissue, and reproductive tissues. Oxidative stress-related biochemical and molecular alterations are captured by a range of biomarkers, such as malondialdehyde (MDA), Total Antioxidant Capacity (TOAC), gluthatione peroxidase (GPx), superoxide dismutase (SOD), paraoxonase-1 (PON1), cytokines, and gene expression profiles, measurable in blood, milk, saliva, and tissues. Integrating these markers enables precision diagnostics, early disease detection, and evidence-based nutritional interventions. Furthermore, computational modeling and spatial-socioeconomic perspectives offer novel approaches to translate molecular redox insights into practical livestock management strategies. By framing OS as a regulated, context-dependent process rather than a simple imbalance of reactive oxygen species, this review advances a conceptual, cross-species framework for understanding, monitoring, and mitigating oxidative stress in livestock. This integrative perspective provides a foundation for targeted antioxidant strategies and sustainable production practices, bridging molecular mechanisms with practical applications in animal health and productivity.}, }
@article {pmid41898576, year = {2026}, author = {Nguyen, M and Oh, S and King, M and Yu, W and Ramadan, AR}, title = {Current Management of Resistant Hypertension in Patients with Intracerebral Hemorrhage.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062716}, pmid = {41898576}, issn = {1422-0067}, mesh = {Humans ; *Hypertension/drug therapy/complications ; *Antihypertensive Agents/therapeutic use ; *Cerebral Hemorrhage/complications/drug therapy ; Calcium Channel Blockers/therapeutic use ; Angiotensin-Converting Enzyme Inhibitors/therapeutic use ; Drug Resistance ; }, abstract = {Approximately 795,000 people experience new or recurrent strokes in the United States each year; between 10 to 20% of these are spontaneous intracerebral hemorrhages (ICH). Uncontrolled hypertension is not only the most common cause of ICH but also a major risk factor for hematoma expansion. Resistant hypertension, defined as persistently elevated blood pressure despite the use of three or more antihypertensives of different classes, is common in patients with ICH. A long-acting calcium channel blocker, angiotensin-converting enzyme inhibitor (ACEi) or angiotensin receptor blocker (ARB), and a thiazide diuretic are generally considered the mainstay for the treatment of resistant hypertension. However, due to the risk of hyponatremia and worsening cerebral edema, thiazide diuretics should be avoided during the first few weeks of ICH. Recent evidence supports the use of a mineralocorticoid receptor antagonist. While resistant hypertension may be idiopathic, a workup of secondary causes should be pursued. Adequate and timely control of elevated blood pressure remains one of the main cornerstones of treatment in patients with ICH. Previous studies have revealed that resistant hypertension in patients with ICH is associated with longer ICU stays, a higher risk of recurrent stroke, and can contribute to renal, cardiac, and neurologic complications. This emphasizes the need for early initiation of oral antihypertensives and adequate blood pressure control at hospital discharge. Landmark studies have shown that early lowering of SBP to 130-150 mm Hg with smooth, sustained BP control is safe and may improve functional outcomes in patients with mild to moderate ICH. After initiating oral antihypertensives with a calcium channel blocker, an ACEi or ARB beta-blocker, and a mineralocorticoid receptor antagonist to maximally tolerated doses, the next line of antihypertensive treatment should be tailored to the patient's co-morbidities, and may include a beta-blocker, central alpha agonist, hydralazine, and minoxidil. In this review, we discuss the epidemiology of resistant hypertension in ICH and its molecular basis, diagnostic workup, and acute and long-term treatment. We present novel mechanisms implicated in hypertensive ICH, including ferroptosis, neuroinflammation, the CNS-gut microbiome axis, and novel therapeutics. We also propose a simple algorithm for the optimal pharmacological management of resistant hypertension in ICH.}, }
@article {pmid41898595, year = {2026}, author = {Makiel, K}, title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062734}, pmid = {41898595}, issn = {1422-0067}, support = {//University of Physical Education, 31-571 Cracow, Poland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology ; *Obesity/diet therapy/metabolism/genetics/microbiology ; *Adipokines/metabolism/genetics ; *DNA Methylation ; *Diet ; Animals ; Inflammation ; Nutrigenomics ; Multiomics ; }, abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.}, }
@article {pmid41898627, year = {2026}, author = {Zhu, Y and Li, S and Li, S and Wang, Y and Du, Y and Zheng, X and Wu, J}, title = {Underestimated and Overlooked Factors in PBC Progression: Bacterial and Fungal Infections.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062766}, pmid = {41898627}, issn = {1422-0067}, support = {82170636//National Natural Science Foundation of China/ ; 2022YFC2304401//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Mycoses/complications/microbiology ; Gastrointestinal Microbiome ; Disease Progression ; *Bacterial Infections/complications/microbiology ; *Liver Cirrhosis, Biliary/microbiology/pathology/epidemiology/etiology ; Dysbiosis/microbiology ; Animals ; }, abstract = {Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by cholestasis, which can progress to end-stage liver disease and even hepatocellular carcinoma. Its onset is typically triggered by complex interactions between genetic and environmental factors. In recent years, epidemiological and mechanistic studies have highlighted bacterial and fungal infections as potential key environmental factors in PBC pathogenesis. Bacteria may be associated with PBC autoimmunity through mechanisms such as molecular mimicry. Gut microbiota dysbiosis has been linked to aberrant immune recognition, altered metabolites, and intestinal barrier disruption, which may contribute to the aggravation of liver injury. Case reports of fungal infections suggest an association with poor prognosis in PBC, although the underlying mechanisms remain to be elucidated. This review systematically summarizes existing clinical epidemiological data, microbiome association studies, and mechanistic evidence; synthesizes the possible molecular mechanisms linking bacterial infections to PBC development and progression; discusses the potential role of the gut microbiota in PBC progression; and analyzes the possible molecular mechanisms underlying the poor prognosis associated with fungal infections in PBC. This study aims to provide valuable insights for developing optimal prevention, diagnosis, and treatment strategies targeting bacterial and fungal infections in PBC.}, }
@article {pmid41898630, year = {2026}, author = {Hernández-Valles, AE and Martínez-Machado, G and Alvarado-Mata, LY and Lopez-Ortiz, C and Nimmakayala, P and Balagurusamy, N and Reddy, UK}, title = {The Role of Diet in Shaping Gut Microbiota and Its Impact on Host Metabolic Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062768}, pmid = {41898630}, issn = {1422-0067}, support = {2024-38821-42101 and 2022-38821-37343//United States Department of Agriculture - National Institute of Food and Agriculture/ ; 2242771 and 1920920//National Science Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diet ; Animals ; Dysbiosis/metabolism/microbiology ; Energy Metabolism ; }, abstract = {Diet is a key modulator of the gut microbiota, thereby influencing host physiology. Microbial colonization begins early in life, influenced by maternal sources, mode of birth, diet, and environmental exposures, and stabilizes into an adult-like microbiome during early childhood. This maturation yields a microbial ecosystem dominated by Firmicutes and Bacteroidetes that contributes to host physiological homeostasis. Gut microorganisms function as an integrated metabolic system that transforms dietary substrates into bioactive metabolites, including short-chain fatty acids (SCFAs), amino acid-derived compounds, and microbial lipids. These metabolites regulate glucose and lipid metabolism, intestinal barrier integrity, and immune modulation. Although many metabolic functions are conserved, their activity is shaped by diet, microbial cross-feeding, and local intestinal conditions, enabling functional specialization within the gut. Disruption of this system, known as dysbiosis, is associated with alterations in microbial diversity and metabolic output that have been linked to metabolic diseases, including obesity and related disorders. Evidence from experimental models and observational studies suggests that these associations may involve interconnected inflammatory and metabolic mechanisms, such as impaired intestinal barrier function, low-grade inflammation, and altered dietary energy harvest; however, causal relationships in humans remain incompletely understood. Beyond peripheral effects, the gut microbiome influences host metabolism via the gut-brain axis, a bidirectional network that integrates neural, endocrine, immune, and metabolic signaling. Microbiota-derived metabolites and gut hormone modulation contribute to appetite regulation, energy balance, and glucose homeostasis, while central neuroendocrine signaling can reciprocally shape the intestinal microbial niche. Collectively, these findings highlight the gut microbiome as a central regulator of host metabolism, whose disruption may contribute to the development of metabolic disease.}, }
@article {pmid41898683, year = {2026}, author = {Çelo, E and Dama, A and Hasho, S and Deda, L}, title = {Topical Probiotics in Diabetic Wound Healing: Emerging Therapeutic Strategies.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062826}, pmid = {41898683}, issn = {1422-0067}, mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Wound Healing/drug effects ; *Diabetic Foot/therapy/microbiology/drug therapy ; Animals ; Administration, Topical ; }, abstract = {Diabetic foot ulcers (DFUs) are among the most serious and costly complications of diabetes, characterised by delayed healing, frequent infections, and a high risk of recurrence. Despite advances in wound care, many current therapies fail to address the multifactorial pathophysiology of diabetic wounds, including vascular dysfunction, immune dysregulation, chronic inflammation, and microbial imbalance. In this context, topical probiotics have emerged as a promising microbiome-based strategy aimed at restoring microbial balance while promoting tissue repair. This review summarises current evidence on the use of topical probiotics in diabetic wound healing, with a particular focus on DFUs, outlining key pathophysiological barriers to healing and examining how probiotic therapies may counteract these processes through antimicrobial, antibiofilm, immunomodulatory, and pro-angiogenic mechanisms. Preclinical studies suggest that topical probiotics may promote accelerated wound closure, reduce bacterial burden, modulate inflammatory responses, and enhance collagen deposition and angiogenesis following topical probiotic application. Early clinical studies investigations remain limited to small pilot studies and case series but have reported preliminary signals of enhanced healing and acceptable short-term tolerability in small exploratory cohorts. In addition, recent advances in probiotic delivery, such as bioengineered dressings, postbiotic formulations, and nano-enabled systems designed to improve stability and therapeutic performance, are also discussed. While existing data indicate biological plausibility and early clinical feasibility, larger, well-designed randomized controlled trials and deeper mechanistic investigations are still required to confirm efficacy, clarify safety in high-risk populations, and enable responsible clinical translation.}, }
@article {pmid41898696, year = {2026}, author = {Moleriu, LC and Lupusoru, R and Marin, RC and Muntean, C and Piroș, T and Vlad, DC and Dumitrașcu, AL and Dumitrașcu, V}, title = {Food as Friend or Foe: A Decadal Narrative Review of Dietary Patterns as Determinants of Gastrointestinal Pathophysiology and Clinical Outcomes (2015-2025).}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062837}, pmid = {41898696}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Diseases/physiopathology/epidemiology/etiology ; Gastrointestinal Microbiome ; *Diet ; *Gastrointestinal Tract/physiopathology ; }, abstract = {Diet is a major modifiable determinant of gastrointestinal (GI) health, influencing disease risk and progression through coordinated effects on the gut microbiome, immune regulation, epithelial barrier integrity, oxidative balance, and epigenetic mechanisms. This narrative review synthesizes epidemiological, mechanistic, and clinical evidence from the past decade to examine bidirectional relationships between dietary patterns and seven common GI disorders: celiac disease, irritable bowel syndrome (IBS), Crohn's disease, ulcerative colitis, Helicobacter pylori-associated gastritis, peptic ulcer disease, and lactose intolerance. Western dietary patterns, characterized by high intake of ultra-processed foods and saturated fats and low fiber consumption, are consistently associated with microbial dysbiosis, impaired barrier function, and enhanced inflammatory signaling. In contrast, Mediterranean and plant-forward dietary patterns show protective associations across multiple GI conditions. Mechanistically, diet influences GI pathophysiology largely through microbiome-derived metabolites, particularly short-chain fatty acids, which regulate epithelial homeostasis, immune tolerance, and inflammatory pathways. Condition-specific dietary strategies remain clinically important. Gluten exclusion is essential in celiac disease, low- fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) approaches provide evidence-based symptom control in IBS, and exclusive enteral nutrition or targeted exclusion diets support remission induction in Crohn's disease. Selected probiotics and emerging postbiotics may provide adjunctive benefits in specific contexts. Despite growing evidence, dietary research remains limited by methodological heterogeneity and interindividual variability. Precision nutrition approaches integrating microbiome profiling and artificial intelligence represent a promising translational direction. Overall, dietary patterns-rather than isolated nutrients-form the foundation of GI dietary therapy.}, }
@article {pmid41703607, year = {2026}, author = {Li, L and Sun, W and Tan, T and Xu, J and Chen, Y and Chen, Y and Gao, G and Ai, X and Zhou, J and Li, Y and Zhang, D and Lei, S}, title = {Limonin attenuates hyperlipidemia by regulating the gut microbiota-bile acid-farnesoid X receptor axis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41703607}, issn = {1479-5876}, support = {2024ZD0532700//National Major Science and Technology Projects of China/ ; 2023AFB302//Natural Science Foundation of Hubei Province/ ; Q20234308//Youth Project of Scientific Research Project of Hubei Provincial Department of Education/ ; 2018YFZD025//Key science and technology project of Jingmen under Grant/ ; 2023YFZD043//Key science and technology project of Jingmen under Grant/ ; 2024ZDYF006//Key science and technology project of Jingmen under Grant/ ; WJ2023M173//Health and Family Planning Commission of Hubei Province/ ; 2022BCE060//Hubei Province key R &amp; D project under Grant/ ; }, abstract = {BACKGROUND: Hyperlipidemia is an established risk factor for cardiovascular disease. Limonin, a natural tetracyclic triterpenoid compound found in the traditional Chinese herb Tangerine peel and citrus fruits, has been shown to ameliorate hyperlipidemia, although the underlying mechanisms of action are unknown. The present study employed a comprehensive approach integrating to assess the efficacy of Limonin in the treatment of hyperlipidemia and to explore its molecular mechanisms.<br><br>METHODS: Hyperlipidemia model was induced by high-fat diet (HFD). The effects of Limonin on hyperlipidemia were evaluated through serum, liver lipid, and Hematoxylin &amp; eosin (H&amp;E). Then, the mechanism of Limonin alleviates hyperlipidemia was explored by network pharmacology. Targeted metabolism was used to measure bile acids (BAs)&#x2019; changes in serum and fecal, and 16&#xa0;S rDNA sequencing of gut microbiota. Finally, the expression of genes and proteins about FXR/FGF15, ASBT, and FGF15/FGFR4 signaling pathways in the distal ileum or liver was detected by qPCR, immunohistochemistry, and Western blotting.<br><br>RESULTS: The results confirmed the significant anti-hyperlipidemia effect of Limonin. Network pharmacology analysis revealed that Limonine alleviates hyperlipidemia is possibly closely pertaining to BAs metabolism. In a mouse model of hyperlipidemia, Limonin altered the colonic BAs profile, especially in terms of elevated levels of conjugated BAs. Limonin reshaped the structure of the gut microbiome by decreasing bile salt hydrolase (BSH)-producing genera, including Lactobacillus, Bacteroides, Clostridium, Streptococcus, and Adlercreutzia. Decreased BSH activity increased levels of conjugated BAs, which inhibited activation of ileum FXR, facilitated BAs synthesis and fecal BAs excretion. The decreased FXR activity resulted in lower expression of FGF15 and ASBT in the distal ileum, lower expression of FGF15 and its receptor in the liver, and increased expression of CYP7A1 in the liver.<br><br>CONCLUSION: Limonin remodels the gut microbiota to reduce BSH activity and to activate BAs synthesis pathways, thereby ameliorating dyslipidemia. These results provide a theoretical basis for clinical investigations into the use of Limonin in anti-hyperlipidemia therapies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07826-7.}, }
@article {pmid41709254, year = {2026}, author = {Parlak, HM and Ozkul, C and Akman, AC and Guncu, GN and Ergunay, K and Akyon, Y}, title = {Submucosal microbiota profile in peri-implant health, peri-implant mucositis, and different severity levels of peri-implantitis.}, journal = {BMC oral health}, volume = {26}, number = {1}, pages = {}, pmid = {41709254}, issn = {1472-6831}, abstract = {BACKGROUND: The unique and complex peri-implant microbiota harbors many species, mostly bacteria, and dysbiotic shift in microbiota induces peri-implant diseases. The aim of the study was to investigate the compositions and differences in submucosal microbial profiles in subject with different peri-implant heath statues, from peri-implant healthy (PH) to advanced peri-implantitis (PI).<br><br>METHODS: Submucosal plaque samples were obtained from 78 individuals with PH, peri-implant mucositis (PM), early, moderate, and advanced PI (PH:16, PM:16, PI-early: 14, PI-moderate: 16, and PI-advanced:16) and analyzed using sequencing of 16S rRNA gene. Differences of submucosal microbiome profiles between groups were evaluated with taxonomic abundances and microbial diversity using the alpha-diversity metrics (observed features, Shannon index, and Chao1 index), beta-diversity metrics (Bray&#x2013;Curtis dissimilarity, unweighted, and weighted UniFrac distance), and linear discriminant analysis effect size analysis.<br><br>RESULTS: According to alpha-diversity and beta-diversity analysis, the submucosal microbiota diversity showed no difference in the PI, PM, and PH sites. Prevotella, Fusobacterium, Bacteroides, Treponema, Porphyromonas, Fretibacterium, and Veillonella genera showed high abundance in the PI groups. At the genus-level, compositional differences between two distinct clinical groups were found. Pseudoramibacter was significantly enriched in PM and PI groups compared to PH. Fretibacterium was the most discriminative taxa between PI-early and PH.<br><br>CONCLUSIONS: Despite similar overall microbial diversity, distinct compositional shifts in the submucosal microbiota were observed across peri-implant health and disease. Specific genera, particularly Fretibacterium and Pseudoramibacter, were associated with disease conditions and may serve as potential candidates for future biomarker research. These findings suggest that microbial composition, in addition to diversity, could be relevant to understanding peri-implant disease processes and may inform the development of diagnostic and preventive strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-07942-2.}, }
@article {pmid41714986, year = {2026}, author = {Lu, S and Zhou, N and Song, X and Song, X and Qiao, X}, title = {Comparison of severe and general Mycoplasma pneumoniae pneumonia in children: a targeted next-generation sequencing based study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41714986}, issn = {1471-2334}, abstract = {BACKGROUND: The incidence and severity of Mycoplasma pneumoniae pneumonia (MPP) in children have increased after the pandemic of COVID-19, raising public concern. However, factors that affect the severity of MPP have not been well described. This study aimed to investigate the influence of Mycoplasma pneumoniae characters, respiratory co-existing pathogens, and host response on the severity of MPP.<br><br>METHODS: Clinical characteristics of 288 children hospitalized for MPP between November 2023 and July 2024 were analyzed retrospectively. Patients were divided into severe MPP (SMPP) and general MPP (GMPP) groups according to disease severity. Targeted next-generation sequencing (tNGS) was employed to analyze the respiratory pathogens of patients.<br><br>RESULTS: Of 288 cases, there were 113 SMPP and 175 GMPP. Compared with GMPP group, children with SMPP had significantly higher levels of neutrophil percentage, Neutrophil to Lymphocyte Ratio (NLR), C-Reactive Protein (CRP), Alanine aminotransferase (ALT), Lactic dehydrogenase (LDH) and D-D dimer (all P&#x2009;<&#x2009;0.05), which reflected a higher host immune response in SMPP group. Meanwhile, tNGS based pathogen analysis showed that Mycoplasma pneumoniae characters (A2063G mutation or not, pathogen concentration) were not associated with the severity of MPP (P&#x2009;>&#x2009;0.05). Furthermore, co-existing pathogens analysis showed that the SMPP group had a lower number of co-detected pathogens, children with human respiratory syncytial virus (RSV) co-existing were more frequent in the SMPP group (all P&#x2009;<&#x2009;0.05). Multivariate analysis showed that lower number of co-detected pathogens (decreased microbial diversity), RSV co-existing, elevated CRP, and LDH were independent risk factors for SMPP.<br><br>CONCLUSION: Collectively, our data showed that respiratory microbiome and host response may play important roles in the pathology of MPP, decreased microbial diversity, RSV co-existing, CRP, and LDH level can predict the severity of MPP.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12914-6.}, }
@article {pmid41879811, year = {2026}, author = {Kaiser, ME and Parikh, MA and Turitto, G and Grutman, G and Frishman, WH and Peterson, SJ}, title = {Processed Foods and Food Dyes: What Are We Eating and What Is the Cardiovascular Risk?.}, journal = {Cardiology in review}, volume = {}, number = {}, pages = {}, doi = {10.1097/CRD.0000000000001256}, pmid = {41879811}, issn = {1538-4683}, abstract = {Ultra-processed foods (UPFs) are industrially manufactured products that contain several additives and may contain high levels of added sugar, fat, salt, or little whole food. They also represent an increasing percentage of the world's diet and are increasingly associated with the development of cardiovascular disease (CVD). The findings of several meta-analyses and extensive, population-based longitudinal studies suggest there is a dose-response relationship between UPF consumption and each of the following outcomes: CVD, stroke, and total CVD-related deaths. Some food additives, especially emulsifiers (like carboxymethylcellulose and mono- and diglycerides), preservatives (like carboxymethylcellulose and mono- and diglycerides), and artificial colors (like tartrazine and sunset yellow), have been proven to independently alter the gut microbiome, induce cellular oxidative stress, and enhance chronic low-level low-grade inflammation. A common mechanistic pathway involves activation of the nuclear factor kappa B family of transcription factors, which mediate the production of pro-inflammatory cytokines, induce endothelial dysfunction, and promote atherogenesis. Thus, reducing UPF serves as a modifiable target for CVD prevention, can be incorporated into dietary guidelines and food-labeling practices to influence public health policy.}, }
@article {pmid41879866, year = {2026}, author = {Finch, JTD and Riegler, M and Cook, JM and Brettell, LE}, title = {Filth Flies, Flowers and Food: Pollination by Flies (Calliphoridae) Does Not Affect the Strawberry Microbiome.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02741-2}, pmid = {41879866}, issn = {1432-184X}, support = {PH16002//Horticultural Innovation Australia Limited/ ; }, }
@article {pmid41879986, year = {2026}, author = {Couradeau, E and Vanegas, J and Betancurt-Anzola, D and Glass, S and Eckert, K and Bechtold, EK and Ellenbogen, JB and Zaragoza, LR and Wrighton, K and Vanegas, JS}, title = {Soil Microbial Diversity in Páramos Wetland of the Colombian Andes Reveals Novel and Unique Features Within a Global Wetland Database.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02738-x}, pmid = {41879986}, issn = {1432-184X}, support = {2325922//NSF/ ; 7006508//USDA Hatch/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; }, abstract = {Tropical wetlands are the largest natural source of methane on Earth, yet they remain the least studied, particularly high-altitude wetlands like those in the Páramo of Chingaza, Colombia. These ecosystems are crucial for water provisioning, carbon sequestration, and biodiversity conservation but are threatened by rapid climate change. While the páramo biome supports thousands of endemic plant species and plays a vital role in balancing carbon inputs and greenhouse gas outputs (CO2 and CH4), its soil microbial diversity and functional roles in soil processes are largely unexplored. To fill this knowledge gap, we conducted amplicon sequencing of the ITS, 16S rRNA, and 18S rRNA genes to examine microbial diversity across three distinct ecosites at Laguna Seca, Chingaza, characterized by different macrotopographies, water-table levels, and vegetation assemblages. Our findings revealed significant variations in microbial community structure, with the peatland ecosite showing the highest diversity across all amplicons. Comparative analysis with global wetland datasets indicated that microbial communities at Laguna Seca share similarities with subarctic Stordalen Mire fen and other peat-forming wetlands. Notably, our targeted assessment identified a diversity of potential methanogens and methanotrophs exclusively within the peatland ecosite, at low but comparable abundance to other wetlands. This suggests that methane cycling in the other ecosites of this wetland may either be less prominent than expected or involve organisms not previously associated with known methane processes. These findings establish a baseline for understanding microbial diversity in tropical high-montane wetlands and underscore the unique ecological significance of páramo peatlands amid climate change.}, }
@article {pmid41880485, year = {2026}, author = {Gupta, S and Geurkink, B and de Rink, R and Plugge, CM and Muyzer, G}, title = {Enhanced activity and tolerance of sulfide-oxidizing bacteria in a dual reactor haloalkaline biodesulfurization system.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag082}, pmid = {41880485}, issn = {1365-2672}, abstract = {AIMS: Studies on haloalkaline biodesulfurization (BD) systems have depicted the process efficiency and active microbial community. This paper aims to unravel the functional potential of BD system's microbial community by investigating its metabolic potential through molecular and kinetic approaches.<br><br>METHODS AND RESULTS: Biomass from all sections of a pilot dual-reactor BD system from six different operations was analysed using kinetic, molecular and genomic approaches. For kinetic analyses, at the end of six runs, biological oxidation (BO) rates of sulfide (0.1-2&#xa0;mmol L-1), thiosulfate (0.1 to 32&#xa0;mmol L-1), and biologically formed sulfur in the BD system (Bio-sulfur) (5&#xa0;mmol L-1) were measured. Highest BO rates were ~ 0.38&#xa0;&#xb5;mol O2&#xa0;mgN-1 sec-1 for sulfide at 1&#xa0;mmol L-1-S HS- for the run with 0.9&#xa0;g L-1 sulfide and 10&#xa0;min HRT (Hydraulic retention time) in anoxic reactor and 0.064&#xa0;&#xb5;mol O2&#xa0;mgN-1 sec-1 at 2&#xa0;mmol L-1 S2O32--S, for the run with 0.5 0.9&#xa0;g L-1 sulfide and 10&#xa0;min HRT in anoxic reactor, cDNA-based qPCR of sqr and fccB genes revealed association with sulfide oxidation efficiency and element sulfur formation. Function predictions via R-based functional prediction tool -Tax4Fun2 indicated a truncated Sox pathway of thiosulfate oxidation.<br><br>CONCLUSIONS: Higher sulfide concentrations boosted biological activity and increased tolerance within the active BD microbiome. Both FccAB and Sqr were prevalent, indicating their essential roles in sulfide oxidation. The predicted truncated Sox system suggests thiosulfate dismutation to sulfate and elemental sulfur.}, }
@article {pmid41880538, year = {2026}, author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, &#xc1;}, title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myag026}, pmid = {41880538}, issn = {1460-2709}, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.}, }
@article {pmid41880553, year = {2026}, author = {Liao, Y and Jiang, R and Zhang, H and Zhang, W}, title = {The dual roles of microorganisms in inflammatory diseases: initiators and regulators.}, journal = {Critical reviews in clinical laboratory sciences}, volume = {}, number = {}, pages = {1-33}, doi = {10.1080/10408363.2026.2637106}, pmid = {41880553}, issn = {1549-781X}, abstract = {Research on the microbiome is reshaping the conceptual foundations of inflammatory diseases. As a dynamic component of the host ecosystem, microbial communities collectively influence inflammatory responses and homeostatic balance through their metabolites, structural signals, and interactions with immune pathways. Dysbiosis can amplify immune activation and metabolic disturbances, leading to persistent inflammation, whereas specific commensal taxa and their metabolites possess the capacity to suppress excessive immune responses and restore homeostasis. This bidirectional regulatory capacity positions the microbiome as a central node that both drives and modulates inflammatory networks. Multi-omics investigations have delineated the systemic architecture of microbe-host interactions, revealing cross-system axes such as the gut-brain, gut-liver, and skin-gut pathways that constitute a signaling framework integrating inflammation and immunity, thereby reshaping our understanding of disease pathogenesis. Within this framework, inflammation is redefined as an adaptive strategy for maintaining systemic stability rather than merely a singular pathological reaction. Therapeutic approaches including fecal microbiota transplantation (FMT), engineered microbial strains, and interventions targeting metabolic signaling are propelling microecological medicine into an era of precision modulation. As systems biology converges with spatial omics, research on the microbiome is shifting from descriptive pathology toward mechanistic control, establishing it as a critical nexus linking immunity, metabolism, and disease evolution. This transformation heralds a paradigm shift in medicine from merely "suppressing inflammation" to actively "reconstructing ecological order."}, }
@article {pmid41880855, year = {2026}, author = {Bhattacharya, S and Kolandhasamy, P and Mandal, A and Rajaram, R and Darbha, GK}, title = {Biofilm-mediated surface depolymerization of multiple synthetic polymers by mangrove-derived bacterial consortia.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141847}, doi = {10.1016/j.jhazmat.2026.141847}, pmid = {41880855}, issn = {1873-3336}, abstract = {Plastic pollution persists across marine and terrestrial ecosystems largely due to the intrinsic resistance of synthetic polymers to biological attack. Despite growing evidence of microbial interactions with plastics, the mechanistic basis and extent of biofilm-mediated polymer deterioration remain poorly constrained. Here, we investigate the capacity of mangrove-derived bacterial consortia to initiate early-stage degradation of major synthetic polymers (PET, PS, LDPE, HDPE, and PP) under controlled laboratory conditions. Over a 120-day incubation under controlled laboratory conditions, consortium-exposed polymers exhibited differential mass loss, surface erosion, and mechanical weakening, with PS 20.14% and PET 8.33% showing the highest susceptibility. Integrated surface and molecular analyses using confocal laser scanning microscopy, atomic force microscopy, scanning electron microscopy energy dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy revealed extensive biofilm formation, nanoscale pitting, oxidative functional group incorporation, and localized polymer chain modification. Tensile testing further demonstrated reductions in mechanical integrity consistent with surface-driven structural weakening. First-order kinetic fits were applied to gravimetric data to provide comparative, non-predictive estimates of degradation dynamics across polymer types. This study provides quantitative and mechanistic evidence that environmentally adapted microbial consortia can promote biofilm-driven surface depolymerization, highlighting mangrove sediments as underexplored reservoirs of plastic-interacting microbes. These findings advance current understanding of early-stage plastic biodegradation and inform future strategies for biotechnological intervention in microplastic-polluted environments.}, }
@article {pmid41881017, year = {2026}, author = {Zhou, J and Zeng, X and Sun, J and Yang, Y and Wang, J and Xiao, X and Fang, P and Liu, Y and Wang, M and Long, Y and Fu, F and Li, W and Du, J and Liang, Z and Nie, S and Luan, S and Li, X and Zhang, H and Peng, Y and Sun, S and Zhu, W and Zhang, L and Shang, Q and Chen, Y and Xu, Y and Chen, L and Ding, Z and Du, D and Guo, AY and Wei, X and Yuan, Y}, title = {Gut microbiota-derived indole-3-lactic acid suppresses anti-PD-1 efficacy in esophageal squamous cell carcinoma.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.019}, pmid = {41881017}, issn = {1934-6069}, abstract = {Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy where the efficacy of anti-PD-1 immunotherapy varies among individuals, possibly influenced by the gut microbiota. Here, we analyze 122 fecal samples from ESCC patients undergoing neoadjuvant immunotherapy and identify an enrichment of Ligilactobacillus salivarius (L. salivarius) in non-responders. Humanized microbiome, orthotopic ESCC mouse models, and single-cell RNA sequencing confirm that L. salivarius-produced indole-3-lactic acid (ILA) suppresses tumor-infiltrating NKG7[+]CD8[+] Tpex cells, impairing anti-tumor immunity. Moreover, ILA-deficient L. salivarius strains abolish ILA production and immune resistance. In vitro assays reveal that ILA targets the aryl hydrocarbon receptor and downregulates nuclear factor κB (NF-κB) signaling in Tpex cells. Pharmacological NF-κB activation restores Tpex function and reverses resistance. Two validation cohorts support the L. salivarius-ILA-NKG7[+]CD8[+] Tpex axis as a resistance mechanism in ESCC patients. These findings highlight L. salivarius and ILA as key modulators of the tumor microenvironment, offering potential strategies for overcoming immunotherapy resistance in ESCC.}, }
@article {pmid41881056, year = {2026}, author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T}, title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1818559}, pmid = {41881056}, issn = {1305-7456}, abstract = {Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.}, }
@article {pmid41881444, year = {2026}, author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML}, title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003864}, pmid = {41881444}, issn = {2052-4439}, mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.<br><br>METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.<br><br>RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95%&#x2009;CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics &#x2264;3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).<br><br>CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.}, }
@article {pmid41881526, year = {2026}, author = {Vahid, F and Loyola-Leyva, A and Bouzas, C and Tur, JA and Ivanova, Y and Doychinov, B and Nikolov, R and Chikalanov, A and De Magistris, T and Halimi, J and Forberger, S and Stahl, C and Evers, S and Devaux, Y and Malisoux, L and Mendon, P and Celebic, A and Vaillant, M and Gantenbein, M and Skhiri, L and Kallas, Z and Garcia, L and Bohn, T and , }, title = {Empowering healthy lifestyle behaviour through personalised intervention portfolios using a healthy lifestyle recommender system to prevent and control obesity in older adults: pilot study protocols from the HealthyW8 project.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e108771}, doi = {10.1136/bmjopen-2025-108771}, pmid = {41881526}, issn = {2044-6055}, mesh = {Humans ; Pilot Projects ; Aged ; *Obesity/prevention &amp; control ; *Healthy Lifestyle ; Male ; Female ; Exercise ; *Health Promotion/methods ; Europe ; }, abstract = {INTRODUCTION: Obesity prevalence has increased globally, imposing a significant burden on individuals and societies. Innovative solutions are, therefore, essential to mitigate its impact.<br><br>METHODS AND ANALYSIS: This protocol outlines the framework of seven independent European pilot studies conducted in Bulgaria, Germany, Luxembourg and Spain, under the EU-Horizon HealthyW8 project. These studies aim to evaluate as primary outcomes feasibility, usage patterns (adherence) and user satisfaction of the Healthy Lifestyle Recommender System (HLRS), a personalised digital tool designed to promote healthy lifestyles through tailored physical activity and meal recommendations, considering emotional aspects. The seven pilot trials will collectively include 240 (around 30 participants/trial) older adults (&#x2265;65 years) with overweight (body mass index (BMI) 25.0-29.9&#x2009;kg/m[2]) over a 3-month period. As a recruitment mitigation strategy, we will extend the age range to include individuals aged &#x2265;55 years and those with normal weight (BMI 18.5-24.9&#x2009;kg/m[2]). Other parameters collected include anthropometric measurements, questionnaires to survey lifestyle (alcohol and tobacco consumption, sleep quality), dietary patterns (food frequency questionnaire and 24-hour recall) and emotional well-being, as well as data collected from wearable devices (smartwatch, accelerometer) to track 24-hour activity patterns. Additionally, two pilot studies will collect blood, urine, saliva (only one partner) and stool samples to explore biomarkers of inflammation, oxidative stress, gut microbiome and circulating miRNAs.<br><br>EXPECTED OUTCOMES: It is hypothesised that participants will use the HLRS consistently enough to assess its feasibility and impact. The findings will contribute to planning and executing long-term trials focused on health outcomes and enhance understanding of the multimodal nature of obesity risk and its comorbidities. This protocol facilitates comparisons across studies in diverse cultural and contextual settings, offering insights into how personal and environmental factors influence the implementation and effectiveness of the HLRS.<br><br>ETHICS AND DISSEMINATION: Ethical approval has been obtained in each country independently. Dissemination efforts will prioritise high-impact journal publications.<br><br>TRIAL REGISTRATION NUMBER: NCT07011368.}, }
@article {pmid41881738, year = {2026}, author = {Park, J and Kim, J and Cho, S and Shin, W}, title = {In vitro platforms for reconstructing skin-microbiome interactions.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2026.02.006}, pmid = {41881738}, issn = {1879-3096}, abstract = {The growing recognition of the skin microbiome in regulating the host's metabolic and immune functions has spurred the development of in vitro platforms designed to recapitulate their intricate interactions, aiding research into both skin-microbiome and microbe-microbe interactions within their distinct niches. Despite these efforts, challenges remain in dissecting skin-microbiome interactions, especially due to the absence of a standardized platform for the long-term coculture of bacterial and mammalian cells. In this review, we highlight the key components in modeling an in vitro skin ecosystem and discuss the therapeutic potential of skin commensals, including recent advances and applications for engineered live biotherapeutics targeting skin diseases, to underscore the translational value of in vitro skin-microbiome interaction studies.}, }
@article {pmid41881804, year = {2026}, author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C}, title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70315}, doi = {10.1111/mec.70315}, pmid = {41881804}, issn = {1365-294X}, support = {FONDECYT N&#xb0;1191769//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Doctoral scholarship N&#xb0;21201700//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. &amp; The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; }, abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.}, }
@article {pmid41882002, year = {2026}, author = {Rumpler, M and van Mierlo, G and Vinten, KT and Giner, MP and Christen, S and Hayat, F and Makarov, MV and Gardeux, V and Russeil, J and Schomakers, BV and van Gijn, L and Hashimi, H and Steiner, C and Giroud-Gerbetant, J and Joffraud, M and Sanchez Garcia, JL and Moco, S and Migaud, ME and Houtkooper, RH and Deplancke, B and Canto, C}, title = {Therapeutic potential of dihydronicotinamide riboside (NRH) on obesity and glucose intolerance in mice.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70965-4}, pmid = {41882002}, issn = {2041-1723}, support = {MSCA-DN-NADIS no. 101073251//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; R21 AAT009908-01//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; }, abstract = {NAD[+] is a crucial metabolic cofactor whose intracellular levels can influence the progression of multiple metabolic and age-related complications. There is therefore a strong interest in using NAD[+] precursors (vitamin B3s) as therapeutic tools, but most current precursors exhibit either poor bioavailability or adverse effects. This study examines the metabolic impact of chronic dietary supplementation with a newly described NAD[+] precursor, dihydronicotinamide riboside (NRH), in mice using a comprehensive approach including phenotyping tests, RNA sequencing in different tissues and microbiome analyses. We show that chronic NRH administration at 100 mg/(kg*day) is well tolerated, yet has minimal metabolic effects in mice on a regular diet. However, NRH mitigates high-fat diet-induced metabolic complications when used as a preventive or as a treatment strategy, including improvements in glucose tolerance, increased hepatic expression of lipid catabolism genes and fat redistribution. These results highlight the potential of NRH as a therapeutic agent, although further studies are needed to optimize its use, as higher doses reveal signs of toxicity.}, }
@article {pmid41882035, year = {2026}, author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK}, title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36646-4}, pmid = {41882035}, issn = {2045-2322}, support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; }, abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.}, }
@article {pmid41882107, year = {2026}, author = {Bertolo, A and Wettstein, R and Valido, E and Capossela, S and Buergin, J and Haumer, A and Speck, N and Nyfeler, N and Widmer, A and Pannek, J and Krebs, J and Stoyanov, J}, title = {Microbial and inflammatory profiling of pressure injuries and urinary tract infections in spinal cord injury: a prospective cohort study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45422-3}, pmid = {41882107}, issn = {2045-2322}, support = {Foko_2018_03//Swiss Paraplegic Foundation/ ; Foko_2018_03//Swiss Paraplegic Foundation/ ; Foko_2018_03//Swiss Paraplegic Foundation/ ; }, abstract = {Pressure injuries (PIs) are common in individuals with spinal cord injury (SCI) and increase the risk of infections, including urinary tract infections (UTIs), which may prolong hospitalisation. However, the role of PIs in the development of postoperative UTIs remains unclear. In this exploratory study, we investigated the relationship between the PI microbiome and urinary bacteria, and examined whether perioperative bacteriuria predicts prolonged hospital stay in patients undergoing reconstructive PI surgery. In this cohort study, 21 male patients with SCI and advanced-stage PIs undergoing reconstructive surgery were evaluated. Microbiome and urinary cytokine profiles were analysed at two postoperative time points: day 3 (early postoperative phase) and day 15 (after completion of antibiotic therapy). DNA from skin, PI tissue, and urine was analysed using 16S rRNA gene sequencing. Asymptomatic bacteriuria was present in 48% of patients on day 3 and 38% on day 15. Dominant urinary bacteria included Enterococcus, Klebsiella, Streptococcus, and Escherichia, which were associated with elevated urinary cytokine levels. High bacterial load (≥ 100,000 bacteria/mL) in urine on day 3 correlated with increased UTI incidence and frequency, although hospitalisation duration was unaffected. By day 15, urinary bacterial load was no longer associated with UTI incidence. The microbiota of PIs and adjacent skin were distinct from urinary microbiota, indicating minimal cross-contamination. Early perioperative high bacterial load is associated with increased urinary inflammation and a higher risk of postoperative UTIs in patients with SCI undergoing PI reconstruction. These findings support early infection monitoring and targeted preventive strategies to improve postoperative outcomes.}, }
@article {pmid41882212, year = {2026}, author = {Noerman, S and Esberg, A and Mack, CI and Ahmed, H and Egert, B and Nordin, E and Brunius, C and Hanhineva, K and Johansson, I and Landberg, R}, title = {Multi-omics analysis of associations between host demographics and saliva metabolome, sugar profiles, and microbiome profiles.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44287-w}, pmid = {41882212}, issn = {2045-2322}, }
@article {pmid41882388, year = {2026}, author = {Wang, Y and Wang, L and Zheng, Y and Wang, R and Zhen, F and Cheng, ZJ and Sun, B and Tsui, SK and An, C}, title = {Integrated multi-omics analysis of gut microbiome and serum metabolome in unipolar and bipolar depression.}, journal = {European archives of psychiatry and clinical neuroscience}, volume = {}, number = {}, pages = {}, pmid = {41882388}, issn = {1433-8491}, support = {2023YFC2506201//National Key Research and Development Program of China/ ; SG2021189//Hebei Provincial Department of Science and Technology/ ; ZF2025052//Government Funded Clinical Medicine Excellent Talents Training Project of Hebei Province/ ; H2023206925//Beijing Engineering and Technology Research Center of Food Additives/ ; }, }
@article {pmid41882398, year = {2026}, author = {Addington, E and Gannon, A and Larcombe, DE and Lawaetz, AC and McHugh, RE and Vahtokari, S and Munnoch, JT}, title = {Microbial Biotechnology in Medicine.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {217-250}, pmid = {41882398}, issn = {0079-6484}, mesh = {Humans ; *Biotechnology/methods ; Synthetic Biology/methods ; Microbiota ; Probiotics/therapeutic use ; Animals ; Precision Medicine ; }, abstract = {The convergence of biology, technology, and medicine has revolutionised healthcare, with microbial biotechnology at the forefront. While many microbes are often considered solely for their infectious properties, many are major producers of natural products, including antimicrobials. Now, not only sources of clinically relevant drugs, they are also being directly engineered for advanced applications such as targeted drug delivery, immune modulation, and precision therapeutics. Microorganisms are key sources of novel antimicrobials, immunomodulatory, and anticancer agents, which synthetic biology and genomics mining can exploit. Bioengineering and exploration of underused microbial taxa offer promising solutions to the problem of rising antimicrobial resistance. Microbes also play crucial roles in modern vaccine development, from live attenuated to recombinant antigen production. The human microbiome has emerged as an interesting player in health, driving innovations in diagnostics and therapies that include next-generation probiotics and microbiota transplants. Furthermore, synthetic biology further empowers the design of 'smart' microbes for in situ therapeutic functions like imaging, biosensing, and targeted treatment. While transformative, these innovations also raise critical ethical and regulatory concerns, including biosafety, ecological impact, data privacy, and equitable access. This chapter explores the multifaceted roles of microbes in medical biotechnology-spanning therapeutics, vaccines, microbiome-based interventions, and engineered systems-underscoring their importance in the evolution of sustainable, personalised healthcare.}, }
@article {pmid41882400, year = {2026}, author = {Hacioglu, O}, title = {Microbiota and Microbiome.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {307-331}, pmid = {41882400}, issn = {0079-6484}, mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; Animals ; Bacteria/genetics ; Host Microbial Interactions ; }, abstract = {The human microbiota represents a complex and dynamic ecosystem composed of microorganisms from various taxonomic groups, including bacteria, viruses, fungi, archaea, and protozoa. These microorganisms inhabit different anatomical regions of the human body, such as the genitourinary system, the gastrointestinal tract, the oral cavity, the skin, and the respiratory tract, exhibiting distinct densities, compositions, and functional characteristics, and interact reciprocally with the host organism. The term microbiota not only defines the diversity and abundance of microorganisms but also encompasses their functional influence on host physiology. At this point, the concept of the microbiome becomes relevant. The microbiome refers to the collective genomic content of all microorganisms comprising the microbiota, that is, their genetic material and the potential biological functions encoded by their genes. Therefore, microbiome analysis enables not only the assessment of microbial diversity, but also of metabolic capacity, signal transduction, immune regulation, and other host-microbe interactions. The microbiota and microbiome play important roles in preserving human health and homeostatic balance. A healthy microbial composition promotes immune system development, aids digestion and nutrient absorption, reduces pathogenic microorganism colonization, and contributes to the integrity of the mucosal barrier. In contrast, dysbiosis, or disruption of microbial equilibrium, has been linked to a variety of pathophysiological illnesses, including inflammatory diseases, metabolic disorders, neurodegenerative diseases, and some neoplasms. Today, microbiome research is not only essential for understanding health and disease mechanisms but also forms the foundation for innovative future medical applications.}, }
@article {pmid41882509, year = {2026}, author = {Seo, JH and Ha, JH and Cho, SH and Kim, KN and Lee, HW}, title = {Comparative analysis of fungal microbiomes in Korean and Chinese chili pepper powders.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70611}, pmid = {41882509}, issn = {1097-0010}, support = {//This work was supported by the Ministry of Education, Republic of Korea (DOI: 10.13039/100009950), and the Jeju Special Self-Governing Province. This research was conducted as part of the Regional Innovation System and Education (RISE) program through the Jeju RISE Center (Project No. 2025-RISE-17-001)./ ; //Regional Innovation System and Education (RISE) program through the Jeju RISE center/ ; 2025-RISE-17-001//Ministry of Education (MOE) and the Jeju Special Self-Governing Province, Republic of Korea/ ; }, abstract = {BACKGROUND: Chili pepper powder plays a crucial role in kimchi fermentation; however, its use may result in fungal contamination. Therefore, analyzing its mycobiome is vital to maintain quality control standards. In this study, we used internal transcribed spacer (ITS)2 amplicon sequencing to compare fungal communities in commercially available Korean and Chinese chili pepper powders widely used in Korea (n = 9 per group).<br><br>RESULTS: Ascomycota was the predominant phylum in the Chinese and Korean chili pepper powders. Chinese powder samples exhibited higher genus-level diversity and were notably enriched in Vishniacozyma, whereas Korean powders showed relative enrichment in Fusarium and Issatchenkia. Species richness tended to be higher in Chinese than Korean samples (2.20&#x2009;&#xb1;&#x2009;0.42 vs. 1.82&#x2009;&#xb1;&#x2009;0.39). Beta diversity analysis revealed a distinct compositional separation between samples based on origin (permutational multivariate analysis of variance, P&#x2009;<&#x2009;0.01). The distribution of potentially toxin-related genera also varied by origin: Aspergillus and Penicillium were more abundant in Chinese powders, whereas Fusarium predominated in Korean powders. Although detection at the genus level does not directly indicate mycotoxin contamination, origin-specific enrichment patterns suggest distinct toxin risk profiles warranting additional investigation.<br><br>CONCLUSION: These findings underscore the importance of systematically monitoring fungal and mycotoxin-producing communities in chili pepper powders and evaluating the impact of kimchi fermentation on mycotoxin persistence and mitigation. Such measures are essential for improving food safety and traceability. &#xa9; 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid41882531, year = {2026}, author = {Kullaya, VI and Rofael, S and Heysell, SK and Thomas, TA and Ongeso, N and Gathii, K and Said, B and Mpagama, S and Mmbaga, BT and McHugh, TD}, title = {Gut microbiome disruption in Tanzanian pulmonary tuberculosis patients: links to treatment, nutritional status, and host immunity.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04882-3}, pmid = {41882531}, issn = {1471-2180}, support = {AREF-325-KULL-F-C0956//Africa Research Excellence Fund (AREF)/ ; }, }
@article {pmid41882573, year = {2026}, author = {Schöttker, B and Kopp-Schneider, A and Biehl, L}, title = {Protocol of the LEONORA randomized clinical trial: Lower gastrointestinal symptom burden by prophylaxis with synbiotics after colorectal cancer surgery.}, journal = {BMC cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12885-026-15903-9}, pmid = {41882573}, issn = {1471-2407}, }
@article {pmid41882673, year = {2026}, author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C}, title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08013-4}, pmid = {41882673}, issn = {1479-5876}, abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.<br><br>METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.<br><br>RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.<br><br>CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.<br><br>TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.}, }
@article {pmid41882707, year = {2026}, author = {Patel, J and Chaudhary, H and Parekh, B and Joshi, R}, title = {Exploring gut microbiome alterations and hormonal imbalances in polycystic ovary syndrome: insights from a comparative study.}, journal = {Journal of ovarian research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13048-026-02081-2}, pmid = {41882707}, issn = {1757-2215}, support = {ANRF/PAIR/2025/000008//Science and Engineering Research Board/ ; }, }
@article {pmid41882727, year = {2026}, author = {Liao, X and Song, W and Wan, Y and Zhang, J and Ren, P and Delaplace, P and Chen, Y}, title = {Dual functions of apigenin in suppressing Phytophthora capsici and shaping the pepper microbiome.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02386-w}, pmid = {41882727}, issn = {2049-2618}, support = {ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; SYS202206//Shandong Provincial Natural Science Foundation/ ; No. 202502AQ370001//Yunnan Department of Science and Technology - Development and adoption of innovative 'green' management tools against insect pest and disease on tomato and pepper in Yunnan/ ; 2024CXPT034//Key R&amp;D Program of Shandong Province, China/ ; }, abstract = {BACKGROUND: Plant resistance to soil-borne pathogens is shaped by the interactions among host genetics, root exudates, and rhizosphere microbiomes. Flavonoids are widely recognized for their antimicrobial and signaling functions, yet their role in mediating metabolite-microbiome-pathogen interactions in pepper (Capsicum frutescens) remains poorly understood.<br><br>RESULTS: Through integrated microbiome, transcriptome, and metabolome analyses, we compared resistant (CA53) and susceptible (CA476) pepper cultivars under challenge by Phytophthora capsici in the pepper rhizosphere. Resistant plants maintained relatively stable transcriptional and metabolic profiles, whereas susceptible plants exhibited a pronounced suppression of the flavonoid biosynthesis pathway, with a marked decline in apigenin levels. Exogenous application of apigenin significantly enhanced pepper resistance by disrupting sporangial cell membrane integrity and thereby inhibiting zoospore release (95% reduction in zoospore release). In addition, apigenin functioned as a central hub metabolite, selectively enriching disease-suppressive rhizosphere microbes and reinforcing host protection.<br><br>CONCLUSION: Our findings uncover a dual role of apigenin in pepper resistance: directly inhibiting pathogen propagation and indirectly reinforcing the recruitment of protective microbiota. These insights highlight the ecological functions of root-derived metabolites in shaping plant-microbiome interactions and provide potential avenues for metabolite-informed strategies in sustainable crop protection. Video Abstract.}, }
@article {pmid41882740, year = {2026}, author = {Täubel, M and Hill, MS and Allard, S and Gilbert, JA and Valkonen, M and Karvonen, AM and Vepsäläinen, A and Pekkanen, J and Kirjavainen, PV}, title = {Environmental microbiota transfer from forest soil into urban homes: a proof-of-principle study.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41882740}, issn = {2049-2618}, support = {296814, 296817//Research Council of Finland/ ; 349427//Research Council of Finland/ ; }, mesh = {Humans ; Dust/analysis ; *Soil Microbiology ; Forests ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota/genetics ; Finland ; RNA, Ribosomal, 16S/genetics ; Fungi/genetics/classification/isolation &amp; purification ; Housing ; Adult ; Air Pollution, Indoor/analysis ; Proof of Concept Study ; Infant ; }, abstract = {BACKGROUND: Urban lifestyles are characterized by reduced encounters of environmental microbe stimuli that activate immunoregulatory pathways. This has been linked to an increased risk of inflammatory diseases, asthma, and allergies. A potential preventative solution is to modify indoor microbial exposures toward health-promoting interactions. Here, we test the feasibility of environmental microbiota transfers into urban homes and quantify the spatiotemporal impact on the built environment microbiota.<br><br>METHODS: House dust microbiota of six Finnish homes was monitored over a 20-week period by collecting settled dust from infant (IBZs) and adult breathing zones (ABZs) and floor dust from different home locations. Microbiota in dust samples was characterized using qPCR and amplicon sequencing of the bacterial and archaeal 16S rRNA gene and fungal ITS1 region. Microbiota transfers were performed with repeated seeding of forest soil onto rugs placed in the home entryway.<br><br>RESULTS: We observed significant, post-intervention increases in the relative abundances of forest soil bacteria in house dust. The magnitude of effect was influenced by building characteristics, spatiotemporal dynamics, and occupant dynamics and was greatest in a home with comparably little additional microbial influx-a home with no pets, low occupancy, and mechanical ventilation. The most pronounced effect was observed in settled dust close to the soil-seeded rugs at IBZ, within the first 2 weeks after each seeding event, though the soil-associated bacterial signal also extended spatially into the living areas of the homes. Increases in bacterial diversity and an asthma protective microbiota index, as well as decreases in the proportion of human-sourced bacteria, were also observed, but only in airborne dust close to the soil-seeded rug. Effects on fungal microbiota or on the bacterial and fungal loads in house dust were inconsistent.<br><br>CONCLUSIONS: We demonstrate that a simple soil-to-rug intervention can modify the bacterial microbiota in airborne particulate matter in residential homes. The introduction of specific environmental soil microbes was most pronounced closest to the source, which is relevant when targeting infant inhalation exposure. While this approach is promising, specifically in highly urbanized settings, dosage and composition of environmental microbiota additions to reach health benefits require further study. Video Abstract.}, }
@article {pmid41882801, year = {2026}, author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM}, title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00554-9}, pmid = {41882801}, issn = {2524-4671}, }
@article {pmid41882807, year = {2026}, author = {McGovern, KC and Silverman, JD}, title = {Scale reliant mixed effects models enhance microbiome data analysis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02377-x}, pmid = {41882807}, issn = {2049-2618}, support = {R01GM148972-01/GM/NIGMS NIH HHS/United States ; R01GM148972-01/GM/NIGMS NIH HHS/United States ; }, abstract = {Linear models, including those used for differential abundance analyses, are frequently used in microbiome research to assess how experimental conditions (e.g., disease state or age) affect microbial abundance. Linear mixed-effects models (MEMs) extend linear models to accommodate complex designs, such as longitudinal sampling or hierarchical study structures. However, when applied to microbiome data, existing MEM approaches suffer from high false positive and false negative rates because sequence counts are compositional - they reflect relative rather than absolute abundances. Current methods attempt to overcome this limitation through normalization, but these approaches rely on strong, often unrealistic assumptions about the unmeasured biological scale (e.g., total microbial load). Here we introduce scale-reliant mixed-effects models (SR-MEM), which extend our earlier scale-reliant inference framework by explicitly modeling uncertainty in the unmeasured scale via user-defined probability distributions. By treating scale as a latent variable rather than fixing it through normalization, SR-MEM enables robust inference for complex experimental designs. SR-MEM can incorporate external scale measurements (e.g., flow cytometry, qPCR) or leverage scale information from independent studies to further improve inference. Across simulations and multiple real-world case studies, SR-MEM consistently controls the false discovery rate while maintaining comparable or higher power than standard approaches relying on normalization or bias correction. In reanalyses of published datasets, SR-MEM yields results that are more reproducible across studies and more consistent with known biological and pharmacological effects. SR-MEM provides a principled and practical framework for mixed-effects modeling of microbiome sequence count data in the presence of unmeasured biological scale. By avoiding normalization-based assumptions and instead propagating scale uncertainty through inference, SR-MEM improves error control and reproducibility in longitudinal and hierarchical studies. An accessible implementation is provided in the ALDEx3 R package.}, }
@article {pmid41883106, year = {2026}, author = {Parker, G}, title = {A further piece of my mind.}, journal = {Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists}, volume = {}, number = {}, pages = {10398562261438777}, doi = {10.1177/10398562261438777}, pmid = {41883106}, issn = {1440-1665}, abstract = {At the conclusion of my academic career, I was privileged when the University of New South Wales convened a Festschrift. This paper captures a number of themes addressed in my presentation at the Festschrift. I overview a long personal focus on models, involving service delivery, diagnostic criteria and management of psychiatric conditions. I also detail a personal 'triple M' model underlying many research studies taken over my career and composed of modelling, measuring and management phases, optimally logically linked. I also argue for the melding of implicit thinking (or 'gut instinct') and explicit thinking in psychiatric research and practice. While my research time has largely concluded, I suggest that psychiatric theorizing and management may well have a new paradigm in play involving the gut microbiome.}, }
@article {pmid41883130, year = {2026}, author = {Kuo, M and Lê Cao, KA and Kodikara, S and Mao, J and Sankaran, K}, title = {Phylobar: an R package for multiresolution compositional barplots in omics studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag151}, pmid = {41883130}, issn = {1367-4811}, abstract = {SUMMARY: Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce phylobar, an R package that interactively links stacked barplots with overview phylogenetic or taxonomic hierarchies. The interface allows users to collapse or expand subtrees, paint color palettes interactively, and search for specific taxa. This allows comparison across taxonomic resolutions that are hidden in static overviews. phylobar works with any omics data with hierarchical organization, including cell type hierarchies, as we demonstrate in a case study of immune cell composition in COVID-19 patients.<br><br>phylobar is available as an R package on GitHub. It uses the htmlwidgets library to link interactive D3 visualizations with R. The interactive plots can be embedded within R Markdown or Quarto notebooks, and views can be exported as vector graphics files. The package is open source and documented at https://mkdiro-O.github.io/phylobar.}, }
@article {pmid41883152, year = {2026}, author = {Zheng, Q and Zhou, Z and Li, T and Xu, J and Zhou, Y and Cui, Y and Wang, K and Wang, N and Li, M and Zhou, L and Tian, J}, title = {Charting the Evolution of Personalized Nutrition: A Comprehensive Bibliometric Survey of Global Research Landscapes and Future Trajectories.}, journal = {Nutrition research reviews}, volume = {}, number = {}, pages = {1-36}, doi = {10.1017/S0954422426100389}, pmid = {41883152}, issn = {1475-2700}, abstract = {Personalized nutrition has emerged as a revolutionary paradigm in nutritional science, shifting from traditional "one-size-fits-all" approaches to tailored dietary recommendations. We conducted a comprehensive bibliometric analysis through a systematic search strategy capturing various conceptualizations of personalized nutrition. The analysis identified 3,159 publications demonstrating three distinct phases: an inaugural phase with minimal activity, a developmental phase showing gradual growth, and a maturation phase exhibiting exponential growth. Five distinct research clusters emerged: clinical nutrition applications for special populations, nutrigenomics and personalized dietary recommendations, metabolic health and weight management, gut microbiome and functional nutrition, and precision nutrition with multi-omics integration. Temporal analysis revealed a clear evolution from genetic foundations toward microbiome research, metabolomics, and computational approaches. Citation analysis highlighted landmark studies that established individual variability in dietary responses, the gut microbiome's role in personalization, and technology-enabled intervention systems as foundational to the field. The convergence of microbiome research, metabolomics, artificial intelligence (AI), and clinical applications creates promising directions for advancing personalized nutrition science. Future research must bridge the gap between mechanistic elucidation and clinical application, leveraging AI-driven predictive models and precision delivery systems to translate biological insights into effective public health strategies.}, }
@article {pmid41883694, year = {2026}, author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A}, title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {50}, number = {}, pages = {e00956}, pmid = {41883694}, issn = {2215-017X}, abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.}, }
@article {pmid41883716, year = {2025}, author = {Abu, Y and Roy, S}, title = {Intestinal dysbiosis during pregnancy and microbiota-associated impairments in offspring.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1548650}, pmid = {41883716}, issn = {2813-4338}, abstract = {The maternal microbiome is increasingly being recognized as a key determinant in various neonatal health outcomes, including offspring immunity, metabolism, brain function, and behavior. While the oral, vaginal, skin, and gut microbiota are significant contributors to the offspring's postnatal gut microbial seeding, the composition and diversity of the maternal gut microbiome during pregnancy seems to be critical in shaping neonatal health outcomes, even prior to birth. Growing evidence suggests that the balance among the microbial groups in the gut and their interactions with the host are crucial for health. Dysbiotic communities in pregnancy and early in life may lead to disease processes in offspring, though the specific processes by which maternal gut microbes affect offspring gut microbial development are unknown. Here, we summarize research examining gut microbial shifts during pregnancy, and their effects on the diversity and composition of the infant microbiome and on early health outcomes. We also discuss current theories for how the maternal gastrointestinal (GI) tract influences neonatal seeding, and how probiotics during the perinatal period may affect offspring health outcomes.}, }
@article {pmid41883788, year = {2026}, author = {Xu, X and Chen, Y and Ye, Q and Xu, B and Yan, X}, title = {Multi-omics analysis reveals maternal gut microbiota-derived short-chain fatty acids and progesterone are associated with offspring birth weight in sows.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781673}, pmid = {41883788}, issn = {1664-302X}, abstract = {INTRODUCTION: Piglet birth weight is a key determinant of preweaning survival and subsequent growth performance, yet the role of maternal gut microbiota in relation to offspring birth weight in sows remains incompletely characterized. This study aimed to investigate the association between maternal gut microbiota in late gestation and offspring birth weight in sows.<br><br>METHODS: Fecal samples were collected from 260 Landrace &#xd7; Yorkshire (LY) sows at gestation day 100, and sows were categorized into high birth weight (HBW; 1.41&#x202f;&#xb1;&#x202f;0.02&#x202f;kg, 16.25&#x202f;&#xb1;&#x202f;0.25 piglets/litter, n =&#x202f;59) and low birth weight (LBW; 1.07&#x202f;&#xb1;&#x202f;0.02&#x202f;kg, 12.19&#x202f;&#xb1;&#x202f;0.22 piglets/litter, n =&#x202f;52) groups based on the average birth weight of live-born piglets and live litter size. We performed 16S rRNA gene amplicon sequencing and fecal untargeted metabolomics, and quantified fecal short-chain fatty acids (SCFAs) and sex hormones.<br><br>RESULTS: Compared with LBW sows, HBW sows showed distinct bacterial community profiles with higher relative abundances of multiple taxa linked to SCFAs production, including Ruminococcus, Oscillibacter, Parabacteroides, and Bacteroides (p&#x202f;<&#x202f;0.05). Untargeted metabolomics revealed a clear separation between groups and enrichment of pathways related to primary bile acid biosynthesis and steroid hormone biosynthesis in HBW sows (p&#x202f;<&#x202f;0.05). Consistently, fecal acetate (p =&#x202f;0.005), propionate (p =&#x202f;0.034), isobutyrate (p =&#x202f;0.007), valerate (p =&#x202f;0.036), as well as progesterone (p =&#x202f;0.016), were significantly higher in HBW sows, and these indices were also positively correlated with piglet birth weight. Spearman correlation analysis showed that gut bacterial taxa enriched in the HBW group were positively associated with primary bile acids and sex hormone-related metabolites, which were also positively correlated with piglet birth weight.<br><br>DISCUSSION: In conclusion, these multi-omics data indicate that higher piglet birth weight is associated with an SCFAs-enriched gut microbial ecosystem accompanied by enhanced bile acid and steroid hormone-related fecal metabolic profiles during late gestation.}, }
@article {pmid41883797, year = {2026}, author = {Sui, C and Qiao, H}, title = {The Type VI secretion system in enteric pathogen colonization: molecular mechanisms, ecological dynamics, and therapeutic potential.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809019}, pmid = {41883797}, issn = {1664-302X}, abstract = {The Type VI Secretion System (T6SS) is a sophisticated, phage-tail-like contractile nanomachine that mediates contact-dependent protein translocation in a wide range of Gram-negative enteric pathogens. As a primary weapon for interference competition, T6SS enables pathogens like Salmonella and Vibrio cholerae to directly eliminate commensal rivals. This targeted elimination allows pathogens to dismantle microbiota-mediated colonization resistance and seize essential nutritional niches. Beyond interbacterial warfare, the system facilitates "exploitative competition" by secreting effectors for the acquisition of limited micronutrients such as iron and zinc. Furthermore, T6SS acts as a crucial virulence determinant by manipulating host cell signaling, disrupting cytoskeletal integrity, and even enhancing intestinal contractions to physically expel competitors. The expression and activity of T6SS are dynamically regulated by gastrointestinal cues, including bile salts, pH fluctuations, and quorum sensing signals, ensuring its activation is precisely timed during infection. Elucidating these multifaceted roles not only deepens our understanding of microbial ecology in the gut but also highlights T6SS as a promising target for microbiome engineering and the development of customizable, precision antimicrobial therapies.}, }
@article {pmid41883802, year = {2026}, author = {Qiao, X and Yan, X and Dong, C and Tao, L and Aili, A and Waheed, A}, title = {Correction: From microbiome collapse to recovery: a roadmap for microbiome-informed grassland restoration under global change.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1819081}, doi = {10.3389/fmicb.2026.1819081}, pmid = {41883802}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1741287.].}, }
@article {pmid41883805, year = {2026}, author = {Liu, F and Shi, L and Yan, S and Zhang, Y and Zhang, M and Han, T and Zhao, X and Li, Z and Niu, N}, title = {Effects of reduced nitrogen on the nifH-harboring soil microbiome in a soybean-maize strip intercropping system.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1770580}, pmid = {41883805}, issn = {1664-302X}, abstract = {INTRODUCTION: Nitrogen (N) is a core limiting factor for crop growth, with approximately 50% of global food production relying on chemical N fertilizer inputs. However, excessive N application results in N use efficiency below 40%, and unabsorbed N triggers environmental problems. Maize-soybean relay strip intercropping (MSSI) enhances vertical resource partitioning, increases land productivity, and optimizes N utilization, but its effects on nifH-marked N-fixing microbiota under reduced N input remain unclear. This study aimed to investigate the abundance and diversity of N-fixing microbiota in response to the MSSI system with reduced N application.<br><br>METHODS: A 2-year field experiment was conducted in two soil textures (sandy loam in Wuji and medium loam in Gaocheng) including three cropping systems: monocropping maize, monocropping soybean, and MSSI. To further explore the underlying mechanism, an N gradient experiment with four fertilizer rates was established in Wuji. At the maturation stage, rhizosphere soil samples were collected, and q-PCR, enzyme activity assays, and high-throughput sequencing were used to analyze N cycle-related marker genes, enzyme activities, and nifH gene abundance and diversity.<br><br>RESULTS: The MSSI system maintained maize yields comparable to monocropped maize, while soybean yields reached 60.1-69.6% of monocropped levels. MSSI significantly increased nifH gene abundance in soybean rhizosphere soil, but reduced the Chao1, Shannon, Simpson, and observed species indices of N-fixing microbiota. Specifically, MSSI decreased N-fixer diversity (Shannon: -18.2%) and richness (Chao1: -12.5%), whereas the 25% reduced N input treatment (ISN25) enhanced diversity (Shannon: +15.7%) by improving community evenness without altering species richness.<br><br>DISCUSSION: Our results demonstrate that the MSSI system significantly alters soil N fertility and the community structure of nifH-marked N-fixing bacteria. The reduced N input combined with MSSI can optimize N utilization by regulating N-fixing microbial communities, providing a theoretical basis for sustainable agricultural practices that balance food security and ecological protection.}, }
@article {pmid41883991, year = {2026}, author = {Yang, J and Yuan, Z and Mei, S and Liu, H and Xiang, Q and Song, E}, title = {Non-Invasive Techniques for Early Detection of Oral Squamous Cell Carcinoma: A Narrative Review.}, journal = {Cancer management and research}, volume = {18}, number = {}, pages = {569352}, pmid = {41883991}, issn = {1179-1322}, abstract = {Oral squamous cell carcinoma (OSCC) is the most common malignant tumor of the oral cavity, accounting for the majority of oral cancers, and early detection is crucial for improving patient survival rates and prognosis. Traditional diagnostic methods have limitations, including invasiveness and diagnostic delays, and are insufficient for early detection and distinguishing between similar diseases. In recent years, with the rapid advancement of molecular biology and biotechnology, a variety of emerging non-invasive diagnostic approaches have provided new strategies for early screening and precise diagnosis of OSCC. This review summarizes the cutting-edge technologies in OSCC diagnosis in recent years, including biomarker-based detection (such as microRNA, circRNA, gene methylation, and salivary proteomics), oral microbiome analysis, optical imaging technologies combined with artificial intelligence, and more. These emerging methods not only offer non-invasive or minimally invasive advantages but also enable the detection of potential molecular changes in the early stages of the disease, allowing for early intervention. Despite the challenges in standardization, sensitivity, and specificity optimization that these new technologies face in clinical applications, they undoubtedly offer vast prospects for early detection and personalized treatment of OSCC. This review aims to achieve the following objectives: First, to systematically evaluate the latest research evidence on various emerging non-invasive diagnostic technologies; second, to comprehensively compare their advantages and limitations relative to traditional methods; and finally, to attempt constructing a clinical translation assessment framework for early-stage multimodal diagnostic technologies in OSCC, thereby guiding future translational strategies.}, }
@article {pmid41883995, year = {2026}, author = {Złoch, M and Sibińska, E and Monedeiro, F and Miśta, W and Arendowski, A and Fijałkowski, P and Pietrowska, M and Mrochem-Kwarciak, J and Jędrzejewska, A and Telka, E and Karoń, K and Rabsztyn, M and Pomastowski, P and Gabryś, D}, title = {Adaptation of MALDI-TOF MS Technique for Tracking Changes in the Urinary Microbiome During and After Radiotherapy for Prostate Cancer.}, journal = {Cancer management and research}, volume = {18}, number = {}, pages = {573379}, pmid = {41883995}, issn = {1179-1322}, abstract = {PURPOSE: The urinary microbiome may influence the development of radiation-induced complications in prostate cancer. However, its dynamics during and after radiotherapy (RT) remain unclear. This study aimed to use matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to characterize and monitor urinary microbiome changes during RT for prostate cancer.<br><br>PATIENTS AND METHODS: Eighty-eight patients with prostate cancer who underwent RT were included. Midstream urine and blood samples were collected at six time points: before gold fiducial implantation (t1), at the start (t2) and end of RT (t3), and at 1, 4, and 7 months post-RT (t4-t6). Microorganisms were cultured under diverse conditions and identified by MALDI-TOF MS. Statistical analyses were used to assess the associations between microbial profiles, RT stages, and biochemical parameters in the urine and blood.<br><br>RESULTS: A total of 1773 microbial isolates were identified in 89% of urine samples, with 79% showing a polymicrobial composition. The microbiota was dominated by Staphylococcus (51.6%), Micrococcus, Enterococcus, Kocuria, and Corynebacterium. Biodiversity decreased at the end of RT but gradually recovered up to seven months post-treatment. Genera such as Actinomyces, Corynebacterium, Staphylococcus, and Streptococcus were significantly correlated with study time course, whereas the abundance of Kocuria rhizophila increased over time. Changes in microbiome composition were strongly associated with glucose levels in urine and blood.<br><br>CONCLUSION: RT triggers a dynamic response in the urinary microbiome, with an initial decline in diversity followed by progressive recolonization. Glucose levels in urine and blood significantly affect microbial composition, suggesting that metabolic factors modulate RT-related microbiome shifts. These findings highlight the interplay between RT, host metabolism, and urinary microbiota, supporting the potential value of glucose monitoring to maintain microbial balance after RT.}, }
@article {pmid41884202, year = {2026}, author = {Kotelevets, SM}, title = {Clinical significance of a possible route of transmission of Candida and Helicobacter pylori associations in gastroduodenal pathology.}, journal = {World journal of gastrointestinal pathophysiology}, volume = {17}, number = {1}, pages = {118294}, pmid = {41884202}, issn = {2150-5330}, abstract = {Fungal and bacterial interactions are widespread in the environment. Such intra-abdominal co-infections may lead to sepsis, potentially resulting in significant mortality. Interactions between invasive fungi (Candida) and pathogenic bacteria [Helicobacter pylori (H. pylori)] appear to be particularly relevant to human infection outcomes. Co-colonization by fungi and bacteria (coinfections) remains a pressing issue among patients with gastrointestinal pathology; however, the transmission routes and pathogenic mechanisms of these microbiome interactions are not yet fully understood. Candida species are known to support the growth of certain bacteria, and studies have observed a significant increase in the colony counts of these bacteria in the presence of fungi. As an opportunistic pathogen, Candida-in association with H. pylori-may contribute to dysbiosis of the oral microflora and other regions of the gastrointestinal tract, potentially facilitating disease progression. Therefore, understanding the interactions between fungi and bacteria is essential for improving early diagnosis and treatment efficacy. Synergistic effects have been identified in the development of resistance to antifungal and antibacterial therapies. Modern treatment strategies should consider focusing on methods to disrupt this synergy, as well as on preventative measures to limit the transmission of Candida-Helicobacter associations between individuals.}, }
@article {pmid41884244, year = {2026}, author = {Salvadori, M and Rosso, G}, title = {Gut-kidney axis: Dysbiosis and renal disease.}, journal = {World journal of nephrology}, volume = {15}, number = {1}, pages = {115357}, pmid = {41884244}, issn = {2220-6124}, abstract = {According United States renal data system the morbidity rate for chronic kidney disease (CKD) is 2.5 times than patients not affected by CKD and the mortality rate is 144.9 per 1000 persons-years. The gut microbiota is involved in uremic toxins (UTs) production. This fact was demonstrated by experiments in rats, which revealed better survival in CKD rats that were deprived of the gut microbiota. In men, UT levels are low in CKD patients without a colon. Diet may affect the gut microbiota through food additives such as prebiotics, probiotics and post biotics. Conservation processes and food processing may also affect the gut microbiota. Other factors are food quantity and composition. The gut microbiota may be the cause of UTs production and accumulation in the blood. Additionally, there is interplay among different organs such as liver, kidney and gut. Several theories have been formulated to justify the interplay between the metabolic dysfunctions. In particular, the increase of species such as Eggerthelia lenta, Fusobacterium nucleatum and Alistipes shahii leads to an increase of the aromatic amino acids degradation, and secondary bile acids and trimethyamine oxide biosynthesis in the intestine. This fact determines an increase of the levels of UT precursors such as indole, p-cresol, phenol, phenylacetaleyde, benzoic acid and trimethylamine. Recent studies document the following. The human microbiome project revealed that the gut microbiota may play an important role in both human health and diseases, including kidney disease. Recently, several studies have shown a strict correlation between the gut microbiota and CKD. Probiotics, prebiotics and synbiotics are possible therapies. Probiotics are living microorganisms that, consumed in adequate quantities, are beneficial for the patient, and act on the intestinal microbiome equilibrium. Lactobacilli and Bifidobacteria are common examples of probiotics. Prebiotics are generally fibers not absorbed by the gut, representing a selective nutrient for the microbiome already present in the gut, which favors their growth and activity. Inulin, fructo-oligosaccharides and other fibers are examples of prebiotics. The association and synergism between probiotics and prebiotics is symbiotic.}, }
@article {pmid41884347, year = {2026}, author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T}, title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2647511}, pmid = {41884347}, issn = {2000-2297}, abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.<br><br>OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.<br><br>DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.<br><br>RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.<br><br>CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.}, }
@article {pmid41884457, year = {2026}, author = {Saeed, NK and Elbeltagi, YM and Al-Beltagi, M}, title = {Unveiling the viral dimension: The paediatric gut virome as a key modulator of gastrointestinal metabolic, and neurodevelopmental health.}, journal = {World journal of virology}, volume = {15}, number = {1}, pages = {118362}, pmid = {41884457}, issn = {2220-3249}, abstract = {Paediatric gut microbiome research has long been bacteriocentric, overlooking the extensive viral component known as the gut virome. Composed of bacteriophages, eukaryotic viruses, and endogenous viral elements, the paediatric gut virome is the most abundant and genetically diverse biological entity in the intestine. Emerging evidence indicates that the virome is a key regulator of microbial ecology, immune maturation, and systemic physiological programming during early life. This narrative review synthesizes current knowledge on the establishment, development, and functional roles of the paediatric gut virome, with emphasis on its interactions with the bacterial microbiome and host immune system. We highlight how early-life viral exposures influence mucosal immune imprinting, epithelial barrier integrity, and immune tolerance, particularly during the first 1000 days of life. Virome dysbiosis is increasingly associated with paediatric gastrointestinal disorders, including inflammatory bowel disease, necrotizing enterocolitis, celiac disease, and functional gastrointestinal disorders. Beyond the gut, the virome also contributes to metabolic regulation, type 1 diabetes risk, and gut-brain axis signaling, influencing neurodevelopment. Mechanistic pathways involving phage-mediated bacterial modulation, innate immune sensing, cytokine signaling, and metabolic intermediates are discussed, positioning the paediatric gut virome as a central regulator of gastrointestinal and systemic homeostasis.}, }
@article {pmid41885217, year = {2026}, author = {Corbett, GA and Murphy, L and Hokey, E and Brien, MO and McEvoy, A and McDonnell, B and Hill, K and Davis, A and Wilson, Z and Callanan, S and Luethe, L and Corcoran, S and McAuliffe, FM}, title = {Research on Preterm Birth Prevention: The Participant Experience.}, journal = {The Australian &amp; New Zealand journal of obstetrics &amp; gynaecology}, volume = {66}, number = {2}, pages = {e70116}, pmid = {41885217}, issn = {1479-828X}, support = {22/FFP-A/10302/SFI_/Science Foundation Ireland/Ireland ; //National Maternity Hospital Foundation/ ; }, mesh = {Humans ; Female ; *Premature Birth/prevention &amp; control ; Pregnancy ; Prospective Studies ; Adult ; *Patient Satisfaction ; Motivation ; Surveys and Questionnaires ; Young Adult ; *Patient Selection ; }, abstract = {BACKGROUND: Research on spontaneous preterm birth (sPTB) is deeply important to the patients it serves. There is an absence of the patient's voice on the experience of research participation.<br><br>MATERIALS/METHODS: This prospective mixed-method study examined the experience of participants of a preterm birth research study. Recruited patients had significant risk factors for spontaneous preterm birth and were offered enrolment in a preterm birth study. Participants enrolled in early pregnancy and continued participation until 6&#x2009;weeks postpartum. At the postnatal visit, they completed a survey on their experience of participation. Responses were analysed using reflexive thematic analysis.<br><br>RESULTS: In total, 112 women completed the study participation survey. Motivations for recruitment included the altruistic goal of protecting other women and families from spontaneous preterm birth (54.5%, 61/112) and interest in the scientific rationale of the study rooted in the microbiome (10.7%, 12/112). 91.0% enjoyed participating in the study. Participant satisfaction with enrolment related to perception of improved clinical care (26.8%, 30/112), continuity of care with the research team (20.5%, 23/112), perceived improved clinical outcome they attributed to study participation (9.8%, 11/112) and symptom benefit from the intervention (1/8%, 2/112).<br><br>CONCLUSIONS: Women at risk of spontaneous preterm birth were motivated for study participation by the goal of protecting other women and families from preterm birth. Participant satisfaction related to perceived improved clinical care and continuity of care. Participants had a strong appetite for results dissemination. These findings highlight the willingness of patients to participate in research, even in the setting of a pregnancy at risk of preterm birth.}, }
@article {pmid41885274, year = {2026}, author = {Belančić, A and Fajkić, A and Wah Lam, Y and Alić, L and Labriffe, M and Pilipović, K and Džidić-Krivić, A and Yee Sy, H and Jankovic, S}, title = {Microbiome-driven PKs: addressing research gaps and shaping future directions beyond the narrative review.}, journal = {Expert opinion on drug metabolism &amp; toxicology}, volume = {}, number = {}, pages = {1-4}, doi = {10.1080/17425255.2026.2650187}, pmid = {41885274}, issn = {1744-7607}, }
@article {pmid41885500, year = {2026}, author = {Coster, D and Margalit, T and Ben-Ami, R and Boursi, B and Shamir, R}, title = {Demography-dependent variability in the human tumor mycobiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0231025}, doi = {10.1128/spectrum.02310-25}, pmid = {41885500}, issn = {2165-0497}, abstract = {UNLABELLED: Recent studies have shown that the tumor mycobiome may have prognostic and diagnostic significance in cancer patients. We aimed to gain a better understanding of how patient characteristics (age, sex, body mass index [BMI], and race) influence the composition of the tumor mycobiome, using the data of these studies. We first tested the data in view of recent critiques of tumor microbiome data processing procedures and concluded that the batch correction and transformation used on it may produce false signals. Instead, we explored 14 combinations of data transformation and batch correction methods on data of 224 fungal species across 13 cancer types. Propensity scores were utilized to adjust for potential confounders such as histological type and tumor stage. To minimize false outcomes, we identified as positive results only those fungi species that showed significant difference in abundance across a demographic factor within a particular cancer type, using data normalized according to all 14 combinations. We observed significant differences in 24 fungal species abundance within tumors for certain demographic characteristics. A total of 20 of these differences were among races in specific cancers. The findings indicate that there are intricate interactions between the mycobiome, cancer type, and patient demographics. Our study highlights the need to account for race in order to understand the role of the mycobiome in cancer development and treatment response. The study also underscores the importance of data processing techniques.<br><br>IMPORTANCE: This study analyzes the demographic-dependent variability of the intratumor mycobiome, providing a novel understanding of fungal abundance across different cancer types and patient demographics. By analyzing over 5,000 tumor samples from The Cancer Genome Atlas, the research identified 24 fungal species with significant abundance variations linked to demographic factors such as race, age, sex, and body mass index. These findings underscore the complexity of the tumor microenvironment and the importance of accounting for demographic diversity in cancer research. The study emphasizes the necessity of using robust data normalization and batch correction techniques to avoid spurious associations in order to ensure the reliability of mycobiome analysis. This work highlights the mycobiome as a new frontier in precision oncology and paves the way for future personalized cancer diagnostics and treatments that account for the influence of demographic factors on tumor biology.}, }
@article {pmid41885558, year = {2026}, author = {Chen, K and Lin, X and Wei, X and Yin, Y and Ye, M and Yang, S}, title = {Divergence in the tomato rhizosphere microbial community structure driven by three soil types.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0303125}, doi = {10.1128/spectrum.03031-25}, pmid = {41885558}, issn = {2165-0497}, abstract = {UNLABELLED: Loess, calcareous, and laterite soils are common in Guangxi, southern China, where tomatoes are widely cultivated. To understand how these soil types affect tomato growth and the associated microbial communities, we analyzed soil fertility and the rhizosphere microbiome. Tomatoes in calcareous soil exhibited higher β-glucosidase activity and microbial biomass carbon, whereas those in laterite soil showed increased acid phosphatase activity and microbial biomass phosphorus. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla across all soils, while Ascomycota and Basidiomycota predominated among fungi. Each soil type hosted distinct microbial communities: loess was enriched with the bacterial genera Ramlibacter and Bradyrhizobium and the fungus Alternaria; calcareous soil favored the bacterium Rubrobacter and the fungus Fusarium, and laterite supported bacteria such as Bacillus and Sphingobium, along with the fungus Curvularia. Given its higher phosphorus availability and the presence of beneficial microbes like Bacillus, laterite soil appears to provide a more favorable environment for tomato cultivation compared to loess and calcareous soils.<br><br>IMPORTANCE: Soil type is a critical but often overlooked factor influencing tomato productivity in southern China, where diverse soils such as loess, calcareous soil, and laterite are extensively cultivated. Understanding how these soils shape rhizosphere microbial communities and soil nutrient dynamics is essential for improving crop performance. This study provides the first comparative assessment of tomato-associated microbiomes across these major soil types in Guangxi. Our findings reveal that each soil fosters distinct microbial assemblages and enzyme activities, with laterite particularly enriched in beneficial taxa such as Bacillus and associated with enhanced phosphorus availability. These insights highlight the importance of soil-specific microbial processes in supporting tomato growth and offer a scientific basis for selecting and managing soils to optimize productivity. The results also contribute to broader efforts to harness rhizosphere microbiomes for sustainable agricultural improvement.}, }
@article {pmid41885716, year = {2026}, author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q}, title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70499}, pmid = {41885716}, issn = {1365-3040}, support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; }, abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.}, }
@article {pmid41885826, year = {2026}, author = {Hervé, V and Lambourdière, J and René-Trouillefou, M and Lopez, PJ}, title = {Patterns of microbial diversity in three aquatic ecosystems of a Caribbean island.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag031}, pmid = {41885826}, issn = {1574-6941}, abstract = {The functioning of various aquatic ecosystems is greatly influenced by the composition of their microbial communities. However, the prokaryotic and eukaryotic organisms present in the microbiome remain to be characterized in the waters of various tropical islands. Here, we used DNA metabarcoding to assess differences in the richness and abundance of prokaryotic and eukaryotic microbial communities in coastal, mangrove, and urban surface waters in Guadeloupe (French West Indies). We found that turnover was an important driving force in these three compartments, and that the urban compartment was the most diverse. We identified 119 prokaryotic and 80 eukaryotic OTUs with differential abundance between these three compartments. Furthermore, functional predictions revealed the importance of photosynthetic organisms (including Bacillariophyceae, Chrysophyceae, Chlorophyceae and Cyanobacteria) in the three compartments, and an enrichment of urban waters in chemoheterotrophic prokaryotes and eukaryotic consumers. Interestingly, we detected several putative harmful algal bloom taxa never before described in Guadeloupe. By cataloging the taxa restricted to particular water bodies, this inventory will facilitate analyses of the long-term effects of urbanization and industrialization on the evolution of microbial assemblages in Guadeloupe.}, }
@article {pmid41885829, year = {2026}, author = {Lewandowski, R}, title = {The gut microbiome as a rainforest: probiotic colonization resistance, functional effects, and next-generation strategies.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnag035}, pmid = {41885829}, issn = {1574-6968}, abstract = {Does taking probiotics really matter? The idea is enticing. Swallow a capsule, add helpful microbes, support immunity, and strengthen the gut. Yet the microbiome is not a vacant landscape waiting for reinforcements. It is a densely woven ecosystem that behaves like an old-growth rainforest. Every niche is filled, every interaction balanced through biochemical negotiation, and any newcomer must face strong colonization resistance. With such a fortified system, what impact can a probiotic truly make? Most strains pass through the adult gut without becoming permanent residents. Still, they are not biologically inconsequential. During transit, they can influence epithelial barrier integrity, alter short-chain fatty acid and bile acid profiles, modulate immune signaling, and participate in cross-feeding interactions that reshape metabolic activity. These effects are best understood as functional ripples rather than structural reconfiguration. Accordingly, probiotic efficacy often reflects transient biochemical and host-microbe interactions, although the balance between transient activity and durable colonization depends on strain and formulation, dosing duration, host factors, and the baseline microbiome ecosystem, including recent disturbances such as antibiotics. Probiotic efficacy should therefore be evaluated using outcomes aligned with the intended mechanism, prioritizing clinical endpoints and biomarkers, supported by complementary compositional and functional microbiome readouts.}, }
@article {pmid41885920, year = {2026}, author = {Wang, J and Zhang, J and Wang, J and Lu, D and Lai, S and Wang, X}, title = {Differences in gut microbiota and faecal metabolomics characteristics in preterm infants with feeding intolerance.}, journal = {Journal of medical microbiology}, volume = {75}, number = {3}, pages = {}, pmid = {41885920}, issn = {1473-5644}, mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; Female ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Metabolomics ; Biomarkers/analysis ; Metabolome ; Bacteria/classification/isolation &amp; purification/genetics ; *Food Intolerance/microbiology/diagnosis ; }, abstract = {Introduction. Feeding intolerance (FI) is one of the most common clinical issues in preterm infants, and there are currently no internationally unified diagnostic criteria.Gap Statement. Screening valuable biomarkers and evaluating their diagnostic value for FI in preterm infants is of great significance.Aim. This study aimed to identify and assess diagnostic biomarkers for feeding intolerance in preterm infants.Methodology. This study included clinical data from 49 preterm infants admitted to a tertiary maternal and child health hospital in Zhejiang's coastal region (January to June 2024). Based on feeding assessments at day 21 postpartum recorded in electronic medical records, infants were divided into feeding-tolerant (FT, n=34) and feeding-intolerant (FI, n=15) groups. Patient data analysis incorporated maternal age, gestational age, parity, antibiotic use, pregnancy complications and neonatal factors (birth weight, Apgar scores, delivery/feeding methods, vomiting, abdominal distension, gastric residuals, kangaroo care and enema use). Faecal samples underwent microbiome and metabolomic profiling to identify diagnostic biomarkers.Results. Baseline data showed no significant differences in maternal-infant characteristics between groups (P>0.05). Dynamic monitoring of feeding tolerance in 21-day-old preterm infants revealed that the incidence of vomiting, abdominal distension, abnormal intestinal morphology and gastric residual volume >30% or >2 ml kg[-1] was significantly higher in the FI group than in the FT group (P<0.001), whereas there was no significant difference in the frequency of nasogastric feeding between the two groups (P>0.05). Microbial analysis revealed enrichment of Escherichia (10.92%) and Klebsiella (6.88%) in FT infants, while FI infants specifically harboured increased Clostridium_P (3.93%), Burkholderia (4.06%) and Limosilactobacillus (4.94%). Metabolomic profiling identified significant pathway differences in ATP-binding cassette transporters (ABC transporters), carbohydrate digestion/absorption and propanoate metabolism. The receiver operating characteristic (ROC) analyses showed that metabolites arginine-proline (Arg-Pro, AUC=0.920), glutamic acid-arginine (Glu-Arg, AUC=0.873), lactaldehyde (AUC=0.900) and genera Clostridium_P (AUC=0.947), Escherichia (AUC=0.765), Staphylococcus (AUC=0.733) and Bifidobacterium (AUC=0.851) exhibited robust predictive value for FI.Conclusion. Our study demonstrates that bacterial genera such as Staphylococcus, Clostridium_P, Bifidobacterium and Escherichia in the gut microbiota, along with metabolites including Arg-Pro, Glu-Arg and lactaldehyde identified in metabolomics, can serve as diagnostic criteria for feeding tolerance in preterm infants. Klebsiella shows a certain degree of diagnostic efficacy but falls into the category of 'low accuracy', requiring comprehensive evaluation considering the research background, sample characteristics and clinical context.}, }
@article {pmid41886413, year = {2026}, author = {Montes-Carreto, LM and Arellano-Hernández, HD and Guerrero, JA and Martinez-Romero, E}, title = {Comparative fecal microbiome analysis of the endangered Volcano rabbit (Romerolagus diazi) reveals a microbial core in contrasting habitats of Central Mexico.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0343260}, pmid = {41886413}, issn = {1932-6203}, mesh = {Animals ; Rabbits/microbiology ; Mexico ; *Feces/microbiology ; *Endangered Species ; *Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; Archaea/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Fungi/genetics/classification/isolation &amp; purification ; }, abstract = {Herbivores show a larger microbial diversity in their guts than omnivores or carnivores. Bacterial symbionts expand the host digestion capacity by fermenting cellulose and hemicellulose. Comparisons between populations in different distribution areas can reveal how environmental conditions affect microbiota, helping to design conservation strategies. The Volcano rabbit (Romerolagus diazi) is the smallest lagomorph in Mexico. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Here we extend our previous microbiome study to another region in Mexico from a high site near an active volcano, the Popocatépetl. In both areas, the most abundant bacterial genera included Acinetobacter, Enterobacter, Streptomyces, Bacteroides, Pseudomonas, Janthinobacterium, Flavobacterium, and Duganella. Among Archaea, Methanosarcina, Halobaculum, Thermococcus, Halorubrum, and Methanobrevibacter were prevalent. Fungal genera such as Fusarium, Ascochyta, Pyricularia, Aspergillus, and Colletotrichum were also identified. Potential functions were identified including carbohydrate, amino acid and nucleotide metabolism. The most abundant enzymes were transferases, hydrolases and oxidoreductases. The PERMANOVA test between areas for Bacteria (p = 0.26), Archaea (p = 0.21) and Fungi (p = 0.48) indicated no significant differences in the taxonomic composition or coding sequences (p = 0.5), although there were differences in relative abundances. Additionally, for archaea, genera that had not been reported previously in Volcano rabbit fecal microbiomes such as Halomicroarcula, Halomicrobium, Haloplanus, and Sulfolobus were identified, with Sulfolobus found exclusive in Izta-Popo. The Volcano rabbit fecal microbiome showed unique bacterial and archaeal profiles. Overall, these microbial communities are likely to contribute to the digestion of plant fibers, phenolic compounds, and other dietary components, underscoring their importance for the health and conservation of these endangered species.}, }
@article {pmid41886872, year = {2026}, author = {Roger, M and Le Monier, P and Bruzac, S and Noël, C and Akcha, F and Bertucci, A}, title = {Tissue differences and changes in the resident bacteriome composition of the Pacific oyster Magallana gigas in relation to trace metal contamination.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120064}, doi = {10.1016/j.ecoenv.2026.120064}, pmid = {41886872}, issn = {1090-2414}, abstract = {Symbiotic microbial communities associated with marine organisms may contribute to the biology and the local adaptation of their host, playing a crucial role in the health of the holobiont. The role of the microbiome of bivalves remains poorly understood despite their high economic value and use as sentinel species to biomonitor water quality. In this study, we used 16S (V3-V4) rRNA amplicon sequencing to investigate the resident bacterial communities associated with the digestive gland, the mantle and the gills of Pacific oysters. We analysed oysters collected from six sites along the French coastline to investigate whether chemical stressors can shape the oyster bacteriome in natural conditions. The resident bacteriome of oysters was dominated by the phyla Proteobacteria, Spirochaetota, Firmicutes and Actinobacteriota with some differences between organs. Chemical analysis revealed differences in trace metal concentration among sites and organs. Statistical analysis showed strong positive or negative correlations between the concentration in some metals and bacterial diversity (ASVs abundance). We identified 316 ASVs associated with As, Cr, Cu, Mn and Zn concentrations in digestive glands, 99 ASVs associated with Ni concentrations in gills, and 116 ASVs associated with Cu concentrations in the mantle. Metal contamination mostly affected members of the core microbiota of oysters such as genera Colwellia and Psychrobacter, evidencing the crucial role of marine pollutants, particularly trace metals, as key parameters of the interactions between hosts and their bacterial partners.}, }
@article {pmid41886887, year = {2026}, author = {Kumar, V and Shukla, R and Gangani, S and Joseph, R and Jain, S and Yadav, H}, title = {Epigenetics and the gut-brain axis: Insights into DNA methylation, aging, and Alzheimer disease.}, journal = {The Journal of pharmacology and experimental therapeutics}, volume = {393}, number = {4}, pages = {104299}, doi = {10.1016/j.jpet.2026.104299}, pmid = {41886887}, issn = {1521-0103}, abstract = {Alzheimer disease (AD) and aging have similar molecular mechanisms that are affected by genetic as well as environmental variables. Based on current research, gut microbiomes contribute to age-specific biological processes and play an essential role in maintaining host homeostasis. Several molecular processes, including the host DNA methylation mechanism, are affected by microbially derived metabolites such as short-chain fatty acids, folate, and choline. This interaction establishes a mechanistic causal relationship that further shapes gene expression, inflammatory balance, and neuronal function in aging and related diseases. In this review, we looked at recent research showing how gut dysbiosis and its associated metabolites impact DNA methylation, which consequently contributes to disease progression in AD and aging. We also talked about how the DNA clock and age-associated methylation drifts can be used for forecasting biological aging. In addition, we discussed recent findings on how microbial and diet-based interventions may restore the methylation patterns that might be involved in aging and neurodegenerative processes. We also implicated the possible use of methylation-based biomarkers in the diagnosis of AD. Additionally, we have also explored the potential therapeutic benefits of using microbiome modulators, dietary modifications, and pharmacological interventions. Next, we highlighted the importance of multiomics and longitudinal studies to build the causal connection underlying methylation dynamics and microbial changes in neurodegeneration. Altogether, this review highlights the potential of the microbiome-methylation axis as an approach to understanding aging and establishing precision strategies to maintain cognitive health. SIGNIFICANCE STATEMENT: This review explores the interplay between DNA methylation and gut microbiota in aging and Alzheimer's disease. It highlights the gut-brain axis and summarizes recent findings on microbiome-driven epigenetic changes and metabolites influencing cognitive decline. The review also emphasizes microbiome-targeted therapeutic strategies for age-related disorders. Overall, it integrates current molecular insights with emerging approaches for the detection, prevention, and management of Alzheimer's disease and associated cognitive challenges.}, }
@article {pmid41887041, year = {2026}, author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z}, title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101810}, doi = {10.1016/j.cbd.2026.101810}, pmid = {41887041}, issn = {1878-0407}, abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.}, }
@article {pmid41887058, year = {2026}, author = {Mayr, C and Dankó, E and Antonielli, L and Kostić, T}, title = {Influence of cabbage farming practice and potato peel addition on the endpoint microbial community in sauerkraut fermentation.}, journal = {International journal of food microbiology}, volume = {454}, number = {}, pages = {111742}, doi = {10.1016/j.ijfoodmicro.2026.111742}, pmid = {41887058}, issn = {1879-3460}, abstract = {The microbial dynamics and lactic acid bacteria (LAB) content of sauerkraut are influenced by various factors. Understanding microbial variations and pathogen-exclusion capacity in spontaneously fermented vegetables is essential for reducing risks in home-style fermentation systems. We investigated the effects of conventional versus organic farming practices and potato peel addition on LAB counts and microbial diversity at days 14 and 21 of fermentation. We tested the susceptibility of different fermentations to the proliferation of a human bacterial pathogen modelled by a surrogate challenge test with Listeria innocua. We monitored the presence of Leuconostoc mesenteroides and Lactiplantibacillus plantarum at different fermentation stages. LAB counts were slightly boosted by potato peel addition until day 14. Day 21 sauerkraut samples with added potato peel sourced from conventional farming practice resulted in significantly higher LAB counts than organic samples. PERMANOVA based on Bray-Curtis dissimilarity indicated dissimilar microbiota between organic and conventional sauerkraut, while potato peel addition showed no significant effect. The presence of distinct taxa in certain samples highlights the strong influence of raw material microbiota on the final fermented product. Cultivation-based analysis combined with qPCR assessment revealed a decline of L. mesenteroides and a progressive increase of L. plantarum during sauerkraut fermentation. The contrasting amplicon sequencing results showing the presence of L. mesenteroides at the later fermentation stage underscore the need to combine cultivation with sequencing to accurately track community succession. The surrogate pathogen challenge test showed no recovery of L. innocua.}, }
@article {pmid41887326, year = {2026}, author = {Alves, ED and Carpena, MX and Bierhals, IO and Matijasevich, A and Barros, AJD and Santos, IS and López-Dominguez, L and Comelli, EM and Bandsma, RHJ and Blum-Menezes, D and Borges, MC and Tovo-Rodrigues, L}, title = {Breastfeeding, early-life feeding practices and adolescent gut microbiota: long-term associations in a birth cohort.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {103101}, doi = {10.1016/j.clnesp.2026.103101}, pmid = {41887326}, issn = {2405-4577}, abstract = {BACKGROUND &amp; AIMS: Breastfeeding plays a critical role in shaping the infant gut microbiome by promoting the growth of beneficial bacteria essential for intestinal health, however, its long-term impact remains poorly elucidated. This study investigates the association between breastfeeding practices and gut microbiota diversity and composition in adolescence.<br><br>METHODS: We analyzed data from 350 participants in the birth cohort, with breastfeeding history at three months as the primary exposure. Additional exposures included breastfeeding duration, and timing and type of complementary food introduction. Gut microbiota was assessed at 12 years through 16S rRNA gene sequencing (V3-V4 region) of DNA from fecal samples. Alpha (Chao1, Simpson, Shannon) and beta diversity (weighted and unweighted UniFrac) metrics, alongside relative taxonomic abundances, were evaluated as primary outcomes.<br><br>RESULTS: No significant differences were observed in microbial diversity between exclusive breastfed (EBF), mixed feeding and non-breastfed groups at three months. However, relative abundance analyses suggested associations between breastfeeding patterns at three months and specific bacterial taxa. Non-breastfed children exhibited a higher relative abundance of Ruminococcus (&#x3b2; = 0.439; 95% CI: 0.11-0.74) compared to EBF, while those who had mixed breastfeeding showed an association with a higher probability of Alloprevotella detection at age 12 (OR = 2.82; CI 95% 1.14; 6.95). These associations did not remain significant after multiple testing correction. Early introduction of liquids (<6 months) was associated with lower Ruminococcus abundance (&#x3b2; = -0.40; 95% CI: 0.72-0.07), whereas early introduction of semi-solid foods was linked to lower odds of Alloprevotella presence (OR = 0.35; 95% CI: 0.15-0.82).<br><br>CONCLUSIONS: Although breastfeeding and early dietary practices may exert lasting effects on adolescent gut microbiota composition, these associations appear modest. Further research with larger cohorts and multi-omics approaches is needed to clarify the underlying mechanisms and clinical implications.}, }
@article {pmid41887353, year = {2026}, author = {Amalraj, S and Karthick, V and Thamarai, R and Suganya, M}, title = {Exposome-induced dysregulation of glycemic homeostasis: Emerging biomarkers for diabetes risk and progression.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {397}, number = {}, pages = {128012}, doi = {10.1016/j.envpol.2026.128012}, pmid = {41887353}, issn = {1873-6424}, abstract = {Environmental exposures throughout life profoundly influence the development and progression of diabetes mellitus. The exposome, representing the totality of environmental exposures from conception to adulthood, interacts with genetic and metabolic pathways, leaving measurable signatures termed biomarkers. These biomarkers encompass indicators of exposure, biological effect, and susceptibility, providing mechanistic insights into glycemic regulation and disease progression. This review synthesizes current evidence on exposome-linked biomarkers in both Type 1 and Type 2 diabetes, highlighting chemical pollutants, dietary patterns, lifestyle factors, psychosocial stressors, and microbiome-derived metabolites as critical contributors to glycemic dysregulation. Advanced omics technologies, including metabolomics, proteomics, transcriptomics, and epigenomics, have facilitated the identification of these biomarkers, enabling a holistic understanding of environmental impacts on diabetes. Integrating exposomics with biomarker research offers potential for early detection, risk stratification, personalized interventions, and improved management of glycemic control. Knowledge gaps remain, particularly in longitudinal exposure mapping, causal inference, and translation into clinical practice. This review provides a comprehensive framework for understanding how environmental imprints shape metabolic health and identifies future directions for research in precision diabetes medicine.}, }
@article {pmid41887418, year = {2026}, author = {Zhang, M and Liao, X and Wang, F and Shen, H and Mao, S and Xu, Z}, title = {Decoding skatole: A comprehensive review on biosynthesis, metabolism, and mitigation in livestock production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134491}, doi = {10.1016/j.biortech.2026.134491}, pmid = {41887418}, issn = {1873-2976}, abstract = {Skatole (3-methylindole) is a potent malodorous compound generated through the microbial degradation of tryptophan in livestock production. Because of its extremely low odor threshold and biological toxicity, skatole is a critical contributor to odor pollution in animal farming systems and poses risks to animal health, product quality, and the surrounding environment. This review synthesizes advances in skatole biosynthesis, absorption and metabolism, migration and regulation mechanisms of skatole, as well as its respective impacts on humans and livestock, with particular emphasis on its dual role as both a pollutant and a potential biomarker of gastrointestinal health. This review systematically examine drivers of skatole formation, including dietary protein, gut microbiota, and environmental conditions. In addition, emerging mitigation strategies, such as nutritional regulation, microbiota-targeted interventions and bioremediation are evaluated. By integrating mechanistic insights with practical applications, this review identifies research gaps to support low-odor, sustainable livestock production.}, }
@article {pmid41887515, year = {2026}, author = {Zhao, X and Song, L and Li, N and Zhang, J and Zhang, Y and Zhao, S and Zheng, N and Zang, C and Wang, J}, title = {Comparative analysis of fecal microbiome, metabolome, and serum metabolome in cows with different milk urea nitrogen phenotypes.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27914}, pmid = {41887515}, issn = {1525-3198}, abstract = {Milk urea nitrogen (MUN), the primary form of non-protein nitrogen (N) in milk, is an indirect indicator of N metabolism in dairy cows. MUN concentrations are modulated by various factors, including dietary composition, physiological status, and environmental conditions. However, the potential roles of host gut microbiota and metabolome in the development of distinct MUN phenotypes remain insufficiently elucidated. Here, we compared fecal microbiota and fecal/serum metabolomes of high-MUN (HMUN) and low-MUN (LMUN) cows (n = 7 per group) under uniform feeding management using 16S rRNA gene sequencing and LC-MS-based metabolomics. Compared with that of LMUN cows, the feces of HMUN cows exhibited relatively higher abundances of UCG-009, UCG-002, and Christensenellaceae_R-7_group and lower abundances of Succinivibrio, Lachnospiraceae_NK3A20_group, Acetitomaculum, Prevotellaceae_UCG-001, and norank_f__Bifidobacteriaceae. Metabolomic analysis revealed that HMUN cows had relatively lower levels of hydroxypropionic acid, N-myristoyl arginine, and N-eicosapentaenoyl tryptophan in feces, and reduced amounts of L-serine, linoleic acid, and butyrate in serum. KEGG pathway mapping revealed that the metabolites relatively elevated in LMUN cows were primarily involved in the β-alanine metabolism pathway. UCG-009 and Christensenellaceae_R-7_group were positively correlated with MUN, whereas Succinivibrio, Lachnospiraceae_NK3A20_group, Anaeroplasma, and Acetitomaculum were negatively correlated. These microbial taxa were also significantly associated with several fatty and amino acid metabolites, including adipic acid, undecenoic acid, dodecanedioic acid, DL-tryptophan, and L-leucine. Collectively, this study revealed certain differences in the gut microbiota and metabolome between cows with high and low MUN levels. These findings suggest that alterations in gut microbial composition and metabolic profiles may contribute to variations in MUN phenotypes and provide new insights into host factors influencing MUN metabolism in dairy cows.}, }
@article {pmid41887569, year = {2026}, author = {Plesz, SB and Szűcs, KF and Ágg, B and Makra, N and Ligeti, B and Demeter, ZO and Adlan, LG and Liszli, P and Szabó, D and Ferdinandy, P and Zádori, ZS and Gáspár, R and Horvath, G and Kekesi, G}, title = {The impact of prebiotic supplementation in a triple-hit rat model of schizophrenia.}, journal = {Neuropharmacology}, volume = {}, number = {}, pages = {110946}, doi = {10.1016/j.neuropharm.2026.110946}, pmid = {41887569}, issn = {1873-7064}, abstract = {Schizophrenia is associated with cognitive deficits and higher stress sensitivity, potentially related to gut-brain axis disturbances, partially due to dysbiosis. To ascertain this phenomenon, we aimed to evaluate these behavioral phenotypes in association with microbiota profile in the triple-hit Wisket rat model of schizophrenia. Furthermore, as a bidirectional approach, the effects of clozapine (CLO) and/or prebiotic (galactooligosaccharide, B-GOS) treatment were also investigated. Male Wistar (control) and Wisket rats were treated for 3 weeks: CLO or its vehicle was administered intraperitoneally, while B-GOS or water was provided ad libitum in drinking bottle. The food-rewarded Ambitus test was used to assess cognition-related behaviors before and during the third week of the treatment. Afterwards, fecal samples were collected to analyse microbiota composition, and smooth muscle electromyography was performed to assess immobilization-induced stress response. B-GOS monotreatment resulted in the highest improvement in cognition-related parameters in Wisket model rats; however, it never reached the performance of control animals. Wisket animals showed higher vulnerability to immobilization-induced stress condition. This group-difference disappeared by each pharmacological treatment, with the most prominent effect of the CLO+B-GOS combination treatment. β-diversity analysis revealed an overall compositional difference of fecal microbiota between treatment groups. Several taxa associated with schizophrenia-model or treatment were significantly correlated with behavioral parameters. Consistent with clinical findings, cognitive impairment with increased stress sensitivity were highlighted in Wisket model rats. To our knowledge, this is the first study on B-GOS prebiotic in a triple-hit schizophrenia model, suggesting microbiome-targeted therapy may aid some schizophrenia-related symptoms.}, }
@article {pmid41887859, year = {2026}, author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z}, title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {409-419}, doi = {10.1016/j.jes.2025.05.033}, pmid = {41887859}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; }, abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.}, }
@article {pmid41887904, year = {2026}, author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P}, title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {867-879}, doi = {10.1016/j.jes.2025.10.021}, pmid = {41887904}, issn = {1001-0742}, mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; }, abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.}, }
@article {pmid41887936, year = {2026}, author = {Han, P and Seneviratne, C and Zhao, Q and Salomon, C and Li, X and Ivanovski, S}, title = {Salivary Microvesicle Methylome and Microbiome Profiles in Periodontitis: An Exploratory Study.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70114}, pmid = {41887936}, issn = {1600-051X}, support = {534-2019//Australian Dental Research Foundation/ ; 2034591//National Health and Medical Research Council/ ; 82001421//National Natural Science Foundation of China/ ; }, abstract = {AIM: Salivary microvesicles (MVs) are nanosized extracellular vesicles from the host and microbiota whose cargo may mirror the biological state of their parent cells. This cross-sectional study aimed to explore the diagnostic power of host methylome and microbiome profiles of MVs in various periodontal disease states.<br><br>MATERIALS AND METHODS: This exploratory study recruited 20 healthy, 16 gingivitis and 26 stage III/IV periodontitis cases. The origins of salivary host-MVs were identified using a multiplex extracellular vesicle (EV) kit. The microbiome and host methylome profiles of MV DNA were analysed using 16S rRNA sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-seq), respectively.<br><br>RESULTS: The periodontitis group showed increased CD63+, CD45+, CD29[+] and CD24[+] MV subpopulations (AUC&#x2009;>&#x2009;0.7), along with significantly higher bacterial outer membrane vesicles (AUC&#x2009;>&#x2009;0.89) from Treponema, Fretibacterium and Treponema denticola, compared to both healthy and gingivitis groups, as well as the non-periodontitis (combining healthy and gingivitis) group. MeDIP-seq identified 1196 differentially methylated regions across 3' UTRs, CDS, introns and intergenic regions (AUC&#x2009;>&#x2009;0.9), distinguishing periodontitis from the other groups. These methylated genes were enriched in inflammation-related pathways, including AMP-activated protein kinase (AMPK) and Toll-like receptor 4 (TLR4) pathways.<br><br>CONCLUSION: This exploratory study found that host methylome and microbiome profiles in salivary MVs reflect periodontal disease status, and hence supports their potential as non-invasive liquid biopsy biomarkers for periodontitis.}, }
@article {pmid41887962, year = {2026}, author = {Marjot, T}, title = {The limits of lifestyle in metabolic disease: How the microbiome shapes exercise response.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2026.03.007}, pmid = {41887962}, issn = {1600-0641}, }
@article {pmid41887976, year = {2026}, author = {Kim, MJ and Sonnenberg, GF}, title = {Diet-induced death: microbiome-mediated lipid stress reduces intestinal ILC3s.}, journal = {Trends in immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.it.2026.03.002}, pmid = {41887976}, issn = {1471-4981}, abstract = {Group 3 innate lymphoid cells (ILC3s) promote gastrointestinal health, dynamically interface with diet and microbes, and become impaired during chronic inflammation or metabolic syndrome. Torrico and colleagues uncover a key pathway rapidly disrupting ILC3 homeostasis in the intestines of humans and mice following the consumption of a high-fat diet.}, }
@article {pmid41888026, year = {2026}, author = {Song, J and Ding, M and Joyce, PWS and Pi, X and Zhang, B and Li, B}, title = {Decoding the HMO‒microbiome axis: bridging maternal milk to infant health outcomes.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649456}, doi = {10.1080/19490976.2026.2649456}, pmid = {41888026}, issn = {1949-0984}, mesh = {Humans ; *Milk, Human/chemistry/microbiology/metabolism ; *Oligosaccharides/metabolism/chemistry ; Infant, Newborn ; *Gastrointestinal Microbiome ; Female ; *Infant Health ; Infant ; Prebiotics ; }, abstract = {Human milk oligosaccharides (HMO) are unique glycans in breast milk that critically mediate interactions between the microbiome and infant health. This review synthesizes recent advances in understanding HMOs as key connectors of maternal and neonatal microbiomes with health outcomes. HMO composition, shaped by genetic factors (e.g., Secretor/Lewis status), lactation stage, maternal diet, and health, exhibits significant structural diversity. Critically, a bidirectional relationship exists between HMOs and the maternal microbiota: the maternal microbiome influences HMO biosynthesis, while HMOs selectively shape the microbial community within breast milk. In neonates, indigestible HMOs function as prebiotics, driving the assembly of a beneficial gut microbiota dominated by Bifidobacterium. This HMO-guided microbial establishment is fundamental to infant health, conferring protection against pathogenic infections (respiratory, gastrointestinal, and urinary), reducing the risk of necrotizing enterocolitis and allergies, and promoting healthy weight regulation, neurodevelopment, and bone mineralization. The modulation of host‒microbe interactions by HMOs underpins these systemic benefits, highlighting their central role as microbial and immunological regulators. Understanding the HMO-microbiome axis provides a holistic framework for elucidating how breast milk components foster infant development and disease resilience.}, }
@article {pmid41888049, year = {2026}, author = {Khalyfa, A and Zhen, L and Joshi, T and Gozal, D}, title = {Gut Luminal Exosomes in Young and Old Mice: Multi-Omic Characteristics and Regulation of Gut Permeability.}, journal = {Aging cell}, volume = {25}, number = {4}, pages = {e70455}, doi = {10.1111/acel.70455}, pmid = {41888049}, issn = {1474-9726}, mesh = {Animals ; *Exosomes/metabolism ; Male ; Female ; Mice ; Mice, Inbred C57BL ; Permeability ; *Aging/metabolism ; *Gastrointestinal Microbiome ; MicroRNAs/metabolism/genetics ; *Intestinal Mucosa/metabolism ; Multiomics ; }, abstract = {Aging is a multifaceted process impacting physiological, genomic, metabolic, and immune functions. This study investigates the role of luminal fecal exosomes (LFEs) in age-associated metabolic dysfunction. We analyzed LFEs from young (3-month) and old (24-month) male and female C57BL/6 mice to characterize age-related differences in exosomal proteomic and miRNA cargos. To explore interactions between LFEs and the gut microbiome, naïve young mice were gavage fed with LFEs from old donors, followed by 16S rRNA sequencing. Gut permeability in vitro and in vivo and systemic metabolic effects were assessed using ECIS, 3D microfluidic models, and insulin sensitivity assays. Bioinformatic analyses identified specific proteins and miRNAs linked to insulin resistance and barrier dysfunction. Heatmaps and principal component analysis revealed distinct differences in LFE profiles between young and old mice. Notably, LFEs from old mice impaired gut barrier integrity and metabolic function in young recipients, with reciprocal effects noted in older mice when receiving LFEs from young mice. Multi-omics profiling, including proteomics and miRNA sequencing, identified age-dependent and gender-related changes in LFE cargo, encompassing host- and GM-derived proteins and miRNAs. These age-specific profiles were associated with pathways implicated in cancer, neurobehavioral changes, and metabolic dysfunction. Our findings highlight that LFEs from old mice are enriched with proteins and miRNAs involved in insulin resistance and gut barrier disruption. Together, these findings identify gut luminal exosomes as age-dependent mediators of microbiome-host communication that contribute to intestinal barrier dysfunction and metabolic decline.}, }
@article {pmid41888125, year = {2026}, author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C}, title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00970-4}, pmid = {41888125}, issn = {2055-5008}, support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; }, abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.}, }
@article {pmid41888318, year = {2026}, author = {Huang, W and Zhang, J and Shan, J and Shen, W and Du, P and Liu, J and Guo, X and Chen, Z and Zeng, W and Lin, Q and Fan, H}, title = {Lactobacillus paragasseri LPG-9 reduces placental inflammation in intrahepatic cholestasis of pregnancy by regulating TGR5 in mice.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09869-4}, pmid = {41888318}, issn = {2399-3642}, support = {32370139//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300085//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Intrahepatic cholestasis of pregnancy (ICP), a liver disorder associated with adverse fetal outcomes, is characterized by elevated bile acid levels and placental inflammation by the TGR5. However, the interplay among the gut microbiome, bile acid metabolism, and ICP-associated placental inflammation remains unexplored. We aimed to investigate the role of the gut microbiota in regulating bile acid metabolism and placental inflammation, and to identify potential probiotic-based therapies for ICP in C57BL/6 mice. Immunohistochemical analysis of human placentas revealed significantly higher inflammation and decreased TGR5 expression in ICP compared with controls. In vivo and in vitro assays confirmed the anti-inflammatory effects of TGR5 activation. Using 16S rRNA sequencing and metabolomics, ICP mice exhibited a distinct gut microbiota composition and reduced abundance of bile salt hydrolase (BSH)-producing bacteria (e.g., Lactobacillus), accompanied by a significant decrease in the proportion of secondary bile acids. Transplanting fecal microbiota from ICP donors into healthy mice reproduced the disease phenotype of ICP, confirming the pathogenic role of gut microbiota dysbiosis. Supplementation with BSH-enriched Lactobacillus paragasseri LPG-9 remodeled the bile acid profile, thereby activating placental TGR5 to inhibit TLR4-NF-κB signaling and promoting hepatic bile acid excretion via BSEP.}, }
@article {pmid41888432, year = {2026}, author = {Marquioni, VM and Hofacker, AC and Villavicencio, JV and Bansept, F}, title = {Modulating microbial intake helps to maintain the gut microbiome diversity.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09867-6}, pmid = {41888432}, issn = {2399-3642}, abstract = {The animal gut is home to a myriad of microbes whose diversity has a proven impact on the host's health. Indeed, lower values of this metric often correlate with pathological status. In this context, processes involved in the gut microbiome assembly have been studied in the search for optimal nutritional habits and medical interventions. While the nutritional content of food has been extensively investigated, its microbial content has comparatively received little attention as an ecological driver of the gut microbiome. Furthermore, while probiotics use is increasing, the question of optimal dose remains open. Here, we fill these gaps by designing a model that tracks the effect of microbial migration bursts - that result from feeding and/or from probiotics administration - on the gut community alpha-diversity. We find that there is a set of feeding parameters (feeding interval and food microbial content) that maximizes the gut Shannon alpha-diversity, which we call the Maximal Diversity Strategy (MDS). Using a combination of numerical and analytical techniques, we show that for large numbers of microbial types, in the diversity maximization scenario, diversity converges to that of the food, and the feeding rate converges to the average clearance rate. These results remain robust both to the choice of distribution for the parameters that describe microbial dynamics and to weak dispersal noise, thus increasing their theoretical significance and potential for empirical exploration. We believe this work can help evaluate how quantitative ecological control can be used to improve the intake protocols of live biotherapeutic products.}, }
@article {pmid41888636, year = {2026}, author = {Wang, S and Tong, C and Wang, R and Liu, F}, title = {IL-17A Inhibitors Therapy Affect Oral Fungal and Bacterial Microbiome in Psoriasis.}, journal = {Experimental dermatology}, volume = {35}, number = {4}, pages = {e70237}, doi = {10.1111/exd.70237}, pmid = {41888636}, issn = {1600-0625}, support = {7254353//Beijing Natural Science Foundation/ ; CYJZ202218//Beijing Chao-Yang Hospital Golden Seeds Fundation/ ; }, mesh = {*Psoriasis/drug therapy/microbiology ; *Interleukin-17/antagonists &amp; inhibitors ; *Mouth/microbiology ; *Mycobiome/drug effects ; Humans ; Male ; Female ; Adult ; Middle Aged ; Aged ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Case-Control Studies ; }, abstract = {Psoriasis is a chronic inflammatory skin disease in which the IL-23/Th17/IL-17 axis plays a central pathogenic role while also contributing to antifungal defence. IL-17-targeting biologics such as secukinumab and ixekizumab are increasingly used in its management. This study aimed to characterize changes in the diversity and composition of oral fungal and bacterial communities in psoriasis patients before and after treatment with IL-17 inhibitors. Oral swabs were collected from psoriasis patients at baseline and after 3 months of IL-17 inhibitor therapy, as well as from healthy controls. Direct microscopy and fungal culture were performed. Microbial DNA was extracted and subjected to amplicon sequencing of the fungal ITS1 region and the bacterial 16S rRNA V3-V4 region using the Illumina HiSeq platform. A total of 36 patients and 38 healthy controls were enrolled in this study. Fungal microbiome analysis revealed significantly increased alpha diversity after treatment compared with baseline (p < 0.05), accompanied by markedly elevated beta diversity (p < 0.001). The dominant fungal genera were Blumeria, Pichia and Aspergillus. The relative abundance of Candida was significantly higher in psoriasis patients at baseline than in controls (16.00% vs. 6.43%, p < 0.05) and decreased significantly after therapy (6.12%, p < 0.05). In the bacterial microbiome, beta diversity decreased significantly following treatment (p < 0.001), whereas alpha diversity increased (p < 0.05). The predominant bacterial genera were Streptococcus, Neisseria and Rothia. After treatment, the relative abundance of Haemophilus was significantly lower than at baseline (9.18% vs. 10.14%, p < 0.05). Streptococcus showed a higher trend in patients versus controls (29.74% vs. 16.48%) and declined post-treatment (23.71%). In conclusion, IL-17 inhibitor therapy in psoriasis alters the oral fungal and bacterial microbiota, with notable shifts in Candida, Haemophilus and Streptococcus. These findings provide new insights into the oral microbial changes associated with biologic therapy and may inform clinical monitoring of mucocutaneous microbial imbalance during treatment.}, }
@article {pmid41888651, year = {2026}, author = {Zhang, H and Cong, J and Hu, X and Lu, D and Kollie, SC and Elolimy, AA and Loor, JJ and Yang, Z and Li, M and Mao, Y and Yang, Z}, title = {Investigating the potential role of propionylcarnitine in milk pentadecanoic acid synthesis in Chinese holstein dairy cows using multi-omics analysis.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12786-9}, pmid = {41888651}, issn = {1471-2164}, support = {YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; }, }
@article {pmid41888669, year = {2026}, author = {Yang, R and Tao, L and Su, W and Zou, F and Wang, Y and Zhang, G and Chen, H and Zhou, X}, title = {Microbial signatures with diagnostic potential in early gastric cancer: insights beyond H. pylori.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04981-1}, pmid = {41888669}, issn = {1471-2180}, support = {82100594//National Natural Science Foundation of China/ ; JSPH-MC-2021-10//Jiangsu Province Hospital (the First Affiliated Hospital with Nanjing Medical University) Clinical Capacity Enhancement Project/ ; }, }
@article {pmid41888912, year = {2026}, author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH}, title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02379-9}, pmid = {41888912}, issn = {2049-2618}, support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; }, abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.<br><br>RESULTS: We discovered that diatoms exude a C6-sulfated &#x3b1;-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.<br><br>CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.}, }
@article {pmid41888988, year = {2026}, author = {Khalil, M and Baffy, G and JohnBritto, JS and Mitten, E and Di Ciaula, A and Portincasa, P}, title = {Potential far-reaching metabolic consequences of cholecystectomy.}, journal = {European journal of clinical investigation}, volume = {56}, number = {4}, pages = {e70198}, doi = {10.1111/eci.70198}, pmid = {41888988}, issn = {1365-2362}, support = {//Prima Project: Tradition &amp; Innovation: promoting sustainable Mediterranean diet by Healthy Foods - B4HT, CUP H93C22000950001/ ; 101080329//PAS GRAS project, Horizon Europe Research and Innovation Action. TheHORIZON-HLTH-2022-STAYHLTH-01-05-twostage/ ; }, mesh = {Humans ; *Cholecystectomy/adverse effects ; Bile Acids and Salts/metabolism ; Gastrointestinal Microbiome/physiology ; Dysbiosis/metabolism ; Liver/metabolism ; Colorectal Neoplasms/etiology ; Receptors, Cytoplasmic and Nuclear/metabolism ; Gallstones/surgery ; Gallbladder/metabolism ; Enterohepatic Circulation ; Receptors, G-Protein-Coupled ; }, abstract = {BACKGROUND: Cholecystectomy is one of the most commonly performed abdominal surgical procedures and is considered the gold standard for symptomatic gallstone disease. Removing the gallbladder, however, is not a neutral process. The gallbladder stores and concentrates diluted cholesterol- and bile acid-enriched hepatic bile and is dynamically involved in the daily enterohepatic circulation of bile acids, with critical local and systemic metabolic effects via agonism of nuclear and membrane-associated receptors such as FXR and GPBAR1.<br><br>METHODS: We performed a narrative review to discuss the mechanisms driving cholecystectomy-associated dysmetabolism and disruption of the gut-liver axis. We reviewed studies that connect cholecystectomy to bile acid-mediated metabolic effects and examine the pathophysiological processes possibly involved in this scenario.<br><br>RESULTS: Experimental and human evidence highlights that cholecystectomy may be linked to several metabolic disorders, also increasing the risk of colorectal cancer. After cholecystectomy, the reservoir and concentrating function of the gallbladder are absent and bile enters the intestine directly. This new anatomical and functional configuration represents a major change in the entero-hepatic circulation of primary and secondary bile acids and in their signalling functions, with altered effects on metabolic receptors and on the gut microbiome. Post-cholecystectomy gut dysbiosis may lead to reduced microbial diversity and diminished capacity to generate beneficial short-chain fatty acids, promoting a pro-inflammatory milieu and altered metabolic homeostasis.<br><br>CONCLUSIONS: Cholecystectomy can predispose to metabolic changes leading to type 2 diabetes mellitus, obesity, metabolic dysfunction-associated steatotic liver disease and cardiovascular diseases.}, }
@article {pmid41889037, year = {2026}, author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS}, title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109518}, doi = {10.1016/j.identj.2026.109518}, pmid = {41889037}, issn = {1875-595X}, abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.<br><br>METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.<br><br>RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.<br><br>CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.}, }
@article {pmid41889114, year = {2026}, author = {Vlk, L and Odriozola, I and Pergl, J and Větrovský, T and Kvasničková, J and Krüger, C and Petružálková, M and Baldrian, P and Vojík, M and Sádlo, J and Petřík, P and Pyšek, P and Kohout, P}, title = {From pathogens to partners: temporal and biogeographical patterns in fungal associations of alien trees.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71094}, pmid = {41889114}, issn = {1469-8137}, support = {DG16P02M041//Ministerstvo Kultury/ ; EXPRO 19-28807X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-20802M//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; }, abstract = {Alien trees reshape belowground fungal communities, but the factors governing the balance between mutualists and pathogens remain unclear. We tested whether residence time, mycorrhizal type, and biogeographical origin shape this balance, and whether alien stands differ from native vegetation. We sampled soils beneath 73 alien tree species in 48 chateau parks and native stands. Using ITS2 metabarcoding with guild assignment, we quantified ectomycorrhizal (ECM) and pathogen fungi and analysed predictors with multivariate models and binomial GLMMs, accounting for spatial structure and covariates. Symbiotic fungal community composition varied with origin, phylogenetic group and mycorrhizal type. With increasing residence time, ECM alien trees showed higher ECM fungal richness and relative abundance; whereas, contrary to enemy accumulation expectations, pathogen richness and relative abundance declined. Alien arbuscular mycorrhizal (AM) trees harboured more pathogens than ECM trees. Alien tree assemblages had a lower ECM fungal share, twice the pathogen relative richness, and threefold higher pathogen relative abundance than native assemblages. Residence time and mycorrhizal type are primary filters shaping belowground trajectories of alien trees, with biogeographical origin patterning community composition. Elevated pathogen loads in alien stands highlight spillover risks to neighbouring vegetation, informing risk assessment and monitoring of alien tree plantings.}, }
@article {pmid41889117, year = {2026}, author = {Ganjayi, MS and Krauss, TA and Demster, GE and Park, S and Anspach, GB and Anthony, SR and Wang, S and Tranter, M and Helsley, RN and Baumann, CW}, title = {Systemic Consequences of Chronic Ethanol Intake: From Microbiome Shifts to Metabolic Impairment.}, journal = {Comprehensive Physiology}, volume = {16}, number = {2}, pages = {e70132}, doi = {10.1002/cph4.70132}, pmid = {41889117}, issn = {2040-4603}, support = {//Osteopathic Heritage Foundation/ ; 23CDA1051959//American Heart Association/ ; R01DK139147/NH/NIH HHS/United States ; K01DK128022/NH/NIH HHS/United States ; R01HL158671/NH/NIH HHS/United States ; }, mesh = {Animals ; *Ethanol/administration &amp; dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice, Inbred C57BL ; *Alcohol Drinking/adverse effects/metabolism ; }, abstract = {Chronic ethanol (EtOH) consumption is a major contributor to multi-organ dysfunction, yet its systemic effects remain incompletely understood. To address this, we utilized a physiologically relevant long-term mouse model, administering 20% EtOH in drinking water for 60 weeks, to investigate the integrated consequences of chronic exposure. EtOH-consuming mice (0.4-0.5 mL/day) exhibited > 30% reductions in chow and fluid intake, resulting in a 12% decrease in total caloric intake compared to controls (p < 0.001). Body mass remained similar until Week 52, after which EtOH-treated mice had lower body mass due to reductions in both lean and fat mass (p ≤ 0.004). Functional assessments revealed impaired treadmill endurance (-17%) and grip strength (-11%) (p ≤ 0.037), while motor coordination remained unaffected (p = 0.203). Chronic EtOH exposure significantly altered gut microbiota composition, reducing Lactobacillus and enriching Faecalibaculum, Clostridium, and Bifidobacterium at the genus level. These changes were accompanied by marked depletion of short-chain fatty acids (p ≤ 0.05). Indirect markers of gut permeability (serum LPS &amp; zonulin) and liver injury (serum ALT &amp; AST, hepatic amyloid content) were elevated, alongside increased total cholesterol and > 62% upregulation of hepatic TNFα, IL-6 &amp; serum amyloid A (p ≤ 0.046). EtOH also induced dyslipidemia and glucose intolerance (p ≤ 0.041), although transcriptomic changes in white adipose tissue were minimal despite elevated free fatty acids. In conclusion, chronic EtOH consumption disrupts energy balance, compromises gut barrier integrity, and impairs hepatic metabolism, collectively driving systemic and metabolic dysfunction. These findings underscore the gut-liver axis as a key mediator of EtOH-induced pathology and highlight the gut microbiome as a promising therapeutic target.}, }
@article {pmid41889411, year = {2026}, author = {Haykal, D and Rossi, A and Kerob, D and Dréno, B}, title = {Post-oncologic skin health: cutaneous recovery and rehabilitation after cancer treatments.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1774381}, pmid = {41889411}, issn = {2234-943X}, abstract = {BACKGROUND: Advances in oncology have markedly improved cancer survival, however, chronic cutaneous sequelae induced by chemotherapy, radiotherapy, targeted therapies, and immunotherapies remain common and may persist long after treatment completion. These long-term skin changes, ranging from xerosis and pruritus to pigmentary alterations, fibrosis, and immune-mediated dermatoses, can substantially impair quality of life and functional recovery.<br><br>OBJECTIVE: To define the evolving role of dermatology in post-oncologic skin health and to critically synthesize mechanistic and clinical evidence supporting long-term dermatologic rehabilitation strategies.<br><br>METHODS: A structured search of PubMed and MEDLINE (2010-2025) identified clinical and mechanistic studies, consensus guidelines, systematic reviews, and cohort data relevant to post-treatment cutaneous sequelae. Eligible publications included human studies addressing chronic skin changes after cancer therapy or evaluating therapeutic approaches applicable to survivorship dermatology. The search yielded 612 records, of which 148 full-text articles were reviewed and 54 met the inclusion criteria for synthesis.<br><br>RESULTS: Post-oncologic skin care extends beyond symptomatic management to encompass restoration of epidermal barrier function, mitigation of chronic inflammation, support of the cutaneous microbiome, and improvement of psychosocial well-being. Mechanistic studies highlight persistent structural, immunologic, molecular, and microbial alterations that underline delayed skin recovery. Within this context, photobiomodulation and selective energy-based modalities may support long-term cutaneous resilience, however robust clinical evidence of their benefit is lacking.<br><br>CONCLUSION: Dermatologists play a central role in survivorship care by transitioning cutaneous management from symptomatic treatment toward preventive, restorative, and rehabilitative strategies that improve long-term quality of life.}, }
@article {pmid41889491, year = {2026}, author = {Zhou, X and Luo, X and Wu, Y and Wang, H and Pan, Z and Wang, J and Xiao, X and Lin, M and Yao, Z}, title = {Co-infection with Pseudomonas aeruginosa and Mycobacterium avium complex in patients with bronchiectasis: coincidence or inevitability?.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1785156}, pmid = {41889491}, issn = {2296-858X}, abstract = {The burden of bronchiectasis is rapidly escalating worldwide, with its airway microbiome shifting from a "single-pathogen" paradigm to "multiple-pathogen coexistence." Both Mycobacterium avium complex and Pseudomonas aeruginosa infections have been demonstrated to exacerbate airway destruction, yet they are rarely examined concurrently. Emerging evidence suggests these pathogens exhibit a long-term coexistence pattern within the same patient, with one dominating when the other recedes. Furthermore, existing studies indicate that the disease burden in coinfected patients is higher than in those with either pathogen alone. However, the specific competitive and synergistic interactions between M. avium complex and P. aeruginosa in bronchiectasis patients remain poorly recognized, posing substantial therapeutic challenges. This review summarizes current understanding of the epidemiology and clinical manifestations of M. avium complex and P. aeruginosa co-infection in patients with bronchiectasis, along with potential mechanisms of microbial interaction between the two pathogens.}, }
@article {pmid41889559, year = {2026}, author = {Kim, M and Puglisi, CH and Hojjat, A and Nagel, E and Vuong, HE}, title = {Maternal environment during pregnancy shapes offspring neural circuitry and social behaviors.}, journal = {Current opinion in physiology}, volume = {47}, number = {}, pages = {}, pmid = {41889559}, issn = {2468-8673}, abstract = {Social interactions encompass complex behaviors that promote individual and group benefits such as communication and cooperation but can also include negative outcomes including competition and conflict. Neural circuits that facilitate social behaviors begin developing in utero and are informed by the maternal environment which include nutritional status, immune state, stress, and microbiome composition. This relationship between the maternal environment during pregnancy and the programming of social circuits and behaviors suggests a critical window of opportunity for early interventions strategies for social disorders, such as autism spectrum disorders. Here, we review recent causal mechanistic findings on how maternal environmental exposures during pregnancy can shape development and function of circuits implicated in social behaviors.}, }
@article {pmid41889579, year = {2026}, author = {Vesnupriya, P and Karukuvelraja, R and Rehanaz, N and Shamna, ME and Saranya, N}, title = {Mind gut harmony: psychobiotics effects on the gut-brain axis and harnessing its effects for the mental health.}, journal = {Journal of food science and technology}, volume = {63}, number = {4}, pages = {613-634}, pmid = {41889579}, issn = {0022-1155}, abstract = {The microbiota-gut-brain axis is gaining attention as a potential therapeutic avenue for treating illnesses of the illnesses of the central nervous system. In recent years, there has been a notable increase in literature examining the connection between the gut microbiome and its impact on overall health and wellness. The microbiota-gut-brain axis is a promising therapeutic target for treating central nervous system diseases and reducing drug adverse effects. Probiotics have been shown in pre-clinical and clinical trials to improve health by modulating the microbiota in the gut-brain axis. Psychobiotics are probiotics that modulate the gut-brain axis (GBA) and regulate the central nervous system to improve gastrointestinal function, as well as have antidepressant and anxiolytic properties via neuronal, humoral, and metabolic mechanisms. Some psychobiotic strains have been shown to reduce inflammation and cortisol levels, thereby degenerative and neurodevelopmental illnesses such as Parkinson's disease, Alzheimer's disease, and autism spectrum disorder can be effectively treated with psychobiotics. Alleviating anxiety and depression symptoms. Neurodegenerative and neurodevelopmental illnesses such as Parkinson's disease, Alzheimer's disease, and autism spectrum disorder can be effectively treated with psychobiotics. This review summarizes the psychobiotic potential on the gut-brain axis for the mental health.}, }
@article {pmid41889649, year = {2026}, author = {Su, R and Ma, J and Li, J and Liu, Y and Ma, T and Wang, J and Mai, Q and Ma, Q and Wang, J and Wang, H and Yang, S and Zhang, X}, title = {Fecal microbiota transplantation ameliorates alcohol-associated liver disease through coordinated restoration of short-chain fatty acid and α-linolenic acid signaling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1744446}, pmid = {41889649}, issn = {1664-302X}, abstract = {BACKGROUND: Alcohol-associated liver disease (ALD) is closely linked to gut microbiota dysbiosis. However, the specific microbial metabolic functions that drive the transition from microbial imbalance to hepatic inflammation and metabolic injury remain unclear, limiting the development of mechanism-based therapeutic strategies.<br><br>METHODS: This study integrated human microbiome analysis with fecal microbiota transplantation (FMT) experiments in an ALD mouse model. Multi-omics approaches, including 16S rRNA gene sequencing, untargeted metabolomics, and immunological profiling, were employed to systematically characterize the interactions among gut microbiota composition, microbial-derived metabolites, and host immune responses.<br><br>RESULTS: We observed that ALD progression was characterized by an early shift in microbial composition followed by a marked decline in microbial diversity, culminating in an ecological collapse of the gut microbiota. FMT from healthy donors significantly improved liver histopathology and serum biochemical parameters, accompanied by restoration of gut microbial diversity and key metabolic functions. Metabolomic analyses revealed enhanced short-chain fatty acid (SCFA) production and activation of &#x3b1;-linolenic acid (ALA)-related metabolic pathways following FMT. These metabolic improvements were associated with reduced inflammatory responses and improved immune homeostasis.<br><br>CONCLUSION: Our findings demonstrate that FMT from healthy donors ameliorates ALD by restoring critical microbial metabolic functions, particularly SCFA production and ALA-related pathways. These results highlight microbial metabolic function as a promising therapeutic target for microbiome-based interventions in ALD.}, }
@article {pmid41889654, year = {2026}, author = {Yu, G and Han, Y and Liu, J and Zhang, Y and Hao, H and Li, M}, title = {Straw-returning of Triticale to field improved the yield of foxtail millet efficiently by modulating soil physicochemical traits and fungal microbiome assembly.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1791055}, pmid = {41889654}, issn = {1664-302X}, abstract = {Green manure-crop rotation systems are effective management practices for maintaining soil health and enhancing crop yield. However, the influence of various green manure-millet rotation systems on soil properties, fungal community structure, and millet yield in the North China Plain remains undetermined. In this study, three types of green manures with foxtail millet rotation experiment were conducted. The physico-lchemica indexes, millet yield and soil fungal community characteristic were detected. Our findings suggest that three green manure-millet rotation systems increased millet yield compared to millet-winter fallow (Si-Le). Among them, the Triticale-millet rotation (Si-Ts) showed the highest yield increase, with a rise of 46.16% in 2021 and 85.7% in 2022. In 2021, compared with Si-Le, the organic matter (OM) in Si-Ts increased by 17.86%, and the available phosphorus (AP) rose by 113.82%. In 2022, in contrast to Si-Le, the alkali-hydrolyzed nitrogen (AHN) in Si-Ts increased by 17.68%, the available phosphorus (AP) by 37.56%, and the available potassium (AK) by 12.56%. Additionally, Si-Ts exhibited the highest diversity of soil fungi and the greatest relative abundance of beneficial genera from the dominant phylum Ascomycota and Mortierellomycota. Moreover, Green manure rotations (particularly Si-Ts) alleviate these constraints by simultaneously augmenting microbial diversity (driven by OM/AK/AHN) and crop yield (driven by AP/OM). Overall, the Triticale-millet rotation is a feasible practice for improving soil conditions, maintaining soil microbial balance, and ensuring high yields of millet. Our findings offer theoretical support for green manure-crop rotation in influencing the soil environment and the sustainable development of the millet industry in the North China Plain.}, }
@article {pmid41889668, year = {2026}, author = {Hong, J and Song, H and Jeong, S and Kim, JS and Choi, H and Kim, C}, title = {Gut and fecal microbiome profiles of the electric eel (Electrophorus varii) revealed by 16S rRNA amplicon sequencing.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112661}, pmid = {41889668}, issn = {2352-3409}, abstract = {We report a 16S rRNA gene amplicon sequencing dataset describing gut and fecal microbiota of the electric eel Electrophorus varii, a freshwater electrogenic fish lacking baseline microbiome references. Fecal and gut samples (n = 3 per group) from an individual eel were analyzed to characterize genus-level taxonomic composition and alpha diversity. The gut samples were strongly predominated by Cetobacterium, whereas the fecal samples contained more heterogeneous community structures. Principal component analysis (PCA) based on Hellinger-transformed relative abundances was applied to primarily separate gut and fecal microbiota samples along the first principal component (PC1) axis (92.8 %). Shannon alpha diversity was significantly higher in fecal microbiota compared with gut microbiota. Although the present dataset is based on triplicate samples from a single individual, expanded studies incorporating multiple electrogenic species and species-level comparisons will be necessary to determine whether electric discharge environments are associated with significant shifts in freshwater fish gut microbiome structure.}, }
@article {pmid41889698, year = {2026}, author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG}, title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1733638}, pmid = {41889698}, issn = {2673-6217}, abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.<br><br>METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69&#xa0;years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.<br><br>RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29&#xa0;years, n = 33; 22.7%), G2 (30-39&#xa0;years, n = 30; 20.7%), G3 (40-49&#xa0;years, n = 27; 18.6%), G4 (50-59&#xa0;years, n = 31; 21.4%), and G5 (60-69&#xa0;years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.<br><br>CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.}, }
@article {pmid41889714, year = {2026}, author = {Rojas-Rodríguez, AL and Jaramillo-Romero, V}, title = {The role of the gut microbiota during the first 2 years of life in the early programming of obesity, type 2 diabetes, and hypertension.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1772889}, pmid = {41889714}, issn = {2296-861X}, abstract = {The first 2 years of life constitute a critical window for the establishment of the gut microbiota and the early programming of cardiometabolic risk. The aim of this review was to analyze the influence of the gut microbiota during the first 2 years of life and its association with obesity, type 2 diabetes, and arterial hypertension. The reviewed studies suggest that early dysbiosis is associated with increased cardiometabolic vulnerability, linked to low-grade inflammation and alterations in energy metabolism. Associations are described between maternal metabolic conditions (such as obesity or gestational diabetes) and a less favorable initial intestinal ecosystem in the child, characterized by lower microbial diversity and reduced abundance of bacteria considered protective. In childhood obesity, longitudinal studies indicate that less mature microbiomes during the first year of life are associated with a higher risk of overweight, particularly when early antibiotic exposure and unhealthy dietary patterns coexist. In contrast, exclusive breastfeeding is associated with more functional microbial profiles. Regarding arterial hypertension, the findings suggest an influence mediated by microbial metabolites such as short-chain fatty acids and mechanisms involved in vascular regulation. Overall, the first 1,000 days represent a priority axis for promoting early-life practices that support a balanced gut microbiota as a potential strategy for cardiometabolic disease prevention.}, }
@article {pmid41872963, year = {2026}, author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ}, title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00825-5}, pmid = {41872963}, issn = {1757-4749}, support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; }, }
@article {pmid41873297, year = {2026}, author = {Katsanos, A and Benekos, K and Karavasili, M and Gorgoli, K and Kostoulas, C and Gartzonika, K and Christodoulou, DK and Katsanos, K and Georgiou, I}, title = {Intestinal Microbiome of Newly Diagnosed Patients With Neovascular Age-Related Macular Degeneration: A 16S rRNA Gene Sequencing Study.}, journal = {Cureus}, volume = {18}, number = {2}, pages = {e103984}, pmid = {41873297}, issn = {2168-8184}, abstract = {BACKGROUND: This study aims to explore differences in the intestinal microbiome between patients with newly diagnosed neovascular age-related macular degeneration (AMD) and controls using 16S rRNA gene sequencing.<br><br>METHODOLOGY: In this cross-sectional study, stool samples from newly diagnosed White patients with neovascular AMD and controls were used for the assessment of the intestinal microbiome. The DNeasy PowerSoil Pro Kit (QIAGEN, Hilden, Germany) was used to extract microbial DNA before sequencing the V3-V4 hypervariable region of the 16S rRNA gene on the Illumina MiSeq system (Illumina, San Diego, CA). Bioinformatic analysis was performed on the Nephele platform using the DADA2 pipeline in R (ClinicalTrials.gov identifier: NCT05757674).<br><br>RESULTS: Thirty-three patients (age: 75 &#xb1; 7 years, 17 women) and 34 age- and sex-matched controls (age: 73 &#xb1; 7 years, 18 women) were analyzed. No differences in height, weight, body mass index, smoking, or systemic comorbidities were noted between the groups. The most prevalent phyla in both groups were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. The most prevalent genus was Bacteroides in both groups. Neither alpha nor beta diversity was different among the groups. The differential abundance analysis using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) showed that some Amplicon Sequence Variants (ASVs) from the Coprococcus genus were more abundant in controls than in patients with AMD, whereas several ASVs from Bacteroides were more abundant in the AMD group.<br><br>CONCLUSIONS: In our sample, the intestinal microbiome of newly diagnosed patients with neovascular age-related AMD showed some small but noteworthy differences compared to matched healthy controls. Some Bacteroides ASVs were enriched in AMD patients, while certain Coprococcus ASVs were more abundant in controls.}, }
@article {pmid41873486, year = {2026}, author = {Pulaski, M and Weber, HC}, title = {Microbiome-derived signaling molecules and the brain-gut axis: emerging mechanisms and clinical implications.}, journal = {Current opinion in endocrinology, diabetes, and obesity}, volume = {}, number = {}, pages = {}, pmid = {41873486}, issn = {1752-2978}, abstract = {PURPOSE OF REVIEW: Recent advances in metabolomics, multi-omics integration, and neurogastroenterology have fundamentally reshaped understanding of the human gut microbiome. Rather than microbial composition alone, emerging evidence highlights microbial secretory and signaling activity as a central regulator of brain-gut communication. Understanding how microbiome-derived molecules interact with epithelial, immune, endocrine, and neural pathways is essential for advancing mechanistic insight and precision interventions in disorders of gut-brain interaction (DGBI).<br><br>RECENT FINDINGS: Recent studies demonstrate that the gut microbiome functions as a metabolic and endocrine signaling system, producing compounds such as short-chain fatty acids, bile acids, tryptophan-derived metabolites, polyamines, and lipid mediators that act on enteroendocrine cells, immune circuits, mechanosensory pathways, and vagal afferents. These signals are integrated centrally through brainstem and cortical networks, shaping gastrointestinal motility, visceral sensitivity, stress responsiveness, and affective processing. Functional dysbiosis and altered microbial signaling - rather than consistent taxonomic changes - appear to be primary modulators of brain-gut axis dysregulation.<br><br>SUMMARY: Emerging data calls for a reframing of gut-brain disorders as conditions of disrupted microbial signaling. Clinically, they support mechanism-based stratification and targeted dietary, microbiome-directed, and neuromodulatory therapies. The findings identify a need for functional biomarkers and targeted molecular approaches to advance precision medicine in DGBIs.}, }
@article {pmid41873937, year = {2026}, author = {Wang, X and Liu, X and Zhou, G and Miao, Y and Zhao, X and Cao, Y and Wang, Z and Deng, D}, title = {A Watermelon-Like Micro/Nano Hierarchical Delivery Platform for Ulcerative Colitis by Regulating Redox Homeostasis and Remodeling Gut Microbiota.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e05873}, doi = {10.1002/adhm.202505873}, pmid = {41873937}, issn = {2192-2659}, support = {2022YFF1100303//National Key R&amp;D Program of China/ ; 82172085//National Natural Science Foundation of China/ ; CPU2022QZ14//Double FirstRate Construction Plan of China Pharmaceutical University/ ; BK20190028//Distinguished Young Scholars/ ; }, abstract = {Ulcerative colitis (UC) is a refractory inflammatory bowel disease marked by mucosal barrier damage, immune dysregulation, and microbial imbalance. Current treatments are limited by systemic toxicity and inadequate targeting. Drawing inspiration from the "watermelon seed and watermelon" concept, this study employs microfluidic technology to encapsulate chondroitin sulfate (CSU) based nanoparticles (NPs) loaded with the antioxidant quercetin (Qu@CSCP) within hyaluronic acid/calcium alginate (HACM) hydrogel microspheres. This process yields a "watermelon-like" micro/nano hierarchical hydrogel microsphere system (QC@HACM) specifically designed for targeted combination therapy of UC. The HACM shell protects Qu@CSCP from the harsh gastrointestinal (GI) environment and enables targeted accumulation in inflamed colon tissue. Owing to its colon-adhesive properties, QC@HACM enhances the expression of tight junction proteins and reshapes the gut microbiota, enriching beneficial probiotics. Upon localized release, Qu@CSCP NPs activate the Nrf2/HO-1 antioxidant pathway, induce M2 macrophage polarization, and modulate the Bax/Bcl-2 ratio to suppress epithelial apoptosis. This dual mechanism effectively relieves oxidative stress and promotes mucosal healing. The therapeutic efficacy of these microspheres was further validated in a murine model of UC, as evidenced by reduced levels of pro-inflammatory cytokines accompanied by restoration of gut microbiota homeostasis. Consequently, this oral delivery platform represents a promising stepwise therapeutic strategy for comprehensive UC management.}, }
@article {pmid41873970, year = {2026}, author = {Valenzuela-Diaz, S and Dikareva, E and Hickman, B and Kiljunen, S and Kolho, K-L and de Vos, W and Salonen, A and Korpela, K}, title = {Impact of phage enrichment on the observed infant gut phageome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0215325}, doi = {10.1128/spectrum.02153-25}, pmid = {41873970}, issn = {2165-0497}, abstract = {The human gut microbiota, particularly during infancy, plays a pivotal role in shaping long-term health outcomes. While research on the bacterial microbiota has advanced rapidly, the infant gut virome-dominated by bacteriophages-remains underexplored due to technical challenges in viral DNA detection and recovery. To address this, we optimized a polyethylene glycol (PEG)-based protocol for phage DNA enrichment tailored to the constraints of infant fecal samples, focusing on maximizing viral yield from minimal input material. We validated the optimized protocol on fecal samples from 41 infants at 1, 6, and 12 months of age and assessed the impact of phage enrichment on the observed gut phageome. The results demonstrate that the optimized protocol improves viral DNA recovery and significantly alters the observed virome composition, especially in older infants. Without appropriate enrichment, key features of the gut virome may be underrepresented or missed entirely. These findings underscore the importance of protocol optimization in virome studies and provide a scalable, cost-effective method for robust infant gut virome profiling.IMPORTANCEUnderstanding the viral component of the infant gut microbiome is essential for uncovering its role in early-life health, yet technical limitations have hindered its study. This work presents a systematically optimized and validated protocol for enriching viral DNA from infant stool samples, designed specifically for low-input material typical of early life. By adapting polyethylene glycol-based precipitation methods, we achieved consistent and scalable recovery of viral DNA across infants of different ages. Application of this protocol revealed key age- and delivery mode-specific differences in phage diversity and replication strategies that were undetectable using standard approaches. Our findings demonstrate that careful protocol optimization is critical for accurate virome profiling in infants and offer a practical solution to overcome longstanding methodological challenges in the field.}, }
@article {pmid41874128, year = {2026}, author = {Yıldırım, S and Zhu, W and Cope, E and Lindemann, S and Suez, J and Shade, A}, title = {Sex-specific microbiome-host interactions: from infection to chronic disease-call for papers.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0015626}, doi = {10.1128/msystems.00156-26}, pmid = {41874128}, issn = {2379-5077}, }
@article {pmid41874175, year = {2026}, author = {Ibarguren-Quiles, C and Blasco, L and López-Causape, C and Bleriot, I and Fernández-García, L and Arman, L and Barrio-Pujante, A and Ortiz-Cartagena, C and Aracil, B and Menéndez-Rodriguez, O and Mariñas-Pardo, L and Cantón, R and Oliver, A and Tomás, M}, title = {Identification and functional insights into new phage tail-like bacteriocins targeting Pseudomonas aeruginosa as new antimicrobials.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0289425}, doi = {10.1128/spectrum.02894-25}, pmid = {41874175}, issn = {2165-0497}, abstract = {The current health crisis caused by multidrug-resistant (MDR) pathogens is one of the health problems of most concern globally. Infections caused by these pathogens, such as Pseudomonas aeruginosa, lead to high rates of complications, particularly in compromised patients such as cystic fibrosis (CF) patients. The need to counteract and minimize the forecast future impact has led to the rescue of phage therapy. The use of bacteriophages has important advantages, including highly specific targeting, self-amplification at the infection site, minimal disruption of the microbiome, safety, and biocompatibility. However, the capacity of bacteria to escape these entities results in a form of resistance that compromises the effectiveness of the therapy. This involves the search for potential alternatives, such as the phage tail-like bacteriocins (PTLBs), also named as tailocins. These high-molecular-weight particles resemble the tail structure of bacteriophages and are characterized by the absence of genetic material, avoiding the development of resistance, one of the major handicaps associated with phage therapy. In this study, we detected 34 different PTLBs in 75 P. aeruginosa genomes, with different serotypes and sequence types, 11 of which were characterized as novel F-type PTLB subtypes (F13-F24). Furthermore, we report that four selected PTLBs (R1, F15, F19, and R3-F24) can deal with bacterial infection, with the R1 and the F15 PTLBs being the most efficient in clearing infection in vitro, yielding a survival rate of more than 75% in the Galleria mellonella larvae in vivo model. This reaffirms the potential of PTLBs to control P. aeruginosa infections, which can cause chronic infections in some patients, such as people with CF, due to its strong impact as a MDR bacterium.IMPORTANCEThe 75 Pseudomonas aeruginosa genomes from people with cystic fibrosis in the study collection included at least one phage tail-like bacteriocins (PTLB) cluster. From the 34 different PTLBs detected in the study collection, 7 were R-type, 10 were complex (R- and F-type encoded), and 14 were F-type PTLBs. Eleven new F-type PTLBs were described in the P. aeruginosa collection under study. An association between the O-antigen present on the surface of the P. aeruginosa isolate and the encoded PTLB subtype was detected. The R1 and F15 PTLB subtypes display high antimicrobial activity both in vitro and in vivo (Galleria mellonella).}, }
@article {pmid41874177, year = {2026}, author = {Poursalavati, A and Laforest-Lapointe, I and Fall, ML}, title = {SS-VIME: a single-source virome-microbiome extraction protocol toward comprehensive soil community analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0332325}, doi = {10.1128/spectrum.03323-25}, pmid = {41874177}, issn = {2165-0497}, abstract = {Integrated analysis of soil microbiomes and their associated viromes is critical for understanding ecosystem function, yet is hampered by the profound spatial heterogeneity of soil, which introduces significant bias when using separate extraction workflows and/or subsampling strategies to capture fungal, bacterial, and viral communities. Here, we present single-source extraction for unified soil virome-microbiome profiling (SS-VIME), a protocol that overcomes this limitation. Based on extended cellulose column chromatography, this method sequentially elutes distinct DNA and double-stranded RNA (dsRNA) fractions from a single soil lysate. We validated the protocol using sterilized soil co-spiked with a ZymoBIOMICS microbial community standard and a synthetic viral dsRNA fragment. Sequencing confirmed that the DNA fraction accurately recovered the theoretical bacterial (16S rRNA gene) and fungal (ITS) community profiles, while the dsRNA fraction demonstrated highly specific recovery of the target viral signature. The protocol was then successfully applied to characterize the complex native communities in environmental soil samples. The SS-VIME protocol provides a streamlined approach for isolating high-quality nucleic acids suitable for downstream applications. By using dsRNA as a proxy for viral activity and eliminating subsample bias, this method provides a robust, accessible, and unified platform to investigate virus-host dynamics in situ, paving the way for a more holistic understanding of the soil microbiome.IMPORTANCEThe study of soil microbes and their viruses, which are central to ecosystem health, is fundamentally limited by technical barriers. Separate extraction workflows for each group introduce sampling bias, obscuring the true ecological relationships within soil's spatially complex micro-environments. Our single-source virome-microbiome extraction (SS-VIME) protocol directly overcomes this by efficiently recovering both microbial DNA and viral double-stranded RNA (dsRNA) from one sample. This unified approach is not only cost-effective but, by using dsRNA as a signature of viral activity, captures a more accurate and representative profile of the soil active virome. SS-VIME provides the foundation for robustly investigating how viruses modulate soil health, carbon cycling, and agricultural productivity, moving the field from correlational studies toward a direct, integrated view of the soil ecosystem.}, }
@article {pmid41874180, year = {2026}, author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV}, title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0264825}, doi = {10.1128/spectrum.02648-25}, pmid = {41874180}, issn = {2165-0497}, abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.}, }
@article {pmid41874246, year = {2026}, author = {Koh, H}, title = {Phylogeny-informed random forests for human microbiome studies.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0345125}, doi = {10.1128/spectrum.03451-25}, pmid = {41874246}, issn = {2165-0497}, abstract = {UNLABELLED: Random Forest is a widely used tree-based ensemble learning algorithm that efficiently captures complex nonlinear relationships and higher-order feature interactions with no distributional assumptions to be satisfied. It is also well-suited to human microbiome studies, where the data are highly skewed, overdispersed, discrete, and irregular. Here, I pay particular attention to the phylogenetic tree information that reflects evolutionary ancestry and functional relatedness among microbial features. Proper incorporation of phylogenetic tree information into microbiome data analysis has provided new insights and improved analytical performance. In this paper, I introduce an extension of the Random Forest algorithm that incorporates phylogenetic tree information, named Phylogeny-Informed Random Forests (PIRF), to improve predictive accuracy in human microbiome studies. The core mechanism of PIRF lies in its localized approach; rather than treating all features as competing globally to be selected or weighted, PIRF identifies informative features within each phylogenetic cluster (i.e., a localized group of microbial features that are evolutionarily and functionally related), thereby enriching functional representations while reducing tree-to-tree correlation. I demonstrate the high predictive accuracy of PIRF, compared with other off-the-shelf tools, across seven benchmark tasks: four classification problems (gingival inflammation, immunotherapy response, type 1 diabetes, and obesity) and three regression problems (cytokine level, age based on oral microbiome, and age based on gut microbiome).<br><br>IMPORTANCE: PIRF is an extension of the Random Forest algorithm that incorporates phylogenetic tree information to improve predictive accuracy in human microbiome studies. PIRF can serve as a useful tool for microbiome-based disease diagnostics and personalized medicine. The software and tutorials are freely available as an R package, named PIRF, at https://github.com/hk1785/PIRF.}, }
@article {pmid41874370, year = {2026}, author = {Liu, C and Dan, L and Wang, X and Chen, L and Yuan, X}, title = {Gut microbiota impact on lung diseases: a mini review of clinical evidence.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0043025}, doi = {10.1128/iai.00430-25}, pmid = {41874370}, issn = {1098-5522}, abstract = {The gut-lung axis represents a bidirectional communication network through which the gut microbiota (GM) influences respiratory health. This mini-review synthesizes clinical evidence on the role of the GM in lung diseases. We focused exclusively on human clinical trials, randomized controlled trials, meta-analyses, and systematic reviews, sourced from major databases after duplicate removal. The evidence indicates that GM dysbiosis is a significant risk factor for the susceptibility and severity of various respiratory conditions, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), and infections, such as COVID-19 and pneumonia. Specific microbial signatures and metabolic profiles, particularly involving short-chain fatty acids (SCFAs), are associated with disease states and outcomes. Interventions like probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) show promise in modulating the GM and improving clinical parameters, though their efficacy can be inconsistent and influenced by confounding factors. In conclusion, the GM is a promising therapeutic target for lung diseases. However, future research must prioritize large-scale, longitudinal clinical trials and deeper mechanistic investigations to establish causality and develop effective, personalized microbiome-based therapies.}, }
@article {pmid41874395, year = {2025}, author = {Park, G and Chakrabarty, P and Efron, PA and Nagpal, R}, title = {Dysbiosis and the gut-brain axis impairment in the pathophysiology of Alzheimer's disease and related dementias: is 'pathobiome' an etiological element?.}, journal = {Essays in biochemistry}, volume = {69}, number = {6}, pages = {}, doi = {10.1042/EBC20253055}, pmid = {41874395}, issn = {1744-1358}, mesh = {Humans ; *Dysbiosis/microbiology/complications/physiopathology ; *Alzheimer Disease/physiopathology/microbiology/etiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Brain/metabolism/physiopathology ; Animals ; *Dementia/physiopathology/microbiology/etiology ; }, abstract = {The gut microbiome plays a pivotal role in host metabolic, cardiovascular, and immune health. Increasing evidence also links it to aging-associated neurocognitive decline and neurodegenerative disorders, including Alzheimer's disease (AD) and related dementias. While the precise mechanisms of the gut-microbiome-brain axis remain incompletely understood, recent findings challenge the traditional view of AD as a disease confined to the central nervous system. Aging-associated gut dysbiosis, marked by loss of beneficial microbes, expansion of opportunistic pathogens, and reduced microbial diversity, can compromise intestinal barrier integrity, leading to 'leaky gut' and increased translocation of microbial components or pathogens into the circulation. These elements may cross a weakened blood-brain barrier, triggering neuroinflammation, amyloid-beta accumulation, tau hyperphosphorylation, and neuronal injury. Such pathobiome-driven inflammatory cascades may initiate or accelerate AD pathology, shifting the etiological perspective beyond the amyloid and tau hypotheses toward systemic and peripheral contributors. Our work and others' have identified distinct dysbiotic microbiome signatures in AD, supporting the possibility that AD pathogenesis may begin in the gut. Restoring microbial homeostasis through targeted interventions could attenuate neuroinflammatory and neurodegenerative processes, offering a novel preventive and therapeutic avenue. This emerging paradigm underscores the need for comprehensive, mechanistic, and longitudinal studies to define how aging-driven microbiome alterations influence the gut-brain axis and contribute to AD progression.}, }
@article {pmid41874416, year = {2026}, author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI}, title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.}, journal = {Nicotine &amp; tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntag057}, pmid = {41874416}, issn = {1469-994X}, abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.<br><br>METHODS: We used osmotic minipumps as an application of chronic nicotine for 15&#xa0;days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24&#xa0;h and 1&#xa0;week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.<br><br>RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24&#xa0;h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.<br><br>CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.}, }
@article {pmid41874734, year = {2026}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM}, title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41874734}, issn = {1573-0972}, abstract = {UNLABELLED: This study explores the root-associated microbiome of Calotropis procera, a drought-adapted, invasive plant thriving in Brazil. We analyzed microbial communities from the root endosphere, rhizosphere, and adjacent soil in two contrasting ecosystems: Caatinga (semi-arid) and Restinga (coastal). Using 16S rDNA sequencing and shotgun metagenomics, we tested three hypotheses: (I) environmental specificity of the rhizospheric bacterial microbiome, (II) continuity of bacterial composition between bulk soil and rhizosphere, and (III) host-driven filtering of the endophytic microbiome. Despite differing soil conditions – more sodium in Restinga and higher organic carbon in Caatinga – microbial profiles in root compartments remained consistent. The root endosphere was enriched with stress-tolerant bacteria and novel archaea, while fungal genera included Fusarium and Puccinia. Results partially supported environmental specificity and showed moderate soil-rhizosphere continuity, with evidence of plant-mediated selection. Host filtering was evident for bacteria and fungi but not archaea. These data indicate a C. procera-mediated regulation of its root microbiome composition, whereby the plant may either selectively recruit specific taxa from prevalent soil microbial communities (e.g., through root exudates) or vertically transmit a conserved subset of its microbiome via seeds. Our study enhances understanding of the C. procera microbiome and its microbial interactions, identifying potential candidates for future biotechnological applications.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04902-4.}, }
@article {pmid41874766, year = {2026}, author = {Tamang, A and Chaudhary, S and Pandey, SS and Hallan, V}, title = {Plant viruses and the microbiome: a complex network shaping plant health and disease resistance.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41874766}, issn = {1432-8798}, support = {CSIR - Indian Institute of Chemical Biology//CSIR - Indian Institute of Chemical Biology/ ; }, mesh = {*Microbiota ; *Plant Diseases/virology/microbiology/immunology ; *Plant Viruses/physiology ; *Plants/virology/microbiology/immunology ; *Disease Resistance ; Host-Pathogen Interactions ; }, abstract = {Plant viruses and microbiomes are pivotal to plant health, growth, and their ability to withstand environmental challenges. However, the extent to which viruses engage in direct or indirect crosstalk with plant-associated microbial communities remains largely unexplored. Traditionally, plant viruses are considered as harmful agents that disrupt normal plant functions, but new research indicates they may also engage in complex interactions with the plant's microbiome. On the other hand, the plant microbiome, comprising a diverse assembly of bacteria, fungi, and other microbes, can influence the plant's responses to viral infections, potentially altering the course of the disease. Thus, we emphasize the intricate interplay between plant viruses and microbiomes, particularly how viruses might "communicate" with microbial communities to alter the host environment or bypass immune defenses. The mechanisms driving these interactions, such as virus-induced shifts in plant metabolism, signaling pathways, and immune responses that indirectly affect microbiome composition are also discussed. The beneficial effect of plant-associated microbial communities against viral infections and the strategy of microbiome-based approaches for managing viral diseases are also focused. By moving beyond the traditional view of pathogen-host interactions, this review will highlight the importance of considering the three-way relationship among plants, viruses, and microbiomes to advance our understanding of plant health and foster innovative solutions for sustainable agriculture.}, }
@article {pmid41874795, year = {2026}, author = {Kwinten, KJJ and Johnson, JE and van Altena, AM and Hoogerbrugge, N and Davidson, EJ and de Hullu, JA}, title = {Prevention strategies for hereditary gynaecological cancer in Lynch syndrome.}, journal = {Familial cancer}, volume = {25}, number = {2}, pages = {}, pmid = {41874795}, issn = {1573-7292}, support = {NIHR304303//NIHR Research Professorship/ ; NIHR203308//NIHR Manchester Biomedical Research Centre/ ; }, abstract = {Lynch syndrome is a hereditary cancer predisposition condition associated with an elevated lifetime risk of colorectal, endometrial, ovarian, and several other malignancies. This review provides an updated overview of evidence-based prevention strategies for gynaecological cancers in patients with Lynch syndrome. Risk-reducing hysterectomy with bilateral salpingo-oophorectomy is the most effective intervention for lowering cancer incidence and mortality, but is associated with surgical morbidity and requires careful consideration of reproductive plans and the adverse consequences of premature menopause. Gynaecological surveillance using transvaginal ultrasound and endometrial biopsy is widely implemented as an alternative; however, available evidence is heterogeneous and indicates no benefit in reducing mortality. Novel approaches—such as biomarker-based detection using DNA methylation analysis of cervicovaginal samples, liquid biopsy techniques, and microbiome profiling—offer promising, non-invasive alternatives but require prospective validation in Lynch-specific populations. Chemoprevention with hormonal agents and aspirin may reduce cancer risk, while vaccine-based prevention strategies are under active investigation. Adoption of a healthy lifestyle is recommended for overall health, although its impact on gynaecological cancer risk in Lynch syndrome remains uncertain. Future research should prioritise prospective trials to establish optimal cancer prevention protocols, validate novel biomarkers and preventive cancer vaccine strategies, and evaluate the long-term effectiveness, acceptability, and cost-effectiveness of combined preventive approaches to improve outcomes in this high hereditary-risk population.}, }
@article {pmid41874898, year = {2026}, author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM}, title = {Protective holobiome promotes strawberry tolerance of biotic stresses.}, journal = {Stress biology}, volume = {6}, number = {1}, pages = {}, pmid = {41874898}, issn = {2731-0450}, support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.}, }
@article {pmid41875058, year = {2026}, author = {Martínez Ruiz, M and Tabor-Simecka, L and Graham, JL and Randolph, C and Fox, R and Lan, R and Pack, L and LeRoith, T and Stanhope, KL and Yeruva, L and Havel, PJ and Piccolo, BD}, title = {Improvement of glucose homeostasis during leptin treatment does not alter the intestinal microbiome in male diabetic UC Davis Type-2 Diabetes Mellitus rats.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00412.2025}, pmid = {41875058}, issn = {1522-1547}, support = {6026-10700-001-00D//USDA | Agricultural Research Service (ARS)/ ; UM1TR004909//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; 1K12TR004924//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; U24DK135074//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; R01AG085572//HHS | NIH | National Institute on Aging (NIA)/ ; }, abstract = {Gut dysbiosis contributes to type 2 diabetes (T2DM) progression according preclinical evidence. Alterations in gut microbiome, energy metabolism, and barrier function were observed in individuals with obesity and insulin resistance. However, it remains unclear whether therapeutic interventions can reverse these alterations. This study aimed to evaluate whether improvements of glucose homeostasis resulting from leptin administration can lead to changes in colonic epithelial metabolism and barrier function in male UC Davis Type 2 Diabetic Mellitus (UCD-T2DM) rats. Male UCD-T2DM rats (age: 173 ± 41 days) with 6 weeks post-onset of diabetes were randomized to receive daily subcutaneous injections of either PBS (control; n=12) or recombinant leptin (0.5 mg/kg; n=12) for four weeks. Metabolic and intestinal outcomes were assessed, including glucose tolerance, insulin sensitivity, GLP-1 levels, gut permeability, microbiota composition, short chain fatty acids (SCFA) content, epithelial hypoxia, intestinal morphology, and gene/protein expression. Leptin treatment significantly reduced food intake and improved glucose homeostasis and insulin sensitivity without affecting body weight. No changes were observed in microbiome composition, gut permeability, or epithelial hypoxic gradients. Ileal villus height was decreased, while colonic crypt depth was not different between leptin-treated rats and control rats. Butyric, isocaproic, and valeric acids levels were increased in colonic content, colonic expression of Pparg and Ldha was downregulated, while PHD2 and Occludin protein levels were upregulated in leptin-treated compared with control. Despite improvements of glucose homeostasis, chronic leptin treatment did not modify gut microbiota or barrier function markers, and colonic metabolic gene expression showed no clear adaptive shift.}, }
@article {pmid41875216, year = {2026}, author = {Castillo-Moral, &#xc1; and Toda-Ferran, C and Bulló, M and Teichenné, J and Escoté, X}, title = {Nutraceuticals and the Microbiota-Gut-Brain Axis: A Pathway for Preventing Cognitive Decline.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuag017}, pmid = {41875216}, issn = {1753-4887}, support = {//Vicente Lopez Program (Eurecat)/ ; //Autonomous Government of Catalonia/ ; 2021 SGR 00213//Departament de Recerca i Universitats de la Generalitat de Catalunya to the Nutrition and Metabolic Health Research Group/ ; 2021 SGR 01556//Precision Nutrition, Wellness and Prevention of Metabolic Diseases/ ; }, abstract = {With the global rise in aging populations, cognitive impairment and neurodegenerative diseases, such as Alzheimer's disease (AD), present a growing public health issue. Current pharmacological treatments primarily target symptoms rather than underlying causes, necessitating the exploration of alternative preventive strategies. Nutraceuticals have emerged as promising candidates for neuroprotection due to their ability to modulate oxidative stress, neuroinflammation, and mitochondrial function. This narrative review aimed to evaluate the neuroprotective potential of nutraceuticals and their interactions with the microbiota-gut-brain axis in preventing age-related cognitive decline. A comprehensive search of the scientific literature using the PubMed, Scopus, and Web of Science databases was undertaken, focusing on publications during the period 2010-2025. Nutraceuticals, including vitamins, omega-3 fatty acids, coenzyme Q10, polyphenols, and isothiocyanates, exhibit neuroprotective properties through antioxidant, anti-inflammatory, and mitochondrial-support mechanisms. The gut microbiota plays a crucial role in regulating the bioavailability and efficacy of these compounds. Microbiome-based interventions, such as prebiotics, probiotics, and fecal microbiota transplantation demonstrate potential in modulating neuroinflammatory responses and supporting cognitive function. Nutraceutical and microbiome-targeted interventions represent promising, low-risk strategies for preventing cognitive decline. Their ability to modulate neuroinflammation and oxidative stress underscores their potential for future clinical applications. Further large-scale studies are needed to validate their efficacy and explore personalized approaches adapted to individual microbiome profiles.}, }
@article {pmid41875499, year = {2026}, author = {Li, F and Liang, X and Li, J and Cui, M and Ho, TE and Li, J and Yuan, Z and Meng, W and Man Lo, EC and Fan, M and Zhang, Z and Jin, L and Chen, X and Lu, H and Jiang, Y}, title = {Oral microbiome perturbations link periodontal health to cognitive ageing in a large community cohort.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106231}, doi = {10.1016/j.ebiom.2026.106231}, pmid = {41875499}, issn = {2352-3964}, abstract = {BACKGROUND: Emerging evidence implicates the oral-brain axis in neurodegeneration, yet large community-based studies remain limited. This study aimed to examine associations between periodontal health, oral microbiome, and cognitive performance, and to explore potential biological pathways underlying these relationships.<br><br>METHODS: We conducted a cross-sectional analysis of 1157 participants from the community-based Taizhou Imaging Study, all of whom underwent comprehensive periodontal examinations, salivary microbiome profiling, and cognitive assessments. Periodontal health and microbiome features were treated as exposures, and cognitive performance as the outcome. Associations between periodontal indices and cognitive scores were assessed using beta regression models adjusted for relevant confounders. Cognition-related microbial features were identified using Multivariate Associations with Linear Models (MaAsLin3), followed by mediation analyses to explore potential pathways linking periodontal health to cognitive function.<br><br>FINDINGS: Five clinical periodontal indices were found to be inversely associated with cognitive performance. Ten microbial genera (e.g., Haemophilus), 21 functional pathways (e.g., FoxO signalling), and two co-abundance modules, including a Treponema module, were significantly related to cognitive function. Mediation analysis suggested that 11 features, including nitrate-reducing taxa and a Treponema-driven inflammatory module, may partially mediate the relationship between periodontal health and cognition.<br><br>INTERPRETATION: These community-based findings reveal microbiome-mediated links along the oral-brain axis and highlight periodontal health and oral microbial homoeostasis as potential targets for early prevention of cognitive decline.<br><br>FUNDING: This work was supported by the National Key R&amp;D Program of China (2023YFC3606300), National Natural Science Foundation of China (82373658), Clinical Research General Project of the Shanghai Municipal Health Committee (202240355), Clinical Research General Project of Shanghai Municipal Health Commission (202440188), Noncommunicable Chronic Diseases-National Science and Technology Major Project (2023ZD0510000), Brain Science and Brain-like Intelligence Technology-National Science and Technology Major Project (2022ZD0211600).}, }
@article {pmid41875611, year = {2026}, author = {Yang, Z and Zhang, F and Yang, S and Anayyat, U and Mo, Y and Ying, Y and Wang, X}, title = {Orally deliverable Perilla frutescens-derived nanovesicles as natural bioactive nanocarriers for colon-targeted colitis therapy via microenvironment reprogramming.}, journal = {Biomaterials advances}, volume = {184}, number = {}, pages = {214832}, doi = {10.1016/j.bioadv.2026.214832}, pmid = {41875611}, issn = {2772-9508}, abstract = {Effective oral therapy for inflammatory bowel disease (IBD) requires overcoming gastrointestinal barriers to modulate the dysregulated mucosal niche. Here, we present edible nanovesicles derived from Perilla frutescens (PLENs) as an intrinsically stable, bioactive nanotherapeutic. Multi-omics profiling defined a robust lipid-bilayer architecture encapsulating a synergistic cargo of proteins, miRNAs, and antioxidant metabolites. This structural integrity enabled PLENs to survive gastrointestinal transit and exhibit preferential fluorescence localization with prolonged retention in the inflamed colonic region, as indicated by in vivo imaging. Upon localization, PLENs executed a "dual-hit" therapeutic strategy: they reprogrammed the immune microenvironment, accompanied by reduced activation of the TLR4/MyD88-NF-κB axis and a phenotypic shift from pro-inflammatory M1 to reparative M2 macrophages. Concurrently, PLENs fundamentally restructured the gut ecosystem, accompanied by enrichment of taxa linked to saccharolytic fermentation and recovery of cecal short-chain fatty acids. Notably, fecal microbiota transplantation (FMT) further supported that this microbial remodeling contributed to the protective phenotype, highlighting the microbiome as an important component of efficacy.}, }
@article {pmid41875802, year = {2026}, author = {Balakrishnan, D and Magudeeswari, P and Surapaneni, M and Kumar, AP and Anantha, MS and Saiprasad, SV and Neelamraju, S and Sundaram, RM}, title = {Genotyping by sequencing of wild interspecific mapping population detected novel genetic locus harbouring OsPT11 for rice yield under nutrient stress conditions.}, journal = {Plant physiology and biochemistry : PPB}, volume = {233}, number = {}, pages = {111231}, doi = {10.1016/j.plaphy.2026.111231}, pmid = {41875802}, issn = {1873-2690}, abstract = {Nutrient deficiency is a major constraint to crop production, severely impairing crop establishment and yield. The development of high-yielding cultivars with enhanced tolerance to limited nutrient availability is therefore essential for sustainable crop production. Wild introgression lines, which have evolved to grow and reproduce under adverse environmental conditions, represent valuable genetic resources and potential donors of traits and genes that confer adaptation to nutrient-limited environments. In this study, wild introgression lines derived from Oryza rufipogon were evaluated across six environments, comprising four environments under the recommended dose of phosphorus (RDP) and two environments under low-phosphorus (low P) conditions. Genotyping-by-sequencing (GBS) enabled the identification of 113 quantitative trait loci (QTLs) associated with key agronomic traits. Of these, 41 major QTLs were detected under RDP, while 21 major QTLs were identified under low P stress, explaining up to 28.06% and 30.23% of the phenotypic variance, respectively. Notably, two major QTLs governing grain yield were consistently detected under low-phosphorus conditions, with favourable alleles enhancing yield derived from O. rufipogon. QTLs for days to 50% flowering, number of tillers per plant, and number of productive tillers per plant were consistently identified across both environments. Furthermore, a QTL hotspot region was detected on chromosome 1, harbouring eight QTLs associated with biomass, total tiller number, productive tiller number, total dry matter, and thousand-grain weight. Candidate gene analysis within this hotspot region identified the Pi transporter gene OsPT11, which is involved in phosphorus acquisition and translocation and plays a key role in activating mycorrhizal symbiosis. These findings suggest that this QTL region represents a promising target for improving grain yield under low-nutrient conditions and may enhance root-microbiome interactions, facilitating more efficient nutrient uptake under stress.}, }
@article {pmid41876480, year = {2026}, author = {Evenepoel, M and Daniels, N and Moerkerke, M and Prinsen, J and Steyaert, J and Boets, B and Joossens, M and Alaerts, K}, title = {The role of the oxytocinergic system in oral microbiome composition in children with autism: evidence from a randomized controlled trial of intranasal oxytocin.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-03964-0}, pmid = {41876480}, issn = {2158-3188}, abstract = {Atypical oxytocinergic functioning and altered microbiome compositions have both been implicated in autism, with growing evidence of interactions between these systems. However, how exogenous oxytocin influences the oral microbiome remains largely unexplored. This exploratory study examined for the first time how oral microbiome alterations link to oxytocinergic signalling in school-aged autistic (n = 80) and non-autistic children (n = 40). Additionally, we investigated the effect of four-weeks of intranasal oxytocin administration in autistic children on oral microbiome compositions immediately post-treatment (T1) and at four-weeks follow-up (T2). At baseline, lower endogenous salivary oxytocin levels were linked to greater microbial evenness and diversity, with twelve genera showing significant associations with oxytocin levels. In autistic children, four weeks of oxytocin administration was associated with significant increases in the abundances of Centipeda immediately post-treatment (T0-T1), alongside decreases in Moraxella (T0-T1), and subsequent reductions in Rothia observed at the four-week follow-up (T1-T2). Particularly, the genus Moraxella emerged as relevant, as lower baseline abundance was associated with higher endogenous oxytocin levels, and a stronger oxytocin-induced downregulation of its abundance correlated with greater increases in endogenous oxytocin levels, accompanied by hypomethylation of the oxytocin receptor gene. All results persisted after adjusting for nutrition and dental care. This exploratory study provides initial evidence for a role of the oxytocinergic system in shaping the oral microbiome in autistic children. These results may facilitate the integration of oral microbiome profiling into autism diagnostic criteria and stimulate future studies on the use of oxytocin as a therapeutic option targeting oral microbiome alterations.}, }
@article {pmid41876505, year = {2026}, author = {Wang, Z and Cao, B and Li, L and Cui, H and Wei, B and Cui, J and Wang, X}, title = {Acid-tolerant injectable bioadhesive for sutureless repair of large gastric perforation.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71031-9}, pmid = {41876505}, issn = {2041-1723}, support = {52573186, 52373162, 82572862//National Natural Science Foundation of China (National Science Foundation of China)/ ; F252056, L256034, L244037, 7262018//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; 2024048519//Beijing Nova Program/ ; }, abstract = {Bioadhesives represent promising alternatives to sutures towards gastric perforation management, however, significant challenges persist concerning instant wet adhesion and durable stability in gastric perforation sealing, particularly in direct contacting with acidic gastric fluids on large perforation injuries. Here we report an injectable acid-tolerant hydrogel composed of FDA-approved components for sutureless repair of large gastric defects. The hydrogel displays rapid in situ gelation, instant wet adhesion, and high burst pressure for efficient sealing despite excessive mechanical challenges, tissue irregularities and gastric juices. The enhanced hydrogen bonding interactions among amide-linked skeleton enable robust acid-tolerant interfaces to accommodate durable adhesion under the fluidically, chemically and mechanically dynamic in-vivo environments. A larger-scale porcine gastric perforation is applied to validate the sealing efficacy via a combined laparoscopic-endoscopic technique. The negligible postoperative adhesion, suppressed inflammation and interference-free transcriptome and microbiome verify the therapeutic outcomes. The proposed bioadhesives hold great promise for clinical treatment of digestive diseases.}, }
@article {pmid41876637, year = {2026}, author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K}, title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.}, journal = {Npj mental health research}, volume = {5}, number = {1}, pages = {}, pmid = {41876637}, issn = {2731-4251}, support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; }, abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.}, }
@article {pmid41876749, year = {2026}, author = {Jamshidi, N and Nigam, SK}, title = {Aryl hydrocarbon receptor in the kidney regulates metabolic cross-talk with the liver and gut microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44083-6}, pmid = {41876749}, issn = {2045-2322}, support = {R01-5R01DK109392/DK/NIDDK NIH HHS/United States ; }, }
@article {pmid41876773, year = {2026}, author = {Xu, Y and Lyu, X and Yang, Y and Akar-Ghibril, N and Telatin, M and Tang, R and Chang, C and Sun, J}, title = {Unmasking the Impact of Air Pollution on Allergic Rhinitis.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {69}, number = {1}, pages = {}, pmid = {41876773}, issn = {1559-0267}, support = {7191008//Beijing Natural Science Foundation-Key Project/ ; }, }
@article {pmid41876795, year = {2026}, author = {Singh, S and Goel, I and Rana, A and Gul, A and Quadri, JA and Mridha, AR and Malhotra, L and Kashyap, N and Radha, B and Nayek, A and Ajmeriya, S and Prasad, J and Dhar, R and Karmakar, S}, title = {IGFBP3 repression driven by inflammation links air pollution to placental and developmental defects.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {41876795}, issn = {1757-4684}, support = {68.10.2023(SK).NCD-II//MOHFW | DHR | Indian Council of Medical Research (ICMR)/ ; R.11012/03/2020-HR//MOHFW | Department of Health Research, India (DHR)/ ; }, abstract = {Air particulate matter (PM2.5 and PM10), can cross the placental barrier, triggering oxidative stress and inflammation that compromise fetal development. These insults lead to placental dysfunction and complications including preterm birth, low birth weight, and preeclampsia. In cell line and placental explant models, urban particulate matter (UPM) increased pro-inflammatory cytokines and oxidative stress pathways, impairing trophoblast invasion, angiogenesis, and nutrient transport, while also altering epigenetic modifications and endoplasmic reticulum function. Rodent studies revealed reduced litter size, placental abnormalities, and fetal growth arrest along with postnatal neurodevelopmental alterations. Human cohorts from high-exposure regions showed elevated low birth weight rates. Proteomic and transcriptomic analyses of rat placenta revealed an inflammatory signature and altered metabolic networks, while gut microbiome dysbiosis suggested links to metabolic disturbances. Importantly, transcriptomic analysis identified IGFBP3 as a major downregulated gene following UPM exposure. IGFBP3, a key regulator of IGF bioavailability, was suppressed by IL1β, establishing inflammation-driven repression as the mechanism. These findings underscore UPM's multidimensional impact on maternal-fetal health and highlight preventive strategies as urgent priorities.}, }
@article {pmid41877100, year = {2026}, author = {Ji, X and Geng, Y and Guo, C and Zhang, S and Li, H and Li, C and Du, Y and Guo, X and Miao, B and Hu, Y and Lv, J and Zhou, Z and Gong, J and Sun, Y}, title = {Analysis of pharyngeal microbiome characteristics in HIV-infected individuals: correlation between the degree of immunosuppression and microbial dysbiosis.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13075-2}, pmid = {41877100}, issn = {1471-2334}, support = {2022YFC2504800//National Key Research and Development Program of China/ ; 102393240020020000003//Enhancement of Communicable Disease Surveillance and Control Technical Capabilities/ ; }, }
@article {pmid41877243, year = {2026}, author = {Lin, YN and Peng, WH and Huang, YC and Lai, CY and Hsu, JR and Wang, JY and Kao, YC and Wu, LL}, title = {Nfil3 integrates circadian rhythm and microbial metabolite signaling to maintain gut-liver immune-metabolic homeostasis under high-fat diet stress.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08000-9}, pmid = {41877243}, issn = {1479-5876}, support = {110-2320-B-002-080-MY3//National Science and Technology Council/ ; 111-2314-B-A49-072//National Science and Technology Council/ ; 112-2314-B-A49-028-MY3//National Science and Technology Council/ ; 113-2321-B-A49-014//National Science and Technology Council/ ; 113-2740-B-A49-003//National Science and Technology Council/ ; 114-2321-B-A49-004//National Science and Technology Council/ ; 114-2740-B-A49-003-//National Science and Technology Council/ ; CI-115-33//Yen Tjing Ling Medical Foundation/ ; PTH110001//TYGH-NYCU Joint Research Program/ ; 11210//Ministry of Health and Welfare/ ; 11310//Ministry of Health and Welfare/ ; }, abstract = {BACKGROUND: Disruption of circadian regulation and gut microbial homeostasis is a hallmark of metabolic dysfunction associated with steatotic liver disease (MASLD). Nuclear factor interleukin 3 (Nfil3) integrates circadian and immune signaling; however, how Nfil3 interfaces with microbiota-associated metabolic cues in MASLD remains incompletely understood. We investigated the role of Nfil3 in linking microbial functional states to hepatic metabolic and immune responses under high-fat diet (HFD) stress and assessed the modulatory impact of probiotic VSL#3 intervention.<br><br>METHODS: We integrated exploratory human peripheral blood mononuclear cell (PBMC) transcriptomic profiling with genetic Nfil3 deletion and probiotic VSL#3 supplementation in HFD-fed mice. Experimental assessments included liver histopathology, metabolic phenotyping, immune flow cytometry, gut epithelial barrier analysis, 16S rRNA microbiome profiling with predictive functional inference, and RT-PCR.<br><br>RESULTS: Exploratory PBMC transcriptomic analysis of obese individuals suggested that NFIL3 may function as a candidate transcriptional node associated with circadian-related genes and short-chain fatty acid (SCFA) sensing receptors in inflammatory signaling pathways. In mice, HFD feeding was associated with increased Nfil3 expression, hepatic steatosis, metabolic dysfunction, immune cell expansion, and impaired intestinal epithelial barrier integrity. Probiotic VSL#3 supplementation mitigated several HFD-associated phenotypes, including weight gain, glucose intolerance, dyslipidemia, transaminase elevation, hepatic lipid accumulation, and gut epithelial permeability, while partially normalizing intrahepatic immune cell composition. Nfil3-deficient mice displayed attenuated responses to several HFD-induced metabolic and inflammatory alterations, with partial phenotypic overlap with probiotic-treated wild-type (WT) mice. Microbiome analyses showed that VSL#3 enriched SCFA- and mucin-associated taxa while suppressing endotoxin-associated bacteria (Desulfovibrionaceae, Romboutsia). Predictive functional profiling suggested restoration of microbial pathways related to amino acid, redox, and energy metabolism, alongside reduced representation of lipopolysaccharide and toxin biosynthesis pathways.<br><br>CONCLUSIONS: These findings support a role for Nfil3 as a regulatory node linking microbial functional potential with immune and metabolic responses in MASLD. Although preclinical in nature, this work provides a mechanistic framework that may inform future translational investigations into how microbiota-associated metabolic reprogramming influences host immune-metabolic homeostasis. Further circadian-resolved and metabolite-level studies, together with human interventional validation, will be required to determine the clinical relevance of the microbiota-Nfil3 axis.}, }
@article {pmid41877267, year = {2026}, author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR}, title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00553-w}, pmid = {41877267}, issn = {2524-4671}, support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; }, abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.}, }
@article {pmid41877434, year = {2026}, author = {Xu, F and Tong, L and Ding, F and Wang, K and Li, P and Xu, M and Bai, C and Chen, Z and Li, J and Xie, Y and Wang, H and Zhang, Q and Liu, J and Zhu, Y and Pang, J and Xu, W}, title = {Plasma membrane H[+]-ATPase OsA1 enhances soil organic phosphorus mineralization via Bacillus cereus recruitment in rice.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71115}, pmid = {41877434}, issn = {1469-8137}, support = {42307419//National Natural Science Foundation of China/ ; 32472825//National Natural Science Foundation of China/ ; U25A20695//National Natural Science Foundation of China/ ; 2024J09028//The Natural Science Foundation of Fujian Province/ ; 2023J01468//The Natural Science Foundation of Fujian Province/ ; SKLAWR-2024-03//Open Research Fund of State Key Laboratory of Efficient Utilization of Agricultural Water Resources/ ; JAT220063//Research Fund of the Education Department of Fujian Province/ ; }, abstract = {Organic phosphorus (P), which accounts for c. 50% of total soil P, is not directly available for plant uptake and must be first mineralized. Plasma membrane (PM) H[+]-ATPase facilitates the mobilization of insoluble inorganic P by energizing the release of organic anions from roots. However, its role in modulating the rhizosphere microbiome to facilitate soil organic P mineralization remains unclear. To address the gap, we investigated the role of PM H[+]-ATPase in recruiting microbiota for soil organic P mineralization through high-throughput sequencing and metabolite analysis. Under low P (LP) conditions in nonsterilized soil, wild-type (WT) rice seedlings exhibited 59%, 73%, and 66% greater shoot P concentration than three PM H[+]-ATPase gene OsA1 mutants, that is, osa1-1, osa1-2, and osa1-3, respectively. Such growth advantage reduced to 33%, 47%, and 39% in sterilized soil, suggesting a microbial contribution. Under LP conditions, organic P mineralization efficiency in the WT rhizosphere was four times greater than under normal P (NP) conditions, whereas no significant difference was observed in the osa1-1 mutant. The abundance of Bacillus was significantly higher in the WT rhizosphere than in osa1-1 under LP. Compared with the osa1-1 rice, WT exhibits significantly higher malate concentration, which could stimulate the growth of Bacillus cereus. Inoculation with B. cereus significantly increased P uptake in both WT and OsA1 mutants compared with the uninoculated control under LP. Together, these findings suggest that OsA1 promoted soil organic P mineralization by recruiting Bacillus through malate exudation. This highlights a cooperative interaction between PM H[+]-ATPase and the rhizosphere microbiome, with important implications for enhancing soil organic P mineralization and P-use efficiency in rice production.}, }
@article {pmid41877507, year = {2026}, author = {Lee, JG and Lim, J and Cho, NJ and Park, S and Gil, HW and Seo, H and Song, HY and Park, SH and Oh, KH and Kim, YL and Bieber, BA and Pisoni, RL and Lee, EY and , }, title = {Xerosis elevates the risk of catheter-related infections in peritoneal dialysis patients.}, journal = {Kidney research and clinical practice}, volume = {}, number = {}, pages = {}, doi = {10.23876/j.krcp.24.275}, pmid = {41877507}, issn = {2211-9132}, abstract = {BACKGROUND: Catheter-related infections, such as exit-site infection and tunnel infection, are major complications in peritoneal dialysis (PD) patients, affecting their prognosis. This study investigates the association between skin conditions and catheter-related infections.<br><br>METHODS: Data from two distinct sources were analyzed: (1) 626 PD patients in the Korean arm of the Peritoneal Dialysis Outcomes and Practice Patterns Study (PDOPPS) and (2) skin microbiome data from 76 dialysis patients at Soonchunhyang University Cheonan Hospital. The relationship between catheter-related infection and self-reported xerosis and pruritus severity was assessed by Cox regression. Risk factors for xerosis and pruritus were evaluated by logistic regression. Furthermore, we discovered the relationship between the severity of pruritus and the relative abundance of Staphylococcus aureus on the skin.<br><br>RESULTS: The risk of catheter-related infections in PD patients increased with xerosis (hazard ratio [HR], 2.71; 95% confidence interval [CI], 1.19-6.18) and pruritus (HR, 2.57; 95% CI, 1.27-5.22), particularly increasing the risk of S. aureus-associated catheter-related infections (xerosis: HR, 5.66; 95% CI, 1.97-16.30; pruritus: HR, 5.93; 95% CI, 2.18-16.15). The relative abundance of S. aureus was notably higher in patients with severe pruritus. Moreover, patients were more likely to exhibit severe xerosis if they owned pets, had higher serum creatinine levels, and elevated calcium-phosphorus product levels.<br><br>CONCLUSION: Xerosis and pruritus significantly increase the risk of catheter-related infections, especially those caused by S. aureus. Instead of relying solely on prophylactic antibiotics for infection prevention, this study highlights the need for new preventive strategies in PD patients, focusing specifically on effective skin management.}, }
@article {pmid41877508, year = {2026}, author = {Liu, X and Li, Z and Liu, H and Xiao, M and Zhang, X and Deng, Y and Tian, B and Sun, Y and Xiao, X}, title = {Diet-microbiota-kidney axis reprogramming: mechanistic insights into microbial metabolite-driven precision nutrition for chronic kidney disease.}, journal = {Kidney research and clinical practice}, volume = {}, number = {}, pages = {}, doi = {10.23876/j.krcp.25.312}, pmid = {41877508}, issn = {2211-9132}, abstract = {Medical nutrition therapy serves as the cornerstone in the management of chronic kidney disease (CKD). While conventional approaches emphasize macronutrient restriction and meal timing adjustments, research highlights the critical mediating role of gut microbiota in translating dietary patterns into physiological effects through metabolite production. Meanwhile, CKD progression is closely associated with dynamic interactions between gut microbiota and their metabolic derivatives. This review introduces the "diet-microbiota- metabolite-kidney axis" framework to elucidate how nutritional components modulate CKD progression via microbial compositional changes and subsequent metabolite alterations. Based on synthesized evidence, this review identifies promising directions for precision nutrition strategies targeting microbial metabolites, including artificial intelligence-assisted dietary planning, engineered bacterial therapies, and metabolite analog development. However, significant interindividual variability in host genetics and baseline microbiota composition necessitates overcoming heterogeneity challenges in nutritional interventions. Consequently, the precise modulation of individualized diet-microbiota-metabolite interactions represents a critical research direction to be prioritized in CKD management.}, }
@article {pmid41877524, year = {2026}, author = {Wight, M and Brooks, CN and Scott Chialvo, CH and West, CA and de Souza, AMA and Bleich, RM}, title = {The impact of weight cycling on gut microbiome richness and diversity in female rats.}, journal = {Physiological reports}, volume = {14}, number = {6}, pages = {e70828}, doi = {10.14814/phy2.70828}, pmid = {41877524}, issn = {2051-817X}, support = {N/A//Appalachian State University (ASU)/ ; 19CDA34660328//American Heart Association (AHA)/ ; 940246//American Heart Association (AHA)/ ; W81XWH2110201//U.S. Department of Defense (DOD)/ ; KL2TR001432//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; P30-CA051008-29S2//HHS | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Rats, Inbred F344 ; Rats ; Feces/microbiology ; *Body Weight ; *Caloric Restriction ; Biodiversity ; }, abstract = {Female Fischer 344 rats were divided into control (access to food ad libitum) and weight cycling (60% diet restriction followed by ad libitum refeeding) groups. The weight cycles consisted of two weeks dietary restriction and three weeks refeeding for three cycles. Fecal microbiome samples were collected following the initial dietary restriction, the initial refeeding, and the final refeeding periods (and corresponding times in control rats). We observed significant differences in alpha diversity between fecal microbiomes following the initial dietary restriction and the final refeeding period. We additionally observed a significant recovery of alpha diversity following the first refeeding period that we did not observe following the third refeeding in the weight cycling group. Differences in relative abundances of taxa included a higher relative abundance of Bacillota (synonym Firmicutes) in the weight cycling group. Species richness of the weight cycling fecal microbiomes significantly decreased across the study period. Inguinal fat tissue was significantly lower in the weight cycling than ad libitum group, yet heart weight and postprandial HOMA-IR were significantly higher. Together, these results suggest that repeated weight cycling from repeated periods of dietary restriction has adverse effects on host condition and microbial diversity, potentially leading to long-term negative health outcomes.}, }
@article {pmid41877779, year = {2026}, author = {Sun, S and Long, F and Su, B and Chen, J and Luo, Y and Zhong, Y and Zhang, G}, title = {The gut microbiome in colorectal anastomotic leakage: from mechanisms to precision.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1781458}, pmid = {41877779}, issn = {2296-858X}, abstract = {Anastomotic leakage after curative colorectal cancer resection remains a frequent and severe complication that increases short-term mortality, worsens long-term oncologic outcomes, and places substantial burdens on individuals and health systems despite advances in surgical technique and perioperative care. Emerging evidence redefines anastomotic failure as not only a technical event but also a biologically driven process in which the gut microbiome regulates inflammation, epithelial repair, and barrier integrity at the healing interface. This review summarizes current data on the dual role of the intestinal microbiome in promoting physiological anastomotic healing and driving pathological leakage when perioperative stressors cause dysbiosis. Mechanistic sections describe how a diverse, metabolically active community supports collagen stability through short-chain fatty acid production, immune regulation, and maintenance of mucus and tight junction architecture. In contrast, the enrichment of microbial groups such as Enterococcus faecalis, Fusobacterium nucleatum, and Alistipes onderdonkii together with fungal and viral shifts, has been associated with extracellular matrix degradation and excessive inflammation. Furthermore, the review examines microbiome-related biomarkers for risk assessment, including DNA-based microbial signatures, metabolite profiles, and host immune markers. It also discusses how integrated multi-omics models combined with machine learning may outperform traditional clinical scores for preoperative and early postoperative prediction. Finally, the article critically evaluates perioperative microbiome-directed strategies ranging from dietary prehabilitation and microbial supplementation to selective decontamination and fecal microbiota transplantation, highlighting promising signals, variability of effect, safety considerations, and key methodological limitations that currently prevent routine implementation. In summary, this review addresses three interconnected domains-mechanisms of microbiome-driven anastomotic failure, microbiome-derived biomarkers for risk stratification, and perioperative intervention strategies-underscoring that AL is best understood as a host-microbiome interaction rather than a purely technical failure. This framing offers surgeons and perioperative teams a biologically rational basis for prevention, yet clinical translation will require causal validation, standardized intervention algorithms, and interpretable computational tools embedded into real-world perioperative practice.}, }
@article {pmid41877865, year = {2026}, author = {Wu, G and Wang, M and Si, Y and Wang, X and Li, H and Wang, L and Wang, R and Zhang, L}, title = {Exploring the causal link between microbiota and tic disorders: a gene sequencing and Mendelian randomization approach.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20812}, pmid = {41877865}, issn = {2167-8359}, mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Tic Disorders/microbiology/genetics ; Genome-Wide Association Study ; Child ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Tic disorders (TD), including Tourette syndrome (TS), are common childhood-onset neurodevelopmental conditions with unclear etiology. Emerging observational data suggest that gut-microbiota (GM) dysbiosis accompanies TD, but causality is unresolved. We aimed to determine whether specific bacterial genera are causally implicated in TD susceptibility.<br><br>METHODS: Two-sample Mendelian randomization (MR) was performed by integrating the largest available GM genome-wide association study (GWAS) (18,340 Europeans, 211 taxa) with the PGC-TS-2019 GWAS (4,819 cases/9,488 controls). Inverse-variance-weighted estimates were complemented with sensitivity analyses and reverse-MR. Findings were validated in an independent pediatric case-control cohort (10 TD vs seven healthy children) profiled by 16S rRNA V3-V4 sequencing; between-group differences were tested with the Mann-Whitney U test.<br><br>RESULTS: Genetically predicted abundance of Anaerotruncus, Butyrivibrio and Ruminococcaceae UCG-002 conferred protection against TS (OR 0.69-0.86, p = 0.014-0.016), whereas Dialister and Ruminiclostridium 6 increased risk (OR 1.28-1.32, p = 0.030-0.041); Sutterella showed no causal effect (p&#xa0;=&#xa0;0.103). No heterogeneity, directional pleiotropy or reverse causation was detected. Sequencing analyses mirrored MR directions: TD cases exhibited significantly lower relative abundance of the protective genera and higher levels of risk taxa compared with controls (p&#xa0;<&#xa0;0.05).<br><br>CONCLUSIONS: By integrating unbiased genetic instrumentation with targeted microbiome profiling, this study offers exploratory evidence suggesting that specific gut bacteria may be associated with TD pathogenesis. Ruminococcaceae UCG-002, Anaerotruncus, and Butyrivibrio emerge as potentially protective taxa, while Dialister and Ruminiclostridium 6 may represent candidate risk markers. These preliminary, mechanistically grounded insights should be considered exploratory and may inform future, larger-scale microbiome-directed precision interventions in TD.}, }
@article {pmid41877915, year = {2026}, author = {Nicolas, CS and Lloret, F and Carton, T and Beuvin, L and Rème, CA}, title = {Beneficial effects of a prebiotic-postbiotic supplement on digestive health and fecal microbiota in dogs and cats.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1797178}, pmid = {41877915}, issn = {2297-1769}, abstract = {Gastrointestinal (GI) disorders are a frequent concern for pet owners and veterinarians. Dietary management of mild GI disorders is often essential in order to correct imbalances in the gut flora. In this context, "biotics," including probiotics, prebiotics, and postbiotics, have received increasing attention for their potential to favorably modulate the gut microbiota and support digestive function. In this study, we investigated the effect of a nutritional supplement containing a specific blend of prebiotics (baobab fruit pulp and acacia gum) and postbiotics (inactivated L. helveticus and selected yeast fractions) on digestive signs exhibited by healthy dogs and cats with mild GI imbalances, such as soft stools, increased quantity of stools or flatulence. The supplement was tested over a 28-day period. Digestive signs were evaluated on 57 dogs and 57 cats and the microbiota analysis was conducted on samples from 35 dogs and 27 cats. Questionnaires completed by the pet owners at regular intervals were used to evaluate digestive signs, while changes in the intestinal microbiota were assessed by fecal sample analysis performed before and after supplementation. The supplement was accepted either alone or mixed with food by 94% of dogs and 91% of cats. In both cats and dogs, the supplementation significantly improved digestive health as of day 7 (p < 0.001). Animals starting the study with impaired stool consistency or high quantity of stools showed significant improvement by day 7. The stool odor also improved from the first week. The proportion of dogs and cats with flatulence was reduced by 45 and 63%, respectively, by day 28 (p < 0.001), and the proportion of pets vomiting was reduced by 51 and 54%, respectively (p < 0.001). The impact on gut microbiota involved mainly changes on multiple subdominant taxa (such as Megamonas and Peptacetobacter in dogs, Anaerotignum and Succinivibrio in cats), without altering the overall microbial community architecture (as shown by diversity indices). Altogether, these results show that the supplement tested (Floragest™ soft chews, Virbac) can help support the digestive health of dogs and cats with mild gastrointestinal disorders.}, }
@article {pmid41878129, year = {2026}, author = {Wang, P and Ye, Y and Mei, K and Chen, B and Kankala, RK and Tong, F}, title = {Nanoscale Approaches to Oro-Dental Tissue Engineering: A Review of Strategies, Composites, and Translational Challenges.}, journal = {International journal of nanomedicine}, volume = {21}, number = {}, pages = {575296}, pmid = {41878129}, issn = {1178-2013}, mesh = {Humans ; *Tissue Engineering/methods ; Dental Pulp/cytology ; Stem Cells/cytology/drug effects ; Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; Animals ; Drug Delivery Systems ; Nanostructures/chemistry ; Mouth ; Nanotechnology/methods ; Dental Implants ; }, abstract = {Oral health is vital to human well-being. As a result, various conditions in the oral cavity, including exposure to dentin and edentulous states, lead to diverse oral issues and tissue loss. Although conventional treatments are available, they often have limitations in drug delivery and tissue regeneration. For example, delivered drugs may fail to disrupt bacterial biofilms, thereby increasing resistance within the oral microbiome and weakening immune responses. Additionally, the limited regenerative capacity of dental pulp cells can lead to serious dental emergencies. To address these challenges, innovative nanoarchitectures have been developed to improve their antimicrobial effects and enhance the regenerative potential of oral tissues for oro-dental tissue engineering. This review discusses different nanotechnological strategies for delivery and subsequent tissue engineering in the oral cavity. We first explore concepts to boost regenerative capacity, emphasizing the roles of various nanomaterials that act as antibacterial agents, activate the differentiation of human dental pulp stem cells, and support their integration with soft oral tissues. Beyond nano-therapeutic strategies involving dental implants, we also discuss nanotoxicity issues and remaining challenges in oral health. Finally, we offer perspectives on translating these developments into clinical practice.}, }
@article {pmid41878283, year = {2026}, author = {Urquhart, DS and Linnane, B and Saunders, CJ and Abkir, M and Georgiopoulos, AM and Dobra, R and Carroll, S and Still, M and Cox, DW and Fitzpatrick, E and Beegan, A and Thursfield, R and Balfe, J and Tarr, A and Lester, K and Cunningham, A and Perrem, L and Davies, JC and McNally, P and , }, title = {ENHANCE: a community partnership charting the evolution of early-life cystic fibrosis disease manifestations in a new era of management.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41878283}, issn = {2312-0541}, abstract = {ENHANCE is a multicentre, longitudinal study examining the natural history of early cystic fibrosis (CF) disease manifestations in children. We hypothesise that the prevalence, presentation and natural history of disease manifestations of CF in young children will change significantly in the next decade with advances in the understanding and treatment of CF, including the use of therapies aimed at improving CFTR function. The study has been co-developed with the CF community, in order to try to answer questions of key importance to people with CF and their caregivers. The study will longitudinally monitor lung health using nitrogen multiple breath washout testing and spirometry, lung structure using spirometry-controlled computed tomography scanning, gastrointestinal health using gut microbiome, gut inflammation and abdominal symptom scores, pancreatic function using faecal elastase, liver function using liver blood tests and liver ultrasound, and sweat chloride. Mental health will be longitudinally assessed using questionnaires for mood (PROMIS, GAD-7), quality of life (CFQ-R) and psychosocial functioning (Pediatric Symptom Checklist). There are three cohorts in the study: infants with CF diagnosed by newborn screening (n=250), children aged 0-6 years and currently attending CF centres (n=200) and healthy newborn infant controls (100). The study will be conducted over 5 years in the first phase with a plan to extend through further phases in the future. We envisage that the study will provide important evidence to enable healthcare staff and families to guide the care of children with CF in the future.}, }
@article {pmid41878551, year = {2026}, author = {Blicharz, L and Bukowska-Ośko, I and Perlejewski, K and Navarro-López, V and Czuwara, J and Waśkiel-Burnat, A and Samochocki, Z and Olszewska, M and Rudnicka, L and Radkowski, M}, title = {Gut Microbiota Influence Host Metabolism and Immune Responses in Atopic Dermatitis: A Next-Generation Sequencing-Based Functional Profiling Study.}, journal = {Clinical, cosmetic and investigational dermatology}, volume = {19}, number = {}, pages = {571034}, pmid = {41878551}, issn = {1178-7015}, abstract = {PURPOSE: Gut dysbiosis has been linked to immune imbalance in allergic diseases, but the underlying mechanisms remain unclear. We aimed to verify whether gut microbiota composition is associated with cellular, metabolic, and immune pathways in atopic dermatitis.<br><br>PATIENTS AND METHODS: Fifty adults with atopic dermatitis and 25 sex- and age-matched healthy controls were enrolled. Gut microbiome composition was assessed using V3-V4 16S rRNA sequencing. Functional pathways were inferred from microbiome data using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States).<br><br>RESULTS: Despite only subtle differences in microbiota composition between patients with atopic dermatitis and controls, PICRUSt analysis identified significant differences in 149 functional pathways. Key pathways enriched in atopic dermatitis involved signal transduction mediated by protein kinases, as well as carbohydrate and lipid metabolism. Downregulated pathways included those related to energy metabolism, amino acid and nucleotide metabolism, antigen processing, and innate immune responses. In patients with atopic dermatitis, microbial diversity increased with EASI scores and IgE levels, correlating with additional predicted functional shifts.<br><br>CONCLUSION: Our results suggest that even subtle structural differences in gut microbiota may exert significant functional effects in atopic dermatitis. Altered pathways could contribute to immune imbalance and impaired epidermal barrier function. These findings underscore the importance of incorporating functional analyses into future gut microbiota studies of atopic dermatitis to help identify therapeutic targets, including candidate probiotic strains for supplementation.}, }
@article {pmid41878631, year = {2026}, author = {MacDonald, KV and Pai, N and Burow, C and deBruyn, JC and Huynh, HQ and Otley, A and Rozario, S and Marshall, DA}, title = {Balancing safety and effectiveness: parent preferences for fecal microbiota transplant and established therapies in pediatric inflammatory bowel disease-results of a multicenter Canadian study.}, journal = {Crohn's &amp; colitis 360}, volume = {8}, number = {1}, pages = {otag016}, pmid = {41878631}, issn = {2631-827X}, abstract = {BACKGROUND AND AIMS: Treatment decision-making in pediatric inflammatory bowel disease (IBD) is complex, with many existing and emerging options. However, little is known about parent preferences for these therapies. This multi-center Canadian study provides the first quantitative data on parent preferences for pediatric IBD treatments and explores characteristics associated with differing preferences.<br><br>METHODS: We conducted a cross-sectional survey including a discrete choice experiment (DCE) with Canadian parents (n&#x2009;=&#x2009;159) of children diagnosed with UC/IBD-U, recruited from four pediatric IBD clinics. The DCE assessed preferences across four treatment attributes: chance of clinical remission, severity and chance of known side effects, severity of rare unknown side effects, and mode of treatment delivery. Latent class modeling was used to explore preference heterogeneity.<br><br>RESULTS: Parents prioritized safety, particularly the risk of rare unknown side effects, followed by likelihood of remission. Latent class analysis identified two distinct groups: one most concerned about rare unknown side effects, and another prioritizing treatment effectiveness. Thirty-eight percent of parents were open to fecal microbiota transplant (FMT), an emerging therapy that uses donor stool to help restore gut microbiome health. Younger parents and those with children experiencing more severe disease and on multiple medications were more likely to accept FMT. Across the cohort, many parents were willing to trade off less desirable delivery modes or increased risk in exchange for better treatment outcomes.<br><br>CONCLUSIONS: Parents value both safety and effectiveness in IBD treatment decisions. Recognizing these preferences may support shared decision-making, particularly when discussing novel therapies like FMT.}, }
@article {pmid41878738, year = {2026}, author = {Xiao, M and Chen, C and Yao, R and Wang, X and Liu, G}, title = {Synergistic nano-bioorganic amendments enhance soil properties and microbial structure in coastal saline soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1720097}, pmid = {41878738}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization threatens global food security and sustainable land use. Ameliorating coastal saline soils with exogenous amendments is crucial. Bio-organic fertilizer (OF) and nano-carbon (NC) are promising green amendments, but their comparative and combined effects on soil properties and microbial communities are not fully understood.<br><br>METHODS: A field experiment was conducted in coastal saline soil (Ninghe District, Tianjin, China). Four treatments were established: control (CK, no amendment), OF application, NC application, and combined application of OF and NC (FC). Soil physicochemical properties and microbial community structure (via 16S and ITS rRNA gene sequencing) were analyzed.<br><br>RESULTS: The FC treatment most effectively improved soil properties, significantly reducing bulk density, pH, salinity, and sodium adsorption ratio (SAR), while increasing porosity, water content, and nutrient (N, P) availability. Soil bacterial diversity (Ace, Chao1, Shannon indices) increased significantly in all amendment treatments compared to CK, with the highest values in NC and FC treatments. Amendment application altered microbial community composition, enriching specific bacterial taxa (e.g., Firmicutes, Desulfobacterota in FC) and fungal taxa. Redundancy analysis identified soil salinity and pH as key drivers of bacterial community structure, whereas fungal communities showed a distinct, less correlated response pattern.<br><br>DISCUSSION: The synergistic application of nano-carbon and bio-organic fertilizer (FC) created a more favorable soil habitat, rapidly ameliorating physicochemical conditions which directionally shaped the bacterial community. Bacterial and fungal communities responded differently to amendments, suggesting divergent assembly mechanisms. The FC strategy demonstrates high potential for the initial restoration of saline-alkali soils by enhancing soil health primarily through rapid physicochemical improvement and modulation of the soil microbiome, particularly bacteria. Future work should focus on functional validation of predicted metabolic shifts and assessment of agronomic outcomes.}, }
@article {pmid41878750, year = {2026}, author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J}, title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.}, journal = {Journal of asthma and allergy}, volume = {19}, number = {}, pages = {464532}, pmid = {41878750}, issn = {1178-6965}, abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.<br><br>METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24&#xa0;healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.<br><br>RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.<br><br>CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.}, }
@article {pmid41878919, year = {2026}, author = {Jiang, C and Peng, B}, title = {Gut microbiota-supportive dietary patterns and rheumatoid arthritis: the mediating role of the systemic immune-inflammation index.}, journal = {Nutricion hospitalaria}, volume = {}, number = {}, pages = {}, doi = {10.20960/nh.06113}, pmid = {41878919}, issn = {1699-5198}, abstract = {BACKGROUND: the gut microbiota has emerged as a potential contributor to autoimmune diseases, including rheumatoid arthritis (RA), through its role in modulating systemic inflammation. However, few studies have evaluated whether adherence to microbiota-supportive dietary patterns is associated with RA in population-based settings.<br><br>METHODS: this study analyzed data from 21.352 adults in the 2010-2020 cycles of the National Health and Nutrition Examination Survey (NHANES). The Dietary Index for Gut Microbiota (DI-GM), ranging from 0 to 14, was used to quantify the extent to which habitual diets support gut microbial health. Logistic regression and restricted cubic spline models were used to examine the association between DI-GM and RA. Mediation analysis was conducted to evaluate whether the systemic immune-inflammation index (SII) mediated this association.<br><br>RESULTS: higher DI-GM scores were significantly associated with lower odds of RA. Each 1-point increase in DI-GM was linked to a 5 % reduction in RA odds [OR = 0.95 (0.92-0.99)]. Compared with individuals in the lowest DI-GM category (0-3), those with scores &#x2265; 6 had significantly reduced odds of RA [OR = 0.81 (0.66-0.99)]. Mediation analysis showed that SII partially mediated the DI-GM-RA association, accounting for approximately 21.3 % of the total effect.<br><br>CONCLUSION: higher adherence to a gut microbiota-supportive dietary pattern was associated with lower odds of RA, partly through reduced systemic inflammation. These findings support the potential value of microbiome-informed dietary strategies in RA prevention.}, }
@article {pmid41879259, year = {2026}, author = {Wang, H and Cao, Y and Zhang, X and Wu, H and Zhou, T and Yang, Y and Ji, K and Wu, J and Xiong, B}, title = {Alterations in the Gut Microbiota of Cirrhosis Patients with Sarcopenia and PH after TIPS.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000001021}, pmid = {41879259}, issn = {2155-384X}, abstract = {BACKGROUND AIMS: TIPS can effectively reduce PH and may associated with improvement in muscle status; however, its impact on the gut microbiota and muscle condition remains unclear. Therefore, this prospective study aimed to evaluate gut microbiota alterations in patients with sarcopenia and PH following TIPS treatment.<br><br>METHODS: Gut microbiota analysis was prospectively conducted in 20 cirrhosis patients with sarcopenia and PH receiving TIPS and their first-degree healthy family between December 2019 and July 2021 in our center. Fecal samples were collected before and 3 months after TIPS and analyzed by 16S rRNA sequencing. Microbial diversity and composition were assessed using standard bioinformatic pipelines. Sarcopenia was defined by L3 skeletal muscle index according to EASL criteria.<br><br>RESULTS: Compared with healthy controls, cirrhosis patients with sarcopenia and PH exhibited significantly reduced &#x3b1;-diversity (Chao1, Shannon, Simpson; all p < 0.001) and distinct &#x3b2;-diversity clustering, confirming gut dysbiosis. Although TIPS did not significantly alter overall &#x3b1;-diversity, a significant increase in the order Burkholderiales and a reduction in Pseudomonadales and Staphylococcales were detected after TIPS. Analysis of the family taxonomic rank revealed that TIPS was followed by an increase in a greater abundance of Ruminococcaceae and Sutterellaceae and decreased levels of Tannerellaceae, Marinifilaceae and Pseudomonadaceae. At the genus level, after TIPS placement, increased levels of Lachnospiraceae_ND3007_group, Intestinibacter, Fusicatenibacter, and Faecalibacterium and lower abundances of Pseudomonas, Prevotella, Peptostreptococcus, Parabacteroides, Muribaculaceae, and Butyricimonas were detected.Sarcopenia reversal was observed in 25% of patients, characterized by enrichment of SCFA-producing genera such as Faecalibacterium and Streptococcus, whereas patients without improvement showed high abundance of Fusicatenibacter and low levels of beneficial taxa.<br><br>CONCLUSION: TIPS induces significant taxonomic shifts without changing overall diversity in cirrhosis patients with sarcopenia and PH, suggesting partial microbial restoration. Enrichment of SCFA-producing bacteria may correlates with improved sarcopenia, whereas pro-inflammatory taxa may indicate poor recovery and higher risk of complications. These findings highlight the gut-muscle-liver axis and support microbiome-based biomarkers and interventions to optimize outcomes after TIPS.}, }
@article {pmid41879296, year = {2026}, author = {Penney, R and Buchanan, LB and Rojas-Vargas, J and Lin, J and Khan, Y and Davidson, J and Wilson, CA and Tai, V and Russo, TA and Hope, TJ and Wilcox, H and Monari, B and Ravel, J and Al, KF and Dave, S and Wang, PZT and Burton, JP and Prodger, JL}, title = {Pathological phimosis is associated with foreskin immune cell infiltration but not microbiota composition.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0072525}, doi = {10.1128/msphere.00725-25}, pmid = {41879296}, issn = {2379-5042}, abstract = {UNLABELLED: The penile microbiota has been implicated in genital inflammation and increased risk of HIV, HPV, HSV-2, and female-partner bacterial vaginosis in adult males, yet its development during childhood and potential role in pediatric foreskin pathologies remain unknown. We characterized the coronal sulcus microbiota of 75 pediatric males (median age 8.5 years; 43% with pathological phimosis) before and after circumcision and compared these profiles to 56 uncircumcised adult men. Pediatric penile microbiota were highly diverse, dominated by strict and facultative anaerobes, and loosely structured compared to adults, who exhibited two distinct, ecologically organized communities. Circumcision markedly reduced anaerobic taxa and increased Corynebacterium and Staphylococcus. Pathological phimosis (the inability to retract the foreskin due to scarring) was associated with increased densities of CD3+ T cells, CD4+ cells, and CD11c+ dendritic cells, suggesting an adaptive immune mechanism; however, pathological phimosis was not associated with microbiota composition. Nonetheless, Mobiluncus was negatively correlated with CD11c+ dendritic cells, while Campylobacter and Peptoniphilus were negatively correlated with CD56+ NK cells, suggesting microbe-immune interactions. Our data suggest pathologic phimosis is driven by adaptive immune responses but not by specific bacteria; the pathology may be driven by differences in host responses to bacteria or by other stimuli, such as fungal antigens. Our data also demonstrate that the transition to adulthood is accompanied by reorganization of penile communities into structured types previously linked to infection risk, highlighting puberty as a potential window for interventions that promote protective adult microbiota and improve lifelong sexual and reproductive health.<br><br>IMPORTANCE: The human penis hosts complex bacterial communities that can influence inflammation, infection risk, and sexual health, but little is known about how these communities form early in life or whether they contribute to childhood foreskin inflammatory disorders. We combined 16S rRNA sequencing with quantitative microscopy to investigate the penile microbiota in boys and its relationship to pathological phimosis, a common condition marked by foreskin scarring. We found that phimosis is associated with infiltration of T cells and dendritic cells, indicating an adaptive immune process, but with no associations with specific bacteria. We also show that penile microbiota reorganize during puberty into structured community types previously linked to HIV and sexually transmitted infection risk. These findings suggest that childhood pathologic phimosis is mediated by adaptive immune responses rather than driven by specific bacterial communities and identify puberty as a critical period for shaping adult penile microbiota, with implications for lifelong genital health.}, }
@article {pmid41879306, year = {2026}, author = {Xia, JY and Sawhney, M and Hussain, HK and Machicado, JD}, title = {Endoscopic management of biliary stricture in primary sclerosing cholangitis.}, journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society}, volume = {}, number = {}, pages = {}, doi = {10.1097/LVT.0000000000000866}, pmid = {41879306}, issn = {1527-6473}, abstract = {Primary sclerosing cholangitis (PSC) is a progressive fibroinflammatory disease characterized by multifocal biliary strictures, recurrent cholangitis, and a markedly increased lifetime risk of cholangiocarcinoma (CCA). Endoscopic retrograde cholangiopancreatography (ERCP) remains central to the diagnosis of CCA and management of PSC-related complications. This review synthesizes current evidence guiding the use of ERCP in patients with PSC, highlighting the importance of careful patient selection to mitigate adverse events. We review traditional ERCP techniques for the evaluation of dominant strictures such as brush cytology, fluorescence in situ hybridization (FISH), and biopsies, which exhibit limited sensitivity for detecting CCA in PSC. We also review the role of advanced endoscopic approaches including cholangioscopy, endoscopic ultrasound, and confocal endomicroscopy, alongside novel molecular diagnostics (next generation sequencing, DNA methylation markers), metabolomics, bile microbiome, and radiomics, which shown promise for risk stratification and CCA detection in PSC. Therapeutically, we review evidence supporting the use of balloon dilation as first line therapy for the management of PSC strictures and discuss settings where plastic stents might be beneficial. Furthermore, we review the endoscopic management of other PSC complications such as cholangitis, stones, acute cholecystitis, and post-transplant strictures. Finally, we provide best practice recommendations to minimize risk of complications, including use of peri-procedural antibiotic prophylaxis, technique modifications, and individualized sphincterotomy decisions. As innovative diagnostic and therapeutic strategies for PSC continue to evolve, rigorous multicenter, prospective studies are needed to assess efficacy, safety, and cost-effectiveness of these strategies prior to widespread adoption.}, }
@article {pmid41879310, year = {2026}, author = {Qin, M and Wen, Y and Li, S and Li, S and Li, X and Lin, Y and Hu, L and Xia, H and Pang, Y and Li, L}, title = {The respiratory microbiome in pulmonary tuberculosis: a meta-analysis reveals niche-specific microbial and functional signatures.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0156325}, doi = {10.1128/msystems.01563-25}, pmid = {41879310}, issn = {2379-5077}, abstract = {UNLABELLED: Tuberculosis (TB) remains a major global health challenge. The close relationship between the microbiome and the host is becoming increasingly notable. While studies on the respiratory microbiome in pulmonary tuberculosis (PTB) exist, a comprehensive understanding of microbial characteristics across the entire respiratory tract is still lacking. To address this, we conducted a meta-analysis by integrating data from common and representative respiratory samples. We integrated 16S rRNA data from 11 public datasets encompassing upper respiratory tract specimens (URTs), sputum, and bronchoalveolar lavage fluid (BALF). Ecological patterns were investigated through co-occurrence networks and neutral community modeling, while taxonomic and functional analyses were conducted with QIIME2 and PICRUSt2. The respiratory microbiota in PTB exhibited dynamic variations while sharing common genera, such as Streptococcus, Prevotella, Veillonella, and Neisseria. Alpha diversity was consistently higher in PTB than in healthy controls, with BALF exhibiting the greatest microbial diversity. Several differentially abundant genera were identified among the three sample types, Serratia being almost exclusively detected in BALF. Notably, the microbial interaction network in sputum was more complex and demonstrated the best fit to the neutral community model. Functional predictions highlighted enriched pathways such as peptidoglycan maturation and ABC transporters, and Bacillus was linked to multiple metabolic pathways. Several KO functions were predicted to be more active in URTs and sputum than in BALF. Our multi-scale analysis delineates a niche-specific biogeography of the respiratory microbiome in PTB. By elucidating community assembly and microbe interplay, we position the respiratory microbiota as an active contributor to TB. This work paves the way for novel microbiota-based diagnostics and ecologically informed therapies.<br><br>IMPORTANCE: Pulmonary tuberculosis (PTB) remains a leading cause of global mortality, yet the ecological principles shaping its respiratory microbiome are poorly understood. By integrating 16S rRNA datasets from upper and lower airway specimens, this study provides the first comprehensive meta-analysis of respiratory microbial diversity and function in PTB. We reveal distinct community structures and functional potentials among upper airways, sputum, and bronchoalveolar lavage fluid, driven by niche-specific ecological processes rather than stochastic assembly. These findings establish a baseline framework for interpreting microbial biogeography across the respiratory tract and highlight potential microbial biomarkers for site-specific monitoring and therapeutic targeting in PTB.}, }
@article {pmid41879323, year = {2026}, author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM}, title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0315525}, doi = {10.1128/spectrum.03155-25}, pmid = {41879323}, issn = {2165-0497}, abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.}, }
@article {pmid41879429, year = {2026}, author = {Valenzuela, CF and Lopez, KM and Iturralde-Carrillo, A and Mancero-Montalvo, R}, title = {Gut feelings about alcohol risk.}, journal = {The American journal of drug and alcohol abuse}, volume = {}, number = {}, pages = {1-4}, doi = {10.1080/00952990.2026.2639481}, pmid = {41879429}, issn = {1097-9891}, }
@article {pmid41879544, year = {2026}, author = {Mochalov, I and Kryvtsova, M and Tsuperiak, S and Mykhailychenko, B and Guzo, N and Kizim, A}, title = {Species composition and antibiotic susceptibility of microorganisms present in the maxillary sinus and other biotopes during the sinus lift procedure.}, journal = {Folia medica}, volume = {68}, number = {1}, pages = {}, doi = {10.3897/folmed.68.e161534}, pmid = {41879544}, issn = {1314-2143}, mesh = {Humans ; *Maxillary Sinus/microbiology/surgery ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Sinus Floor Augmentation/methods ; Microbial Sensitivity Tests ; Male ; Female ; }, abstract = {Lateral sinus lift is a common procedure in the field of dentistry, employed for the purpose of preparing the maxilla for subsequent dental implantation. This procedure is associated with a significant risk of intra- and postoperative complications, largely attributable to the presence of pathogenic microorganisms within the oral cavity and maxillary sinus.}, }
@article {pmid41699596, year = {2026}, author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X}, title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41699596}, issn = {1479-5876}, support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; }, abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored.<br><br>METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N&#x2009;=&#x2009;8) and high-fat diet group (HFD group, N&#x2009;=&#x2009;18). Successfully modeled mice were further assigned to model group (group B, N&#x2009;=&#x2009;8) and exercise group (group C, N&#x2009;=&#x2009;8). Group C underwent a 6-week treadmill exercise program (12&#xa0;m/min, 60&#xa0;min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics.<br><br>RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P&#x2009;<&#x2009;0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-&#x3b1;, NLRP3, IL-1&#x3b2;, and IL-18 significantly increased (P&#x2009;<&#x2009;0.05 or P&#x2009;<&#x2009;0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-&#x3b1; and other indicators in obese mice (P&#x2009;<&#x2009;0.05 or P&#x2009;<&#x2009;0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise.<br><br>CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.}, }
@article {pmid41807420, year = {2026}, author = {de Oliveira Ignacio, MA and Marconi, C and Bidinotto, LT and Balsanelli, E and Belleti, R and da Silva, MG and Duarte, MTC}, title = {Characteristics associated with Lactobacillus-depleted vaginal microbiota in women with different sexual behavior.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41807420}, issn = {2045-2322}, support = {2018/14770-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2015/04224-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, abstract = {UNLABELLED: The aim of this study was to compare the vaginal microbiome of women with different sexual behaviors and to examine characteristics associated with Lactobacillus-deprived community state type IV. In this prospective study performed in a community-based population in a city of approximately 150,000 inhabitants in Southeast region of Brazil, vaginal swabs were obtained of 109 participants, including women who only had sex with women (n = 54) and women who only had sex with man (n = 55). Sociodemographic data, sexual and intimated hygiene practices of the participants were also assessed. Vaginal microbiota was assessed by sequencing the hypervariable regions V3 and V4 of 16 S ribosomal nucleic acid gene (Illumina 250 PE). Alpha diversity (Shannon index) was compared between the two groups by the Mann-Whitney test. Logistic regression analyses were performed to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between covariates with the Lactobacillus-deprived community state type IV. Results showed that overall distribution of vaginal CSTs did not differ between the two study groups (P = 0.19). However, alpha diversity was increased in women that only have sex with women (P = 0.0018). Lactobacillus-deprived community state type IV was associated with lower income (OR: 4.15, 95% CI: 1.04–16.46) and use of sex toys (OR: 3.97, 95% CI: 1.09–14.45). In conclusion, nearly one-third of women that only have sex with women had a sub-optimal vaginal microbiome and show evidence of sex transmissibility of CST-IV associated organisms.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34977-2.}, }
@article {pmid41868365, year = {2026}, author = {Li, J and Li, Q and Wang, M and Xu, S and Zhang, D}, title = {Crop rotation-driven changes in secondary metabolites of potato rhizosphere soil exert stronger regulation on soil microbial community.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768797}, pmid = {41868365}, issn = {1664-302X}, abstract = {INTRODUCTION: Crop rotation promotes ecological effects and production by regulating belowground processes, particularly the shaping of the rhizosphere soil microbiome. Rhizosphere metabolites are a key driver of belowground processes and play a crucial role in shaping soil microbial community composition. However, the rhizosphere metabolites of different potato rotations have rarely been reported, and the regulation of key metabolites on the rhizosphere soil microbiome remains unclear.<br><br>METHODS: This study measured agronomic traits of potatoes, collected potato rhizosphere soils from three crop rotations, including potato monoculture (P-P), maize (Zea mays)-potato rotation (M-P), cowpea (Vigna unguiculata)-potato rotation (V-P), to determine rhizosphere soil metabolites and analyze defense metabolites, and assess the soil bacterial and fungal diversity and community composition.<br><br>RESULTS: Compared to monoculture, the potato rotations had positive effects on growth and yield. Potato rotations had more primary metabolites, such as amino acids and carbohydrates and conjugates, but significantly reduced secondary metabolites with defensive functions in rhizosphere soils including phenols and other benzene derivatives, flavonoids, alkaloids and other N-containing compounds, and terpenoids. Potato rotation systems supported higher diversity of bacteria and fungi and enriched beneficial bacteria such as biocontrol, nitrogen fixation, C degradation, denitrification, and pollutant degradation bacteria, while suppressing pathogenic fungi in the rhizosphere soils. Rhizosphere soil metabolites strongly correlated with the microbial community composition. The secondary metabolites, which are predominantly alkaloids, terpenoids, and flavonoids, exerted a dominant regulatory effect on the composition of soil microbial community.<br><br>DISCUSSION: These results demonstrate the important regulation of rhizosphere metabolites on soil microbial community composition, deepening our understanding of the benefits of crop rotation via the belowground effect.}, }
@article {pmid41868371, year = {2026}, author = {Bel Mokhtar, N and Stathopoulou, P and Asimakis, E and Augustinos, A and Salgueiro, J and Alleck, M and Sookar, P and Dembilio, &#xd3; and Segura, DF and Tsiamis, G}, title = {Evolutionary dynamics of type VI secretion systems in fruit fly-associated Enterobacter.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755534}, pmid = {41868371}, issn = {1664-302X}, abstract = {Species in the genus Enterobacter are widely distributed and occupy diverse ecological niches. Although many species within this genus have been extensively isolated and characterized, their symbiotic associations with Tephritidae fruit flies remain understudied, particularly through comparative genomic analyses. To address this gap, we conducted a whole-genome comparative analysis of thirteen Enterobacter strains isolated from the most economically significant fruit fly species: Anastrepha fraterculus, Bactrocera dorsalis, Bactrocera zonata, Ceratitis capitata, and Zeugodacus cucurbitae. The results revealed that different fruit flies harbor distinct Enterobacter species, with Enterobacter hormaechei being the most prevalent across hosts. Notably, distinct E. hormaechei subspecies were associated with specific hosts, suggesting a potential host-driven adaptation and coevolution. Pangenome analysis highlighted a dynamic genetic structure among these strains, with significant differences in the core, shell, and species-specific gene composition. The high proportion of metabolism-related genes in the core genome suggests a conserved role in essential biological functions, whereas the enrichment of mobile genetic elements (prophages and transposons) and cell motility genes within the shell and species-specific genomes highlights the genomic plasticity and potential host-specific adaptations. Three distinct subtypes of T6SS (type VI secretion systems) gene clusters, T6SS_C1, T6SS_C2, and T6SS_C3, were detected across Enterobacter strains. T6SS_C1 and T6SS_C2 were identified in most Enterobacter strains, whereas T6SS_C3 cluster was restricted to a single isolate. Although these clusters contained thirteen core T6SS genes, they were characterized by different gene synteny and effector/immunity gene content, suggesting that different Enterobacter strains may utilize distinct mechanisms for interbacterial interactions, host manipulation, and environmental adaptation. Overall, our findings reveal the genetic basis of the symbiosis between Enterobacter species and fruit flies, shedding light on their evolutionary dynamics, diversity of T6SS, and functional traits. These results open new avenues for developing microbiome-based strategies for pest management, including the targeted manipulation of microbial communities to enhance sterile insect technique (SIT) outcomes.}, }
@article {pmid41868375, year = {2026}, author = {Gao, Y and Wang, Z and Cheng, J and Fu, Y and Wang, Y and Sun, Y and Geng, G and Sun, Y}, title = {Effects of Sphingomonads on sugar beet growth and rhizosphere microbiota under continuous cropping.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1793515}, pmid = {41868375}, issn = {1664-302X}, abstract = {INTRODUCTION: Sugar beet is a crucial sugar crop, and its yield and quality are vulnerable to the adverse effects of continuous cropping. Plant growth-promoting rhizobacteria function as biological control agents and exhibit high potential for crop growth promotion.<br><br>METHODS: In this study, soil subjected to continuous sugar beet cropping was selected as the experimental substrate to evaluate the effects of Sphingobium abikonense strain W2, Sphingomonas panni strain W9, Sphingomonas sp. strain W13, and their mixed bacterial suspension on sugar beet seedling growth and soil properties using pot experiments. High-throughput sequencing was used to characterize changes in the rhizosphere soil microbial community structure.<br><br>RESULTS: The results indicated that Sphingomonads inoculation significantly improved the agronomic performance of sugar beet seedlings, as evidenced by increased plant height, stem diameter, aboveground and root fresh weight, and enhanced nitrogen and phosphorus uptake. In addition, inoculation increased soil pH, available potassium content, and sucrase activity. Microbial community analysis revealed that all inoculation treatments markedly altered the diversity and composition of the rhizosphere microbiome. Compared with the continuous cropping control, the inoculated soils exhibited a significantly higher abundance of Pseudomonadota, exceeding that observed under crop rotation. Moreover, beneficial genera (e.g., Pseudomonas, Cupriavidus, Massilia, and Novosphingobium) were enriched. Functional prediction demonstrated a significant enhancement of key metabolic processes, including ureolysis and xylanolysis.<br><br>CONCLUSION: Overall, Sphingomonad inoculation effectively regulated the structure and function of the rhizosphere microbial community, improved soil enzyme activity and nutrient availability, and promoted sugar beet seedling growth. This study provides a theoretical foundation and potential biocontrol strategy for mitigating continuous cropping obstacles in sugar beet cultivation.}, }
@article {pmid41868536, year = {2026}, author = {Liu, Y and Wang, S and Liu, Y and Yu, D and Wang, Q and Tian, Y and Ma, L}, title = {Impact of Dupilumab on the Skin Microbiome in Children Aged 6-12 years with Moderate-to-Severe Atopic Dermatitis.}, journal = {Journal of asthma and allergy}, volume = {19}, number = {}, pages = {570878}, pmid = {41868536}, issn = {1178-6965}, abstract = {PURPOSE: We aimed to investigate alterations in the skin microbiome following treatment and discontinuation of dupilumab in children with atopic dermatitis (AD).<br><br>METHODS: In all, 24 pediatric AD patients and 10 pediatric health volunteers (HVs) were included. AD patients were treated with dupilumab for 16 weeks and following by a 12-week discontinuation. Cutaneous samples were collected from HVs, and AD patients at baseline and during dupilumab application period (Week 2, Week 4, Week 8, Week 12, and Week 16) and discontinuation period (Week 22 and Week 28) to conduct sequencing targeting the 16s rRNA V3-V4 regions. Clinical severity was assessed using the Eczema Area and Severity Index (EASI), Individual Signs Score (ISS), Children's Dermatology Life Quality Index scores (CDLQI), Patient Oriented Eczema Measure (POEM), and peak pruritus Numerical Rating Scale (NRS itch).<br><br>RESULTS: Dupilumab treatment significantly improved AD characteristics, with reductions in EASI, ISS, CDLQI, POEM, and NRS itch scores (all P < 0.01). Concurrently, 16s rRNA sequencing indicated decline in Staphylococcus aureus abundance and increase in microbial diversity. These changes began to reverse upon treatment discontinuation, coinciding with a trend toward worsening EASI scores. Moreover, a dupilumab-responsive reduction in other bacterial genera such as Aggregatibacter, and Megasphaera were observed; and these alterations could be reversed after treatment cessation.<br><br>CONCLUSION: We provided a dynamical pattern of skin bacterial community during and after dupilumab therapy in pediatric AD patients. Our findings suggest that the therapeutic action of dupilumab may extend to modulating a wider range of bacteria than previously recognized. The roles of our identified candidate microbial taxa require further investigation in larger and functional studies.}, }
@article {pmid41868611, year = {2026}, author = {Jimenez-Arenas, P and Ferrer, M and Ruiz-Rivera, M and Júlvez, J and Bustamante, M and Gascon, M}, title = {The relationship between the gut microbiota and neuropsychological development and behaviour during childhood and adolescence: a systematic review of epidemiological studies.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {53}, number = {}, pages = {101212}, pmid = {41868611}, issn = {2666-3546}, abstract = {Mounting evidence suggests that early-life microbial colonization might shape cognitive development and behaviour. This systematic review summarizes current research on the relationship between the gut microbiota and neuropsychological development and behaviour in children and adolescents (0-18 years). Following PRISMA guidelines, we conducted a comprehensive search across MEDLINE, Scopus, and Web of Science, identifying 78 eligible studies covering both clinical neurodevelopmental disorders and general-population neuropsychological outcomes. We observed a high heterogeneity across studies regarding study design, statistical analyses and the consideration of confounding factors (e.g., diet, medication use), gut microbiota determinations and the assessment of neurobehavioural outcomes. Only 42% of studies used longitudinal designs, and confounding factors were frequently unaddressed. Microbiome alterations in autism spectrum disorder (n = 23 studies) included community structure shifts, elevated Clostridium and Sutterella, and reduced Blautia, Lactobacillus, and Bifidobacterium. Functional and metabolomic analyses suggest immunomodulatory and neuroactive processes as main contributors, including elevated levels of the short-chain fatty acids propionate and valerate. For attention-deficit/hyperactivity disorder (n = 7) findings were less consistent. Associations were modest in the general paediatric population, with Veillonella and Bifidobacterium appearing across multiple studies being more abundant in children with enhanced neuropsychological development. Overall, the evidence highlights potential microbial signatures associated with neurodevelopment, yet methodological limitations constrain causal inference. Most of the studies were of poor to fair quality, often due to technical shortcomings in microbiome assessment and statistical limitations. Future research should prioritize standardized exposure/outcome assessment protocols and multi-omics integration, while underlining the potential of methodological rigour in translating findings into clinically actionable knowledge.}, }
@article {pmid41868718, year = {2026}, author = {Jia, S and Liu, P and Zhang, H and Zeng, H and Chen, G and Zhao, L}, title = {Why the COPD Microbiome Matters: How Airway Microbes Shape Disease Severity and Treatment Response.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {21}, number = {}, pages = {531521}, pmid = {41868718}, issn = {1178-2005}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy/diagnosis/physiopathology/immunology/drug therapy ; *Microbiota ; *Lung/microbiology/drug effects/physiopathology/immunology ; Dysbiosis ; *Bacteria/drug effects/immunology/pathogenicity/growth &amp; development/classification ; Severity of Illness Index ; Treatment Outcome ; Host-Pathogen Interactions ; Disease Progression ; *Respiratory System/microbiology ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease caused by multiple factors, with diverse clinical manifestations leading to varying treatment outcomes. Dysbiosis of the respiratory microbiome is one of the key contributors to this variability.<br><br>OBJECTIVE AND METHODS: Due to differences in microbial detection technologies and sample collection methods, studies on the characteristics of respiratory prokaryotic microbiota and how these microbes influence host functions in COPD patients have yielded variable results. In this review, we conducted a comprehensive search of relevant literature from PubMed, ScienceDirect, and Elsevier, summarizing studies on the characteristics and functional analyses of prokaryotic microbiota under various technical approaches. The goal was to identify common patterns of microbiota changes in COPD across different disease states, as well as individual microbial influences on host functions.<br><br>RESULTS: Compared with healthy adults, in stable-phase COPD patients, the relative abundance of Prevotella species in the Bacteroidetes phylum is significantly reduced. During acute exacerbations, the predominant microbiota is composed of Moraxella, Haemophilus, and Streptococcus species from the Proteobacteria and Firmicutes phyla. Clinical indicators in COPD patients are correlated with the abundance of Streptococcus (Firmicutes) and Prevotella (Bacteroidetes) species. Furthermore, the different phyla of respiratory prokaryotic microbiota are associated with innate immunity, metabolism, and inflammation factors related to COPD.<br><br>CONCLUSION: This review summarizes evidence on dynamic changes in the airway prokaryotic microbiome during COPD progression. It highlights the dual role of these microbial changes as biomarkers of disease progression and modifiable targets for personalized care. Observed patterns-such as reduced Prevotella abundance in stable disease and the dominance of Moraxella, Haemophilus, and Streptococcus during acute exacerbations-provide a basis for stratifying patients and designing individualized treatment plans. Microbiome analysis may aid in early identification of high-risk patients for preventive strategies, guide pathogen-specific antimicrobial or immunomodulatory therapy, and allow treatment response to be monitored through microbial shifts. By linking distinct microbial profiles to host immune and inflammatory pathways, this approach supports the development of tailored interventions to restore microbial balance. These strategies could improve clinical outcomes and advance precision medicine in COPD management.}, }
@article {pmid41868793, year = {2026}, author = {Yan, N and Zhang, Y and Wang, S and Hu, S and Ruan, L and Wang, Y and Feng, W and Xiong, W and Zhang, W and Wei, Y and Yao, C}, title = {CAMK1D as a potential therapeutic target for gut microbiota-driven promotion of lung adenocarcinoma development.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20985}, pmid = {41868793}, issn = {2167-8359}, mesh = {Humans ; *Adenocarcinoma of Lung/genetics/microbiology ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Calcium-Calmodulin-Dependent Protein Kinase Type 1/genetics/metabolism ; Mendelian Randomization Analysis ; }, abstract = {BACKGROUND: The gut microbiome is closely associated with malignant tumors; however the specific mechanisms by which it contributes to the development of lung adenocarcinoma remain unclear. In this study, we performed a two-sample bidirectional Mendelian randomization (MR) analysis to assess the causal relationship between the gut microbiome and lung adenocarcinoma. By identifying single nucleotide polymorphism markers linked to gut microbiome species, we aimed to discover potential biomarkers for lung adenocarcinoma. These findings may offer new insights into the role of the gut microbiome in the prevention and treatment of lung adenocarcinoma.<br><br>METHODS: We used genome-wide association study (GWAS) summary statistics to assess the association between the gut microbiome and lung adenocarcinoma through two-sample MR analysis. Sensitivity analyses were performed to confirm the robustness of the findings. Reverse MR analysis and GWAS data integration were employed to identify potential genetic and therapeutic targets. Bioinformatics analysis and quantitative Real-Time PCR (qRT-PCR) were utilized to validate gene expression and explore the underlying mechanisms of key genes.<br><br>RESULTS: Our analysis identified two bacterial taxa, Prevotella9 and Parabacteroides, as being causally associated with lung adenocarcinoma, both showing positive causal relationships. Sensitivity analyses confirmed the robustness of these associations. The reverse MR analysis revealed no evidence of reverse causality. GWAS data identified 15 genes (DNAH1, PDE10A, DOCK2, INSYN2B, DNAI3, SUOX, LINC01505, SULT4A1, NT5ELP, LINC02895, calcium/calmodulin dependent protein kinase 1D (CAMK1D), ENSG00000253557, BCAS3, C18orf63, MYO18B) that passed the summary-data-based MR test. The transcriptomic data revealed that five genes (CAMK1D, BCAS3, DNAH1, PDE10A, and C18orf63) were differentially expressed between lung adenocarcinoma patients and healthy individuals. Through qRT-PCR validation, the CAMK1D gene was markedly upregulated in lung adenocarcinoma cell lines, whereas BCAS3, DNAH1, PDE10A, and C18orf63 genes exhibit ed substantially reduced expression.<br><br>CONCLUSION: Our study identified specific gut microbial taxa as risk factors for lung adenocarcinoma and proposes CAMK1D as a microbiota-related candidate biomarker and potential therapeutic target that may inform personalized treatment and drug development strategies in the future.}, }
@article {pmid41868872, year = {2026}, author = {Kyrochristou, I and Kyrochristou, G and Fousekis, F and Katsanos, K and Schizas, D and Vlachos, K and Lianos, GD}, title = {Determinants of the healthy gut microbiome: core features, modifying factors and normal functions.}, journal = {Annals of gastroenterology}, volume = {39}, number = {2}, pages = {191-201}, pmid = {41868872}, issn = {1108-7471}, abstract = {The human gut microbiome represents a complex and dynamic ecosystem that is central to maintaining health and preventing disease. Defining a "normal" gut microbiome remains challenging, given the significant variability arising from host physiology, lifestyle, genetics, geography and environmental exposures. This review synthesizes current evidence regarding the composition and functions of the gut microbiota in healthy individuals from diverse populations. At the taxonomic level, healthy gut microbial communities are typically dominated by the phyla Firmicutes and Bacteroidetes, with additional contributions from Actinobacteria and Proteobacteria. However, substantial inter-individual and regional differences are observed, such as a higher prevalence of Prevotella in populations consuming fiber-rich Eastern diets, and greater Bacteroides abundance in Western cohorts. Anatomical location and health status also influence alpha-diversity, underscoring the need to interpret diversity metrics within context. Furthermore, the gut microbiome performs essential functional roles across multiple organ systems, including fermentation of dietary fibers into short-chain fatty acids, regulation of immune responses, modulation of the gut-brain axis, maintenance of intestinal barrier integrity, and support of cardiovascular and hepatic functions. These findings support the conceptualization of the microbiome as a multifunctional organ system that integrates host and environmental signals. In summary, a healthy gut microbiome is best understood as a dynamic equilibrium, characterized by functional resilience and adaptability, rather than a fixed microbial profile. Interpreting this variability is crucial for developing targeted interventions to prevent disease.}, }
@article {pmid41869364, year = {2026}, author = {Wang, B and Zhang, Y and Lin, L and Wang, S and Yang, S}, title = {Psoriasis: microbiome dysbiosis and pathogenic mechanisms.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1714515}, pmid = {41869364}, issn = {1664-3224}, mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Psoriasis/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Animals ; *Microbiota/immunology ; Skin/immunology/microbiology ; }, abstract = {Psoriasis is a chronic immune-mediated inflammatory disease whose pathogenesis is a triad of genetic predisposition, immune dysregulation, and environmental triggers. This review provides a novel, in-depth synthesis arguing that microbial dysbiosis is not merely an associative phenomenon but a central regulatory node within this triad, actively shaping immune responses and clinical phenotypes. We move beyond cataloging microbial shifts to construct a detailed mechanistic framework of the gut-skin axis. Gut dysbiosis; characterized by reduced diversity, a diminished Bacteroidetes/Firmicutes ratio, and depleted SCFA producers, compromises intestinal barrier integrity, reduces systemic immunoregulatory tone via diminished SCFA signaling, and promotes Th17 polarization. This systemic inflammation is directly communicated to the skin. Concurrently, cutaneous dysbiosis, featuring Staphylococcus aureus dominance and fungal alterations, disrupts the local barrier, provides chronic antigenic stimulation, and amplifies IL-17-driven inflammation, creating a self-sustaining loop. Crucially, we analyze how specific infections (HCV, H. pylori, Streptococcus) act as environmental triggers by sharing or activating these very pathways. The bidirectional relationship with therapy is dissected: while biologics induce drug-specific microbiome shifts that often correlate with clinical normalization, they also carry infection risks that must be strategically managed. Emerging microbiome-targeted interventions like specific probiotics show promise but are hampered by methodological inconsistencies. This review uniquely highlights the causality gap and proposes that future breakthroughs require a shift from correlation to mechanism. We conclude that the microbiome is a dynamic interface between genes and environment in psoriasis; its successful integration into diagnostic and therapeutic paradigms demands standardized multi-omics approaches, functional validation, and personalized medicine strategies that target this critical axis.}, }
@article {pmid41869707, year = {2026}, author = {Wang, Z and Fu, Y}, title = {Bacteria weigh up costs and benefits of mobile weapons.}, journal = {eLife}, volume = {15}, number = {}, pages = {}, pmid = {41869707}, issn = {2050-084X}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteria/genetics/metabolism ; }, abstract = {Gaining the ability to kill rival microbes is not always an advantage for bacteria in complex gut microbiomes.}, }
@article {pmid41869810, year = {2026}, author = {Zhang, C and Sun, Z and Lin, Y and Long, W and Zhang, R and Huang, H and Liang, W}, title = {Pulmonary mucoid Pseudomonas aeruginosa infection and association with higher species richness and stronger inflammatory immune response.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0229525}, doi = {10.1128/spectrum.02295-25}, pmid = {41869810}, issn = {2165-0497}, abstract = {The mucoid phenotype of Pseudomonas aeruginosa (PA) is regarded as a comprehensive adaptive stress response to difficult environmental circumstances. However, there is little knowledge about the relationship between the prevalence of mucoid PA and species richness and immune inflammatory response. A case-control study was conducted in hospitalized patients with pulmonary infections caused by mucoid and non-mucoid PA. Sputum samples were subjected to 16S rDNA sequencing to characterize microbial diversity and taxonomic composition, while serum levels of TNF-α, IL-6, IL-8, IL-10, and IL-17 were measured using enzyme-linked immunosorbent assays. Subsequent statistical analysis using R 4.0 revealed significant correlations between differentially abundant microbial taxa and cytokine profiles. Compared to the non-mucoid PA group, the mucoid PA group demonstrated significantly higher α-diversity indices in terms of species richness, as indicated by the Chao1 (P = 0.0015) and Observed-species metrics (P = 0.0014). Furthermore, distinct β-diversity patterns were observed between the two groups (P < 0.05). LefSe analysis revealed significant enrichment of Veillonella spp., Haemophilus spp., Porphyromonas spp., Prevotella spp., Actinomyces spp., Lactobacillus spp., and Rothia spp. in the mucoid PA group, while Stenotrophomonas spp., Acinetobacter spp., Parvimonas spp., and Serratia spp. dominated in the non-mucoid PA group. The mucoid PA infections showed marked elevation of IL-8 (P = 0.0137), TNF-α (P = 0.0048), IL-10 (P = 0.0042), IL-17 (P = 0.0220), and IL-6 (P = 0.0001). Spearman correlation revealed Veillonella spp./Rothia spp./Porphyromonas spp./Prevotella spp. positively correlated with IL-10/TNF-α/IL-17/IL-6, whereas Haemophilus spp. showed a negative relationship with IL-17. Stenotrophomonas spp. exhibited strong negative correlations with IL-10/IL-6, and Serratia spp. was inversely associated with TNF-α in non-mucoid PA infections. Clinically distinct microbial ecosystems in mucoid PA correlate with exacerbated inflammation. This phenotype-driven dichotomy provides actionable biomarkers for stratified antimicrobial/immunomodulatory therapies in chronic lung disease.IMPORTANCEThis study holds significant clinical and scientific importance, as it elucidates the critical differences between mucoid and non-mucoid Pseudomonas aeruginosa (PA) infections in pulmonary patients. By demonstrating that mucoid PA infections are associated with distinct microbial ecosystems (higher species richness and different taxonomic compositions) and more severe inflammatory responses (elevated TNF-α, IL-6, IL-8, IL-10, and IL-17), the research provides crucial insights into phenotype-specific pathogenesis. The identified correlations between specific bacterial species (e.g., Veillonella/Rothia with pro-inflammatory cytokines) offer potential biomarkers for clinical stratification. These findings are particularly valuable for developing targeted therapeutic strategies, as they suggest mucoid PA infections may require different antimicrobial/immunomodulatory approaches compared to non-mucoid variants. The study bridges an important knowledge gap in understanding how bacterial phenotypic adaptation influences host-microbiome interactions and disease outcomes in chronic lung infections.}, }
@article {pmid41869813, year = {2026}, author = {Mancabelli, L and Palomba, E and Magni, F and Chatenoud, L and Olgiati, I and Buracchi, C and Bugarin, C and Gaipa, G and Abbruzzese, C and Filippini, M and Forastieri, A and Fumagalli, R and Geraldini, F and Picetti, E and Terranova, L and Vaschetto, R and Zoerle, T and Ventura, M and Citerio, G and Gori, A and Bandera, A and Alagna, L and Turroni, F}, title = {Microbial signatures and host immune responses associated with the development of ventilator-associated pneumonia among patients with neurological injuries.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0319325}, doi = {10.1128/spectrum.03193-25}, pmid = {41869813}, issn = {2165-0497}, abstract = {Ventilator-associated pneumonia (VAP) remains a leading complication in mechanically ventilated patients, yet the contribution of the respiratory microbiota remains poorly understood. The PULMIVAP study is a multicenter, longitudinal cohort investigation of respiratory microbiota composition and host immune responses in critically ill adults intubated for non-pulmonary conditions. A total of 146 intubated adult patients were enrolled across eight Italian ICUs, forming matched groups of 73 with VAP and 73 without. Oropharyngeal swabs and endotracheal aspirates were collected at intubation and either at VAP diagnosis or at a matched point in controls for a total of 584 biological samples. Metataxonomic analyses revealed substantial temporal shifts in microbial communities across both upper and lower respiratory compartments, with a trend toward reduced microbial richness in patients who developed VAP. Several genera, such as Corynebacterium, were more abundant in no-VAP patients, whereas Escherichia-Shigella and Peptoniphilus were enriched in VAP samples. Cytokine-microbiota correlation analysis suggested a pro-inflammatory signature in VAP patients, with Citrobacter positively associated with IFN-γ and TNF-α, while several commensal genera were inversely correlated with inflammatory mediators. Additionally, taxa associated with VAP correlated with lower PaO2/FiO2 ratios, implicating them in disease severity. Consistently, several bacteria, such as Corynebacterium, appeared to be linked to better respiratory outcomes, suggesting protective or risk-associated microbial profiles. Overall, these findings highlight the complex interplay between microbial communities and mucosal immunity in the pathogenesis of VAP. The identification of condition-associated microbial and immunological signatures may inform future strategies for risk stratification and targeted prevention.IMPORTANCEVentilator-associated pneumonia (VAP) remains a major complication of mechanical ventilation, yet most microbiome studies have focused on late-stage infection or single airway compartments, limiting insight into early microbial dynamics associated with VAP risk. By longitudinally characterizing upper and lower airway microbiota before and during VAP development, this study provides new insights into microbial and immune patterns associated with susceptibility and disease severity in humans. These findings contribute to the current understanding of VAP pathogenesis by suggesting a role for early airway dysbiosis and local immune responses alongside clinical factors. Remarkably, the identification of taxa associated with risk or protection supports the potential for microbiota-informed monitoring and future risk stratification strategies during mechanical ventilation.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04849039.}, }
@article {pmid41869814, year = {2026}, author = {Yang, K and Yang, Z and Li, H and Liu, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T}, title = {Effects of heavy metal exposure on oral microbial communities in women with different menopausal status.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0312325}, doi = {10.1128/spectrum.03123-25}, pmid = {41869814}, issn = {2165-0497}, abstract = {This study investigates the effects of long-term heavy metal exposure on the oral mucosal microbiota in women. By measuring both external environmental heavy metal exposure and internal heavy metal exposure indicators in the human body, it aims to elucidate the complex interactions between external environmental exposure and internal exposure, as well as their potential association with menopausal status. We analyzed oral microbial composition, function, and co-occurrence networks in 47 women from polluted and control areas. Heavy metal exposure significantly altered oral microbial diversity and functional pathways, with molybdenum (Mo) exhibiting a uniquely strong influence. Key metabolic pathways related to cardiovascular disease and carbohydrate metabolism were enriched in specific groups. Network analysis revealed a loss of keystone species and structural simplification in postmenopausal women from the polluted area. These findings suggest that heavy metal exposure alters oral microbial communities, and these alterations correlate with shifts in host metabolic pathways that are known to be associated with menopausal hormonal changes, potentially impacting women's health during this transition.IMPORTANCEThis study reveals, for the first time, how chronic heavy metal exposure and menopause interact to disrupt the female oral microbiome. We identify Mo as a key metal, correlating strongly with specific bacteria and linked to downregulated cardiovascular and metabolic pathways. Critically, postmenopausal women in polluted areas exhibit a severe loss of keystone species and a collapsed microbial network structure. These findings position the dysregulated oral microbiome as a potential mechanistic link between environmental metal exposure and the heightened systemic risks-such as metabolic disorders and chronic inflammation-observed in postmenopausal women, highlighting new targets for preventive health strategies.}, }
@article {pmid41869817, year = {2026}, author = {Chong, Q and Cheng, M and Cao, Q and He, J and Xiao, M and Li, Y and Wang, Z and Wang, J and Zhang, K and Gou, H}, title = {Systematic evaluation of phage cocktail-ciprofloxacin combination therapy against multidrug-resistant Salmonella Typhimurium induced gut dysbiosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0264025}, doi = {10.1128/spectrum.02640-25}, pmid = {41869817}, issn = {2165-0497}, abstract = {Phage therapy, despite its promise as a novel therapeutic alternative for multidrug-resistant (MDR) bacterial infections, is hampered by clinical limitations such as narrow host range and therapeutic inconsistency. This research has engineered a phage-antibiotic synergistic therapy enabling precision eradication of drug-resistant Salmonella Typhimurium (S. Typhimurium). From slaughterhouse wastewater and fecal samples, three Felixounavirus phages (TSP_TW2, TSP_SW1, and TSP_SJ5) were isolated. Compared to the clinical phage repository, these phages demonstrated more superior broad-spectrum activity, successfully lysing over 85% of the tested wild-type isolates. The in vitro study, validated by laser confocal fluorescence imaging demonstrates that compared to solitary phage, phage cocktail delays the emergence of resistance to 24 h while also achieving effective biofilm eradication. In the murine intestinal infection model, the experimental group treated with phage cocktail in combination with ciprofloxacin (CIP) demonstrated significant therapeutic effects, reaching 90% survival rate, restoring the CD4[+]/CD8[+] T cell balance, and decreasing the levels of pro-inflammatory factors, which were significantly superior to those of phage or CIP alone. In addition, the susceptibility of S. Typhimurium to β-lactams, quinolones, and observed four- to eightfold reduction in tetracycline minimal inhibitory concentration (MIC) demonstrated effective restoration of antibacterial activity after therapeutic intervention. 16S rRNA high-throughput sequencing showed that the index of intestinal flora diversity of mice in the treatment group was not significantly difference to healthy control group, while specifically promoting the growth of beneficial microbial populations such as Lactobacillus spp. The innovative phage-antibiotic combination therapy established in this study demonstrated dual therapeutic advantages: effective clearance of antimicrobial-resistant strains and maintenance of enteric microbiome homeostasis, thereby offering a clinically promising strategy for controlling infections caused by antimicrobial-resistant S. Typhimurium.IMPORTANCEFoodborne Salmonella infections threaten global public health, as conventional antibiotics accelerate resistance and disrupt microbial balance. We pioneer a synergistic phage-ciprofloxacin cocktail strategy that overcomes multidrug-resistant Salmonella infection through three key advances: First, it delays resistance evolution while eradicating biofilm matrices; second, the therapy synergistically enhances antibiotic sensitivity to restore efficacy of critical drugs; and third, the combined approach maintains optimal gut microbiota balance during pathogen clearance. By using environmentally derived phages with minimized antibiotic dosing, this strategy achieves targeted removal of resistant pathogens-including invasive biofilms-without collateral damage to commensal flora. Crucially, it prevents systemic inflammation and preserves intestinal barrier function. This ecologically sustainable paradigm provides a dual-defense mechanism against infections and microbiome dysbiosis, positioning phage-antibiotic synergy as a transformative tool for containing foodborne disease threats.}, }
@article {pmid41869825, year = {2026}, author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G}, title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {15578666261428562}, doi = {10.1177/15578666261428562}, pmid = {41869825}, issn = {1557-8666}, abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.}, }
@article {pmid41869845, year = {2026}, author = {Suk, K and Lee, WH}, title = {Peptidoglycan recognition proteins in the brain: Role in neuroinflammation and behavioral consequences.}, journal = {Histology and histopathology}, volume = {}, number = {}, pages = {25064}, doi = {10.14670/HH-25-064}, pmid = {41869845}, issn = {1699-5848}, support = {RS-2024-00408736//National Research Foundation of Korea (NRF), Korean government/ ; }, abstract = {Peptidoglycan recognition proteins (PGRPs) constitute an evolutionarily conserved family of pattern recognition molecules that detect bacterial peptidoglycan. While their antimicrobial functions have been well characterized in peripheral immunity, recent discoveries have unveiled critical roles for PGRPs in central nervous system inflammation and behavior. Among the four mammalian PGRP family members, PGLYRP1 exhibits unique expression in brain microglia and demonstrates potent pro-inflammatory properties in neurological contexts. Recently, PGLYRP1 has been shown to function as a key amplifier of neuroinflammation through a novel TREM1-Syk-Erk1/2-Stat3 signaling axis, establishing a positive feedback loop with TNF-α that perpetuates microglial activation. This review synthesizes current understanding of PGRP biology in the nervous system, with particular emphasis on molecular mechanisms of PGLYRP1, cellular sources, and behavioral consequences. We examine the structural basis of peptidoglycan recognition, cell-type-specific expression patterns, signaling pathways, and integration with other innate immune systems. Furthermore, we explore emerging connections between gut microbiome-derived peptidoglycan, blood-brain barrier penetration, and neuropsychiatric disorders. Critical knowledge gaps remain regarding physiological versus pathological roles of PGLYRP1, therapeutic targeting strategies, and translational potential. Understanding PGLYRP1-mediated neuroinflammation provides novel mechanistic insights into microbiome-brain communication and offers promising therapeutic avenues for neuroinflammatory and neurodegenerative diseases.}, }
@article {pmid41869887, year = {2026}, author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J}, title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e20332}, doi = {10.1002/advs.202520332}, pmid = {41869887}, issn = {2198-3844}, support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; }, abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.}, }
@article {pmid41869963, year = {2026}, author = {Zhong, X and Chen, W and Sun, Q and Zhang, S and Yang, J and Min, W and Li, W}, title = {Crisaborole Reduced the Staphylococci but Increased Cutibacterium on the Skin Microbiome of Children with Atopic Dermatitis.}, journal = {Dermatitis : contact, atopic, occupational, drug}, volume = {}, number = {}, pages = {17103568261431028}, doi = {10.1177/17103568261431028}, pmid = {41869963}, issn = {2162-5220}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a common, recurrent skin disease in children, associated with an imbalance in the skin microbiome. Topical corticosteroids (TCS) cream is the first-line drug for treating AD. However, its long-term use is prone to the development of adverse reactions. Crisaborole, a nonsteroidal medication, is effective and well-tolerated for long-term maintenance treatment and flare reduction in adult and pediatric patients with mild-to-moderate AD. However, the effect of crisaborole on the skin microbiome remains unknown.<br><br>OBJECTIVE: The study aimed to compare the effects of topical crisaborole treatment and TCS treatment on microbial abundance and diversity in AD lesions.<br><br>METHODS: A cross-sectional study was conducted involving 30 children with mild-to-moderate AD and 10 healthy controls. Patients with AD were divided into three groups (untreated, TCS, and crisaborole; n = 10 each) based on baseline status. Skin samples were collected directly from the healthy child, the untreated lesions, and after a 2-week treatment period. The skin microbiome was analyzed using 16S rRNA gene sequencing.<br><br>RESULTS: Compared to the untreated AD group, both TCS and crisaborole treatments significantly reduced the relative abundances of Staphylococcus and Pseudomonas, while increasing the abundances of Streptococcus and Cutibacterium (formerly Propionibacterium). Alpha diversity of the skin microbiome was significantly increased after both treatments. However, the microbial profile of the crisaborole group was more distinct from the healthy control group than the TCS group was. Furthermore, the crisaborole group showed significant enrichment of taxa from the phylum Actinobacteria, including the genus Cutibacterium and species acnes.<br><br>CONCLUSIONS: Although the efficacy of crisaborole in treating mild-to-moderate AD in children is not equivalent to that of TCS, crisaborole could still remarkably improve the clinical symptoms of patients and partially restore the microbial diversity on the skin surface of children with AD.}, }
@article {pmid41869966, year = {2026}, author = {Yu, T and Fan, H}, title = {Host-microbiota interactions: a novel insight into the aryl hydrocarbon receptor in Parkinson's disease.}, journal = {Postgraduate medical journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/postmj/qgag017}, pmid = {41869966}, issn = {1469-0756}, abstract = {BACKGROUND: Parkinson's disease (PD) is regarded as the second most common neurodegenerative disease. Accumulating evidence suggested an emerging effect of the dysregulation of the gut-brain axis in the neurodegenerative disease pathogenesis, mediated particularly by microbiota-derived metabolites in PD. The aryl hydrocarbon receptor (AHR) is of great importance in regulating central nervous system inflammation by sensing microbiota-derived metabolites.<br><br>STRATEGY: AHR is a transcription factor activated by ligands, which can be activated locally or remotely by endogenous microbial metabolites. AHR signaling suppressed inflammation by activating anti-inflammatory and immunosuppressive responses, promoting intestinal host-microbiome homeostasis. The pathogenesis of PD is related to the activation of microglia and the occurrence of neuroinflammation. There is increasing attention that alterations in the intestinal flora and decreased AHR activity were closely associated with PD.<br><br>CONCLUSION: The AHR-gut microbiota axis garnered increasing attention in PD research. In this review, we synthesize current clinical and preclinical evidence linking the AHR-gut microbiota axis to PD pathogenesis, and we highlight that pharmacological targeting of this pathway represents an emerging therapeutic strategy for PD.}, }
@article {pmid41870062, year = {2026}, author = {Weingarten, EA and Fernando, BM and Freitas, MR and Indest, KJ}, title = {Cave microbial communities are structured by environmental matrix and depth and can be characterized with field-portable assays.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0031226}, doi = {10.1128/aem.00312-26}, pmid = {41870062}, issn = {1098-5336}, abstract = {UNLABELLED: Terrestrial caves are unique ecosystems characterized by environmental stability, nutrient limitation, and absence of light, yet they host diverse microbial communities with ecological and public health relevance. Microbiome studies of caves have typically been limited in scope, sampling only select environments or cave depths. We conducted a broad survey of microbial diversity in three natural limestone caves and two abandoned mines spanning continental, subtropical, and arid climates in the United States. Using amplicon sequencing of 382 samples composed of soil, rock, water, air, and bat and rodent feces, microbiome composition was found to be primarily structured by cave location, followed by environmental matrix (soil, water, air, etc.), and transect distance from the cave entrance. Significant heterogeneity was observed both between and within caves, underscoring the need for spatially explicit and multi-matrix sampling to capture representative community profiles. Portable DNA extraction and quantitative PCR (qPCR) technologies for onsite detection of microbial pathogens were further validated, demonstrating comparable results to laboratory-based workflows and reducing sample-to-result turnaround time from several days to less than 2 h. Pathogen panels detected zoonotic and waterborne agents of human health concern, including Salmonella and Legionella, directly from cave environments. Collectively, our findings establish a methodological framework for robust microbiome characterization in subterranean ecosystems and highlight the feasibility of field-deployable genetic tools for both biodiversity mapping and rapid pathogen surveillance. These approaches will enable more systematic monitoring of cave environments, with applications for ecology, conservation, and public health.<br><br>IMPORTANCE: Caves and mines represent extreme and isolated environments that harbor unique microbial communities, yet they remain among the least studied environments on Earth. Understanding how these communities are structured across different habitats and locations is essential for both ecological research and public health monitoring. In this study, we surveyed microbiomes across multiple caves and environmental materials to reveal how location, substrate type, and depth shape microbial diversity. We also demonstrated that portable DNA extraction and analysis tools can be used in the field to rapidly detect microorganisms, including potential pathogens, without the need for laboratory infrastructure. These results provide new insight into how microbial life is distributed in subterranean ecosystems and establish practical methods for monitoring microbial diversity and detecting pathogens in remote environments.}, }
@article {pmid41870087, year = {2026}, author = {Wang, X and Wu, W and Yang, B and Liu, Y and Xu, Y and Wang, L and Lv, X and Gao, J and Lu, M and Yu, A and Li, N and Chen, Q and Lu, L and Zhao, D}, title = {Additive effects of fecal microbiota transplantation and infliximab on gut microbiome and metabolome in refractory inflammatory bowel disease patients.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0077425}, doi = {10.1128/msystems.00774-25}, pmid = {41870087}, issn = {2379-5077}, abstract = {UNLABELLED: Fecal microbiota transplantation (FMT) is an emerging therapy for inflammatory bowel disease (IBD), yet its efficacy in patients refractory to conventional treatments and its underlying mechanisms require further elucidation. We studied 37 IBD patients (15 ulcerative colitis [UC], 22 Crohn's disease [CD]) refractory to conventional therapies and 16 healthy donors. FMT monotherapy from a single donor induced week-4 clinical response in 12 UC and 9 biologic-naïve CD patients, with all responders sustaining remission and most achieving endoscopic remission by week 14. Integrated multi-omics revealed FMT restored microbial diversity and profoundly reorganized host-microbiota-metabolite networks. In nine refractory CD patients (7 infliximab [IFX] non-responders, 2 FMT non-responders), IFX-FMT combination led to week-4 response in 6 patients, all of whom attained clinical and endoscopic remission by week 14, with more complete microbial-metabolic restoration than monotherapy. Our findings establish that FMT induces remission in refractory IBD via ecosystem network rewiring, and that IFX-FMT exhibits additive effects, supporting further trials of microbiome-directed adjunctive strategies.<br><br>IMPORTANCE: This study provides mechanistic and clinical insights into the therapeutic effects of fecal microbiota transplantation (FMT) in inflammatory bowel disease (IBD), particularly when combined with the anti-tumor necrosis factor (anti-TNF) biologic infliximab (IFX). While both FMT and IFX achieve response in approximately 60% of IBD patients, their combined influence on the gut microbial and metabolic landscape in refractory disease has been poorly understood. Here, we demonstrate that FMT monotherapy restores gut microbial diversity and reconfigures host-microbiota-metabolite networks, correlating with clinical and endoscopic remission in patients refractory to conventional treatments. Furthermore, in Crohn's disease patients unresponsive to either therapy alone, combined IFX-FMT induced more complete microbial and metabolic normalization and achieved remission where monotherapy had failed. These findings reveal ecosystem-level network rewiring as a central mechanism of FMT efficacy and establish the additive potential of combining microbiome-targeted and immunomodulatory therapies. This work supports the development of microbiome-informed adjunctive strategies for severe or refractory IBD, highlighting an actionable path toward personalized, mechanism-based treatment regimens.<br><br>CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT07149441.}, }
@article {pmid41870088, year = {2026}, author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S}, title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0010426}, doi = {10.1128/msystems.00104-26}, pmid = {41870088}, issn = {2379-5077}, abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.}, }
@article {pmid41870192, year = {2026}, author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM}, title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261433762}, doi = {10.1177/15578100261433762}, pmid = {41870192}, issn = {1557-8100}, abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.}, }
@article {pmid41870248, year = {2026}, author = {Deng, Y and Zhen, X and Xia, R and Zhu, R and Zhang, G and Chen, P and Lai, J and Tao, R}, title = {Integrated Microbiome and Metabolome Analysis for Characterization and Discrimination of Saliva, Semen, Vaginal Secretions, and Their Mixtures.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c05356}, pmid = {41870248}, issn = {1520-6882}, abstract = {Body fluid identification (BFID) and estimation of time since deposition (TsD) are valuable yet challenging in forensic practice. Previous studies have demonstrated that integrating microbial and metabolomic profiles provides complementary biological insights. Therefore, this study performed untargeted metabolomic profiling and full-length 16S rRNA sequencing on fresh saliva (SA), semen (SE), vaginal secretions (VF), and their mixtures (SA-VF and SE-VF), with additional microbial analysis after 15 and 30 days of indoor exposure. Results showed the single-fluid samples exhibited specific dominant bacterial taxa, whereas the two mixture samples contained detectable bacterial signatures from both constituent fluids. Untargeted UHPLC-QTOF/MS analysis revealed unique metabolic signatures for each body fluid, enriched in biologically relevant pathways like steroid and bile acid metabolism. Moreover, we putatively identified characteristic metabolites, including α-solanine, candicidin, and megalomicin C1, some of which are rare microbial antibiotics. Owing to the exploratory nature and associated constraints of nontargeted approaches, these results serve as a provisional reference for identifying potential candidates. Integration of metabolomic and microbiome data uncovered strong metabolite-microbe correlations, highlighting microbially influenced metabolic networks unique to each body fluid type. Using differential microbes and metabolites individually as input features, the random forest model achieved BFID accuracies of 80 and 83.1%, respectively; however, integrating both sets of features increased accuracy to 100%. In contrast, microbial-based TsD prediction performed well for single-fluid samples but showed reduced effectiveness for mixed samples. Overall, our research highlights the powerful predictive potential and improved predictive accuracy of the integration of microbiome and metabolome data in BFID.}, }
@article {pmid41870398, year = {2026}, author = {Handoko, C and Singh, A and Dharmage, SC and Hu, YJ and Dashper, SG and Bertelsen, RJ and Lowe, AJ and Lopez, DJ}, title = {The Impact of Early Childhood Caries on Asthma Trajectories During the First 15 Years of Life.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.70307}, pmid = {41870398}, issn = {1398-9995}, support = {//Australian Institute of Family Studies/ ; }, }
@article {pmid41870630, year = {2026}, author = {da Costa, JP and Fraiz, GM and Bonifácio, DB and Milagro, FI and Bressan, J}, title = {Sex-specific differences in salivary microbiota composition and their associations with metabolic health in adults with excess body weight: a secondary cross-sectional analysis.}, journal = {Clinical oral investigations}, volume = {30}, number = {4}, pages = {}, pmid = {41870630}, issn = {1436-3771}, abstract = {OBJECTIVES: Growing evidence links the oral microbiome to obesity-related outcomes, yet the influence of sex-related biological differences on salivary microbial profiles remains insufficiently explored. This exploratory study aimed to characterize the composition, abundance, and diversity of the salivary microbiota in Brazilian men and women with excess body weight and to examine its associations with cardiometabolic markers.<br><br>MATERIALS AND METHODS: This cross-sectional secondary analysis of a randomized controlled trial (REBEC: RBR-9832wsx) included 59 adults with excess body weight. Salivary microbiota was profiled through amplification of the 16&#xa0;S rRNA V4 region, and bioinformatics analyses were performed using the Microbiome Analyst (v2.0). Associations between microbial taxa and clinical variables were assessed using Spearman&#x2019;s correlation.<br><br>RESULTS: Men exhibited greater alpha diversity at the family level by higher Shannon (p&#x2009;=&#x2009;0.015, rrb = 0.4) and Simpson (p&#x2009;=&#x2009;0.003, rrb = 0.5) indices. Sex-specific microbial differences were identified: men showed higher levels of genera Tannerella, Lachnoanaerobaculum, and Actinomyces, as well as the putative species-level taxons Tannerella serpentiformis and Lachnoanaerobaculum umeaense, whereas women demonstrated greater abundance of genera Campylobacter, Granulicatella, Moryella, and Scardovia. Among women, Granulicatella genera was positively associated with triglycerides and the TyG index.<br><br>CONCLUSION: Men and women with excess body weight exhibited distinct salivary microbiota profiles, with differences in both diversity and taxonomic composition.<br><br>CLINICAL RELEVANCE: Sex-specific differences in salivary microbiota composition may be associated with variations in metabolic markers. These findings are exploratory and hypothesis-generating, providing insight into sex-related patterns in the oral microbiome and may help inform future research exploring personalized approaches to cardiometabolic risk assessment.}, }
@article {pmid41870676, year = {2026}, author = {Božac, E and Žučko, J and Braut, A and Špalj, S and Peršić Bukmir, R and Toplak, N and Hladnik, M and Vitezić, BM}, title = {Supragingival dental biofilm microbiomes of tobacco heating system smokers, cigarette smokers and non-smokers.}, journal = {Clinical oral investigations}, volume = {30}, number = {4}, pages = {}, pmid = {41870676}, issn = {1436-3771}, mesh = {Humans ; *Biofilms ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Microbiota ; *Smokers ; RNA, Ribosomal, 16S ; *Non-Smokers ; Middle Aged ; *Gingiva/microbiology ; DNA, Bacterial ; Heating ; }, abstract = {OBJECTIVES: The study compared the bacterial composition of supragingival dental biofilm (SDB) among smokers and non-smokers (NS).<br><br>MATERIALS AND METHODS: This cross-sectional study included 60 subjects allocated into three groups: tobacco heating system smokers (THSS), cigarette smokers (CS) and NS. SDB samples were collected, and bacterial DNA was extracted and prepared for next generation sequencing of the 16s rRNA gene hypervariable regions. Bioinformatic pipelines were applied to assess microbial diversity and taxonomic composition.<br><br>RESULTS: No significant differences were observed in alpha diversity (Observed taxa and Shannon index) or beta diversity (Bray-Curtis index) among groups. In contrast, significant differences in microbiome bacterial composition were identified across multiple taxonomic levels. At the genus level, Alysiella (p&#x2009;=&#x2009;0.016) and Propionibacterium (p&#x2009;=&#x2009;0.025) were most abundant in THSS, whereas Actinobaculum (p&#x2009;=&#x2009;0.004), Avibacterium (p&#x2009;=&#x2009;0.015) and Haemophilus (p&#x2009;=&#x2009;0.030) predominated in NS. At the species level: Alysiella filiformis (p&#x2009;=&#x2009;0.006) and Streptococcus thermophilus (p&#x2009;=&#x2009;0.025) were most abundant in THSS, Streptococcus lactarius (p&#x2009;=&#x2009;0.05) in CS, and Prevotella multiformis (p&#x2009;=&#x2009;0.016) and Lactobacillus salivarius (p&#x2009;=&#x2009;0.018) in NS group.<br><br>CONCLUSIONS: Distinct differences in bacterial composition of SDB were observed among THSS, CS and NS. The increased abundance of anaerobic bacteria with cariogenic potential in THSS and CS suggests a more dysbiotic profile and increased pathogenic potential compared to NS.<br><br>CLINICAL RELEVANCE: Variations in SDB bacterial composition may influence the pathological potential of dental biofilms in smokers and non-smokers.}, }
@article {pmid41870852, year = {2026}, author = {Ellis, JR and Powell, EJ and Tomasovic, LM and Warman, A and Chien, A}, title = {The cutaneous microbiome as a dynamic photoprotective interface against solar radiation.}, journal = {Photochemical &amp; photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology}, volume = {}, number = {}, pages = {}, pmid = {41870852}, issn = {1474-9092}, }
@article {pmid41871006, year = {2026}, author = {Londoño-Sierra, DC and Restrepo-Mesa, SL and Costa Antunes, AE and Sivieri, K and Martínez-Galán, JP}, title = {Enhancing the microbiome in the maternal-infant dyad: Perspectives from maternal and infant nutrition.}, journal = {Archivos argentinos de pediatria}, volume = {}, number = {}, pages = {e202510860}, doi = {10.5546/aap.2025-10860.eng}, pmid = {41871006}, issn = {1668-3501}, abstract = {Establishing the microbiome is an important milestone for infant health. The type of delivery, gestational age, antibiotic use, and infant feeding practices significantly impact this process. However, interest in the effects of maternal diet and nutrition has grown. The objective of this review is to present an update on the microbiota in the mother-child dyad and the role of maternal nutritional status and diet in its modulation. Scientific articles in electronic databases were reviewed. Adherence to established dietary guidelines during pregnancy and lactation, as well as otherrecommendations based on the study of foods that are sources of fiber, unsaturated fatty acids, and fermented foods, is a good starting point for promoting a healthy microbiome from the early years of life.}, }
@article {pmid41871143, year = {2026}, author = {Nguyen, AT and Kim, A and Fernando, C and Kularatne, BMDN and Palmer, DRJ and Hill, JE}, title = {Ligand-binding properties of substrate binding proteins of a maltose uptake system in Gardnerella swidsinskii.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {3}, pages = {}, pmid = {41871143}, issn = {1465-2080}, mesh = {*Maltose/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; Oligosaccharides/metabolism ; Glycogen/metabolism ; Operon ; Ligands ; Protein Binding ; Gene Expression Regulation, Bacterial ; Substrate Specificity ; *Maltose-Binding Proteins/metabolism/genetics ; }, abstract = {Glycogen and its breakdown products, maltose and malto-oligosaccharides, are important carbon sources for vaginal bacteria including Gardnerella species. MusEFGKI transport systems for maltose and malto-oligosaccharides have been identified in all Gardnerella species; however, unlike in other species, the Gardnerella swidsinskii operon encodes two substrate-binding proteins (SBPs) (MusE1345, MusE1346, ~60% amino acid identity). Two SBPs could allow binding of additional ligands, providing a competitive advantage to G. swidsinskii relative to other species with only one SBP. Our objectives were to determine if both genes are expressed in G. swidsinskii and compare the specificity and affinity of G. swidsinskii MusE SBPs for glycogen breakdown products. Gene expression analysis showed the presence of a polycistronic transcript spanning both SBP encoding genes; however, musE1346 transcripts were more abundant, likely due to the presence of an additional promoter identified in the intergenic region. No difference in the relative expression of either gene was observed in isolates grown in media supplemented with glycogen or maltotriose. Predicted structures of both SBPs were highly similar and characteristic of previously characterized maltose-binding proteins. Both proteins had a high affinity for maltose, maltotriose and maltotetraose (K d 10[-6] to 10[-7] M) and much lower affinities to maltopentaose and maltohexaose (K d 10[-3] to 10[-4] M). Our results demonstrate that the affinities of G. swidsinskii MusE SBPs for maltose and malto-oligosaccharides are similar under the same experimental conditions.}, }
@article {pmid41871593, year = {2026}, author = {von Seth, E and Karlsen, TH and Tanaka, A and Ponsioen, C and Bergquist, A}, title = {Primary sclerosing cholangitis.}, journal = {Lancet (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1016/S0140-6736(25)02582-6}, pmid = {41871593}, issn = {1474-547X}, abstract = {Primary sclerosing cholangitis is a rare, chronic cholestatic liver disease characterised by biliary inflammation and fibrosis. Inflammatory bowel disease co-occurs in 50-80% of individuals with primary sclerosing cholangitis and there is an increased risk for hepatobiliary and colorectal cancers. Primary sclerosing cholangitis presentation is highly variable but there is usually a slowly progressive fibrosis of the bile ducts with strictures, development of liver fibrosis and cirrhosis, and eventually a need for liver transplantation, after which primary sclerosing cholangitis can reoccur. Primary sclerosing cholangitis is diagnosed mostly at the asymptomatic stage but, as the disease advances, people often have itching, fatigue, upper right abdominal pain, recurrent cholangitis, or complications related to portal hypertension. There are few treatment options and its exact cause and pathogenesis remain unclear. It is widely believed that both genetic and environmental factors are important, with the intestinal microbiome increasingly recognised as crucial to disease development, progression, and outcomes. This Seminar explores the clinical features of primary sclerosing cholangitis, summarises the current understanding of its pathogenesis, and gives insights into the challenges and opportunities in managing the disease.}, }
@article {pmid41871875, year = {2026}, author = {Zhang, Y and Xu, X and Wang, S and Yin, X and Zhang, B and Zhu, Z and Ji, R and Zhu, J and He, H and Cheng, S and Han, Z and Xie, T and Zhang, X and Wang, Y and Shen, S and Kou, Y and Bao, S and Liu, Y and Cao, B and Bonny, C and Guo, X and Segal, E and Tan, Y and Shen, L and Peng, Z}, title = {Fecal microbiota transplantation combined with anti-PD-1 therapy in refractory microsatellite-stable gastric cancer: a phase I feasibility and safety study.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {3}, pages = {}, doi = {10.1136/jitc-2025-013823}, pmid = {41871875}, issn = {2051-1426}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; *Stomach Neoplasms/therapy/drug therapy ; Middle Aged ; Aged ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Feasibility Studies ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Adult ; }, abstract = {BACKGROUND: The discovery and therapeutic application of immune checkpoint inhibitors (ICIs) have significantly improved clinical outcomes in cancer treatment. However, the response rate is still low in gastrointestinal (GI) cancers. The gut microbiome's impact on immune modulation is a promising area for overcoming resistance to immunotherapy.<br><br>METHODS: This study (NCT04130763) is an open-label, single-arm, single-center, phase I study assessing the safety and efficacy of fecal microbiota transplantation (FMT) from healthy donors in 10 patients with advanced GI cancer resistant to anti-programmed death-ligand 1 (PD-(L)1) treatment. 10 patients with histologically confirmed, unresectable, or metastatic GI cancers (8 gastric, 2 colorectal) who were refractory to anti-PD-(L)1 treatment were enrolled. Patients received initial FMT treatment via oral capsules (60 capsules), followed by a combination therapy phase, where maintenance FMT (10 capsules per treatment) was paired with nivolumab at 3&#x2009;mg/kg every 2&#x2009;weeks for six cycles. Serial biomarker assessments were conducted through both fecal and blood sampling.<br><br>RESULTS: The combination of FMT and anti-PD-1 treatment was well tolerated with no serious adverse events. The objective response rate was 20% and the disease control rate was 40%. Clinical benefits were associated with colonization of donor-derived immunogenic microbes, and an activated immune status reflected by peripheral immune cell populations. Moreover, microbial signatures were identified for anti-programmed cell death protein-1 (PD-1) responsiveness and validated in an independent cohort.<br><br>CONCLUSIONS: This phase I study demonstrates the feasibility and safety of combining FMT with anti-PD-1 therapy in patients with ICI-refractory gastric cancer. The observed preliminary efficacy signals and identified microbial signatures generate hypotheses for future trials to investigate microbiome-based approaches to enhance immunotherapy efficacy.<br><br>TRIAL REGISTRATION NUMBER: NCT04130763.}, }
@article {pmid41871943, year = {2026}, author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB}, title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336675}, pmid = {41871943}, issn = {1468-3288}, abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.<br><br>OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.<br><br>DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] &#xd7; interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.<br><br>RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7&#x3b1;-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.<br><br>CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.}, }
@article {pmid41871945, year = {2026}, author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT}, title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337436}, pmid = {41871945}, issn = {1468-3288}, abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.<br><br>OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.<br><br>DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.<br><br>RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.<br><br>CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.}, }
@article {pmid41872049, year = {2026}, author = {Carpay, NC and Kamphorst, K and van Elburg, RM and Vlieger, AM}, title = {Antibiotics in the first week of life are not associated with functional gastrointestinal disorders at 9-12 years of age.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70402}, pmid = {41872049}, issn = {1536-4801}, support = {//None/ ; }, abstract = {OBJECTIVES: Dysbiosis due to early-life antibiotics may contribute to the development of functional gastrointestinal disorders (FGIDs). This follow-up study of a birth cohort primarily investigates the association between antibiotic treatment in the first week of life and the presence of FGIDs at 9-12 years. Secondarily, it examines whether a history of infantile colic or current food allergy is associated with FGIDs.<br><br>METHODS: A prospective observational birth cohort of 436 term-born infants was followed up at the age of 9-12 years; 151 received intravenous antibiotics in the first week of life due to suspected early onset sepsis (AB+) and 285 did not (AB-). Participants filled out questionnaires on the presence of FGIDs (Rome IV questionnaire) and food allergies, and FGID diagnoses were reported by general practitioners. Statistical analyses included chi-squared tests and multivariable logistic regression.<br><br>RESULTS: 306 of 388 eligible participants (79.5%) participated in the follow-up study: 109 (35.6%) AB+ and 197 (64.4%) AB-. FGID prevalence at 9-12 years was similar in AB+ and AB- (any FGID: odds ratio [OR] 1.083, 95% confidence interval [CI] 0.608-1.932). Infantile colic was not significantly associated with FAPDs after adjusting for confounders (adjusted OR 2.007, 95% CI 0.978-4.003, p&#x2009;=&#x2009;0.051). Children with a food allergy were more likely to have a functional abdominal pain disorder (FAPD) (adjusted OR 4.028, 95% CI 1.532-10.286).<br><br>CONCLUSIONS: No statistically significant association was observed between first-week antibiotics or infantile colic and FGIDs at 9-12 years of age, but FAPDs were significantly more prevalent in children with food allergies.}, }
@article {pmid41872068, year = {2026}, author = {Ben-Assa, N and Naddaf, R and Carasso, S and Dagan, O and Sason, A and Gefen, T and Geva-Zatorsky, N}, title = {Intra-species competition combats vancomycin-resistant enterococci.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2647529}, pmid = {41872068}, issn = {1949-0984}, mesh = {Animals ; *Vancomycin-Resistant Enterococci/physiology/virology/drug effects/genetics/growth &amp; development ; Mice ; *Enterococcus faecalis/physiology/virology/drug effects/genetics/growth &amp; development ; *Gram-Positive Bacterial Infections/microbiology/therapy ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics/physiology ; Humans ; *Antibiosis ; Vancomycin/pharmacology ; Female ; }, abstract = {Vancomycin-resistant Enterococcus (VRE) is a leading cause of multidrug-resistant infections in hospitalized patients, yet no reproducible microbiota therapies exist to selectively displace it. Here we harness intra-species competition within Enterococcus to suppress VRE colonization. Through in vitro screening and mouse colonization models, we identified a single antibiotic-susceptible strain, E. faecalis X98, that significantly reduced VRE burden both in vitro and in mouse experiments, whereas multi-strain consortia failed due to competitive interference among consortium members. In parallel, we subjected the vancomycin-sensitive strain E. faecalis OG1RF to phage selection, which produced a prophage-integrated derivative with convergent glycosyltransferase mutations that secreted a VRE-killing factor, conferring enhanced antagonism even without exogenous phage. These findings reveal ecological and evolutionary principles for selecting strains as targeted microbial therapeutics. Exploiting intra-species antagonism and phage-driven evolution provides a practical framework for developing microbiota-based interventions that minimize collateral damage to the microbiome while addressing antibiotic-resistant pathogens.}, }
@article {pmid41872195, year = {2026}, author = {DeVito, VL and Karamched, BR}, title = {Signed, sealed, delivered: a generalizable model for living biotherapeutic dosing and metabolism.}, journal = {NPJ systems biology and applications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41540-026-00685-4}, pmid = {41872195}, issn = {2056-7189}, abstract = {Living Biotherapeutic Products (LBPs) offer a promising therapeutic strategy for metabolic disorders rooted in gut microbiome dysfunction, yet quantitative frameworks for predicting their efficacy remain underdeveloped. We introduce the Bacterial Compartment Absorption and Transit (BCAT) model, a pharmacokinetic-pharmacodynamic framework that couples probiotic transit, endogenous microbiome metabolism, and enzymatic transformation within a unified dose-optimization setting. Building on the classical CAT model, BCAT incorporates mechanistically-derived colon compartments and treats dosing time as a control variable. We validate BCAT against clinical data for native choline metabolism and SYNB1618 probiotic trials, achieving 5% mean prediction error compared to ~30% for prior two-compartment models. Applying BCAT to trimethylaminuria (TMAU), we predict that ~10[9] CFU of engineered probiotic, administered 3-4 h before meals, achieves 95% reduction in systemic trimethylamine, matching healthy hepatic clearance. Global sensitivity analysis identifies enzyme expression level as the dominant design parameter, enforcing the broad applicability of this model. The BCAT framework generalizes to any gut microbiome-mediated metabolic disorder and provides quantitative dosing targets to guide live biotherapeutic development.}, }
@article {pmid41872294, year = {2026}, author = {Vaughn, SN and Pavlovsky, JC and Heiman, JA and Jackson, CR}, title = {Contrasting spatial and temporal structuring of seawater and sediment bacterial communities in coastal environments.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45076-1}, pmid = {41872294}, issn = {2045-2322}, }
@article {pmid41872423, year = {2026}, author = {Papagiannidou, A and Mitropoulou, M and Papantzikos, K and Petropoulou, D and Tsilingiris, D and Magkos, F and Dalamaga, M}, title = {Hypomagnesemia: A Clinical and Nutritional Update.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {41872423}, issn = {2161-3311}, abstract = {PURPOSE OF REVIEW: Hypomagnesemia, defined as low serum/plasma magnesium concentration, is a highly prevalent yet underrecognized electrolyte disorder with extensive clinical, metabolic, and nutritional implications. This review provides an updated synthesis of magnesium physiology, dietary determinants, homeostatic regulation, diagnostic challenges, and therapeutic strategies, with particular emphasis on recent meta-analyses and large-scale epidemiological evidence linking hypomagnesemia to multisystem disease.<br><br>RECENT FINDINGS: Accumulating evidence has shown consistent associations between low serum or dietary magnesium and increased risk of cardiometabolic disorders (hypertension, type 2 diabetes mellitus, metabolic syndrome, and cardiovascular disease), neuropsychiatric conditions (migraine, depression, cognitive impairment, and dementia), osteoporosis, immune dysregulation, and adverse outcomes in hospitalized, critically ill, and chronic kidney disease patients. Mechanistic studies have clarified the roles of TRPM6/7 channels, tight junction claudins, and basolateral magnesium transporters in intestinal and renal magnesium handling, elucidating pathways underlying both inherited and acquired deficiencies. Research has also highlighted the contribution of modern dietary patterns, food processing, mineral-depleted drinking water, medication use (notably proton pump inhibitors, diuretics and chemotherapeutic agents), and gut microbiome alterations to widespread subclinical deficiency. Meta-analyses of RCTs indicate that magnesium supplementation confers modest but clinically relevant improvements in blood pressure, glycemic control, inflammatory markers, endothelial function, migraine frequency, and depressive symptoms, particularly in individuals with baseline hypomagnesemia. However, serum magnesium remains an insensitive biomarker of total body magnesium status, and consensus on optimal diagnostic thresholds and replacement strategies is lacking.<br><br>SUMMARY: Magnesium deficiency contributes to a wide spectrum of multisystem disorders, and is driven by dietary insufficiency, gastrointestinal and renal losses, medication use, chronic disease, and altered microbiome function. Meta-analytic evidence supports its role as a modifiable risk factor across cardiovascular, metabolic, neurological, skeletal, and immune disorders. Dietary modification, optimized supplementation, and correction of underlying causes of deficiency remain central to management. Future research should focus on improved diagnostic tools, personalized dosing approaches and long-term outcomes of magnesium repletion. Enhancing clinical awareness and integrating magnesium evaluation into routine care may reduce the growing burden of hypomagnesemia.}, }
@article {pmid41872585, year = {2026}, author = {Gokalp, S and Dinleyici, EC and Muluk, C and Inci, A and Aktas, E and Okur, I and Ezgu, F and Tumer, L}, title = {Alterations in gut microbiota composition in children with methylmalonic acidemia, propionic acidemia, and maple syrup urine disease.}, journal = {European journal of clinical nutrition}, volume = {}, number = {}, pages = {}, pmid = {41872585}, issn = {1476-5640}, support = {TGA-2021-7036//Gazi &#xdc;niversitesi (Gazi University)/ ; }, abstract = {AIM: Methylmalonic acidemia (MMA), propionic acidemia (PA), and maple syrup urine disease (MSUD) are rare monogenic disorders that are described as intoxication-type inborn errors of metabolism (IEMs). They usually present in early life, and long-term management requires strict dietary protein restriction, which may significantly alter gut microbiota composition. Despite growing interest in microbiome research, limited data exist on gut microbiota in these disorders, and no study is available for MMA and MSUD. We aimed to describe the gut microbiota compositions in children with MMA, PA, and MSUD.<br><br>METHOD: A total of eight patients (Five MMA, one PA, and two MSUD), and 11age-matched healthy controls were enrolled. All patients were following a medically supervised, protein-restricted diet. Fecal sample was collected from each participant, and gut microbiota composition was evaluated with 16S rRNA sequencing.<br><br>RESULTS: Patients with MMA, PA, and MSUD exhibited significantly altered gut microbiota composition compared to healthy controls. Alpha diversity analysis revealed reduced microbial richness in patients, with significantly lower Chao1 and observed OTU indices (p&#x2009;<&#x2009;0.05). Beta diversity metrics demonstrated distinct clustering between groups, indicating significantly different microbial community structures. Higher relative abundances of opportunistic or dysbiotic taxa have been seen in patient group, while controls were enriched in beneficial taxa like Faecalibacterium prausnitzii, Ruminococcus, and Lactobacillus. LEfSe analysis identified 17 taxa enriched in patients-including members of Proteobacteria, Sphingobacteriia, and Streptococcus anginosus-and 6 taxa enriched in controls, notably Faecalibacterium prausnitzi.<br><br>DISCUSSION: This is the first descriptive study of the gut microbiota composition of MMA, PA, and MSUD patients. These findings indicate an association between long-term dietary management and altered microbiota composition, although causality cannot be inferred due to the cross-sectional study design. The observed alterations suggest that the gut microbiota may represent a novel therapeutic target in the management of IEMs.}, }
@article {pmid41872600, year = {2026}, author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E}, title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41872600}, issn = {1546-170X}, abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.}, }
@article {pmid41872622, year = {2026}, author = {Lee, H and Oh, Y and Seo, TW and Choi, YB and Kim, S and Cheon, S and Lee, DG and Kang, S and Han, K and Heo, YM and Mun, S}, title = {Exploring Cyclo (-Gly-Pro) for inflammation modulation in atopic dermatitis: a study on streptococcal postbiotics.}, journal = {Genes &amp; genomics}, volume = {}, number = {}, pages = {}, pmid = {41872622}, issn = {2092-9293}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by intense itching and eczematous lesions, significantly affecting quality of life. Complex interactions involving genetic predispositions, environmental factors, and immune dysregulation contribute to AD pathogenesis, with impaired skin barriers and Staphylococcus aureus playing critical roles. Recent interest in postbiotics, beneficial compounds derived from probiotics, has opened potential therapeutic avenues.<br><br>OBJECTIVE: This study investigates the postbiotic solution derived from three human skin-derived Streptococcus isolates, to identify a core bioactive compound and its therapeutic role in AD.<br><br>METHODS: Using GC-MS and GC-FID, we quantified Cyclo (-Gly-Pro) and assessed its impact on inflammatory biomarkers in an AD-like keratinocyte cell model. The effect of different incubation temperatures on the compound's production was also analyzed. Furthermore, 16S V3-V4 amplicon sequencing was performed to analyze changes in the skin microbiome of AD patients following treatment.<br><br>RESULTS: Cyclo (-Gly-Pro) was consistently present across all strains, with production inversely related to incubation temperature, peaking at 25&#xa0;&#xb0;C. Our findings suggest that optimized production conditions and potential synergistic effects with other postbiotic components could enhance therapeutic efficacy.<br><br>CONCLUSION: These results support further in vivo research to elucidate the mechanisms and validate the compound's role in AD treatment strategies, potentially leading to novel dermatological therapies.}, }
@article {pmid41872902, year = {2026}, author = {Rojas, CA and Smith, R and Oliver, R and Jospin, G and Corral, I and Ganz, HH}, title = {Temporal variability is an inherent feature of the healthy canine microbiome assessed by full-length 16S rRNA gene sequencing.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00546-9}, pmid = {41872902}, issn = {2524-4671}, }
@article {pmid41872951, year = {2026}, author = {Matei, DE and Rosser, EC}, title = {The gut-joint axis in juvenile idiopathic arthritis.}, journal = {Arthritis research &amp; therapy}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13075-026-03786-x}, pmid = {41872951}, issn = {1478-6362}, support = {KENN 21 22 09//Kennedy Trust for Rheumatology Research/ ; KENN 21 22 09//Kennedy Trust for Rheumatology Research/ ; 094//FOREUM/ ; }, }
@article {pmid41865111, year = {2026}, author = {Oliveira, AGG and Dias, MF and Haq, IU and Ferreira, JFG and Silva, CP and Moreira, M and da Silva Lanna, MC and Santos Rodrigues, LD and de Mâcedo Farias, L and Magalhães, PP}, title = {Seasonal and Source-Associated Microbiome Dynamics in Brazilian Drinking Water.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02735-0}, pmid = {41865111}, issn = {1432-184X}, }
@article {pmid41865193, year = {2026}, author = {Mathkor, DM and Aldairi, AF and Faidah, H and Babalghith, AO and Johargy, AK and Ahmad, F and Haque, S and Bantun, F}, title = {The role of breastfeeding in modulating antimicrobial resistance in neonates: a systematic review.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {41865193}, issn = {1530-0447}, abstract = {Antimicrobial resistance (AMR) is a growing health concern in neonates. Breastfeeding potentially plays a pivotal role in modulating neonatal gut microbiota, thereby influencing the acquisition and transmission of AMR genes (ARGs). This systematic review evaluates the links between breastfeeding and the origin of neonatal gut microbiota and AMR. Selection of pertinent studies published between 2015 and 2025 focusing on major outcome measures of neonatal AMR and ARG transfer was performed on scholarly databases. Following quality assessment, 22 studies met the inclusion criteria for further consideration. Evidence consistently demonstrates that breast milk is an active contributor to the microbial and genetic landscape of the neonatal gut microbiome. Further, studies implicated breast milk as a source of ARG transfer in neonates. Other reports indicated that exclusive breastfeeding and human milk-associated bioactive compounds promoted the colonization of beneficial commensals, limited colonization of multidrug-resistant species, and suppressed horizontal transfer of ARGs. Interestingly, maternal factors, such as maternal antibiotic history, lifestyle, and overall health status, appeared to influence the links between breast milk and transmission and impact of ARGs in neonates. In conclusion, while breastfeeding-based strategies are important to neonatal AMR mitigation, further mechanistic studies are required to establish causal pathways. IMPACT: Breastfeeding has an active role in altering neonatal gut microbiota and influences antimicrobial resistance (AMR) acquisition. This review synthesizes evidence from 2015-2025 indicating that breastfeeding is both a source of antimicrobial resistance genes (ARGs) and contains bioactive components that suppress ARG transmission and promote beneficial colonization. Maternal factors, such as antibiotic exposure, lifestyle, and overall health, potently influence these links. Mechanistic comprehension of the links between breastfeeding, neonatal microbiome, and AMR acquisition may allow identification of prevention strategies against neonatal infections. The analyses underscore the need for longitudinal, mechanistic studies to determine causal relationships and long-term effects of breastfeeding on neonatal AMR.}, }
@article {pmid41865545, year = {2026}, author = {Yu, F and Feng, H and Yu, Z and Jiang, J and Li, S and Meng, J}, title = {Dissolved nitrogen and phosphorus trigger Euglena sanguinea blooms via Burkholderiaceae enrichment and extracellular polymeric substance stimulation.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129428}, doi = {10.1016/j.jenvman.2026.129428}, pmid = {41865545}, issn = {1095-8630}, abstract = {As representative landscape water bodies, urban park ponds are typically shallow and hydrologically isolated, making them highly susceptible to algal blooms. This study focused on recurrent summer-autumn blooms of Euglena sanguinea in Hefei Binhu Forest Park. These blooms form thin, red, oil-slick-like surface scums that severely suppress aquatic photosynthesis. We investigated phytoplankton community succession and its drivers by collecting surface biofilm, mid-depth water, and bottom sediment samples from three representative ponds during the 2024 bloom season. Results revealed extensive E. sanguinea blooms in July-August, with surface cell density reaching 9.86 × 10[6] cells/L (42% of total) and biomass attaining 98.61 mg/L (94% of total). This bloom peak coincided with a 2.5-fold increase in surface dissolved total nitrogen (DTN) and phosphorus (DTP). Concurrently, the surface biofilm exhibited a peak extracellular polymeric substance (EPS) concentration of 43.92 mg/L and a film-forming rate of 90.73%, structurally supported by the predominance of large algal-bacterial aggregates (>64 μm), which accounted for nearly 80% of the particulate composition. The bounding EPS (BEPS), rich in tryptophan-like proteins, corresponded with peak biofilm hydrophobicity. Critically, this nutrient-enriched microenvironmental transformation selected for a low-diversity, high-dominance microbiome. Burkholderiaceae dominated the August biofilm (23%), contrasting sharply with sediment communities (dominated by Steroidobacteraceae, 7%) and post-bloom October biofilms (dominated by Sporichthyaceae, 21%). Mechanistic path analysis revealed that DTN and DTP stimulated bloom expansion not by directly promoting algae, but by enriching Burkholderiaceae and stimulating EPS production. These findings elucidate a microbially mediated pathway linking nutrient enrichment to E. sanguinea bloom formation, challenging the conventional direct nutrient-bloom paradigm. The study provides mechanistic blueprint for targeted, microbiome-informed management of urban landscape water blooms.}, }
@article {pmid41865546, year = {2026}, author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C}, title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129432}, doi = {10.1016/j.jenvman.2026.129432}, pmid = {41865546}, issn = {1095-8630}, abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.}, }
@article {pmid41865576, year = {2026}, author = {Wu, Y and Qin, L and Zhang, Y and Jia, Y and Lü, Y and Wang, N and Zheng, H and Li, L and Zhang, Z}, title = {Co-exposure to polystyrene microplastics and glyphosate induces gut microbiota dysbiosis and cognitive impairment in honeybees.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141796}, doi = {10.1016/j.jhazmat.2026.141796}, pmid = {41865576}, issn = {1873-3336}, abstract = {Microplastics, as emerging persistent environmental contaminants, can act as vectors for the absorption of other pollutants in ecosystems, such as pesticide residues. However, the combined toxicological effects of microplastics and pesticides on pollinators remain poorly understood. Here, we evaluated the toxicity of polystyrene microplastics (PS) and glyphosate (GLY), both individually and in combination, in honeybees (Apis mellifera). While no significant changes in body weight gain or food consumption were observed after 20 days of exposure, co-exposure to PS and GLY significantly increased bee mortality and induced midgut damage and microbial dysbiosis. In the gut, pathways associated with cell proliferation and differentiation, along with genes related to oxidative stress, detoxification, and immunity, were significantly downregulated. Furthermore, the combination of PS and GLY impaired sucrose responsiveness, a key cognitive behavior in bees. Brain transcriptomics indicated a downregulation of serotonergic synapse-related genes, which were correlated with shifts in core gut bacteria such as Snodgrassella and Lactobacillus. Our findings demonstrate that co-exposure to PS and GLY exacerbates gut homeostasis disruption and impairs cognitive behavior, suggesting a potential role of the gut-brain axis. This study extends our understanding of the combined ecological risks posed by multiple environmental contaminants to bees as insect pollinators and emphasizes the need for comprehensive hazard assessments in insect conservation.}, }
@article {pmid41865725, year = {2026}, author = {Wang, S and Sun, H and Lv, X and Li, J and Du, D and Guo, F and Zhang, C}, title = {Ultrasound-assisted extraction optimization of Fructus Tribuli polysaccharides: How stir-frying processing alters structures and enhances antihypertensive efficacy.}, journal = {Ultrasonics sonochemistry}, volume = {128}, number = {}, pages = {107829}, doi = {10.1016/j.ultsonch.2026.107829}, pmid = {41865725}, issn = {1873-2828}, abstract = {Fructus Tribuli (FT), the dried ripe fruit of Tribulus terrestris L., is recognized for its antihypertensive properties, which are enhanced by stir-frying without adjuvants. However, research on its polysaccharides with therapeutic potential remains limited. This study optimized the ultrasound-assisted extraction (UAE) of FT polysaccharides (FP) using response surface methodology, yielding a maximum extraction yield of 2.182 ± 0.29% under the conditions of liquid-solid ratio 20:1 mL/g, 51 min, 62 °C, and precipitation ethanol concentration of 95%. Subsequently, FP and stir-fried FT polysaccharides (SFP) were isolated, and their structural differences and antihypertensive effects were systematically compared. Structural analysis revealed notable differences between FP and SFP. Furthermore, the extraction resulted in a higher polysaccharide yield for SFP. In spontaneously hypertensive rats, both FP and SFP attenuated hypertension and vascular injury, modulated gut microbiota, increased short-chain fatty acids, and enhanced intestinal barrier function effects that were more pronounced with SFP. Mechanistically, both polysaccharides inhibited the aortic TLR4/MyD88 pathway. These results suggest that stir-frying modifies polysaccharide structure, thereby improving gut microbiome regulation, barrier protection, and vascular outcomes, highlighting the value of processing in enhancing polysaccharide efficacy. Thus, stir-frying amplifies therapeutic effects through bioactive macromolecular remodeling, advancing the understanding of Traditional Chinese medicine processing principles.}, }
@article {pmid41865866, year = {2026}, author = {Wang, Y and Wang, D and Wang, H}, title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {}, number = {}, pages = {111996}, doi = {10.1016/j.cbpa.2026.111996}, pmid = {41865866}, issn = {1531-4332}, abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.}, }
@article {pmid41865944, year = {2026}, author = {Zou, C and Liang, L and Zhao, M and Lin, L}, title = {Chlorogenic acid enhances gut microbiota regulatory effect and anti-inflammatory of Lycium barbarum polysaccharide by simulated fermentation.}, journal = {International journal of biological macromolecules}, volume = {356}, number = {}, pages = {151538}, doi = {10.1016/j.ijbiomac.2026.151538}, pmid = {41865944}, issn = {1879-0003}, abstract = {The intricate interplay between dietary components, the gut microbiome, and host immunity is a core of intestinal immune research. Lycium barbarum polysaccharide (LBP)-chlorogenic acid (CGA) complex exhibits proliferative activity of Bacteroides and strong inhibitory effect on Staphylococcus aureus, but lacks of the microbial fermentation characteristics and immunomodulatory effect. Herein, in vitro fecal bacteria microbiota and macrophages models were employed to investigated the regulatory capacity of the LBP-CGA complex on intestinal microbiota and immunomodulatory activities of its metabolites. Results showed that LBP and LBP-CGA both readily fermentable. Fermentation led to significant molecular weight and pH reductions, nearly 85% polysaccharide degradation. Notably, LBP-CGA complex was more favorable to increase the relative abundance of Sutterella, Veillonella, Faecalibacterium and contents of SCFAs than LBP. Interesting, LBP fermentation product possessed the potential for immune-enhancing, with the polysaccharide fraction was the key active component. Conversely, LBP-CGA complex fermentation product elicited the potential for immune-suppressive response, with dihydrocaffeic acid of CGA metabolites was critical contributors. The data further indicated LBP-CGA exhibited better immunomodulatory of intestinal microbiota probably due to the proliferation of Bacteroides. Bacteroides may improve the bio-transformation of CGA and produce more dihydrocaffeic acid, which may in turn potentiate the immunosuppressive activity of the LBP-CGA complex fermentation product. To summarize, the results revealed that CGA elevated the ability of LBP to regulate the intestinal microbiota and to potential exert immunosuppression. This study offers profound insights into the development of LBP-CGA complex as a prebiotic with excellent anti-inflammatory effect.}, }
@article {pmid41866241, year = {2026}, author = {Chauhan, S and Kumari, P and Deepa, N and Chanotiya, J and Trivedi, PK and Singh, A}, title = {Proteomic insights into plant-endophyte interactions: advancing understanding of mutualistic symbiosis and plant resilience.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-20}, doi = {10.1080/07388551.2026.2618190}, pmid = {41866241}, issn = {1549-7801}, abstract = {Endophytic microorganisms are a vital part of the plant microbiome, contributing significantly to the plant's growth, development, and stress tolerance. Proteomics investigations have significantly enhanced our comprehension of the interactions between plants and endophytes, illuminating the complex molecular mechanisms that govern these mutually beneficial relationships. The review aims to integrate the latest developments in proteomic research concerning endophyte-plant interactions, emphasizing on elucidating the molecular mechanisms that underlie the benefit imparted to the host plant by the symbionts. The special focus of the review is to discuss the proteome level changes happening at the early recognition events, primary and secondary metabolism, signaling pathways, and defense mechanisms. By underscoring critical proteomic signatures, the review aspires to offer insights into how these interactions enhance plant health, increase stress resilience, and promote overall growth. The article discusses the potential applications of proteomics in agriculture and environmental sciences, emphasizing its role in crop resilience against biotic and abiotic stresses, optimizing biocontrol strategies, and improving nutrient use efficiency. The article also highlights that despite the advancements, critical gaps persist including the necessity for a deeper understanding of the temporal dynamics of proteomic responses, the specificity of protein-protein interactions, and the influence of environmental factors on the proteome induced by the endophytes. The review concludes by proposing future directions for proteomics research in plant-endophyte interactions for developing a more comprehensive understanding of the intricate molecular dialogues for developing a more sustainable and resilient agricultural systems.}, }
@article {pmid41866413, year = {2026}, author = {Berkelmann, D and Zuñiga-Umaña, JM and Chaverri, P and Solano, W and Gatica-Arias, A}, title = {Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866413}, issn = {1573-0972}, support = {111-C1-472//Vicerrector&#xed;a de Investigaci&#xf3;n, Universidad de Costa Rica/ ; }, mesh = {*Plant Diseases/microbiology ; *Coffea/microbiology ; Plant Leaves/microbiology ; *Basidiomycota/genetics/classification/isolation &amp; purification ; DNA, Fungal/genetics ; Costa Rica ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; *Fungi/genetics/classification/isolation &amp; purification ; Coffee/microbiology ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.}, }
@article {pmid41866421, year = {2026}, author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R}, title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866421}, issn = {1573-0972}, }
@article {pmid41866543, year = {2026}, author = {Lu, Q and Chen, S and Shan, B and Wei, A and Luo, Y and Wu, L and Jiang, Q and Chen, Z}, title = {Rhizosphere microbiome dynamics and hormonal interactions regulating tiller development in sugarcane cultivars.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-38474-y}, pmid = {41866543}, issn = {2045-2322}, support = {32201392//National Natural Science Foundation of China/ ; 2024GXNSFBA010329//Natural Science Foundation of Guangxi Province/ ; Guike AA24263045//Guangxi Major Science and Technology Program/ ; }, abstract = {Sugarcane tillering is a key determinant of crop productivity, yet the integrated roles of rhizosphere microbiome dynamics, nutrient status, and hormone signaling in regulating tiller development remain poorly understood. Here, we compared rhizosphere microbial communities, endogenous hormone profiles, and nutrient element concentrations in sugarcane cultivars with contrasting tillering capacities. High-tillering varieties exhibited significantly greater microbial diversity and more complex co-occurrence network structures in the rhizosphere, characterized by enrichment of Acidobacteriota, Chloroflexi, and Planctomycetes and functional pathways related to nitrogen fixation, phosphorus solubilization, and auxin biosynthesis. In contrast, low-tillering varieties harbored simplified, stress-adapted microbial consortia and prioritized pathways linked to oxidative stress response and heavy metal detoxification. Hormonal analysis revealed that high-tillering cultivars maintained higher levels of growth-promoting hormones-particularly auxin (IAA) and active cytokinins-in tiller buds while low-tillering cultivars accumulated elevated abscisic acid (ABA) and inactive cytokinin conjugates. Nutrient analysis indicated that high-tillering genotypes possessed higher nitrogen and phosphorus contents, supporting vigorous axillary bud activation and shoot proliferation, whereas low-tillering varieties accumulated more zinc and manganese, potentially reflecting stress adaptation. Network-level integration of microbial, hormonal, and nutrient profiles underscored genotype-specific feedback between rhizosphere microbiota and plant physiological states, highlighting modular associations that link microbial hubs with tissue-specific nutrient and hormone signatures. Our findings reveal a systems-level mechanism by which rhizosphere microbial community structure and function interact with plant-nutrient-hormonal status to regulate tillering in sugarcane. These insights provide a basis for microbiome-informed strategies to enhance sugarcane productivity through integrated nutrient-hormonal-microbe management.}, }
@article {pmid41866581, year = {2026}, author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW}, title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45459-4}, pmid = {41866581}, issn = {2045-2322}, support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; }, }
@article {pmid41866722, year = {2026}, author = {Chen, SJ and Wayne, CD and Jacobs, TH and Besner, GE}, title = {Rethinking probiotic delivery: new hope for preventing necrotizing enterocolitis.}, journal = {Expert opinion on drug delivery}, volume = {}, number = {}, pages = {}, doi = {10.1080/17425247.2026.2648748}, pmid = {41866722}, issn = {1744-7593}, abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is a devastating disease of the gastrointestinal tract that mainly affects premature newborns, with mortality rates exceeding 50% in the most severe cases. Despite decades of research the disease persists, there is no known cure, and treatment consists of supportive care only. Dysbiosis of the gut microbiome has been implicated as a contributing factor to the development of NEC. With a deepening understanding of the therapeutic efficacy of probiotics in reversing intestinal dysbiosis, a potential avenue to prevent this disease has emerged.<br><br>AREAS COVERED: Through review of the literature related to probiotics in NEC and novel oral delivery methods for probiotics, we will discuss what is known about preventing NEC with commercially available probiotics. We will discuss the challenges imposed on probiotic therapy by the September 2023 FDA warning on probiotic administration to premature babies. We will also examine novel delivery methods for probiotics that can enhance their beneficial capabilities.<br><br>EXPERT OPINION: By obtaining approval for novel oral probiotic delivery technologies including biofilm formation and prebiotic co-ride, the risk of NEC in premature infants could be significantly decreased.}, }
@article {pmid41866998, year = {2026}, author = {Ebigbo, N}, title = {The esophageal microbiome: mechanisms and clinical implications.}, journal = {Current opinion in gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOG.0000000000001170}, pmid = {41866998}, issn = {1531-7056}, abstract = {PURPOSE OF REVIEW: Interest in the esophageal microbiome has expanded rapidly, yet its functional and clinical relevance remains incompletely defined. This review synthesizes emerging evidence on host-microbe interactions in esophageal diseases, with a focus on mechanistic pathways and translational potential.<br><br>RECENT FINDINGS: Recent studies demonstrate that esophageal microbes influence epithelial differentiation, barrier integrity, and inflammatory signaling in conditions such as eosinophilic esophagitis and Barrett's esophagus. Microbial metabolism, particularly bile acid transformation, links microbial composition to epithelial stress responses and neoplastic progression. In esophageal cancer, tumor-associated microbes modulate epigenetic regulation and suppress antitumor immunity. Integrative multiomics approaches have further identified microbial signatures associated with disease progression and treatment response.<br><br>SUMMARY: The esophageal microbiome influences disease pathogenesis and has potential for risk stratification and therapeutic targeting. Future progress will depend on longitudinal studies, improved functional resolution, and integration of microbial data with epithelial and immune biology to enable clinical translation.}, }
@article {pmid41867064, year = {2026}, author = {Nikam, R and Pax, K and Beverly, ML and Kumar, PS}, title = {Mapping the subgingival HerBiome and HisBiome over the human healthspan.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70098}, pmid = {41867064}, issn = {1943-3670}, support = {/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: Understanding the intricate relationship between sex, age, and the oral microbiome is crucial for deciphering the onset and progression of numerous age-related oral and systemic diseases.<br><br>METHODS: Subgingival plaque was collected from 781 periodontally and systemically healthy females and 160 males spanning 0 to 80 years. 16S amplicon sequencing was performed. 80 million sequences were annotated and analyzed through the QIIME pipeline, principal components analysis (PCA) used for dimensionality reduction, LefSe to identify driver species, beta dispersion to measure inter-subject variability, and machine learning algorithm (RandomForest package in R [RF]) to validate the results. Causal mediation models were implemented to investigate the influence of aging on the male and female microbiomes.<br><br>RESULTS: PCA demonstrated significant class separation based on sex (p&#xa0;<&#xa0;0.001, permutational multivariate analysis of variance [PERMANOVA]). Males demonstrated higher alpha diversity (p&#xa0;<&#xa0;0.001, Wilcoxon signed-rank test of the Shannon diversity index), but also higher inter-subject heterogeneity p&#xa0;<&#xa0;0.001, ANOVA). RF identified males with 0.99 sensitivity, 0.15 specificity, and accuracy of 85%. Age exerted an almost complete mediation effect, with significant differences in the trajectory and pattern of aging between males and females. Females&#xa0;>&#xa0;30 demonstrated a lower microbial diversity (p&#xa0;<&#xa0;0.001) and higher levels of Fusobacterium nucleatum (p&#xa0;<&#xa0;0.001), while the male microbiome remained highly personalized throughout the lifespan, without defined patterns of aging.<br><br>CONCLUSIONS: Sex and age interact to influence the subgingival microbiome. These findings might explain differing disease susceptibilities in either sex, as well as informing personalized prevention and intervention based on age and sex. Further studies using granular -omics approaches are needed to advance our knowledge.<br><br>PLAIN LANGUAGE SUMMARY: Periodontal (gum) diseases are caused by a breakdown in the intricate balance between bacteria that live under the gumline and the local immune response. Since periodontal diseases have been reported to be more common in men than in women, we set out to investigate whether these bacterial communities are intrinsically different between the 2 sexes, and whether these differences are sustained over the lifespan. Using deep-sequencing technology to analyze the microbiomes of 941 individuals, we discovered that sex at birth is indeed a determining factor in the types of bacteria that live under the gums. Aging trajectories and patterns also differ between men and women, with women demonstrating a distinct shift after 30 years of age, and men showing no definite age-based change. These findings have important implications for the cause of periodontitis in either sex, as well as the potential to personalize therapy based on age and sex.}, }
@article {pmid41867134, year = {2026}, author = {Piraccini, BM and Micali, G and Fulgione, E and Guida, S and Caldarola, G}, title = {Experts' view on the management of scalp seborrheic dermatitis in Italy.}, journal = {The Journal of dermatological treatment}, volume = {37}, number = {1}, pages = {2644012}, doi = {10.1080/09546634.2026.2644012}, pmid = {41867134}, issn = {1471-1753}, mesh = {Humans ; *Dermatitis, Seborrheic/diagnosis/drug therapy ; Italy ; Antifungal Agents/administration &amp; dosage/therapeutic use ; Algorithms ; *Scalp Dermatoses/diagnosis/drug therapy ; *Dermatologic Agents/administration &amp; dosage/therapeutic use ; Severity of Illness Index ; Acne Vulgaris/drug therapy/diagnosis/complications ; Adolescent ; Diagnosis, Differential ; }, abstract = {BACKGROUND: Acne vulgaris is a common skin disorder that negatively affects adolescents' quality of life. Recent evidence suggests that combining isotretinoin with desloratadine may enhance treatment outcomes.<br><br>OBJECTIVES AND METHODS: This study aimed to develop a practical algorithm for SSD management in Italy, by gathering insights from Italian dermatology experts on diagnosis, treatment and long-term management of SSD.<br><br>RESULTS: According to literature review and clinical experience, accurate diagnosis of SSD requires medical history, clinical evaluation, disease severity assessment and trichoscopy. The differentiation of SSD from psoriasis, eczema, and tinea capitis is essential to guide appropriate treatment, which should counteract the main pathogenic mechanisms underlying the disease and be tailored to the severity of clinical manifestations. Topical antifungals are the first-line treatments due to their efficacy in reducing Malassezia colonization. The use of topical anti-inflammatory agents, including corticosteroids, is useful for moderate-to-severe cases, but should be limited due to potential adverse effects. Selenium disulfide may be a useful option for both acute symptom control and long-term maintenance because of its antifungal, sebostatic, keratolytic, and microbiome-restoring properties, associated with a high degree of patient satisfaction. Systemic antifungals may be considered in refractory cases.<br><br>CONCLUSION: This experts' view provides a structured approach to SSD management in Italy, integrating clinical experience and scientific evidence.}, }
@article {pmid41867523, year = {2026}, author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S}, title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.}, journal = {ACS omega}, volume = {11}, number = {10}, pages = {16913-16921}, pmid = {41867523}, issn = {2470-1343}, abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.}, }
@article {pmid41867679, year = {2026}, author = {Biagioli, V and Matera, M and Cavecchia, I and Illiceto, M and Pennazzi, L and Luongo, G and Lugli, S and Striano, P}, title = {Beyond breastfeeding: a One Health Decalogue for nurturing the infant microbiota.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1784544}, pmid = {41867679}, issn = {2296-861X}, abstract = {BACKGROUND: Early-life nutrition is a key determinant of infant gut microbiota development, immune maturation, and long-term health outcomes. Although breastfeeding is widely recognized as the optimal feeding strategy, many mothers are unable to breastfeed, underscoring the need for practical, evidence-based guidance to support infant health beyond breastfeeding. A One Health approach enables the integration of nutritional, microbial, clinical, environmental, and socio-cultural factors that influence maternal-infant dyads.<br><br>METHODS: A narrative review of the literature was conducted using PubMed, Scopus, and Google Scholar, focusing more on works published from 2020 to 2026. Evidence was synthesized on maternal and infant nutrition, breast milk bioactive components, infant formula feeding, gut microbiota development, and short- and long-term health outcomes in non-breastfed infants. Based on this interdisciplinary evidence, a translational "One Health Decalogue" was developed for mothers who are unable to breastfeed.<br><br>FINDINGS: The reviewed literature highlights that infant nutrition, particularly in the absence of breastfeeding, significantly influences gut microbiota composition, immune programming, metabolic regulation, and neurodevelopment. Key modifiable factors include formula composition, feeding practices, maternal health status, environmental exposures, caregiver education, and psychosocial support. The proposed One Health Decalogue synthesizes these elements into 10 actionable principles aimed at supporting microbial resilience, promoting healthy development, and reducing health inequalities when breastfeeding is not possible.<br><br>CONCLUSION: Translating scientific evidence into practical tools is essential to support infants who cannot be breastfed. The One Health Decalogue presented in this review provides a comprehensive, interdisciplinary, and translational framework for healthcare professionals, families, and public health policies, fostering informed nutritional choices and holistic strategies to optimize infant health beyond breastfeeding.}, }
@article {pmid41867689, year = {2026}, author = {Zhong, L and Qing, Y and Liu, J}, title = {The role of enteral nutrition and parenteral nutrition in the management of inflammatory bowel disease: a bibliometric analysis (1999-2025).}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1767514}, pmid = {41867689}, issn = {2296-861X}, abstract = {OBJECTIVES: As a chronic disease often accompanied by malnutrition, Inflammatory Bowel Disease (IBD) has encountered many difficulties in long-term management. Enteral nutrition (EN) and parenteral nutrition (PN) are important methods to help improve nutritional status and support the remission of the disease. However, although increasing attention has been directed toward this kind of nutritional therapy, there is still a lack of detailed and accurate bibliometric analysis in this field. Therefore, the goal of this study is to find out the research trends and hot spots, and provide reference for future academic exploration and clinical practice.<br><br>METHODS: On November 26th, 2025, publications concerning EN, PN in IBD published from 1999 to 2025 were retrieved from two databases: Web of Science Core Collection and Scopus. In this study, R software, Microsoft Excel, VOSviewer and CiteSpace are used to measure and visually analyze the articles.<br><br>RESULTS: A total of 3,245 documents were reviewed, indicating a trend of power-law growth. The USA and UK lead in global collaboration, with China being third in volume but with less cooperative intensity. The study identifies a clear progression from early "total parenteral nutrition" and "corticosteroids" to "exclusive enteral nutrition". Citation bursts occurring in the years 2020 to 2025 included "Mediterranean diet," "gut microbiome," and "Crohn's disease exclusion diet," pointing to an emerging focus in personalized, whole-food-based therapies and microbiome modification.<br><br>CONCLUSION: The research on nutritional therapy of IBD demonstrates a rapid increase, which shows that it is becoming more and more important in helping patients control their illness. In the future, we need more high-quality research to turn these data into useful and multidisciplinary treatment guidelines.}, }
@article {pmid41867705, year = {2026}, author = {Barrodia, P and Saw, AK and Jeter-Jones, SL and Chang, CC and Shao, J and Arslan, E and Singh, AK and Satpati, S and Jenq, RR and Rai, K and Piwnica-Worms, H}, title = {Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.06.710208}, pmid = {41867705}, issn = {2692-8205}, abstract = {UNLABELLED: Fasting enhances small intestinal regeneration after radiation but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKK 's metabolic output. AKK -conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK -dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of persister stem cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu , Olfm4 , Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister stem cells for rapid regeneration of the intestinal epithelium following radiation-induced injury.<br><br>SIGNIFICANCE STATEMENT: Fasting changes the gut microbiome, but how these changes help the body recover from damage is not well understood. We found that fasting increases a helpful bacterium, Akkermansia muciniphila , which produces propionate, which drives epigenetic changes by modifying histones and regulating gene activity. These changes promote the expansion of persister stem cells that help the intestine recover after radiation. This study shows how fasting and gut bacteria work together to protect healthy tissue and suggests that diet or microbial treatments could help reduce side effects of cancer radiotherapy.}, }
@article {pmid41867794, year = {2026}, author = {Alviter-Plata, A and Ahmari, N and Gadient, J and Brammer-Robbins, E and Martyniuk, CJ and Zubcevic, J}, title = {Loss of Bone Marrow β1/β2-Adrenergic Receptors Reprograms Host-Microbiota Interactions and Protects Against Diet-Induced Obesity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.05.707516}, pmid = {41867794}, issn = {2692-8205}, abstract = {The gut ecosystem is shaped by multiple factors with the immune system being one of the major determinants in shaping its composition in health and disease. On the other hand, the immune system regulates its responses through the action of the sympathetic nervous system (SNS) in part through beta-adrenergic receptors 1/2 (ADRB1/2). In the past years, a clear link has been established between the immune system, SNS, and the modification of nutrient absorption by the gut microbiota in the development of diet-induced obesity. We have previously shown in male mice transplanted with bone marrow cells ADRB1/2 knock-out mice (KD) showed mild immunosuppression and microbiota changes. Post-recovery, mice were challenged with high-fat diet (HFD) for two weeks ad libitum . Our findings show that KD mice are protected against diet-induced adiposity and weight gain. Additionally, these mice showed an increase in residual calorific values and a decreased expression of the fatty acid transporter FAT/CD36. Suggesting a decreased absorption of lipids in the KD mice. Gut microbiota analysis showed that KD microbiota composition on a HFD remained stable with a significant enrichment in the Bacteroidetes phylum , which is depleted in obesity. This was associated with a switch from triglycerides to diglyceride fecal profile. Moreover, microbiome culture showed a decrease in triglycerides after an incubation with 0.1% of HFD lipid extract. Suggesting a potential role of the Bacteroidetes phylum in the metabolism of these lipids. Our findings demonstrate not only that the gut microbiota can modify nutrient absorption and susceptibility to diet-induced obesity but also that the immune system contributes to selective depletion of microbial members that would otherwise thrive on dietary lipids. Revealing a novel mechanism by which host immunity sculpts the gut ecosystem in ways that influence metabolic outcomes.}, }
@article {pmid41867919, year = {2026}, author = {Morrin, ST and Buck, RH and Hill, DR}, title = {A unique blend of five human milk oligosaccharides supports recovery of infant microbiome composition and function after ex vivo antibiotic use.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1765159}, pmid = {41867919}, issn = {2296-2360}, abstract = {Human milk oligosaccharides (HMOs) are the third most abundant solid component of human breast milk, with well-established prebiotic and immunomodulatory functions. HMOs serve as selective substrates to support the growth of beneficial microbes in the developing gastrointestinal tract. At the same time individual HMOs have been shown to also exert selection against pathogens via direct anti-adhesive mechanisms. A longstanding hypothesis has held that HMOs act in concert and with other bioactive components of milk, and that this complex matrix of milk components collectively accounts for both the benefits to microbiome development and reduced risk of infectious disease associated with breastfeeding. The prebiotic activity of a diverse blend of fucosylated, acetylated, and sialylated HMOs was examined using microbiota cultured in an ex vivo model of the infant gastrointestinal tract before, during and after the supplementation of common childhood antibiotics. The anti-adhesive activity of this blend against infant-prevalent bacterial pathogens was tested using in vitro cultured intestinal epithelial cells. Taken together, this data suggests that a blend of 5 specific HMOs acts through multiple selection mechanisms to shape the development of the microbiota and interrupt opportunistic microbial pathogenesis.}, }
@article {pmid41868041, year = {2026}, author = {Yu, S and Shu, W and Zhang, J and Cheng, S and Shen, X and Chen, G and Zhang, T and Dong, K and Zhang, J and Wang, H}, title = {Gut Microbiota-Immune Interactions in Endometrial Cancer: Causal Mediation and Subtype-Specific Mechanisms.}, journal = {International journal of women's health}, volume = {18}, number = {}, pages = {583327}, pmid = {41868041}, issn = {1179-1411}, abstract = {PURPOSE: In this study, we applied two-sample Mendelian randomization (MR) to explore the causal effects between gut microbiota (GM), immune cells, and endometrial cancer (EC) subtypes and to assess whether immune cells mediate the impact of GM on EC.<br><br>PATIENTS AND METHODS: Using two-sample Mendelian randomization and mediation analysis, we analyzed GWAS data: GM (Dutch Microbiome Project; N=7738), EC subtypes (IEU Open GWAS; N=331,588), and immune traits (N=3757). We assessed the effects of the causal gut microbiota on EC subtypes and immune trait mediation.<br><br>RESULTS: Subtype-specific causal relationships were identified.Overall EC: Four positive (e.g. genus Erysipelotrichaceae noname) and three negative (e.g. species Bacteroides faecis) microbial causal effects; three mediated by immune traits (e.g. Ruminococcus obeum via CD86+ myeloid DC AC). Endometrioid EC: Five negative (e.g. class Bacilli) and two positive (e.g. species Aspergillus senegalensis) effects; three immune-mediated (e.g. Bacilli via IgD+ CD38br % lymphocytes). Non-endometrioid EC: Two positive (e.g. species Bacteroides stercoris) and one negative (species Ruminococcus bromii) effect; one mediated (Ruminococcus bromii via CD8br NKT % lymphocytes).<br><br>CONCLUSION: Immune traits significantly mediated causal pathways from GM to EC development. It also highlighted the distinct causal relationships and immune-mediated mechanisms across the three major EC subtypes (overall, endometrioid, and non-endometrioid). These subtype-specific insights into the gut-immune-cancer axis provide novel perspectives for developing therapeutic strategies targeting GM and the immune microenvironment in different EC subtypes.}, }
@article {pmid41868135, year = {2026}, author = {Wen, P and Zhuo, X and Xue, S}, title = {Fatty acid-related immune network in psoriasis: metabolic regulation of innate and adaptive immunity.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1731683}, pmid = {41868135}, issn = {1663-9812}, abstract = {Psoriasis is a chronic inflammatory skin disorder driven by dysregulation of the Treg/Th17 axis, where enhanced Th17 activity promotes keratinocyte proliferation and inflammation, while impaired Treg function exacerbates immune dysregulation. Emerging evidence highlights peroxisome proliferator-activated receptor γ (PPARγ) as a key regulator of fatty acid oxidation (FAO), a metabolic pathway critical for Treg differentiation and function. PPARγ activation enhances FAO via upregulation of CD36, CPT1, and AMPK signaling, while suppressing glycolysis, thereby skewing the Treg/Th17 balance toward immune tolerance. Concurrently, short-chain fatty acids (SCFAs), microbial metabolites with immunomodulatory properties. ameliorate psoriatic inflammation by promoting Treg expansion, inhibiting Th17 polarization, and modulating innate immune cells (neutrophils, dendritic cells, and macrophages). SCFAs exert their effects through receptor-dependent signaling and epigenetic mechanisms (HDAC inhibition), while derivative compounds and probiotic interventions enhance therapeutic potential. This review summarizes mechanistic insights into PPARγ-driven FAO and SCFA-mediated immunomodulation, proposing novel metabolic and microbiome-targeted strategies for psoriasis treatment.}, }
@article {pmid41868170, year = {2026}, author = {Zhang, J and Zhang, M and Wu, X and Jing, H and Li, P and Wang, W and Guo, X and Zhao, Z and Zhu, S and Wang, Y}, title = {Circulating Butyrate Attenuates Cetuximab Efficacy in Colorectal Cancer Through EGFR and AMPK-Wip1 Signaling.}, journal = {Drug design, development and therapy}, volume = {20}, number = {}, pages = {574116}, pmid = {41868170}, issn = {1177-8881}, mesh = {*Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Cetuximab/pharmacology ; Humans ; ErbB Receptors/metabolism/antagonists &amp; inhibitors ; Signal Transduction/drug effects ; *AMP-Activated Protein Kinases/metabolism ; *Butyrates/pharmacology/blood ; Animals ; Mice ; Cell Proliferation/drug effects ; Drug Screening Assays, Antitumor ; *Adaptor Proteins, Signal Transducing/metabolism ; *Antineoplastic Agents, Immunological/pharmacology ; Neoplasms, Experimental/drug therapy/pathology/metabolism ; Dose-Response Relationship, Drug ; Mice, Nude ; Tumor Cells, Cultured ; }, abstract = {BACKGROUND: Cetuximab is an approved therapy for metastatic colorectal cancer (CRC) with wild-type RAS and BRAF; however, additional resistance mechanisms beyond genetic mutations remain poorly understood. Butyrate, a key metabolite produced by the gut microbiome and present in the circulatory system, has been reported to supply cellular energy and modulate the epidermal growth factor receptor (EGFR) downstream signaling pathway. However, whether butyrate affects the resistance to cetuximab is still unknown.<br><br>METHODS: In this work, Cell Counting Kit-8 (CCK-8) and colony formation assays were used to evaluate the efficacy of cetuximab. Glycolysis/oxidative phosphorylation (OXPHOS) Assay Kit was applied to assess metabolic activity. Human Phospho-Kinase Array and RNA sequencing were employed to screen targets of butyrate. Overexpression plasmids and short hairpin RNAs (shRNAs) targeting these molecules were transfected into cells for further validation. Subcutaneous tumor and pulmonary metastasis models were used for in vivo studies.<br><br>RESULTS: The findings showed that physiological concentrations of butyrate increased cetuximab resistance in KRAS wild-type cells only. Further investigation found that butyrate upregulated EGFR signaling through facilitating the binding reaction between epidermal growth factor (EGF) and EGFR. In parallel, butyrate activated AMP-activated protein kinase (AMPK)-wild-type p53-induced phosphatase 1 (Wip1) signaling, leading to suppression of p53 and p38 mitogen-activated protein kinase (p38 MAPK)-mediated pro-apoptotic signaling. These two mechanisms are the reason that butyrate attenuates the efficacy of cetuximab. Results of subcutaneous tumor and pulmonary metastasis models exhibited a similar conclusion to in vitro experiments.<br><br>CONCLUSION: Butyrate reduces cetuximab efficacy in KRAS wild-type colorectal cancer through EGFR and AMPK-Wip1 signaling, and may represent a candidate predictive biomarker for treatment response.}, }
@article {pmid41868349, year = {2026}, author = {Liang, J and Huang, T and Li, J and Yang, Z and Ni, J and Wang, Y}, title = {The chemistry of the nitrate-nitrite-nitric oxide pathway: regulating muscle oxygenation and exercise performance.}, journal = {RSC advances}, volume = {16}, number = {17}, pages = {15723-15735}, pmid = {41868349}, issn = {2046-2069}, abstract = {Nitric oxide (NO) is a pleiotropic signaling molecule fundamentally involved in regulating skeletal muscle physiology, including blood flow, contractility, and metabolism. For decades, the synthesis of NO was attributed solely to the l-arginine-dependent nitric oxide synthase (NOS) enzymes. However, the discovery and characterization of the nitrate-nitrite-NO pathway have revealed an alternative, NOS-independent mechanism for NO generation. This pathway is particularly significant under hypoxic and acidic conditions, which are characteristic of exercising skeletal muscle. Dietary inorganic nitrate, abundant in green leafy vegetables and beetroot, is sequentially reduced to nitrite and then to bioactive NO. This review critically examines the intricate chemistry underpinning this pathway, from the initial enzymatic reduction of nitrate by both mammalian and microbial reductases to the diverse chemical routes of nitrite reduction to NO within the muscle milieu. We delve into the specific roles of key proteins such as xanthine oxidoreductase, deoxyhemoglobin/deoxymyoglobin, and mitochondrial complexes in catalyzing these transformations. Furthermore, we explore how NO generated via this pathway modulates muscle oxygenation through vasodilation and regulation of mitochondrial respiration. The ergogenic potential of dietary nitrate supplementation is discussed in the context of human exercise performance, highlighting the significant controversies, methodological challenges, and sources of inter-individual variability, including genetics and the microbiome. This review aims to provide a comprehensive, chemistry-focused perspective on the nitrate-nitrite-NO pathway, bridging fundamental biochemical mechanisms with their physiological consequences in exercise.}, }
@article {pmid41868361, year = {2026}, author = {Zhang, Y and Pang, Y and Tan, H and Xian, R and Liang, J and Wen, Q and Li, Z and Yan, L and Xie, Z and Li, J and Fu, W and Zhou, P}, title = {Electroacupuncture alleviates comorbid obesity and depression via the gut-brain axis: orchestrating SCFA-producing bacteria and hippocampal synaptic plasticity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772788}, pmid = {41868361}, issn = {1664-302X}, abstract = {INTRODUCTION: Comorbid obesity and depression (COMBD) represents a complex metabolic-neuropsychiatric challenge with limited therapeutic options. While Electroacupuncture (EA) is effective for both metabolic and mood disorders, the systemic mechanisms-particularly the interplay between the gut microbiome and hippocampal plasticity-remain elusive.<br><br>METHODS: We established a COMBD rat model using a high-fat diet combined with chronic unpredictable mild stress (CUMS). An integrated multi-omics approach comprising 16S rDNA sequencing, LC-MS/MS serum metabolomics, and hippocampal transcriptomics was utilized to decipher the therapeutic mechanisms of EA.<br><br>RESULTS: EA treatment significantly attenuated body weight gain and reversed depressive-like behaviors. Crucially, EA restructured the dysbiotic gut microbiota, specifically increasing the abundance of short-chain fatty acid (SCFA)-producing bacteria. This microbial restoration was strongly correlated with a reprogrammed serum metabolic profile. In the hippocampus, transcriptomic analysis identified Cd74 as a pivotal upstream regulator modulated by EA. Furthermore, EA mitigated hippocampal oxidative stress and restored synaptic plasticity, evidenced by increased dendritic spine density and upregulated synaptic protein expression.<br><br>CONCLUSION: Our findings suggest that EA ameliorates COMBD via a coordinated "Microbiota-Metabolism-Brain" axis. Specifically, EA creates a neuroprotective milieu by promoting beneficial SCFA-producing bacteria and regulating metabolic signals, which subsequently targets hippocampal Cd74 to restore synaptic plasticity. This study provides a novel mechanistic basis for the clinical application of EA in treating complex metabolic-mood comorbidities.}, }
@article {pmid41868364, year = {2026}, author = {Yin, J and Wang, H and Cui, Y and Zhou, X and Zhang, S and Yin, H}, title = {Bacteriophage-mediated gut microbiota regulation: a bibliometric landscape analysis (2005-2024).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768117}, pmid = {41868364}, issn = {1664-302X}, abstract = {OBJECTIVE: This study systematically evaluates the current situation, knowledge structure and development trend of bacteriophage-mediated intestinal microbiota regulation research from 2005 to 2024 through literature measurement analysis.<br><br>METHOD: Retrieve relevant research from the Web of Science core collection, Scopus and PubMed databases. After screening according to inclusion criteria, CiteSpace, VOSviewer, and R-bibliometrix were employed for bibliometric and visualization analysis. This systematically mapped publication trends, collaboration networks among countries/institutions/authors, core journals, and research hotspots.<br><br>RESULTS: Thousands of relevant studies were included. From 2005 to 2024, the number of papers published in microbiology journals showed a step-by-step increase, reaching a peak of 355 articles in 2022. The United States and China are the main contributors. University College Cork in Ireland and San Diego State University in the United States have become core research institutions, and Colin Hill is listed as the most influential author. The Frontiers in Microbiology has published the largest number of papers, and Microbiome and Nature Communications have become platforms for the publication of high-impact research results. The research focus has shifted from the description of early bacteriophage-bacterial binary interaction to exploring the ternary relationship of "bacteriophage-microbiota-host health." In recent years, short-chain fatty acids, microbiota disorders and clinical intervention have become the core research directions. This study included 16 clinical trials on phage-mediated gut microbiota regulation, 14 of which were based on moderate to high-quality clinical evidence, indicating that research design in this field has advanced from the initial observational stage to the intervention verification stage.<br><br>CONCLUSION: This research systematically sorts out the research progress of 20&#x202f;years in the field of bacteriophage-mediated intestinal microbiota regulation through the method of literature metrology. The research clearly outlines the evolutionary trajectory of this field from basic description to mechanism exploration to clinical transformation. Future research should focus on the following directions: clarifying the molecular mechanism of the interaction of core diseases, establishing a standardized research framework, and carrying out large-scale multi-center clinical trials to promote the transformation of this field from basic research to clinical application.}, }
@article {pmid41859031, year = {2026}, author = {Motlak, M and Gill, C and Guzzardi, E and Barlow, S and Guilarte, G and Choudhary, S}, title = {Alcohol Use and Hidradenitis Suppurativa: An Unclear Relationship.}, journal = {Skin appendage disorders}, volume = {}, number = {}, pages = {}, pmid = {41859031}, issn = {2296-9195}, abstract = {BACKGROUND: Hidradenitis suppurativa (HS) may be linked to behavioral factors that exacerbate inflammation, gut microbiome, and healing.<br><br>SUMMARY: This review evaluates current evidence on the relationship between alcohol consumption and HS. Emerging studies show high incidences of alcohol and substance use disorders in HS patients. However, observational studies remain inconsistent: HS patients may experience higher alcohol-related burden, yet its association to disease progression and baseline severity remains unclear. Limitations of existing studies include self-reported exposures of alcohol, heterogeneous outcome measures, and potential confounding factors, such as stress.<br><br>KEY MESSAGES: Biologic plausibility remains, as alcohol can promote dysbiosis, inflammation, and oxidative stress that may influence disease activity and healing. This review highlights the need for larger, controlled trials that determine whether the reduction or elimination of alcohol may improve HS outcomes.}, }
@article {pmid41859075, year = {2026}, author = {Chen, M and Zhang, J and Yang, H and Lei, L and Yang, L and Wang, S and Yu, H}, title = {JK5G postbiotics modulate gut microbiota and metabolome to alleviate cancer-related pain: a randomized controlled trial with multi-omics integration.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1764491}, pmid = {41859075}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; Middle Aged ; Female ; *Probiotics/administration &amp; dosage ; *Cancer Pain/metabolism/microbiology/therapy/etiology ; Quality of Life ; Double-Blind Method ; Adult ; Metabolomics/methods ; Aged ; Feces/microbiology ; Multiomics ; }, abstract = {INTRODUCTION: Cancer-related pain remains a critical clinical challenge, with existing opioid-based therapies often yielding inadequate relief and significant side effects. This study investigates the therapeutic potential of JK5G postbiotics-a formulation of inactivated Lactobacillus strains and metabolites-in modulating the gut-microbiome-immune axis to alleviate pain in cancer patients.<br><br>METHODS: This study employs a randomized, double-blind, placebo-controlled trial design involving 149 participants divided into two groups: a control group receiving patient-controlled subcutaneous analgesia (PCSA) plus placebo, and an experimental group receiving PCSA plus JK5G postbiotics. The primary outcomes were changes in gut microbiota composition assessed by 16S rRNA gene sequencing, and quality of life (QoL). The secondary outcomes included fecal metabolomics, adverse effects (AEs), blood inflammatory cytokines, and lymphocyte subsets. This study was registered at www.chictr.org.cn(ChiCTR2500108811).<br><br>RESULTS: JK5G supplementation significantly improved pain scores, QoL, and cognitive and social functioning compared to controls. Microbiome analysis revealed enrichment of beneficial taxa such as Akkermansia muciniphila and Bifidobacterium, alongside suppression of pathogenic Escherichia-Shigella. Machine learning identified five core microbial biomarkers (Akkermansia muciniphila, Bifidobacterium, Escherichia-Shigella, Blautia, Streptococcus), with SHAP analysis highlighting Akkermansia muciniphila and Bifidobacterium as top contributors. Metabolomic profiling demonstrated upregulation of 236 metabolites, including kynurenic acid and butyric acid, with tryptophan and butyrate metabolism emerging as key altered pathways. Immune profiling showed elevated CD3[+]CD4[+] T cells and reduced TNF-&#x3b1; levels, while MIMOSA2 analysis linked microbial taxa to metabolic shifts, such as correlations between Ruminococcus torques and butyric acid.<br><br>CONCLUSION: These findings suggest that JK5G may contribute to the amelioration of cancer-related pain by reshaping gut microbiota, modulating host metabolism, and enhancing immune responses. This study highlights the potential of JK5G postbiotics as an adjunct therapy, supporting the need for further validation in larger cohorts and mechanistic investigations to advance its clinical translation.<br><br>CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/showproj.html?proj=285304, identifier ChiCTR2500108811.}, }
@article {pmid41859112, year = {2026}, author = {Chen, H and Lou, G and Meng, F and Zhang, Y and Kuang, H and Yang, D}, title = {Critical role of reproductive tract microbiota and derived metabolites in inflammation, tumor immunity, and tumorigenesis of gynecological cancers: a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1734792}, pmid = {41859112}, issn = {1664-3224}, mesh = {Humans ; Female ; *Genital Neoplasms, Female/metabolism/immunology/microbiology/therapy/etiology ; Animals ; *Microbiota/immunology ; *Carcinogenesis/immunology ; Inflammation/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; *Genitalia, Female/microbiology/immunology ; }, abstract = {Gynecological malignancies, including ovarian, cervical, and endometrial cancers, present significant clinical challenges due to the epidemiological complexity and limitations in current therapeutic strategies. Emerging evidence highlights the critical role of the microbiome and its metabolites in modulating tumor initiation, progression, and treatment responses. This review explores the intricate mechanisms through which gut and reproductive tract microbiota influence gynecological cancers via immune regulation, metabolic reprogramming, and epigenetic modifications. Key microbial metabolites, such as short-chain fatty acids, bile acids, and estrogen-metabolizing intermediates, serve as molecular bridges in host-microbe communication, impacting chemotherapy resistance and immunotherapy efficacy. Furthermore, we discuss the translational potential of microbiome-targeted interventions, including probiotics, fecal microbiota transplantation, and precision microbial therapies, as innovative approaches for diagnosis, prognosis, and treatment. Understanding the microbiota-reproductive axis offers novel insights into overcoming therapeutic resistance and improving patient outcomes in gynecologic oncology.}, }
@article {pmid41859191, year = {2026}, author = {Su, Y and Xia, Y}, title = {Gut microbiota dysbiosis and depression: Bidirectional interactions, mediating pathways, and microecological therapeutics.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101372}, pmid = {41859191}, issn = {2665-9271}, abstract = {The microbiota-gut-brain axis (MGBA) is increasingly recognized as a key target for ameliorating major depressive disorder (MDD). This review systematically synthesizes evidence on the bidirectional relationship between gut microbiota dysbiosis and MDD, and delineates the core mechanisms-such as neuroinflammation, neurotransmitter metabolism, and hypothalamic-pituitary-adrenal (HPA) axis dysregulation-through which this axis influences depressive pathogenesis. Further, the intestinal microbiota characteristics related to MDD, the main regulatory pathways, and the potential efficacy of microbiome-targeted intervention measures-including psychobiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary strategies-were sorted out. In the clinical assessment and drug research of depression, the assessment tools are mainly divided into two categories: clinician-rated and self-reported. These two types are often used together to provide multi-dimensional evidence of therapeutic efficacy. Evidence suggests that stress-related intestinal permeability may initiate gut dysbiosis, which in turn can impair barrier function, promote neuroinflammation, disrupt neurotransmitter synthesis, and overactivate the HPA axis, potentially exacerbating depressive symptoms. Interventions targeting the gut microbiota may help reshape microbial communities, increase short-chain fatty acids (SCFAs) and 5-Hydroxytryptamine (5-HT), and dampen inflammatory and stress responses, thereby offering a promising, non-pharmacological avenue for alleviating MDD. This review not only offers a theoretical foundation for microbiota-based therapeutics in MDD but also highlights pathways toward developing safe, effective non-pharmacological strategies for depression management.}, }
@article {pmid41859194, year = {2026}, author = {Armah, J and Alzahid, S and Pei, Q and Cousin, L and Fanfan, D and Heldermon, C and Lyon, D}, title = {Associations among physical activity, diet, non-lifestyle characteristics and the gut microbiome of cancer patients: A scoping review and network analysis.}, journal = {Oncoscience}, volume = {13}, number = {}, pages = {85-103}, pmid = {41859194}, issn = {2331-4737}, abstract = {Lifestyle factors, such as physical activity and dietary modifications can beneficially modulate the gut microbiome of cancer patients, however their effects are often shaped by non-modifiable variables. This review and network analysis aims to synthesize current evidence on how both lifestyle and non-lifestyle factors affect the gut microbiome in cancer patients. A systematic search was conducted on Scopus, CINAHL, PubMed and Web of Science to produce 51 eligible studies for this review. A chi-square test of independence indicated that the distribution of gut bacteria function categories was significantly associated with the category of influencing factor (Χ[2] = 390.87, p = 0.032). Across studies, high physical activity and healthy diets were associated with increased abundances of saccharolytic/short-chain fatty acids and lactic acid-producing bacteria, alongside decreased abundances of pathogenic or opportunistic bacteria. However, these associations may also be influenced by non-lifestyle characteristics such as chemotherapy, age, and cancer type or stage which could mask the benefits of lifestyle interventions. This study highlights the limited but growing evidence linking physical activity, diet and the gut microbiome in cancer populations. Progress in this field will require larger, more integrative designs that account for non-lifestyle confounders and apply advanced analytical approaches to capture complex interactions.}, }
@article {pmid41859443, year = {2026}, author = {Whitaker, BK and Gdanetz, K and Vaughan, MM and McCormick, S and Becker, T}, title = {Wheat mycobiome dynamics driven by interseasonal crop-crop transfer and Fusarium head blight.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1778987}, pmid = {41859443}, issn = {1664-302X}, abstract = {INTRODUCTION: Fusarium head blight (FHB) is a devastating disease of wheat that causes mycotoxin contamination in grains. Diseases like FHB have traditionally been managed with integrated strategies; but this has led to a proliferation of fungicide-resistant pathogens and soil erosion while full disease control has remained elusive. Leveraging the microbiome for more sustainable management is an alternative, however, translation of promising strategies is hampered by our limited understanding of crop microbiome differences across plant development and tissue types.<br><br>METHODS: We characterized fungal communities using amplicon sequencing across five developmental timepoints in wheat leaves and wheat heads, as well as in maize debris from the previous growing season. Samples were collected from two locations in Illinois, USA. We assessed how tissue type, site, developmental stage, and wheat variety contributed to mycobiome composition. Source-sink relationships among debris, leaves, and heads were evaluated, and taxa associated with high and low FHB conditions were identified. Network analyses were used to determine the roles of key fungal taxa in wheat head and maize debris microbiomes.<br><br>RESULTS: Mycobiome composition varied strongly by tissue type, though site and developmental timepoint were also important contributors. Host variety conditionally explained mycobiome variation in wheat heads, but not in leaves or debris. We also identified debris as a major fungal source to leaves early in development, but not later-and found that leaves were never a large inoculum source to head mycobiomes at either developmental stage tested. Taxa enriched under high FHB conditions in wheat heads belonged to the Ascomycota (Cladosporium, Pseudopithomyces), while taxa enriched under low FHB conditions primarily belonged to the Basidiomycota (Filobasidium, Sporobolomyces, Tilletiopsis, Entyloma). Fusarium spp. were important nodes in wheat head and maize debris microbiome networks.<br><br>DISCUSSION: This work shows that fungal movement from crop to crop across seasons, and between plant tissues within a season, shape phyllosphere microbiome dynamics and can indicate potential disease outcomes in the FHB pathosystem. As microbiome-based disease management develops alongside rapid growth in the biologicals industry and increased recognition of microbial roles in agriculture, this work highlights several promising directions. These include identifying basidiomycetous yeasts associated with low FHB, pinpointing taxa correlated with Fusarium in wheat heads and maize debris, and demonstrating that applying biocontrols to wheat leaves is unlikely to affect pathogen spread to heads. Future research should focus on controlled tests of microbe-microbe interactions and their impacts on plant immunity, disease suppression, and yield.}, }
@article {pmid41859445, year = {2026}, author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W}, title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783810}, pmid = {41859445}, issn = {1664-302X}, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.}, }
@article {pmid41859446, year = {2026}, author = {Bai, L and Wang, Z and Wang, H and Ma, B}, title = {Comprehensive evaluation of environment adaptability in wild and captive lenok (Brachymystax lenok): from the perspective of antioxidant capacity, immune response and gut microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1764670}, pmid = {41859446}, issn = {1664-302X}, abstract = {INTRODUCTION: The intestinal microbiota is considered an adaptive trait closely associated with reintroduction success and may contribute to the ecological fitness of B. lenok.<br><br>METHODS: In this study, intestinal morphology, digestive enzyme activity, immune parameters, and gut microbiota composition were compared between wild and farmed B. lenok to elucidate differences in intestinal and hepatic health under distinct aquatic environments.<br><br>RESULTS: Histological analysis showed that villi in the hindgut of wild individuals were longer and denser than those of farmed ones. Although the intestinal structure of farmed B. lenok remained intact, their villus morphology and density differed significantly from those of the wild group. Compared with the farmed group, wild B. lenok showed higher hepatic immune/antioxidant activity (elevated alkaline phosphatase (AKP), acid phosphatase (ACP), lysozyme (LYZ), and catalase (CAT), as well as glutathione (GSH) content) and up-regulated liver immune-related genes (c3, foxo1, igM, il-10, lyz, etc.), while farmed fish displayed higher intestinal stress markers (CAT, malondialdehyde (MDA) and a pro-inflammatory signature (il-6, il-1&#x3b2; upregulated). Microbiota profiling revealed higher abundance of Firmicutes and Bacteroidetes but a trend of decreasing Proteobacteria in the wild group.<br><br>DISCUSSION: Collectively, these findings demonstrate significant differences in intestinal morphology, digestive function, and microbial community composition between wild and farmed B. lenok. This study provides new insights for improving post-stocking adaptability in reintroduction programs and proposes novel conservation strategies for biodiversity restoration.}, }
@article {pmid41859449, year = {2026}, author = {Han, Y and Huang, H and Zhang, Z and Li, X and Li, T and Zong, S}, title = {Microbiome and metabolome dynamics in phloem and rhizosphere of Pinus tabuliformis against Dendroctonus valens infestation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1754801}, pmid = {41859449}, issn = {1664-302X}, abstract = {Microbial communities play essential roles in mediating plant defenses against insect pests. However, how host-associated microbiota and metabolites jointly respond to bark beetle infestation remains largely unexplored. Here, we integrated microbiome and metabolome profiling to elucidate how Pinus tabuliformis regulates its phloem and rhizosphere responses under varying levels of Dendroctonus valens infestation. Both bacterial and fungal diversity, as well as the relative abundance of dominant taxa such as Erwinia and Pseudoxanthomonas, shifted significantly with infestation intensity. Concurrently, key plant defense metabolites-including terpenoids, jasmonates, and polyphenols-were markedly elevated. Pathway enrichment analysis indicated that the phloem was characterized by enhanced phenylpropanoid and flavonoid biosynthesis, whereas the rhizosphere soil accumulated terpenoids and polyketides, implicating both compartments in resistance modulation. In the phloem, differential bacterial and fungal taxa displayed distinct positive and negative correlations with phenylpropanoid intermediates and downstream derivatives, while in the rhizosphere, bacteria from Bacillota and fungi such as Candida and Ogataea were strongly linked to diterpenoids, sesquiterpenoids, flavonoids, and indole derivatives. These findings demonstrate that P. tabuliformis mounts a compartment-specific, microbiome-associated metabolic response to D. valens infestation, providing new insights into the ecological roles of symbiotic microbiota in plant defense and offering a mechanistic foundation for microbe-based pest management strategies.}, }
@article {pmid41859450, year = {2026}, author = {Jia, J and Chen, L and Liu, Q and Wang, K and Zhao, K and Ren, X and Gao, X and An, J}, title = {Correction: Enhancement of soil microbial community stability by earthworms and collembolans in soil from abandoned coal mine land.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1803716}, doi = {10.3389/fmicb.2026.1803716}, pmid = {41859450}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1636784.].}, }
@article {pmid41859452, year = {2026}, author = {Jia, C and Zhu, W and Yuan, Y and Xie, Q}, title = {How gut microbiota contribute to neuropsychiatric disorders: evidence from neuroimaging studies.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1760096}, pmid = {41859452}, issn = {1664-302X}, abstract = {The interaction between the gut microbiota and central nervous system (CNS) diseases has emerged as a major focus in neuroscience and microbiome research. Accumulating evidence shows that gut microbiota influence the pathogenesis of neurodevelopmental, neurodegenerative, autoimmune, and psychiatric conditions via the microbiota-gut-brain axis. However, the underlying mechanisms are complex and not yet fully elucidated. Advances in multimodal magnetic resonance imaging, positron emission tomography, and diffusion tensor imaging, now enable in vivo visualization of associations between gut microbial alterations and abnormalities in brain structure and function, providing new perspectives for understanding the role of gut microbiota in CNS pathology. This review systematically reviews neuroimaging-based research linking gut microbiota to neurological diseases (e.g., Alzheimer's disease, multiple sclerosis, traumatic brain injury), and psychiatric disorders (e.g., schizophrenia, and autism spectrum disorder). It highlights the mediating roles of microbial metabolites, immune-inflammatory responses, and neuroimmune pathways, and discusses future directions integrating multi-omics data with neuroimaging technologies, as well as their potential clinical applications. What distinguishes this review from its predecessors in the same field is its explicit neuroimaging-driven framework rather than general mechanistic discussion.}, }
@article {pmid41859467, year = {2026}, author = {Szydłowicz, M and Zajączkowska, &#x17b; and Chabowski, M and Nowicki, M and Łukianowski, B and Gajdzis, P and Kváč, M and Calderón, EJ and Le Gal, S and Kicia, M}, title = {Multi-site screening for Pneumocystis jirovecii in lung cancer: possible tumour tissue colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1755638}, pmid = {41859467}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/complications/pathology ; *Pneumocystis carinii/isolation &amp; purification/genetics ; Male ; Female ; Middle Aged ; Aged ; Genotype ; Aged, 80 and over ; *Pneumonia, Pneumocystis/microbiology/diagnosis ; DNA, Fungal/genetics ; Lung/microbiology ; Adult ; *Pneumocystis Infections/microbiology/diagnosis ; Polymerase Chain Reaction ; }, abstract = {OBJECTIVES: Recent studies suggest that various tumour types can be colonized by different microorganisms, but data on unusual opportunistic fungus - Pneumocystis jirovecii - remain scarce. Lung cancer patients are considered one of the risk groups for its infection. Since P. jirovecii tends to distribute focally within the lungs, this study aimed to determine whether it can be detected in lung tumour tissue.<br><br>METHODS: Fragments of neoplastic tissue (NPL), normal adjacent tissue (NAT) and respiratory secretions (RS) were collected from 70 patients with histologically confirmed primary lung cancer. DNA was extracted and analysed by nested-PCR targeting the mtLSU rRNA and CYB loci, followed by genotyping.<br><br>RESULTS: Pneumocystis jirovecii was detected in fourteen samples derived from 8/70 individuals (11.4%): two NPL, six NAT and six RS. In two patients, Pneumocystis was detected in all three specimen types; both were diagnosed with the same histological malignancy grade (G3, P=0.036). The genotype distribution varied across sample types in most cases.<br><br>CONCLUSIONS: The ability of Pneumocystis to colonize NPL may be linked to the stage of tumour advancement, suggesting that local tumour-related factors could influence its colonization. These findings support further investigation of the lung microbiome in the context of tumour-associated microenvironments and their potential utility as complementary biomarkers in lung cancer.}, }
@article {pmid41859469, year = {2026}, author = {Zafeiropoulou, K and Hageman, IL and Mu, T and Davids, M and Li Yim, AYF and Joustra, VW and Hakvoort, TBM and Satsangi, J and Chronas, K and Koelink, PJ and Wildenberg, ME and van den Wijngaard, RM and D'Haens, GR and de Jonge, WJ}, title = {Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn's disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1741002}, pmid = {41859469}, issn = {2235-2988}, mesh = {Humans ; *Crohn Disease/drug therapy/microbiology/pathology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/pathology ; Biopsy ; Middle Aged ; *Tumor Necrosis Factor-alpha/antagonists &amp; inhibitors ; Treatment Outcome ; Adalimumab/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infliximab/therapeutic use ; Ustekinumab/therapeutic use ; Intestinal Mucosa/microbiology/pathology ; Biological Therapy ; }, abstract = {INTRODUCTION: Crohn's disease (CD) is commonly treated with biologic therapies, including anti-TNFα agents, vedolizumab (VDZ), and ustekinumab (USTE), yet only a subset of patients respond to these treatments. This study aimed to evaluate the potential of the gut microbiome to predict treatment response.<br><br>METHODS: Adult CD patients initiating anti-TNF&#x3b1; (infliximab or adalimumab), VDZ or USTE were enrolled. Pre-treatment ileal and/or colonic biopsies were collected endoscopically. Treatment response after 26-52 weeks was defined by &#x2265;50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (&#x2265;3-point HBI decrease or remission [HBI &#x2264;4] without systemic steroids) or a biochemical response (&#x2265;50% or &#x2264;5 mg/L CRP reduction and &#x2265;50% or &#x2264;250 &#x3bc;g/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA gene sequencing of biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNF&#x3b1;-induced CD14[+]CD206[+] macrophages was tested in mixed lymphocyte reactions (MLRs).<br><br>RESULTS: A total of 125 patients were included: 39 on anti-TNF&#x3b1;, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies, anti-TNF&#x3b1; responders had significantly higher pre-treatment &#x3b1;-diversity, and 3.9% of &#x3b2;-diversity variation associated with response. Among six models, the anti-TNF&#x3b1; colonic model performed significantly better than random (AUC = 0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNF&#x3b1;. When tested in MLRs, pretreatment with M. gnavus and B. luti led to a reduction in macrophage polarization, with a significantly stronger effect observed for M. gnavus compared with B. luti.<br><br>DISCUSSION: Taken together, this study demonstrates that the colonic mucosal microbiome prior to anti-TNF&#x3b1; treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker.}, }
@article {pmid41859568, year = {2025}, author = {Adnan, D and Engen, PA and Villanueva, M and Raeisi, S and Ramirez, V and Naqib, A and Green, SJ and Bishehsari, F and Barnes, LL and Keshavarzian, A and Dhana, K and Voigt, RM}, title = {Oral microbiome brain axis and cognitive performance in older adults.}, journal = {NPJ dementia}, volume = {1}, number = {}, pages = {}, pmid = {41859568}, issn = {3005-1940}, support = {R01 AG052583/AG/NIA NIH HHS/United States ; R01 AG056653/AG/NIA NIH HHS/United States ; }, abstract = {The human oral microbiota is a community of microorganisms that reside in the oral cavity, including lingual, buccal, and saliva, each niche with a distinct microbial composition. Alterations in oral microbiota have been associated with an increased risk of Alzheimer's disease (AD). This study used data from 143 older adults in the MIND trial to evaluate the association between oral microbiome and cognitive function. Oral niche-specific differences (saliva, buccal, and lingual), as well as the microbiome composition differences (α and β diversity), were associated with cognitive function. A lower abundance of Gemella and a higher abundance of anaerobic pro-inflammatory bacteria (e.g., Parvimonas, Treponema, Dialister) were linked to a lower Cognitive Z Score. Porphyromonas, previously linked to AD, was not associated with cognition. The outcomes suggest that oral microbiota may be a biomarker for cognitive function. Further research is required to assess whether oral microbiota-directed strategies can positively impact cognitive decline.}, }
@article {pmid41859724, year = {2025}, author = {Fei, Y and Lei, Z and Wang, Y and Joshua, M and Guo, L and Li, L}, title = {Overview of multi-omics approaches for pulmonary sarcoidosis.}, journal = {EC pulmonology and respiratory medicine}, volume = {14}, number = {1}, pages = {}, pmid = {41859724}, support = {R21 ES036375/ES/NIEHS NIH HHS/United States ; }, abstract = {PURPOSE: Here, we review recent findings in the transcriptome, proteome, metabolomics, and microbiome of pulmonary sarcoidosis and highlight differentially expressed genes, specific pathways, mechanisms, microorganisms, metabolites, and targeted therapeutics in the field.<br><br>RECENT FINDINGS: The transcriptome and proteome of pulmonary sarcoidosis have been widely studied in recent years. Many differentially expressed genes and signaling pathways have been identified. Several proteins have been identified as potential molecular markers of pulmonary sarcoidosis. The microorganisms and metabolites of patients with sarcoidosis also have certain specificity. We compared pulmonary sarcoidosis with other diseases, such as idiopathic pulmonary fibrosis, tuberculosis, and chronic beryllium disease, and found some differential diagnoses. Based on the identified pathways and mechanisms, targeted therapeutic strategies have been proposed.<br><br>SUMMARY: Many differentially expressed genes have been identified, including CBX8, CCL5, CXCL9, CXCL11, GBP1, GBP5, LINC01278, MMP12, PSMB9, STAT1, and TLE3, as well as the related enriched pathways, such as the IFN-&#x3b3;, IL-1, IL-17, MHC, T-cell receptor, TNF, Th1, and Th2 signaling pathways. Proteins such as ABCG1, Apo A-I, CXCR5, MMP12, PD-1, PPAR&#x3b3;, and vitamin D-binding protein, together with the Fc galactosylation status of IgG4, are potential molecular markers for pulmonary sarcoidosis. Many specific microorganisms and metabolites in patients with sarcoidosis have also been found. Targeted drugs such as infliximab, nintedanib and rituximab have been proposed according to the discovered pathways and mechanisms.}, }
@article {pmid41859763, year = {2026}, author = {Qin, YF and Zhang, WR and Wang, L and Wang, YF and Lin, D and Cai, TG and Li, HZ and Huang, QS and Rillig, MC and Zhu, D}, title = {Extracellular vesicles drive stress-induced antibiotic resistance spread in soil.}, journal = {Environmental science and ecotechnology}, volume = {30}, number = {}, pages = {100681}, pmid = {41859763}, issn = {2666-4984}, abstract = {Antimicrobial resistance threatens millions of lives annually, yet its acceleration by non-antibiotic pollutants remains poorly understood. Artificial sweeteners, now ubiquitous in soils and waters, are known individually to promote conjugative transfer of resistance genes, but real environments contain complex mixtures whose collective impact is unknown. Extracellular vesicles (EVs) released by stressed bacteria serve as protected, long-range vectors for antibiotic resistance genes (ARGs), yet whether sweetener diversity modulates this pathway has never been tested. Here we show that increasing artificial-sweetener diversity dramatically enriches ARGs, virulence factors and mobile genetic elements inside soil-derived Evs, driving compositional shifts in 30.5% of EV-associated genera while leaving the bulk microbiome largely undisturbed. EVs originate from a small, fast-growing Pseudomonadota subset that upregulates vesicle-biogenesis genes in response to oxidative and membrane stress; these vesicles selectively package chromosomal resistance traits and transfer phenotypic resistance to recipient Escherichia coli. This stress-induced decoupling reveals EVs as rapid, hidden mediators of resistome mobilization that community-level surveys miss. By demonstrating that pollutant diversity itself drives resistance dissemination through nanoscale vectors, our findings establish EVs as a critical new indicator within the One Health framework and call for revised environmental risk models that account for chemical complexity rather than single-compound exposures.}, }
@article {pmid41859944, year = {2026}, author = {Jiang, M and Gomez, A and Seelig, DM and Gallaher, DD}, title = {Prune (dried plum) consumption does not reduce colonic tumor formation but drives beneficial changes in the gut microbiome of rats.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo03398e}, pmid = {41859944}, issn = {2042-650X}, abstract = {Previous research has highlighted the potential benefits of prune consumption, including a changed gut microbiome composition and a reduction in colon cancer risk factors. This study investigated whether prune consumption reduced colon tumor development and led to positive changes in the large intestinal microbiome in a chemically induced colon cancer model in rats. Male Wistar rats were fed one of three diets: 5% (by energy) prune, 10% prune, or a prune-free control. Rats were fed the diets for 32 weeks. Rats received weekly injections of 1,2-dimethylhydrazine for 15 weeks to induce colon tumorigenesis. Colonic tumor number or size did not differ among the diet groups. However, there was a trend toward fewer small intestinal tumors in the 10% prune diet group (p < 0.1). Groups fed prune had heavier cecum tissue, indicating greater large intestinal fermentation. The prune diets increased taxonomic richness and altered bacterial species composition. Specifically, prune consumption was associated with increased abundance of Methanosphaera genus and taxa from the Lachnospiraceae family, such as Blautia and Coprococcus. Prune diets also increased total cecal SCFA amount, notably butyrate. However, 24 hour fecal excretion of p-cresol, indole, and total bile acids did not differ significantly among the groups. While prune consumption did not show a significant reduction in colonic tumor formation, potential benefits were noted in a trend towards reducing small intestine tumors, increasing large intestinal fermentation and SCFA production, and increasing microbial richness, suggesting prune consumption may provide other health benefits.}, }
@article {pmid41859980, year = {2026}, author = {Akebota, N and Ma, RF and Yang, HQ and Li, YD and He, K and Liu, HY and Tang, KY and Zhu, Y}, title = {Behavioral smearing and physiological secretions drive divergent microbiome assembly during breeding in the crested ibis.}, journal = {Zoological research}, volume = {47}, number = {2}, pages = {361-373}, doi = {10.24272/j.issn.2095-8137.2025.407}, pmid = {41859980}, issn = {2095-8137}, mesh = {Animals ; *Microbiota/physiology ; *Birds/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Feathers/microbiology ; Seasons ; Reproduction/physiology ; Bacteria/classification/genetics ; }, abstract = {Host-microbiota interactions represent a key axis in animal adaptation, especially in species displaying pronounced seasonal variation in behavior and physiology. In avian species, behavioral processes associated with reproduction may influence symbiotic microbial communities, yet the underlying mechanisms remain poorly resolved. The endangered crested ibis (Nipponia nippon) exhibits a distinctive seasonal transition in plumage coloration, shifting from white in the non-breeding period to gray during breeding, a change linked to smearing behavior and deposition of black secretions from the neck region. In the present study, 16S rRNA sequencing across three body sites was performed to profile body surface microbiomes during breeding (gray-feather) and non-breeding (white-feather) stages. Breeding individuals exhibited lower microbial diversity, consistent with an influence of black neck secretions on microbiome structure. Microbial communities were differentiated more strongly by season than by body site, and microbial similarity among body sites increased during breeding, supporting redistribution of microbes through smearing behavior. Community assembly also showed clear season- and site-specific variation. Neck feathers exhibited a 36.5% better fit to the neutral model, indicating a stronger contribution of stochastic assembly, likely associated with microbial dispersal during smearing of black secretions. In contrast, neck skin showed a 36.3% lower neutrality and 11.87% more host-selected variants, indicating stronger deterministic selection associated with breeding-related secretions. These findings support a dual regulatory framework during breeding, in which behavioral smearing promotes microbial dispersal while physiological secretion strengthens host filtering. Such coordinated regulation likely drives seasonal microbiome variation and contributes to seasonal adaptation. Overall, this work provides novel insight into the integration of behavior and physiology in shaping host-microbiota interactions during critical life stages and establishes a microbiome-based perspective for crested ibis conservation.}, }
@article {pmid41859990, year = {2026}, author = {Szczepanik, K and Kierończyk, B and Szymkowiak, P and Taciak, M and Barszcz, M and Tuśnio, A and Gawin, K and Dobrowolski, P and Świątkiewicz, M}, title = {Effects of Hermetia illucens larvae full-fat meal and astaxanthin on the microbiome and histomorphology of the large intestine in piglets.}, journal = {Polish journal of veterinary sciences}, volume = {29}, number = {1}, pages = {17-29}, doi = {10.24425/pjvs.2026.158497}, pmid = {41859990}, issn = {2300-2557}, mesh = {Animals ; Swine/microbiology/anatomy &amp; histology ; *Animal Feed/analysis ; Larva ; *Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Xanthophylls/pharmacology/administration &amp; dosage ; *Intestine, Large/anatomy &amp; histology/microbiology/drug effects ; Animal Nutritional Physiological Phenomena ; *Diptera ; }, abstract = {This study evaluated the effects of Hermetia illucens (HI) larvae full-fat meal and astaxanthin (AST) on large intestine histomorphometry, microbiota activity, and composition in pigs. Forty-eight pigs (8.7 kg) were divided into six groups: control (0HI), 2.5% HI (2.5HI), 5% HI (5HI), 2.5% HI + AST (2.5HI+AST), 5% HI + AST (5HI+AST), and AST alone (AST). The experiment lasted from 35 to 70 days of age. HI meal increased mucosal thickness (p<0.01), crypt depth (p<0.05), and width (p<0.05). Goblet cell counts increased in the 2.5HI (p<0.05), while enterocyte numbers decrease in the AST group (p<0.01). Dietary HI meal reduced concentrations of total short-chain fatty acids (SCFA), including butyrate (p<0.05), whereas AST increased acetic acid levels in multiple intestinal regions (p<0.05). Both additives modified microbial populations: AST increased total bacterial counts (p<0.001), while 2.5% HI meal reduced the abundance of the Bacteroides-Prevotella cluster (p<0.001). Significant interactions were detected for Lactobacillus/Enterococcus spp. and Enterobacteriaceae (p<0.001). HI meal decreased p-cresol concentrations in the middle colon (p<0.05), whereas AST reduced phenol in the distal colon (p<0.05) and indole in the middle colon (p<0.05). AST increased ammonia levels in the proximal colon (p=0.001). These findings suggest that HI meal and AST modulate intestinal fermentation, exhibit anti-inflammatory effects, and regulate microbial populations, potentially reducing harmful metabolites and odor emissions. Their dietary combination may have positive implications for intestinal health.}, }
@article {pmid41860010, year = {2026}, author = {Medenica, S and Prelević, V and Zanković, N and Maggio, V and Rizzo, M}, title = {Cardiorenometabolic medicine as a new subspecialty in the light of novel pharmaceuticals with dual or triple benefits.}, journal = {Expert opinion on drug safety}, volume = {}, number = {}, pages = {}, doi = {10.1080/14740338.2026.2648248}, pmid = {41860010}, issn = {1744-764X}, abstract = {INTRODUCTION: There is a lack of clinical models which include comprehensive and holistic care of patients with cardiorenometabolic diseases and isolated care of those patients usually leads to poor clinical outcomes. Cardiometabolic diseases, encompassing conditions like type 2 diabetes, obesity, and atherosclerotic cardiovascular disease, represent a major global health burden. Their frequent coexistence due to shared mechanisms necessitates an integrated care approach, reflecting a critical paradigm shift. Therefore, necessity for a new integrated clinical model which include all those specialties should be the focus of a new, modern interdisciplinary approach.<br><br>AREAS COVERED: This review synthesizes mechanistic insights, safety data, and emerging interventions for cardiorenometabolic disease management. It examines cornerstone therapies like SGLT2 inhibitors and GLP-1 receptor agonists, highlighting their profound cardiovascular, renal, and metabolic benefits. Newer dual/triple incretin therapies are also discussed for their potential in weight loss and cardioprotection. Safety considerations, including genitourinary infections and gastrointestinal intolerance, are addressed. Additionally, emerging research on gut microbiota - derived metabolites and sleep optimization as modifiable risk pathways is explored. The literature search included papers published as of July 2025, identified using PubMed.<br><br>EXPERT OPINION: We advocate a holistic, risk-adapted approach integrating pharmacologic, behavioral, and metabolic dimensions to optimize patient outcomes and truly transform cardiometabolic care.}, }
@article {pmid41860216, year = {2026}, author = {Chatman, CC and Olson, EG and Ricke, SC and Majumder, EL-W}, title = {Exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0246925}, doi = {10.1128/aem.02469-25}, pmid = {41860216}, issn = {1098-5336}, abstract = {UNLABELLED: The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards: nitrate, atrazine, and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low-dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high-dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. Both contaminant types significantly altered the cecal microbiomes as determined by the enrichment of the genera Fournierella and Ruminococcus and an unclassified Coriobacteriaceae genus. Untargeted metabolomics revealed distinct but convergent patterns of metabolic reprogramming across exposures. Chemical mixtures modulated pathways linked to xenobiotic metabolism, pyruvate and thiamine metabolism, and other cofactor-dependent processes, consistent with a shift from oxidative, biosynthetically intensive metabolism toward glycolysis, fermentation, and detoxification. In contrast, PE fibers selectively suppressed oxidative and cofactor/vitamin pathways while perturbing bile acid, sphingolipid, and aromatic compound metabolism, indicating a simplified, maintenance-oriented energy state. Despite these pronounced metabolomic shifts, histopathology revealed no overt intestinal or systemic lesions in any treatment group, highlighting altered microbial activity despite the absence of gross pathological lesions and supporting a silent dysbiosis phenotype.<br><br>IMPORTANCE: Environmental contaminants in groundwater are increasingly common, yet their combined effects on animal health remain poorly understood. The current study shows that even low-level exposure to agricultural chemical mixtures and microplastics can alter the gut microbial metabolism in broiler chickens without intestinal damage. These subclinical shifts, characterized by altered energy pathways, cofactor scarcity, and microbial restructuring, highlight a form of silent dysbiosis. Our findings emphasize the need to integrate microbiome- metabolic endpoints into environmental risk assessments to predict earlier, more meaningful, functionally relevant impacts.}, }
@article {pmid41860224, year = {2026}, author = {Bintarti, AF and Sulesky-Grieb, A and Colovas, J and Marolleau, B and Boureau, T and Simonin, M and Barret, M and Shade, A}, title = {Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0301925}, doi = {10.1128/spectrum.03019-25}, pmid = {41860224}, issn = {2165-0497}, abstract = {Drought is a critical risk for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither a strong response of the Red Hawk microbiomes to drought nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity, while its root had no legacy effect observed. This study demonstrates that below-ground plant microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries are useful to inform generalities and build theory toward prediction on microbiome responses to global change.IMPORTANCEDrought remains an important challenge in crop agriculture because of climate change, and plant microbiome management has potential to support plant resilience to drought. Here, we investigated the impact of drought and drought legacy across two generations on the root and rhizosphere microbiomes of the drought-susceptible legume common bean, a key staple food crop with production widely distributed across the Americas, Africa, Europe, and Asia, and which is of critical importance for food security in many of its production regions. Despite host plant decline with drought, the effects of drought on the microbiomes were either not observed, inconsistent, or weak, suggesting overall microbiome resistance and limited drought legacy. This work provides insights into how the stability of the below-ground plant microbiome can be driven by stress resistance, offering a different perspective on how the microbiome could be managed to support crops facing drought.}, }
@article {pmid41860424, year = {2026}, author = {Guo, Y and Liu, W and Qiu, K and Si, H and Zhang, Y and Huang, Y and Yang, Y and Xie, Y}, title = {Linking Bacterial Diversity to Rhizosphere Ecological Stoichiometry and Nutrient Availability in a Clonal Desert Plant.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag076}, pmid = {41860424}, issn = {1365-2672}, abstract = {AIMS: This study aimed to examine the relationships between rhizosphere (RS) microorganisms of the desert pioneer plant Psammochloa villosa and soil nutrient availability, with the goal of clarifying microbial mechanisms supporting its persistence in desertified regions and identifying potential targets for microbiome-based management.<br><br>METHODS AND RESULTS: Using absolute quantification of 16S rRNA gene and ITS sequencing, microbial communities in the RS of P. villosa were compared with those in bulk soil (BS). The results showed that the rhizosphere of P. villosa had significantly lower total phosphorus (TP) but higher carbon-to-phosphorus (C/P) and nitrogen-to-phosphorus (N/P) ratios than BS, while the available nitrogen-to-available phosphorus ratio (AN/AP) was 4-5 times higher than N/P. This pattern suggests that the RS experiences stronger phosphorus limitation than BS. A lower fungi-to-bacteria (F/B) ratio in the RS relative to BS was positively associated with TP and negatively associated with soil C/P and N/P ratios, indicating a bacterial-dominated community under phosphorus-limited conditions. Structural equation modeling further indicated that rhizobacterial diversity strongly promoted the acquisition of available nutrients by significantly affecting soil organic carbon (SOC), TP, and stoichiometric balance.<br><br>CONCLUSIONS: These results indicate that bacterial diversity is tightly linked to the regulation of ecological stoichiometry and nutrient availability under P-limited conditions in the rhizosphere of P. villosa.}, }
@article {pmid41860558, year = {2026}, author = {Bloom, P and Khanna, S}, title = {Fecal microbiota transplantation in chronic liver disease: Current and future state of the art.}, journal = {Hepatology communications}, volume = {10}, number = {4}, pages = {}, pmid = {41860558}, issn = {2471-254X}, mesh = {*Fecal Microbiota Transplantation/methods/trends/adverse effects ; Humans ; Gastrointestinal Microbiome ; *Liver Diseases/therapy ; Chronic Disease ; }, abstract = {Chronic liver diseases are associated with changes in gut microbiome composition and function. Early data suggest that fecal microbiota transplantation (FMT) may treat several chronic liver diseases, especially cirrhosis, hepatic encephalopathy, and alcohol-associated liver disease. Well-powered and multisite studies are needed to better understand which indications and subpopulations hold promise for FMT. At present, there is variability in the screening, processing, and administration of FMT. Some of this variability is inherent to the nature of FMT, but some of the variability could be standardized to optimize safety and efficacy. Ultimately, we may find that narrowed and donor-independent microbiome therapeutics are superior tools to provide a consistently effective result in chronic liver disease. Regulation of FMT for chronic liver disease indications in the United States will continue to require the rigid regulatory framework of other drugs, requiring an Investigational New Drug (IND) application.}, }
@article {pmid41860619, year = {2026}, author = {Fu, X and Chen, Y and Wang, Y and Chen, B and Chen, M and Lyu, J and Sun, H and Wang, Z and Xu, J and Li, GL and Ren, D}, title = {Microbiota in Chronic Suppurative Otitis media: association with Postoperative Tympanic membrane outcomes.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41860619}, issn = {1432-0614}, mesh = {Humans ; *Otitis Media, Suppurative/microbiology/surgery ; *Microbiota ; Female ; Male ; Chronic Disease ; Middle Aged ; Adult ; *Tympanic Membrane/microbiology/surgery ; Pseudomonas aeruginosa/isolation &amp; purification/genetics ; Biomarkers ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Tympanic Membrane Perforation/microbiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Chronic suppurative otitis media (CSOM) is a prevalent condition with global health implications due to its impact on hearing and quality of life. Conventional treatments often fail because of bacterial biofilms and antimicrobial resistance. Effective treatment of CSOM depends on the precise determination of the middle ear microbiota; however, current microbial detection methods do not meet this need. Postoperative reperforation may compromise surgical outcomes. If the risk of perforation can be predicted immediately after surgery, sensitive antibiotics could be administered proactively for early intervention to optimize treatment efficacy. This study introduces 2b-RAD sequencing for the microbiome (2b-RAD-M), a novel technology designed to provide a comprehensive profile of the CSOM microbiota and identify diagnostic biomarkers that predict postoperative outcomes. We analyzed ear swabs from patients with postoperative perforation (PO), nonperforation (NPO), and otosclerosis (CON) using microbial diversity, relative abundance, and composition analyses. Bacillus_A_bombysepticus and Pseudomonas aeruginosa were identified as potential biomarkers, with Bacillus_A_bombysepticus demonstrating superior diagnostic accuracy (area under curve (AUC) = 0.92) compared to P. aeruginosa (AUC = 0.25). Functional predictions revealed that biological activities related to gene regulation, substance metabolism, and DNA repair were more prominent in the PO group. This study offers new insights into CSOM pathogenesis and progression, proposing Bacillus_A_bombysepticus as a novel biomarker for predicting postoperative outcomes that can indicate an increased risk of tympanic membrane reperforation for the first time. KEY POINTS: 2b-RAD-M technology enables comprehensive CSOM microbiota profiling and biomarker identification. Bacillus_A_bombysepticus (AUC = 0.92) outperforms Pseudomonas aeruginosa in diagnostic accuracy. Bacillus_A_bombysepticus predicts postoperative tympanic membrane reperforation via functional activity analysis.}, }
@article {pmid41860655, year = {2026}, author = {Gu, Z and Song, C and Kang, X and Liu, T and Du, M and Wang, X and Zhao, H and Liu, J and Zhang, Y}, title = {Highly diverse and anaerobe-dominated vaginal microbiota in women living with HIV: a cross-sectional study.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {41860655}, issn = {1439-0973}, support = {DTKF202303//Beijing Key Laboratory of Emerging Infectious Diseases Support/ ; ZYLX202126//Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support/ ; }, abstract = {INTRODUCTION: Although highly active antiretroviral therapy (HAART) suppresses HIV viral load and extends life, rising non-AIDS-defining events (NADEs) underscore the importance of long-term health, including reproductive tract health in women living with HIV (WLWH). This study compared vaginal microbiota in WLWH versus women without HIV infection (WLWNH) to inform reproductive health assessment and intervention.<br><br>METHODS: Vaginal swabs from 76 WLWH and 74 WLWNH (Beijing Ditan Hospital, Sept-Oct 2022) underwent 16S rRNA gene sequencing. We used hierarchical clustering to categorize community state types (CSTs I-V) and Adonis for inter-group differences. Pearson correlation assessed relationships between CD4 + T cells and differential bacteria, while Spearman correlation evaluated microbial co-occurrence network interactions (visualized via Gephi0.10.1). Neutral community modeling evaluated assembly processes.<br><br>RESULTS: WLWH exhibited higher vaginal microbial diversity. Compared to WLWNH, Gardnerella vaginalis showed higher relative abundance in WLWH CST III (P&#x2009;=&#x2009;0.001). Additionally, urogenital pathogens Aerococcus christensenii and Ureaplasma urealyticum were significantly enriched in WLWH CST III (P&#x2009;=&#x2009;0.028, P&#x2009;=&#x2009;0.033; AUC&#x2009;=&#x2009;0.704, 0.721, respectively) and CST IV (P&#x2009;=&#x2009;0.024, P&#x2009;=&#x2009;0.031; AUC&#x2009;=&#x2009;0.657, 0.646, respectively). In CST III, CD4&#x2009;+&#x2009;T cell counts correlated positively with Aerococcus christensenii (r&#x2009;=&#x2009;0.49, P&#x2009;=&#x2009;0.044). Neutral community modeling demonstrated that microbiota assembly in WLWH was primarily shaped by stochastic processes (R[2]&#x2009;=&#x2009;0.37 vs 0.219) with significantly restricted microbial dispersal (Nm&#x2009;=&#x2009;9 vs14).<br><br>CONCLUSIONS: WLWH exhibit a distinct, highly diverse vaginal dysbiosis enriched with anaerobic and urogenital pathogenic bacteria. This post-HIV infection dysbiosis may predispose women to subsequent genital infections; future longitudinal research comparing pre- and post-infection microbiome dynamics will be crucial for optimizing gynecological management.}, }
@article {pmid41860665, year = {2026}, author = {Abedi, A and Moghaddam, MM and Kachuei, R and Fooladi, AAI}, title = {Exploring the role of metabolic disorders and gut microbiome in immune checkpoint regulation in cancer: PI3K/AKT/mTOR focus.}, journal = {Journal of physiology and biochemistry}, volume = {82}, number = {1}, pages = {}, pmid = {41860665}, issn = {1877-8755}, }
@article {pmid41860729, year = {2026}, author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Ledesma-Hernandez, G and Cuezva, S and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V}, title = {Habitat Specialization and Airborne Dispersal Shape the Microbiome of a Gypsum Karst Cave.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02745-y}, pmid = {41860729}, issn = {1432-184X}, }
@article {pmid41861238, year = {2026}, author = {Yao, ML and Dai, Y and Zhang, W}, title = {Natural Products from the Oral Microbiome.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051024-050248}, pmid = {41861238}, issn = {1545-4509}, abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.}, }
@article {pmid41861247, year = {2026}, author = {Allen, WJ and Williams, S and Collinson, I}, title = {The Great Escape: Protein Trafficking from the Bacterial Cytosol to the Outer Membrane.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051024-011856}, pmid = {41861247}, issn = {1545-4509}, abstract = {To protect their delicate, carefully curated contents from the world, bacteria encase themselves within a protective envelope made up of sugars, lipids, and proteins. Cell envelopes give bacteria their characteristic shapes, provide rigidity and mechanical stability, and form a selective antechamber-granting access only to a desirable subset of environmental substances. Yet this protective layer is a double-edged sword: Its effectiveness at keeping things out also makes it difficult for things to leave, including the proteins required to interface with the outside world and form the envelope itself. Bacteria have solved this problem by constructing an array of proteinaceous nanomachines that expend energy to selectively shuttle proteins and other building blocks to their intended destinations. Here, we present an overview of our current understanding of how these transporters work, focusing on the major, conserved machines that ferry proteins across the cell envelope throughout the domain Bacteria. The emphasis is on recent discoveries and open questions, with the hope that answering these will provide new avenues to help combat the rising threat of antimicrobial resistance and the rapidly expanding list of diseases linked to human microbiome composition.}, }
@article {pmid41861743, year = {2026}, author = {Addazii, D and Pinheiro, ACAS and Nissen, L and Tappi, S and Bordoni, A and Rocculi, P and Gianotti, A}, title = {Bridging the gap of gut microbiome effects of new food additives in food risk assessment: MICODE gut model to test new chitosan from seafood waste.}, journal = {Food chemistry}, volume = {512}, number = {}, pages = {148927}, doi = {10.1016/j.foodchem.2026.148927}, pmid = {41861743}, issn = {1873-7072}, abstract = {EFSA and FAO outlined guidelines to address data and methodological gaps in assessing the impact of food compounds on gut microbiota (GM) and human health, emphasizing the need for in vitro GM models and standardized biomarkers to integrate GM data into food safety risk assessments. Food texturizers are widespread in processed foods enhancing texture and stability, yet their effects on GM remain unclear. This study investigates three additives: a chitosan from seafood waste (CHIW), a chitosan standard (CHIC), and hydroxypropyl methylcellulose (HPMC), using fructo-oligosaccharides (FOS) as a prebiotic control. A standardized in vitro gastrointestinal model simulating digestion and colonic fermentation, combined with qPCR and GC-MS, assessed their influence on microbial composition and metabolic output, under the hypothesis that distinct carbohydrate polymers differently affect GM. CHIC and CHIW, derived from crustacean waste, promoted beneficial bacteria (Clostridium group IV, Bifidobacteriaceae) and boosted SCFAs production, including butyrate and propionate, with CHIW showing stronger prebiotic effects. HPMC was associated with reduced abundance of Lactobacillaceae and harmful metabolites. These findings support our hypothesis, demonstrate the responsiveness of in vitro GM models to dietary polymers, and reinforce the potential of GM-based screening in food safety assessment, suggesting native chitosan as a promising alternative to synthetic additives.}, }
@article {pmid41861747, year = {2026}, author = {Fennessy, A and Slattery, L and Shelley, O and Reyes, LF and Martin-Loeches, I}, title = {Infectious complications of burns in the intensive care unit.}, journal = {Journal of critical care}, volume = {94}, number = {}, pages = {155519}, doi = {10.1016/j.jcrc.2026.155519}, pmid = {41861747}, issn = {1557-8615}, abstract = {BACKGROUND: Severe burn injury is associated with profound physiological derangement and remains a major cause of infection-related morbidity and mortality worldwide. Disruption of the skin barrier sustained immune dysregulation, prolonged intensive care unit (ICU) exposure, and extensive use of invasive devices create a uniquely infection-prone host environment. Infectious complications, particularly those caused by multidrug-resistant organisms (MDROs), continue to account for a substantial proportion of deaths in critically ill burn patients despite advances in surgical and critical care management.<br><br>OBJECTIVES: This narrative review aims to provide a comprehensive, clinically focused overview of infectious complications in critically ill burn patients, integrating current evidence on epidemiology, pathophysiology, microbial dynamics, diagnostic strategies, and contemporary management approaches relevant to daily ICU practice.<br><br>SOURCES OF EVIDENCE: A narrative synthesis of the published literature was performed, including international guidelines, observational studies, randomised trials, systematic reviews, and translational research focusing on burn-related infections, antimicrobial resistance, diagnostics, and emerging therapies.<br><br>CONTENT: The review examines the multifactorial pathophysiology underlying infection susceptibility following major burns, including loss of the cutaneous barrier, hyperinflammatory responses followed by immune paralysis, and burn-induced hypermetabolism. Dynamic patterns of microbial colonisation, biofilm formation, microbiome disruption, and the global rise of MDROs are explored. Diagnostic challenges in distinguishing colonisation from invasive infection are discussed, alongside traditional and advanced diagnostic modalities such as quantitative tissue cultures, biomarkers, multiplex molecular assays, and next-generation sequencing. Contemporary management strategies are reviewed, emphasising early surgical source control, pharmacokinetically optimised antimicrobial therapy, antimicrobial stewardship, and rigorous infection prevention and control practices. Emerging adjunctive therapies, including bacteriophage therapy, nanotechnology-based antimicrobials, microbiome-directed interventions, and immunomodulatory approaches, are also highlighted.<br><br>IMPLICATIONS: Effective infection management in burn patients requires an integrated, multidisciplinary approach that combines rapid diagnosis, early surgical intervention, tailored antimicrobial therapy, and robust infection prevention strategies. Advances in molecular diagnostics, precision medicine, and microbiome science hold promise for improving outcomes and mitigating the growing burden of antimicrobial resistance in burn ICUs.<br><br>CONCLUSIONS: Infectious complications remain a leading determinant of outcome following severe burn injury. Optimising infection care through early recognition, precise diagnostics, coordinated surgical and antimicrobial strategies, and emerging precision-based interventions is essential to reduce infection-related morbidity and mortality in this vulnerable patient population.}, }
@article {pmid41861866, year = {2026}, author = {Kalimuthu, S and Leung, YY and Neelakantan, P}, title = {Oral mucositis in cancer therapy: A review of the clinical landscape and the emerging role of microbiome-host interactions.}, journal = {Critical reviews in oncology/hematology}, volume = {222}, number = {}, pages = {105282}, doi = {10.1016/j.critrevonc.2026.105282}, pmid = {41861866}, issn = {1879-0461}, abstract = {Oral mucositis (OM) is a debilitating toxicity of chemotherapy and radiotherapy that compromises nutrition, quality of life, treatment adherence, and overall cancer outcomes. Despite its clinical impact, therapeutic options remain limited, and our descriptive analysis of the clinical trial landscape reveals about 93.75% attrition rate from clinical success to regulatory approval, highlighting the limitations of single-pathway strategies that target epithelial injury alone. Emerging evidence implicates oral microbiome as an active contributor to OM initiation, inflammatory amplification, and delayed healing, interacting dynamically with host immune responses to shape disease trajectory. These insights support a shift toward multi-targeted therapeutic frameworks that concurrently address epithelial protection, host-immune modulation, and microbial dysbiosis. This approach is increasingly reflected in the growing pipeline shift toward multifunctional compounds and microbiome-based approaches. This suggests that successful OM management will require the integrated antimicrobial and anti-inflammatory approaches, potentially guided by patient-specific microbiome profiling.}, }
@article {pmid41861946, year = {2026}, author = {Wang, ST and Li, L and Yang, Q and Zhang, GF}, title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.}, journal = {Environmental research}, volume = {299}, number = {}, pages = {124314}, doi = {10.1016/j.envres.2026.124314}, pmid = {41861946}, issn = {1096-0953}, abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.}, }
@article {pmid41862052, year = {2026}, author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P}, title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.}, journal = {Life sciences}, volume = {393}, number = {}, pages = {124336}, doi = {10.1016/j.lfs.2026.124336}, pmid = {41862052}, issn = {1879-0631}, abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.<br><br>METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.<br><br>KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p&#xa0;<&#xa0;0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.<br><br>SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.}, }
@article {pmid41862063, year = {2026}, author = {Reytor-González, C and Frias-Toral, E and Annunziata, G and Simancas-Racines, D and Barrea, L}, title = {Obesity-Focused Dietary Interventions in Breast Cancer Care: A Comprehensive Review of Medical Nutrition Therapy Approaches and Efficacy in Prevention and Treatment.}, journal = {Seminars in cancer biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcancer.2026.03.002}, pmid = {41862063}, issn = {1096-3650}, abstract = {Obesity is associated with an increased risk of developing breast cancer, particularly in postmenopausal women, through mechanisms such as excessive estrogen production, insulin resistance, and chronic low-grade inflammation, all of which promote tumor initiation and progression. Alterations in the gut microbiota, frequently observed in obesity, further exacerbate this risk by influencing estrogen metabolism, modulating immune responses, and promoting systemic inflammation, thereby creating a microenvironment conducive to breast cancer growth. Medical nutrition therapy plays a crucial role in managing these interrelated conditions, with dietary interventions such as the Mediterranean diet, ketogenic diet, and intermittent fasting showing potential to reduce weight, improve metabolic health, modulate the gut microbiome, and positively influence inflammatory and hormonal signaling. While short-term outcomes are promising, long-term studies are required to confirm their effects on breast cancer survival and recurrence. Personalized nutrition-accounting for genetic, epigenetic, and microbiome profiles-is emerging as a highly effective approach to enhance therapeutic outcomes. Integrating targeted nutritional strategies into breast cancer treatment protocols is essential to improve prognosis, optimize therapy responses, and enhance patients' quality of life. This narrative review examines the role of nutritional therapies in the prevention and management of obesity and breast cancer, emphasizing their impact on tumor biology, treatment efficacy, and patient health.}, }
@article {pmid41862100, year = {2026}, author = {Cordeiro, J and Macela, C and Kleiner, R and Vaskovich-Koubi, D and Moura, LIF and Satchi-Fainaro, R and Florindo, HF}, title = {Harnessing the power of microbiome, nanotechnology, and immunity against cancer.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {114839}, doi = {10.1016/j.jconrel.2026.114839}, pmid = {41862100}, issn = {1873-4995}, abstract = {The human microbiome has emerged as a key player in health and disease, including cancer, which remains one of the leading causes of mortality worldwide. Although advances in understanding the tumor immune microenvironment and the development of immunotherapies have transformed cancer treatment, clinical efficacy remains limited by suboptimal response rates and severe side effects. Recent integrative research in cancer biology, immune-oncology, and cancer microbiome research, enabled by omics technologies and advanced bioinformatics, has begun to reveal intricate links between the microbiome, cancer progression, and immune modulation. These findings underscore the microbiome's pivotal role in shaping both therapeutic efficacy and resistance mechanisms. Currently, nanotechnology, propelled into mainstream success through the development of COVID-19 mRNA vaccines, is offering new tools for precision oncology. Nanomaterials are now being explored not only for targeted drug delivery but also for monitoring and modulating the microbiome, with significant potential for biomarker discovery and personalized medicine. In this article, we explore the role of the microbiota in tumorigenesis and cancer therapy, with a particular focus on its crosstalk with the immune system. We highlight emerging microbiota-targeted therapeutic strategies and discuss how nanotechnology-based systems are being designed to modulate the microbiome-immune-cancer axis. Finally, we discuss future directions in leveraging the convergence of microbiome science, nanotechnology, and immunotherapy to advance cancer treatment.}, }
@article {pmid41862195, year = {2026}, author = {Raithel, M and Zlatou, V and Kremenevski, I and Hagel, AF and Konturek, P}, title = {[Endogenous Alcohol Production in the Human Micro- and Mycobiome: Auto-Brewery Syndrome].}, journal = {Zeitschrift fur Gastroenterologie}, volume = {64}, number = {3}, pages = {270-276}, doi = {10.1055/a-2772-7942}, pmid = {41862195}, issn = {1439-7803}, mesh = {Humans ; *Ethanol/metabolism ; *Dysbiosis/diagnosis ; *Gastrointestinal Microbiome/physiology ; *Mycobiome/physiology ; Syndrome ; Dietary Carbohydrates/adverse effects/metabolism ; }, abstract = {Pathological changes in the human microbiome and mycobiome can lead to endogenous production of toxic metabolites, including alcohol. Auto-brewery syndrome (ABS) is characterized by endogenous alcohol formation after high-carbohydrate intake in cases of dysbiosis or underlying disease.Cases described since 1948 were analyzed up to May 2025 via selective literature review regarding symptoms, pathophysiology, diagnostics, and therapy. Syndromes not clearly attributable to endogenous alcohol (e.g., autointoxication, intestinal fermentation syndrome) were excluded.Around 30 cases show variable clinical features with neuropsychiatric, gastrointestinal, and hepatological symptoms, sometimes causing emergencies or accidents. Alcohol is produced by microbial or mycotic overgrowth (e.g., E. coli, Klebsiella, Saccharomyces, Candida) following carbohydrate intake. Diagnosis requires detailed personal and external history, exclusion of other causes, and, if needed, monitored carbohydrate challenge with alcohol measurement. Treatment focuses on carbohydrate reduction, antibiotics or antifungals, and management of underlying conditions.ABS is rare but causes endogenous alcohol-related symptoms that must be considered in medical and legal evaluation of unexplained symptoms or incidents.}, }
@article {pmid41862269, year = {2026}, author = {Wakamatsu, N and Yoshioka, Y and Habu, M and Ariyoshi, W and Yamasaki, R}, title = {Surfactin selectively suppresses acidogenicity in Streptococcus sobrinus without inhibiting growth or biofilm formation.}, journal = {Journal of oral biosciences}, volume = {68}, number = {2}, pages = {100756}, doi = {10.1016/j.job.2026.100756}, pmid = {41862269}, issn = {1880-3865}, mesh = {*Biofilms/drug effects/growth &amp; development ; *Peptides, Cyclic/pharmacology ; *Lipopeptides/pharmacology ; Lactic Acid/metabolism ; Hydrogen-Ion Concentration ; Dental Caries/prevention &amp; control/microbiology ; Humans ; *Streptococcus/drug effects/growth &amp; development/metabolism ; }, abstract = {OBJECTIVES: Dental caries are caused by organic acids produced by cariogenic bacteria through carbohydrate metabolism. Suppression of acid production without disrupting the oral microbiome is a promising preventive strategy against dental caries. Surfactin, a naturally derived biosurfactant, has several biological activities. However, its effects on acid production by cariogenic bacteria remain unclear. In this study, the effects of surfactin on lactate production, growth, biofilm formation, and metabolic activity of Streptococcus sobrinus, were investigated.<br><br>METHODS: In vitro assays were performed to distinguish surfactin-mediated suppression of acidogenic metabolism from its effects on bacterial growth or biofilm formation, combined with molecular and enzymatic analyses to explore the underlying regulatory mechanisms.<br><br>RESULTS: Surfactin significantly reduced lactate production in planktonic and biofilm-associated S. sobrinus, and it delayed environmental pH reduction in the presence of sucrose. Notably, these effects were observed without inhibition of bacterial growth or biofilm formation. There were no significant changes in the expression of lactate production-related genes, and lactate dehydrogenase activity was not inhibited by surfactin. In contrast, in the MTT assay, there was a transient reduction in metabolic activity, accompanied by delayed initiation of growth.<br><br>CONCLUSION: These findings indicate that surfactin selectively attenuates acidogenicity in S. sobrinus, without markedly affecting bacterial viability or biofilm architecture, which is consistent with an anti-virulence mode of action. Although further validation in more complex oral environments and comprehensive safety assessments are required, this study provides fundamental evidence supporting the potential of naturally derived biosurfactants as a basis for future preventive strategies for caries.}, }
@article {pmid41862311, year = {2026}, author = {Berry, AA}, title = {Gut check: converging evidence links microbiome to malaria risk.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.03.004}, pmid = {41862311}, issn = {1471-5007}, abstract = {Beyond genetics and immunity, the gut microbiome may be an underappreciated determinant of malaria parasite burden. Gustin et al. demonstrated that pre-infection microbiome composition predicts the level of Plasmodium parasitemia in both rhesus macaques and human volunteers, with convergent evidence pointing to Bifidobacterium as a potentially protective genus.}, }
@article {pmid41862401, year = {2026}, author = {Mutalik, VK and Inman, JL and Chang, H and Arkin, A and Mao, JH}, title = {Phage therapy in oncology: opportunities for cancer prevention and treatment.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2026.02.001}, pmid = {41862401}, issn = {1471-499X}, abstract = {Bacteriophages (phages) are emerging as programmable biological therapeutics in oncology, extending beyond their traditional antimicrobial applications. This review proposes a phage-microbiome-immune-oncology axis that links microbial dynamics, immune modulation, and engineered phages to guide precision cancer prevention and therapy. Phages can eliminate cancer-associated bacteria, remodel the tumor microenvironment, enhance antitumor immunity, and deliver targeted therapeutic payloads. However, several critical challenges must be addressed to realize this therapeutic potential, particularly host immune responses that limit repeat dosing, inefficient tumor penetration, and the need for rigorous clinical validation. By examining phage-host-tumor interactions through robust model systems and highlighting translational opportunities, this review establishes phage therapy as a promising frontier in precision oncology that warrants accelerated clinical development.}, }
@article {pmid41862452, year = {2026}, author = {Du, Z and Li, M and Lin, K and Xing, B and Ou, Y and Lin, Z and Song, W and Chen, J and Li, J and Li, J and Xiao, M}, title = {High-resolution phage-host assignment through key proteins using large language models.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70613-x}, pmid = {41862452}, issn = {2041-1723}, abstract = {Viral sequences in diverse environments remain largely uncharacterized, impeding our comprehension of their genetic makeup, biological interactions, and potential applications. This underscores an urgent need for innovative analytical methods. Here, we present the VirHost Hunter framework, which employs phage tails and lysins, bypassing the requirement for full genomes, for efficient and high-resolution host assignment. By harnessing Protein Language Models and Vision Transformers, VirHost Hunter captures protein functional homology despite sequence dissimilarity, significantly boosting prediction accuracy. In the scenario of disease-associated gut bacteria, the calibrated VirHost Hunter surpasses existing methods, doubling phage host assignments, expanding taxonomic reach, and revealing previously uncharacterized phages targeting gut bacteria, including Akkermansia and Prevotella. Therefore, we establish a gut phage lysin database, enabling the synthesis of a lysin that effectively and specifically targets an obesity-promoting bacterium. VirHost Hunter's precision and scalability mark a significant leap forward in virome research and present a promising avenue for microbiome therapies.}, }
@article {pmid41862473, year = {2026}, author = {Daniels, M and Wijayagunasekera, D and Berry, D}, title = {Widespread effects of catecholamines on growth of human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00948-2}, pmid = {41862473}, issn = {2055-5008}, support = {Grant-DOI 10.55776/ESP558//Austrian Science Fund/ ; }, abstract = {The interactions between hosts and their microbiomes are driven in part by chemical communication, which influences immune responses, metabolism, and microbial community structure. Neuroendocrine signals are central to this bidirectional communication, forming the basis of microbial endocrinology. Although host-derived hormones, including catecholamines, are known to affect microbial physiology, much of the existing literature focuses on a limited number of model organisms or complex in vivo systems, where disentangling direct microbial responses from host-mediated effects is challenging. As a result, systematic comparative analyses of direct bacterial responses under controlled conditions remain scarce. Here, we performed a systematic in vitro screen under anaerobic conditions to assess catecholamine effects on the growth dynamics of phylogenetically diverse human gut bacteria. Catecholamines altered multiple growth parameters in a species-specific manner, with effects detectable at nanogram concentrations. Multivariate analyses, including principal component analysis and non-metric multidimensional scaling, revealed lineage-associated response patterns across taxa. Although derived from monoculture experiments, these intrinsic responses provide a comparative framework for understanding how direct hormone-microbe interactions may contribute to microbiome dynamics under host stress. Overall, this study provides a quantitative cross-species dataset to inform future systems-level investigations in microbial endocrinology.}, }
@article {pmid41862558, year = {2026}, author = {Soriano-Lerma, A and Soriano-Suárez, JS and Garcia-Rodriguez, M and Alferez, MJ and Soriano, M and Salcedo, JAG and Lopez-Aliaga, I}, title = {Molecular study of the small intestine dysbiosis derived from iron deficiency anaemia.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44373-z}, pmid = {41862558}, issn = {2045-2322}, support = {Contratos PUENTE//Universidad de Granada/ ; [P_FORT_CENTROS_2023/09][AS1] , [P_FORT_GRUPOS_2023/102]//Universidad de Almer&#xed;a/ ; PID2020-120481RB-100/AEI/10.13039/50110001103//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PI21/00497//Instituto de Salud Carlos III/ ; }, }
@article {pmid41862676, year = {2026}, author = {Shim, SY and Lee, J and Linh, LTY and Kim, SR and Choi, HS and Lee, MG and Hwang, SG}, title = {Effects of short-term application of organic manure on the growth of forage maize (Zea mays L. cv. Kwangpyeongok) and soil bacterial communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45179-9}, pmid = {41862676}, issn = {2045-2322}, abstract = {While chemical fertilizers (CF) ensure rapid crop growth, relying exclusively on them can disrupt natural nutrient cycling and lead to environmental concerns such as nutrient imbalance. In contrast, organic amendments offer a sustainable alternative by promoting resource circulation; however, their efficacy is often variable and difficult to control, depending on complex interactions among application rates, plant types, and field conditions. Therefore, gaining comprehensive insights into their optimal use is essential to maximize agricultural benefits. This study evaluated the effects of composted Hanwoo manure (HM) applied at standard (HM_1x) and quadruple (HM_4x) rates on forage maize growth and soil microbial communities compared with CF and no treatment (NT). Growth parameters indicated that plant length was highest in the CF (219.33 cm) and HM_4 × (217.30 cm) groups, followed by HM_1 × (176.78 cm) and NT (172.02 cm). Soil analysis indicated that organic matter (OM) and available phosphorus (P2O5) were significantly higher in HM-treated soils than in NT. Microbiological analysis revealed distinct shifts in community composition linked to these chemical changes. In HM-treated soils, the relative abundance of Proteobacteria and Candidatus Saccharibacteria, known for their roles in OM decomposition and nutrient cycling, significantly increased. Conversely, the CF group showed a higher prevalence of Saprospiraceae, a phosphorus-removing bacterium, which is consistent with the observed reduction in available phosphorus in both soil and plant tissues in the CF treatment. Collectively, this study demonstrates that applying sufficient amounts of composted HM, where appropriate, can result in crop growth comparable to that of CF. Notably, we observed that such growth performance coincided with specific patterns in soil microbial communities related to nutrient availability. By highlighting these co-occurring trends, our research offers valuable insights into the biological dynamics of compost application for sustainable agriculture.}, }
@article {pmid41862790, year = {2026}, author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H}, title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04966-0}, pmid = {41862790}, issn = {1471-2180}, support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; }, }
@article {pmid41863277, year = {2026}, author = {Ely Arman, NI and Makpol, S}, title = {The Link between Gut Microbiome, Amyloid-Beta Deposition, Brain Inflammation, and Alzheimer's Disease: A Review of Current Literature.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/011570159X416900251207210728}, pmid = {41863277}, issn = {1875-6190}, abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by amyloid-beta (Aβ) plaques, neurofibrillary tangles, and cognitive decline. AD has gained increasing global attention. As the aging population continues to grow, the economic burden on individuals, families, and healthcare systems rises, emphasizing the urgent need for early detection and natural therapeutic approaches to address these challenges. The gut microbiota regulates essential physiological functions, including digestion, nutrient absorption, and inflammatory signaling. Dysbiosis, or changes in gut microbiome composition, is marked by the overgrowth of pathogenic bacteria and depletion of beneficial species. Gut dysbiosis is also linked to pathological features of AD, such as increased Aβ deposition, compromised intestinal and blood-brain barrier integrity, and neuroinflammation through the brain-gut microbiome axis (BGMA). However, the connection between the gut microbiome and AD pathological hallmarks remains unclear. This narrative review aims to explore current research on the relationship between gut dysbiosis and the pathological features of AD, with the goal of highlighting the role of the gut system in brain function and AD pathogenesis. Vitamin E, due to its antioxidative and anti-inflammatory properties, may serve as a promising natural option for modulating the gut microbiome while potentially delaying AD progression and promoting a balanced microbial composition.}, }
@article {pmid41863409, year = {2026}, author = {Kaur, S and Bhandari, N and Mahajan, S and Mehta, D and Chauhan, S and Kumar, V and Rohilla, M and Mehta, S and Dhankhar, S}, title = {Molecular Pathways of Microbiota-derived Neuromodulation: An Integrative View.}, journal = {Current neurovascular research}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115672026427392260131184931}, pmid = {41863409}, issn = {1875-5739}, abstract = {INTRODUCTION: The gut microbiota, also called "the forgotten organ", is a complex and dynamic ecosystem of microorganisms that is fundamental to human physiology, neurobiology, and disease. This review examines the intricate relationships between the gut microbiota and the nervous system via the microbiota-gut-brain (MGB) axis. It discusses their endocrine, immunological, and neural pathways.<br><br>METHODS: A thorough literature search was performed across databases including PubMed, Scopus, Web of Science, and Google Scholar, using keywords such as "gut microbiota," "microbiota- gut-brain axis," "neuromodulation," "serotonin," "dopamine," "GABA," "norepinephrine," "prebiotics," "probiotics," and "faecal microbiota transplantation"..<br><br>RESULTS: This article explains how the gut microbiota impacts significant body's chemical messengers such as serotonin, dopamine, GABA, and norepinephrine. These are essential for brain functioning. All of these diseases have evidence linking inflammation of the gut and the brain. Furthermore, gut dysbiosis has been responsible for some of the most serious disorders of mankind through pandemics and plagues.<br><br>DISCUSSION: Moreover, prebiotics, probiotics, faecal microbiota transplantation (FMT), synbiotics, diet, and bioactive substances such as curcumin and flavonoids are new treatment approaches. These strategies help bring back a normal balance of gut microbes for mental and neurological health. Even though preclinical studies have shown promise, bringing it to humans is not simple. Issues like the strain, the individual, and sustained use make it a substantial challenge.<br><br>CONCLUSION: Future directions of work should combine and focus human-based research efforts with precise and personalized microbiome modulation, allowing us to leverage the gut-brain axis therapeutically.}, }
@article {pmid41863708, year = {2026}, author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H}, title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {41863708}, issn = {2509-2723}, abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.}, }
@article {pmid41863784, year = {2026}, author = {Giannakogeorgou, A and van den Ende, T and Verhaar, BJH and de Clercq, N and van Laarhoven, HWM and Nieuwdorp, M}, title = {Targeting the gut microbiota as treatment for obesity and cancer cachexia.}, journal = {Expert opinion on emerging drugs}, volume = {}, number = {}, pages = {}, doi = {10.1080/14728214.2026.2650180}, pmid = {41863784}, issn = {1744-7623}, abstract = {INTRODUCTION: Obesity and cancer cachexia represent two seemingly contrasting yet interrelated ends of the metabolic disorder spectrum, both characterized by disrupted energy homeostasis, inflammation and neuroendocrine dysfunction, and associated with increased morbidity and mortality. Existing treatments often fail to address the complex underlying pathophysiological mechanisms. Emerging research highlights the role of the gut microbiome in the pathophysiology of both conditions and how it can serve as a novel therapeutic target.<br><br>AREAS COVERED: This review explores shared and distinct pathways linking obesity and cancer cachexia. Key systems discussed include the gut-brain axis as well as skeletal muscle and adipose tissue metabolism. We discuss how the gut microbiota influences these processes through (diet-derived) gut microbial metabolites that affect specific signaling pathways. The review evaluates the efficacy and limitations of current anti-obesity and cachexia therapies and summarizes clinical and preclinical interventions targeting the gut microbiome, including pre-, pro-, postbiotics and fecal microbiota transplantation.<br><br>EXPERT OPINION: The gut microbiota holds potential as a therapeutic target in metabolic diseases, offering opportunities for precision medicine based on microbial and metabolic profiles. While early microbiota-based therapies show promise, further investigation into mechanistic pathways and novel engineered microbiota is essential to develop effective treatments for obesity and cachexia.}, }
@article {pmid41864264, year = {2026}, author = {Merrick, B and Mullish, BH and Goldenberg, SD and Khanna, S and Ahuja, V and Hvas, CL and Makharia, GK and Williams, HRT}, title = {A global evaluation of the use of faecal microbiota transplant (FMT).}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108574}, doi = {10.1016/j.ijid.2026.108574}, pmid = {41864264}, issn = {1878-3511}, abstract = {BACKGROUND: Faecal microbiota transplant (FMT) is an effective therapy for recurrent Clostridioides difficile infection (CDI); its use is increasingly being investigated for other indications. Although regional surveys and national registries have provided insight into local practices, a comprehensive global overview of FMT access, implementation and governance is lacking.<br><br>METHODS: A survey regarding key aspects related to FMT use was disseminated electronically to members of the World Gastroenterology Organisation, European FMT Network, and International Society of Infectious Diseases. Responses were analysed both descriptively and using appropriate statistical methods.<br><br>FINDINGS: 80 responses were obtained from 55 countries. FMT was available in significantly more Tier 1/2, than Tier 3/4, nations (24/28 vs 8/27; p<0.001). In countries lacking access to FMT reasons included: lack of expertise/infrastructure; financial constraints; regulatory uncertainty; and perceived lack of clinical need. Most countries using FMT employed both upper and lower gastrointestinal administration routes; 18/32 (56%) used capsulised FMT. Almost all countries with access to FMT used it to treat CDI, albeit with different thresholds for the number of CDI episodes prior to use. There were many non-CDI indications for FMT in current use. Payment for stool donation was reported by 10 countries.<br><br>INTERPRETATION: This is the first global overview of FMT availability and governance, highlighting substantial international inequities and considerable heterogeneity in regulation, clinical use, donor screening, and cost. Standardisation of practice and targeted support for lower income countries is needed to ensure equitable access and to promote safe, high-quality delivery as FMT and microbiome-based therapeutics continue to evolve.}, }
@article {pmid41864269, year = {2026}, author = {Melchiorri, S and Besutti, VM and Castagliuolo, I}, title = {Blastocystis spp. in Fecal Microbiota Transplantation: Evidence, Policy, and the Screening Paradox.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108548}, doi = {10.1016/j.ijid.2026.108548}, pmid = {41864269}, issn = {1878-3511}, abstract = {OBJECTIVES: Fecal microbiota transplantation (FMT) is an established treatment for recurrent Clostridioides difficile infection (rCDI). However, the detection of Blastocystis spp. in potential donors remains controversial and often leads to donor exclusion, despite uncertain pathogenicity. This review aims to critically evaluate the available evidence on Blastocystis spp. transmission through FMT, its clinical impact, and the implications of current donor screening strategies.<br><br>METHODS: A narrative review of the literature was performed using PubMed, Embase, and Web of Science. Studies reporting Blastocystis spp. detection in FMT donors or recipients, transmission events, clinical outcomes, diagnostic methods, and microbiome associations were included and analyzed.<br><br>RESULTS: Across published reports, 34 FMT recipients were exposed to Blastocystis spp.-positive donor material. Transmission was limited to common subtypes (ST1-ST3), was transient, and was not associated with adverse clinical outcomes or reduced efficacy of FMT for rCDI. No cases of symptomatic infection were reported. Frozen stool preparations appeared to abolish parasite viability. Molecular screening methods markedly increased detection rates compared with microscopy, frequently identifying low-burden colonization of uncertain clinical relevance. Available data suggest that Blastocystis spp. carriage may coexist with a healthy microbiome and does not negatively impact FMT outcomes.<br><br>CONCLUSIONS: Current evidence indicates that Blastocystis spp. transmission through FMT in immunocompetent adults is clinically benign. Routine donor exclusion based solely on Blastocystis spp. detection may therefore be overly restrictive. A risk-based approach incorporating parasite burden, subtype, host factors, and processing methods may better balance patient safety with donor availability, supporting more sustainable FMT programs.}, }
@article {pmid41864480, year = {2026}, author = {Rauf, M and Naveed, A and Asghar, MU}, title = {Post-acute sequelae of COVID-19: A disorder of impaired innate immune resolution - A narrative review.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {285}, number = {}, pages = {110701}, doi = {10.1016/j.clim.2026.110701}, pmid = {41864480}, issn = {1521-7035}, abstract = {Post-acute sequelae of COVID-19 (PASC) affect millions of people worldwide and are increasingly recognized as a disorder of failed innate immune resolution rather than a persistent viral infection. Emerging evidence shows that residual SARS-CoV-2 antigens, host-derived alarmins, reactivated latent viruses, and mucosal microbiome-derived products from oral-nasopharyngeal and gut reservoirs sustain the chronic activation of pattern-recognition receptors, inflammasomes, and complement pathways. In parallel, deficits in specialized pro-resolving mediators, impaired efferocytosis, and persistent tissue injury prevent physiological termination of inflammation. These unresolved cues drive long-lasting epigenetic and metabolic reprogramming of hematopoietic stem cells and myeloid lineages, creating maladaptive trained immunity states characterized by hyper-responsiveness or exhaustion of these cells. Thromboinflammatory processes, including aberrant NETosis and sustained interface signalingling, further reinforce self-perpetuating inflammatory circuits. Together, these pathways give rise to reproducible molecular endotypes, including thromboinflammatory, interferon-driven, and neuroinflammatory phenotypes, which explain clinical heterogeneity. Framing PASC as a disorder of impaired immune resolution within a mucosal microbial viral context provides a unifying mechanistic scaffold for biomarker identification and host-directed therapies. This review proposes that restoring active resolution programs, rebalancing metabolic-epigenetic networks, and dismantling pathogenic innate feedback loops are promising strategies for reversing the chronic immune imprint of PASC.}, }
@article {pmid41864590, year = {2026}, author = {Raj, DS and Gao, B and Sohn, MB and Brydges, C and Srivastava, A and Rabb, H and Cheung, AK and Fiehn, O and Kendrick, C and Gassman, JJ and Tariq, A and Isakova, T and Fried, LF and Wolf, M and Raphael, KL and Middleton, JP and Abdalla, Y and , }, title = {Response to the "Letter to the Editor: ''Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism''.".}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.jrn.2026.02.010}, pmid = {41864590}, issn = {1532-8503}, }
@article {pmid41864593, year = {2026}, author = {Xu, K and Qian, Y and Zhao, C}, title = {Letter to the Editor Regarding "Prebiotic Administration to CKD Patients Modifies Their Microbiome and Metabolism".}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.jrn.2026.01.010}, pmid = {41864593}, issn = {1532-8503}, }
@article {pmid41857652, year = {2026}, author = {Russell, A and Gore, R and Wood, JL and Robert, KA}, title = {Characterising the gut microbiome of six Australian marsupials reveals captivity constrains microbiome.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00545-w}, pmid = {41857652}, issn = {2524-4671}, abstract = {BACKGROUND: The gut microbiome is an ecosystem of microbes that live within the host's digestive tract and are a vital component of host health. An increasing number of studies are investigating microbiome differences in wild and captive-managed populations to assist in species conservation and improve captive welfare. The gut microbiota of Australian marsupials has not been extensively studied but has long been recognised as having an important functional role in the digestive physiology and health of those in care. We used 16S rRNA gene sequencing to characterise and compare the faecal bacterial communities of six species of Australian marsupials from captive or wild origins over a large temporal and spatial scale.<br><br>RESULTS: We found the microbiome of captive marsupials had reduced microbial richness and diversity in two species, the brushtail possum and the Eastern grey kangaroo. Captivity was associated with gut microbiome compositional differences for half of the species tested. These compositional changes were accompanied by less pronounced seasonal variability in captivity.<br><br>CONCLUSIONS: This study provides valuable baseline data and demonstrates that captivity significantly alters the gut microbiota, suppressing its natural seasonal variability. These findings enhance our understanding of the gut microbiome in Australian marsupials. Future research should focus on determining the functional importance of these microbial communities and develop strategies to address any microbiome deficiencies in managed populations. Such efforts could ultimately improve the success of captive rearing and reintroduction programs.}, }
@article {pmid41857729, year = {2026}, author = {Li, P and Guo, S and Zhang, Y and Hu, H and Cheng, T and Xu, B and Zeng, K and Huang, T and Dong, Z and BenHuo,  and Lin, J and Wen, H and Sun, B}, title = {Multimodal deep learning for inflammatory bowel disease: a new frontier in cellular and molecular biomarker discovery to clinical translation.}, journal = {Journal of biological engineering}, volume = {20}, number = {1}, pages = {}, pmid = {41857729}, issn = {1754-1611}, abstract = {Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is a chronic, relapsing condition with heterogeneous clinical phenotypes and variable therapeutic outcomes. Deep learning (DL), combined with high-throughput sequencing and multi-omics, has advanced precision management by enabling integration of genomic, transcriptomic, microbiome, metabolomic, imaging, and clinical data. DL applications include molecular biomarker discovery, automated endoscopic and histopathological image analysis, patient stratification, disease monitoring, and prediction of therapeutic response, such as anti-TNF-α efficacy. Convolutional neural networks (CNNs) demonstrate exceptional performance in image interpretation and automated scoring. Challenges for clinical translation include limited multi-center datasets, inconsistent annotations, low interpretability, and privacy concerns. Addressing these issues through interpretable, efficient, and privacy-preserving DL frameworks, along with temporally resolved cross-institutional datasets, will facilitate real-time monitoring and personalized care, reshaping IBD diagnosis, treatment, and long-term management.}, }
@article {pmid41857737, year = {2026}, author = {Lei, C and Wu, J and Fu, Z and Jin, R and Hu, B and Xu, K and Cheng, C and Shi, T and Gong, D and Huang, C and Qin, J}, title = {The microbiome of host saliva, gastric fluid, and gastric mucosa as accurate diagnostic tools for gastric cancer detection.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07953-1}, pmid = {41857737}, issn = {1479-5876}, }
@article {pmid41857777, year = {2026}, author = {Xu, T and Qiu, X and Hang, Q and Qi, X and Mei, H and Guo, J and Zheng, Y and Ji, M and Xu, Q and Wu, B}, title = {Oral microbiome and Frailty: Insights from NHANES 2009-2012 and Mendelian Randomization Analysis.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glag079}, pmid = {41857777}, issn = {1758-535X}, abstract = {BACKGROUND: Frailty is associated with increased risks of disability, hospitalization, and mortality. Emerging evidence suggests that the oral microbiome may influence frailty development, but population-based evidence is limited and causal relationships remain unclear. This study explored the link between oral bacteria and frailty, using genetic analysis to investigate causality.<br><br>METHODS: We analyzed data from 2,696 adults aged &#x2265;50&#x2009;years in NHANES 2009-2012. Oral microbiome diversity was assessed using 16S rRNA gene sequencing. Frailty was measured using a 36-item Frailty Index. Survey-weighted linear regression and restricted cubic spline models examined associations between four &#x3b1;-diversity indices and frailty. &#x3b2;-diversity was quantified using Bray-Curtis dissimilarities and compared by frailty status using PERMANOVA. Bidirectional two-sample Mendelian randomization (MR) using GWAS data assessed causal relationships between taxa and frailty.<br><br>RESULTS: Lower &#x3b1;-diversity across all four indices were associated with higher frailty scores (P&#x2009;<&#x2009;0.050). &#x3b2;-diversity differed by frailty (P&#x2009;=&#x2009;0.001). MR analyses indicated that in saliva, Campylobacter_A, Saccharimonadaceae, and TM7x were protective, whereas Gemella was associated with increased frailty risk. In tongue samples, Saccharimonadaceae was a risk factor, while Fusobacterium, TM7x, and Solobacterium showed protective effects.<br><br>CONCLUSIONS: Oral microbiome diversity is inversely associated with frailty in U.S. adults, and MR analyses identify specific oral taxa potentially involved in frailty development. These findings provide population-level evidence and genetic support for the oral microbiome as a potential modifiable target to promote healthy aging.}, }
@article {pmid41857807, year = {2026}, author = {Heidari, H and Vincent, M and Lawrence, DA}, title = {Integrating exposomics and multi-omics with dysbiosis biomarkers for clinical and environmental connections implicated in neuropathology. Cause and cure cluses.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfag034}, pmid = {41857807}, issn = {1096-0929}, abstract = {Multi-omic investigations into environmental effects on health and disease are aided by inclusion of microbial microbiomes with assessment of mirobes producing metabolites that differentially modulate host organ functions. The gut microbiome is key because many environmental toxicants enter the body orally and may disrupt gut microbes that help digest food, as well as the microbiome-gut-brain axis, which produces regulatory metabolites with systemic effects. Environmental stressors may differentially alter brain development and function, even among identical twins, in that over time, there may be divergence due to epigenetic effects from the environment, including microbes within the microbiome. The diversity of microbiomes is presented as playing a key role in the influence of organs on each other, health, and the development of disorders. The gut microbes and their metabolites may cause mitochondria to produce less ATP and more reactive oxygen species (ROS). The metabolites produced by microbes during the digestion of foods can nourish or harm a person's cellular and molecular functions and vary depending on each person's exposome. The detrimental effects of environmental stressors are discussed, focusing on how altered levels of neuropeptides, neurotransmitters, and the inflammatory/anti-inflammatory balance affect health and disorders. During ATP production, dysfunctional mitochondria may produce more ROS, which can lead to inflammation and oxidative stress, causing cell damage and disrupting products needed for neuronal development, connections, and functions. The balance between inflammatory/anti-inflammatory biomarkers and metabolites and between oxidants/antioxidants is discussed in relation to some clinical connections; for example, the proportions of CD4 and CD8 T cells in HIV patients and the ROS-to-glutathione ratio in inflammatory bowel disease and septic patients. These imbalances are reviewed regarding brain development and functions leading to anxiety, depression, and dementia. The integration of multi-omics, dysbiosis, and mitochondrial dysfunction with a person's clinical evaluation is discussed to inform the formulation of prevention measures and therapeutic interventions regarding environmental effects on the microbiome-gut-brain axis and physical and mental health.}, }
@article {pmid41857857, year = {2026}, author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G}, title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e115290}, doi = {10.1136/bmjopen-2025-115290}, pmid = {41857857}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; }, abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.<br><br>METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.<br><br>ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charit&#xe9;-Universit&#xe4;tsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.<br><br>TRIAL REGISTRATION NUMBER: DRKS00036475.}, }
@article {pmid41858059, year = {2026}, author = {Zeng, J and Wang, R and Gu, Z and Li, J and Huang, M and Shen, Q and Wang, M and Guo, S}, title = {Nitrate-constructed fungal communities and rhizosphere metabolites confer resistance to Fusarium wilt in cucumber.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71110}, pmid = {41858059}, issn = {1469-8137}, support = {32402674//National Natural Science Foundation of China/ ; 42577134//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Provincial Special Project for Carbon Peak Carbon Neutrality Science and Technology Innovation/ ; }, abstract = {Nitrogen fertilization regimes are a critical determinant of soilborne disease outcomes in intensive agriculture, yet the mechanisms through which different nitrogen forms exert their influence remain poorly understood. Our study investigates how nitrate and ammonium nutrition differentially modulate the severity of Fusarium wilt in cucumber by altering the rhizosphere microbiome and metabolome. We utilized a split-root system to study the effects of nitrate and ammonium on disease progression, integrating ITS amplicon sequencing and gas chromatography mass spectrometry metabolomics. Nitrate nutrition promoted the recruitment of beneficial fungal taxa and the accumulation of antifungal metabolites, which collectively suppressed pathogen growth and enhanced plant health. By contrast, ammonium supply created a rhizosphere environment conducive to pathogen growth by selectively enriching pathogenic fungi and driving metabolic reprogramming, which ultimately heightened plant susceptibility. Split-root experiments revealed that local nitrate application stimulated resveratrol accumulation and enriched Funneliformis in the rhizosphere. In vitro inhibition assays showed that resveratrol directly suppressed Fusarium mycelial growth, and pot experiments demonstrated that exogenous resveratrol application and inoculation with Funneliformis both enhanced plant performance. Our findings reveal how nitrogen forms regulate plant-microbe-metabolite interactions to determine soilborne disease outcomes, providing a foundation for nutrition-based management strategies that can reduce fungicide reliance through natural suppression.}, }
@article {pmid41858079, year = {2026}, author = {Mbong Ngwese, M and Loum, S and Berg, L and Tyakht, AV and Youngblut, ND and Adegnika, AA and Kremsner, P and Ley, RE and Marsh, JW}, title = {Genomic and phenotypic characterization of a human gut Methanobrevibacter intestini strain G0370_i3 isolated in Gabon.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/17460913.2026.2645510}, pmid = {41858079}, issn = {1746-0921}, abstract = {AIMS: Methanogens are methane-producing archaea that are present in the human gut. Yet, their adaptation to diverse human lifestyles remains poorly understood. Here, we report the isolation of Methanobrevibacter intestini G0370_i3 from the stool of a healthy adult from Southern Gabon, Africa, where inhabitants maintain traditional subsistence lifestyles with diets distinct from industrialized populations.<br><br>MATERIALS AND METHODS: M. intestini was enriched from human stool, phenotypically characterized, and sequenced.<br><br>RESULTS: G0370_i3 growth relied on the presence of H2 and CO2 and could also grow on formate, in contrast to reports for the type strain. The genome encoded pathways for amino acid biosynthesis, cofactor metabolism, and secondary metabolite production. We identified 23 mobile genetic elements and five defense systems, indicating horizontal gene transfer and antiviral defense. No prophage regions were detected.The genome also encoded uridine diphosphate (UDP)-sugar metabolism pathways, indicating capacity for energy storage and cell wall adaptability. Genes encoding adhesin-like proteins suggest capabilities for host interaction. Phenotypically, G0370_i3 is a coccobacillus, grows optimally at 37&#xb0;C, and tolerates antibiotics, salt, and oxygen stress.<br><br>CONCLUSIONS: These findings highlight the stress resilience and selective metabolic capabilities of M. intestini and underscore the importance of representing African populations in microbiome research.}, }
@article {pmid41858134, year = {2026}, author = {Odendaal, J and Fishwick, K and Correia, GDS and Lee, YS and Makwana, K and Black, N and Southcombe, J and Thornton, J and Larsen, K and Hussain, Q and Hawkes, A and Kandiyil, A and Muter, J and Brighton, PJ and Vrljicak, P and Lucas, E and Granne, I and Bouliotis, G and Bennett, PR and Brosens, J and MacIntyre, DA and Quenby, S}, title = {CD138 expression in the endometrium associates with endometrial timing and inflammatory status but not microbiota composition.}, journal = {Human reproduction (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/humrep/deag032}, pmid = {41858134}, issn = {1460-2350}, support = {//Efficacy and Mechanism Evaluation (EME) Programme/ ; 17/60/22//National Institute for Health and Care Research and Medical Research Council partnership/ ; //Tommy's National Centre for Miscarriage Research, and the Imperial National Institute for Health and Care Research Biomedical Research Centre Pregnancy and Prematurity/ ; //Genesis Research Trust/ ; }, abstract = {STUDY QUESTION: What is the relationship between constitutive CD138 expression in the endometrium and the reproductive tract microbiota composition?<br><br>SUMMARY ANSWER: The presence of CD138+ cells in endometrial stroma is cycle-dependent and associated with impaired luteal phase endometrial timing but not altered vaginal or endometrial microbial composition.<br><br>WHAT IS KNOWN ALREADY: CD138-diagnosed chronic endometritis (CE) is associated with adverse reproductive outcomes including recurrent pregnancy loss (RPL) in uncontrolled studies. However, CD138 is constitutively expressed in the endometrium, potentially confounding the reported associations between CE, adverse endometrial function, and early pregnancy loss.<br><br>STUDY DESIGN, SIZE, DURATION: Translational cohort study of a subset of 103 samples derived from 737 women embedded within the CERM trial, a double-blinded, randomized interventional trial evaluating the impact of pre-pregnancy antibiotic treatment for CE in RPL patients.<br><br>Women aged &#x2265;18 to <42&#xa0;years, with a history of two or more first-trimester consecutive miscarriages were recruited from specialist RPL clinics. Endometrial biopsies, vaginal, ectocervical, and endometrial swabs were obtained 10&#x2009;&#xb1;&#x2009;4&#x2009;days following a positive home ovulation test. Additional samples, including proliferative endometrium, were obtained from the Tommy's National Reproductive Health Biobank. Endometrial biopsies were processed for CD138 expression analysis and immunohistochemistry (IHC), histological dating based on Noyes' criteria, and molecular timing analysis. Metataxonomic profiling of microbiota was performed by sequencing of bacterial 16S ribosomal RNA genes alongside cytokine analysis.<br><br>IHC revealed three patterns of CD138 immunoreactivity: predominantly membranous punctate staining, predominantly diffuse staining, and a mixed pattern. CD138 is constitutively expressed on the basolateral membrane of glandular epithelial cells and a subset of non-immune stromal cells. Stromal expression was very high (>200 CD138-positive stromal cells/10&#xa0;mm2) in 26 out of 27 proliferative endometrial samples. While CD138 immunoreactivity in the stroma declines markedly following ovulation (Mann-Whitney U-test; P&#x2009;<&#x2009;0.005), gene expression analysis demonstrated a reduction in SDC1 expression encoding CD138/syndecan-1, across the menstrual cycle. When compared to CD138-negative samples, conspicuous diffuse staining in the stromal compartment was associated with significantly earlier endometrial histological dating (P&#x2009;<&#x2009;0.01) and lower molecular timing ratios (P&#x2009;<&#x2009;0.01). Poor correlation between CD138 and immunoreactivity was demonstrated. Sequencing of paired vaginal and ectocervical swabs and endometrial Tao brush samples collected from 114 patients demonstrated tightly interconnected microbial composition throughout the reproductive tract. No significant difference in vaginal, ectocervical, or endometrial community state type with CD138 expression was demonstrated. Analysis of supernatants of vaginal and ectocervical swabs and Tao Brush revealed an inverse correlation between the severity of stromal CD138 immunoreactivity in endometrial stroma and secreted levels of IL-10, TNF-&#x3b1;, and VEGF (q&#x2009;<&#x2009;0.05).<br><br>LARGE SCALE DATA: Microbial and Metataxonomic raw data are available in the European Nucleotide Archive (Projects PRJEB83331 and PRJEB83332).<br><br>This study relied on patient-reported ovulation-based timing. This was, however, associated with the provision of validated ovulation tests. In addition, the study is limited by lack of collection of data on the underlying fertility-related co-morbidities due to exclusion of known contributory co-morbidities at the point of recruitment.<br><br>This study challenges the purported relationship between CD138+ CE and the pathophysiology of CE-associated RPL. The findings indicate endometrial CD138 levels are non-immune and non-bacterial driven and are associated with endometrial immaturity. CD138-based CE testing and treatment should not be performed outside of a research context.<br><br>Funding was provided by the Efficacy and Mechanism Evaluation (EME) Programme a National Institute for Health and Care Research and Medical Research Council partnership (17/60/22). Further funding was from Tommy's National Centre for Miscarriage Research, and the Imperial National Institute for Health and Care Research Biomedical Research Centre Pregnancy and Prematurity Theme. G.D.S.C. is supported by the Genesis Research Trust. All authors report no direct conflict of interest.<br><br>TRIAL REGISTRATION NUMBER: ISRCTN23947730.}, }
@article {pmid41858163, year = {2026}, author = {Li, N and Wang, J and Qiu, G and Han, Z and Zhang, C and Yu, H}, title = {Synergistic Utilization of KOH-Modified Biochar and Nitrogen-Fixing Bacteria for Recovering Tetracycline-Contaminated Agricultural Soil and Promoting Crop Growth.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c16832}, pmid = {41858163}, issn = {1520-5118}, abstract = {Tetracycline (TC) contamination in agricultural soils poses a serious threat to crop production and ecosystem health. However, sustainable remediation strategies capable of both efficiently degrading antibiotics and simultaneously restoring impaired nitrogen cycling functions remain lacking. This work developed a synergistic system combining KOH-modified biochar (KOB) with two TC-resistant nitrogen-fixing bacteria (TCNFB): Chryseobacterium lathyri Cbl and C. elymi Cbe. Cbl showed superior TC degradation (47.3%) and nitrogenase activity (0.08 mmol of C2H4 g[-1] min[-1]). In pot experiments, the KOB-Cbl composite increased soybean biomass by 45.21% through rhizosphere microbiome restructuring, enhanced community stability, upregulation of nifD/H/K genes, suppressed denitrification, and elevated phytohormone levels. KOB's high surface area and pyridinic nitrogen enriched Chryseobacterium, enabling colocalized TC degradation and nitrogen fixation. This work reveals an agricultural soil remediation strategy based on synergistic interactions between functional materials and microorganisms, providing an effective pathway for concurrently addressing antibiotic pollution and enhancing crop growth.}, }
@article {pmid41858365, year = {2026}, author = {Lommer, C and Schroeder, L and Amato, C and Dhakal, K and Kotian, C and Quiroga, D and Paskett, ED and Fu, MR and McAlearney, AS and Collins, S and King, TA and McLaughlin, SA and Myers, SP}, title = {Pharmacotherapy agents in prevention and treatment of breast cancer-related lymphedema: a systematic scoping review.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1751628}, pmid = {41858365}, issn = {2234-943X}, abstract = {BACKGROUND: Breast cancer-related lymphedema (BCRL) is a common and life-long adverse event affecting ~20% of breast cancer survivors. As existing non-pharmacologic management is burdensome, expensive, and variably effective, this systematic scoping review aims to identify pharmacologic and herbal agents for prevention and treatment for BCRL.<br><br>METHODS: PubMED, Embase, Web of Science Core collection, and the Cumulative Index to Nursing and Allied Health Literature were searched for studies published in English between 1993 and 2025 that investigated the preventative or therapeutic effect of pharmacologic or herbal agents on BCRL among adult stage I-III breast cancer patients. Studies describing interventions with systemically absorbed anti-inflammatories, anti-thrombotics, anti-coagulants, and blood product components were included. Systematic reviews, protocols for ongoing clinical trials, preclinical and non-human studies, editorials, and studies not exclusive to BCRL were excluded. Three reviewers screened and extracted data between June and August 2025. The primary outcomes of interest were reduction in BCRL incidence or severity.<br><br>RESULTS: Of the 217 articles screened, 37 were included in the final review. After full text review, 13 were excluded for repetitive data, non-English language, or irrelevant outcomes. The 24 studies included in the analysis investigated anti-diabetic, herbal, anti-inflammatory, anti-hypertensive, immunomodulatory, and microbiome modifying agents, and venoactive flavinoid derivates. Three studies explored the role of pharmacologic/herbal agents in BCRL prevention. While thiazolidinediones, anti-hypertensives, and non-steroidal anti-inflammatory drugs (NSAIDs) had no effect on BCRL incidence, glucagon-like peptide-1 receptor agonists (GLP-1 RA) were associated with BCRL prevention. In the 21 studies that assessed the effect of pharmacologic/herbal agents in BCRL treatment, NSAIDs/steroids, anti-hypertensives, microbiome/synbiotic supplements, and doxycycline showed no benefit and data for flavonoid-derived venoactive agents and herbal products were inconsistent. Immune-modulating therapies were associated with improved BCRL signs/symptoms in three studies.<br><br>CONCLUSION: This systematic scoping review found limited evidence suggesting that GLP-1 RAs may reduce the risk of BCRL and that immunomodulatory agents may improve signs/symptoms of BCRL. Rigorous prospective trials using standardized limb volume/edema, quality-of-life (QoL), and symptom measures and longer follow-up are needed to inform clinical practice aimed at preventing and treating BCRL.<br><br>https://www.crd.york.ac.uk/PROSPERO/, identifier CRD420251055134.}, }
@article {pmid41858617, year = {2026}, author = {Chen, N and Zhao, S and Yin, Z and Khan, S and Guo, J and Zhao, M}, title = {The potential of Protaetia brevitarsis as a functional food that enhances immune function and gut microbiota in mice.}, journal = {iScience}, volume = {29}, number = {4}, pages = {114939}, pmid = {41858617}, issn = {2589-0042}, abstract = {The issues of global hunger, malnutrition, and the increasing prevalence of diseases present considerable challenges to public health, emphasizing the urgent need for functional foods possessing immune-enhancing attributes. This study investigated the effects of Protaetia brevitarsis (Lewis) (PB), an edible insect, on immune modulation and gut microbiota composition in ICR mice. 160 male mice in four groups were treated with diets with different PB additions (0, 5%, 10%, and 20%). The results demonstrated that PB improved the cellular immune response of T cells (p ≤ 0.05), phagocytosis activity of macrophages (p ≤ 0.05), and humoral immunity in terms of elevated levels of serum hemolysin, IgG, and TNF-α (p ≤ 0.05), compared to the CK (100% basal diet) group. The gut microbial dynamics among treatments showed an increased microbiota diversity and abundance of beneficial bacteria, including Muribaculaceae and Muribaculum at genus level and Bacteroidota at phylum level with the increased PB (p ≤ 0.05). In conclusion, PB can enhance the immune function and gut microbiota, highlighting its potential as a functional food.}, }
@article {pmid41858644, year = {2026}, author = {Khorshidi Asl, Z and Jafari, F and Rezazadeh, F and Kamyabi, H}, title = {Burning Mouth Syndrome and the Oral Microbiome: Unveiling Potential Links.}, journal = {Biomedicine hub}, volume = {11}, number = {1}, pages = {23-37}, pmid = {41858644}, issn = {2296-6870}, abstract = {BACKGROUND: Burning mouth syndrome (BMS) is a chronic neuropathic orofacial pain condition that remains challenging to manage due to its unclear etiology and limited treatment options. While multiple systemic factors have been proposed, emerging evidence suggests that oral microbial dysbiosis may contribute to neuroinflammatory and pain-related mechanisms. However, the role of the oral microbiota in BMS remains insufficiently understood.<br><br>SUMMARY: This review examines current evidence regarding the potential association between oral microbiota and BMS, with emphasis on hormonal regulation, immune function, and micronutrient balance. A comprehensive literature search identified studies reporting systemic alterations in patients with BMS. Available evidence suggests that BMS may be associated with changes in sex hormones, thyroid hormones, and neuroendocrine stress responses, potentially influenced by oral microbial composition. Alterations in immune mediators, particularly interleukin-6, and micronutrient imbalances such as vitamin B12 deficiency have also been reported in a subset of patients. These interconnected pathways may contribute to peripheral and central neuropathic pain mechanisms underlying BMS symptoms.<br><br>KEY MESSAGES: (i) Oral microbiota may interact with hormonal, immune, and micronutrient pathways relevant to BMS. (ii) The relationship between oral dysbiosis and BMS appears complex and potentially bidirectional. (iii) Further clinical and mechanistic studies are needed to clarify these interactions and inform targeted therapies.}, }
@article {pmid41858664, year = {2026}, author = {Han, C and Luo, W and Peng, G and Tan, D and Liu, R and Cao, Y}, title = {Metarhizium anisopliae reshapes the citrus rhizosphere microbiome to enhance fruit quality via nutrient cycling.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1784405}, pmid = {41858664}, issn = {1664-462X}, abstract = {The rhizosphere microbiome is a critical regulator of nutrient acquisition and plant growth in citrus. Here, we evaluated the effects of the entomopathogenic fungus Metarhizium anisopliae CQMa421 on soil nutrient status, rhizosphere bacterial community structure, and fruit quality in citrus using soil physicochemical assays, plant physiological measurements, and 16S rRNA amplicon high-throughput sequencing. CQMa421 application markedly reshaped soil properties, increasing available potassium by 128.50% and organic matter by 75.05%. In addition, total nitrogen, alkali-hydrolyzable nitrogen, and available phosphorus increased by 112.68%, 155.30%, 305.74% respectively, while soil pH decreased by 0.4 units. CQMa421 treatment significantly increased leaf total nitrogen content and elevated fruit vitamin C by 12.00%. Microbial community profiling showed an enrichment of putatively beneficial taxa, including Proteobacteria and Firmicutes, in treated soils. Functional prediction suggested enhanced nutrient cycling potential, with increased representation of genes associated with carbohydrate metabolism and inorganic ion transport. Collectively, these results indicate that M. anisopliae CQMa421 acts as a plant growth-promoting fungus by enhancing soil nutrient availability and restructuring the rhizosphere microbiome, thereby improving the overall nutrient status of the soil and enhancing citrus fruit quality.}, }
@article {pmid41858670, year = {2026}, author = {Mattei, V and Sergeant, K and Saracchi, M and Bulgari, D and Kunova, A and Pizzatti, C and Cortesi, P and Renaut, J and Pasquali, M}, title = {Differential modulation of tomato root exudates by Streptomyces strains underlies contrasting control of Fusarium oxysporum f. sp. lycopersici.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1759226}, pmid = {41858670}, issn = {1664-462X}, abstract = {INTRODUCTION: Rhizosphere microbiome is affected and modulated by the complex mixtures of bioactive molecules that are released by plant roots. In this work, two promising plant growth-promoting strains of Streptomyces spp. (DEF17 and DEF19) were evaluated for their capacity to modulate tomato roots and exudates metabolic profile and influence Fusarium oxysporum f. sp. lycopersici (Fol).<br><br>METHODS: Dual culture assays, chemotropism assays, and in planta pathogenesis assays were performed to evaluate the capability of the strains to inhibit Fol growth, repel Fol conidia, and induce plant defense mechanisms both in vitro and in vivo. Finally, untargeted LC-MS/MS analysis was performed to understand which metabolites are produced and released by tomato roots after plant-bacteria interaction occurs.<br><br>RESULTS: This study indicates that herbal formulas that could regulate the composition and proportion of gut microbiota have a positive effect in three stages (perioperative, postoperative, and advanced) of GC and CRC. They could promote the recovery of postoperative gastrointestinal function, increase tumor response, improve performance status, and reduce the incidence of adverse events. Herbal formulas exerted anti-cancer efficacy through multiple mechanisms and pathways; among them, the regulation of gut microbiota has not been paid enough attention. To further support the conclusion and better understand the role of gut microbiota in the treatment of GC and CRC, more rigorously designed, large-scale, and multicenter RCTs that focus on herbal formulas and gut microbiota are needed in the future.<br><br>DISCUSSION: Together, these results indicated that tomato plant protection against Fol is consistent with DEF17 through exudate-mediated modulation, highlighting a gap between in vitro antagonism and in planta efficacy.}, }
@article {pmid41858674, year = {2026}, author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z}, title = {Microbiome and plant relationship: a symbiosis against phytopathogens.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1722279}, pmid = {41858674}, issn = {1664-462X}, abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.}, }
@article {pmid41858792, year = {2026}, author = {Raber, J and Sharpton, TJ}, title = {Diet, gut microbiome, and cognition in neurodegeneration: a review and methodological framework.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1771904}, pmid = {41858792}, issn = {1663-4365}, abstract = {The gut microbiome influences brain function through the gut-brain axis via synthesis of neurotransmitters, production of metabolites affecting epithelial barrier integrity and immune modulation and signaling through the vagus nerve. In humans, microbiome diversity reflects healthy aging and predicts survival, while dysbiosis is increasingly implicated in neurodegenerative conditions including Alzheimer's disease, Parkinson's disease, multiple sclerosis, and ALS. Fecal transplant studies in germ-free mice demonstrate that microbiome alterations are sufficient to induce cognitive and neuropathological phenotypes, supporting causality in preclinical models. Genetic risk factors and environmental exposures affect both neurodegeneration risk and microbiome composition. In this review, we synthesize evidence from human cohorts and preclinical models on the gut-brain axis in cognitive health and disease. We then present a methodological framework for diet-microbiome-cognition research, addressing causal inference through mediation analysis, supervised approaches for deriving diet scores, validation strategies, and individual heterogeneity. This framework can guide development of microbiome-targeted dietary interventions to improve cognitive outcomes.}, }
@article {pmid41858899, year = {2026}, author = {Kumar, M and Singh, S and Ojha, R and Kriti, M and Park, G and Verma, V and Pal, N and Sharma, P and Shubham, S and Pandey, MK and Parasannanavar, DJ and Sarma, DK and Tiwari, RR and Nagpal, R}, title = {Gut microbiome disparities reflect type 2 diabetes progression and medication status.}, journal = {iScience}, volume = {29}, number = {3}, pages = {115156}, pmid = {41858899}, issn = {2589-0042}, abstract = {Type 2 diabetes mellitus (T2D) prevalence is rapidly increasing in India, yet microbiome signatures linked to disease progression and oral antidiabetic therapy remain underexplored. We performed full-length 16S rRNA sequencing of fecal samples from prediabetics (PDs), untreated newly diagnosed T2D (UKT2D), and clinically diagnosed T2D patients (KT2D), alongside biochemical, anthropometric, and medication data. Despite comparable glycemic control and insulin resistance between UKT2D and KT2D groups, gut microbial diversity was significantly reduced in KT2D, coinciding with antidiabetic drug use, primarily metformin. Lactobacillus abundance increased with disease progression, while Clostridium_sensu_stricto_1 was associated with glucose homeostasis and insulin sensitivity. β diversity differed only between controls and PD, with no other pairwise differences. Collectively, these results indicate that T2D progression and oral antidiabetic medications remodel the gut microbiome in this south Asian cohort and highlight the need to reassess antidiabetic treatment efficacy using larger longitudinal studies.}, }
@article {pmid41856961, year = {2026}, author = {Narimatsu, Y and Pleguezuelos-Manzano, C and Hornikx, D and Goerdeler, F and Jaroentomeechai, T and Flores, K and Narimatsu, S and Boot, C and Hansen, L and Durbesson, F and Vincentelli, R and Comstock, L and Clevers, H and Taleb, V and Corzana, F and Henrissat, B and Clausen, H and Hurtado-Guerrero, R and Büll, C}, title = {Discovery of a secreted Bacteroides fragilis mucinase that cleaves mucins with bis-T O-glycans through a carbohydrate binding module-dependent mechanism.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644983}, pmid = {41856961}, issn = {1949-0984}, mesh = {*Bacteroides fragilis/enzymology/genetics/metabolism ; *Mucins/metabolism/chemistry ; *Polysaccharides/metabolism/chemistry ; Humans ; *Bacterial Proteins/metabolism/genetics/chemistry ; Substrate Specificity ; Glycoside Hydrolases/metabolism/genetics ; Gastrointestinal Microbiome ; Carbohydrate Binding Modules ; }, abstract = {Degradation of mucins at the host-microbial mucus interphase involves glycosidases that release monosaccharides from O-glycans and mucinases that cleave the mucin protein backbone. Mucinases recognize and cleave peptide bonds at specific sequence motifs with varying O-glycan structures required and/or permissible. Mucinases that digest mucins with intact O-glycans can potentially destroy the protective mucus, while mucinases that only digest mucins with partially degraded O-glycans may serve at a later stage of nutrient sourcing from mucins. Here, we discovered nine CBM-bearing M60-like mucinases across gut commensals and opportunists, including a conserved Bacteroides fragilis mucinase denoted HC11. We also investigated the previously described Bacteroides thetaiotaomicron mucinase BT4244, which together delineates two functional classes with distinct preferences: BT4244 for bis-Tn (GalNAcα1-O-Ser/Thr) and HC11 for bis-T (Galβ1-3GalNAcα1-O-Ser/Thr) O-glycans. Both mucinases harbor carbohydrate-binding modules (CBM32) that bind their cognate O-glycan motifs and are required - together with the catalytic domains - for efficient cleavage of extended mucin domains, which is consistent with cooperative engagement, but are not required for the cleavage of short glycopeptides. We show B. fragilis strains secrete HC11 and degrade mucins only after the removal of sialic acids. Together, these findings expand the mucinase repertoire by nine enzymes spanning commensals and opportunists, demonstrate that CBM32 domains are essential for efficient cleavage of extended mucin substrates likely by promoting multivalent engagement and substrate positioning, and nominateidentify CBM-catalytic cooperation as a mechanism and intervention point for controlling mucus turnover and barrier integrity.}, }
@article {pmid41857136, year = {2026}, author = {Dutta, S and Khanh, NV and Lee, YH}, title = {Rhizosphere and endophytic bacterial communities of the endangered alpine modest primrose and their plant growth-promoting potential.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41389-3}, pmid = {41857136}, issn = {2045-2322}, abstract = {Plant microbiomes play critical roles in host growth and stress resilience, yet remain underexplored in alpine ecosystems. We investigated the rhizosphere and endophytic bacterial communities of an endangered alpine modest primrose (Primula modesta var. hannasanensis), which is endemic to the high-altitude regions of Korea. Using 16 S rRNA gene amplicon sequencing, we compared the bacterial communities in wild and cultivated populations. The rhizosphere microbiota exhibited greater diversity than the root endophytes, and cultivated plants harbored more diverse and compositionally distinct endophytic communities than wild plants, suggesting that cultivation influences the microbial structure. We isolated bacterial strains from these communities and identified Leifsonia lichenia JBCE310 and Chryseobacterium piperi JBCE316 as significantly enhancing seed germination and seedling growth of Primula malacoides and Arabidopsis thaliana. The co-inoculation yielded synergistic effects that were likely mediated by phytohormone production. These results highlight the functional potential of alpine plant-associated bacteria and provide potential microbial candidates for the conservation and ex situ propagation of endangered alpine flora.}, }
@article {pmid41857189, year = {2026}, author = {Dalamaga, M and Rozani, S and Petropoulou, D}, title = {Why Is Colorectal Cancer Occurring Earlier? Metabolic Dysfunction, Underrecognized Carcinogens, and Emerging Controversies.}, journal = {Current obesity reports}, volume = {15}, number = {1}, pages = {}, pmid = {41857189}, issn = {2162-4968}, }
@article {pmid41857249, year = {2026}, author = {Ríos Colombo, NS and Perez-Ibarreche, M and Lanka, P and Ross, RP and Hill, C}, title = {Establishing and analyzing the Simplified Human Intestinal Microbiota (SIHUMI) as a versatile in vitro gut microbiome model with qPCR-based strain-level tracking.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {41857249}, issn = {1750-2799}, support = {101027450//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101027450//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {A major challenge in microbiome research is the inherent complexity and inter-individual variability of the human gut microbiota. To address this, we have developed a detailed protocol for establishing and analyzing a Simplified Human Intestinal Microbiota (SIHUMI)-a defined, in vitro bacterial consortium composed of seven fully sequenced and anaerobically culturable human gut commensals. This model enables highly reproducible and controlled experiments, in which the individual growth of each member can be quantitatively tracked over time (up to 48 h) via species-specific qPCR. The protocol outlines optimized and standardized steps, including consortium setup, time-resolved sample collection, DNA extraction and qPCR analysis. It can be used to evaluate community dynamics in response to interventions such as nutrients, antimicrobials or other xenobiotics. The system is readily adaptable: additional strains can be incorporated, including pathogens (e.g., Clostridioides difficile), to transform it into an infectious disease model. In addition, we describe two optional rapid methods for assessing interspecies interactions and provide an open-source web app for generating interaction network plots. This enables exploration of ecological mechanisms and potential off-target effects. The entire workflow-from setup to data acquisition-can be completed within 1 week. This qPCR-based protocol offers a validated and accessible platform for gut microbiome research, providing a standardized, strain-level and time-resolved alternative to 16S- or fluorescence-based workflows and enabling quantitative, scalable analysis of defined microbial communities.}, }
@article {pmid41857413, year = {2026}, author = {Yang, L and Peery, RC and Zhou, S and Chen, X and Farmer, LM and Gutierrez, F and Fowler, S and Zhang, L and Salamat, JM and Riggins, K and Shi, J and Shen, L}, title = {Weaning drives microbiome-mediated epigenetic regulation to shape immune memory in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41857413}, issn = {2058-5276}, support = {6-FY18-135//March of Dimes Foundation (March of Dimes)/ ; R21HD101035//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD100914//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01CA233472//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {During weaning, the transition to solid food diversifies the gut microbiome, triggering a programmed immune response critical for long-lasting mucosal immunity. Previous work showed that the gut microbiome mediates epigenetic development in intestinal stem cells (ISCs) during suckling, but what happens during weaning is unclear. Here, genome-wide profiling revealed that weaning-driven microbiome changes shape the DNA methylome and transcriptome of murine ISCs in an IFNγ-dependent manner. Specifically, we observe demethylation of enhancer elements essential for MHC class II genes, which results in a transcriptional memory that persists through differentiation into adulthood. IFNγ blockade, or low-dose penicillin to target Gram-positive bacteria, in early life impaired microbiome-mediated epigenetic control and mucosal immunity, and exacerbated colitis. Murine organoids primed with IFNγ showed rapid, amplified transcriptional responses upon secondary stimulations. These findings reveal that early-life events alter the gut microbiome and these changes reprogramme ISC epigenetic memory to shape mucosal immunity.}, }
@article {pmid41857429, year = {2026}, author = {Xiao, S and Wang, M and Martin, TG and Scott, B and Fang, X and Liu, X and Yang, Y and Fu, S and Truong, SD and Gugel, JF and Maas, GL and Mullen, MP and Hill, JH and Li, VL and Markhard, AL and Zhao, M and Qi, W and Reghupaty, SC and Zhao, M and Spaas, J and Wei, W and Moholdt, T and Hawley, JA and Voldstedlund, CT and Richter, EA and Chen, X and Svensson, KJ and Bernstein, D and Leinwand, LA and Xu, Y and Long, JZ}, title = {Python metabolomics uncovers a conserved postprandial metabolite and gut-brain feeding pathway.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {41857429}, issn = {2522-5812}, support = {R01DK124265//U.S. Department of Health Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes Digestive Kidney Diseases)/ ; K99DK141966//U.S. Department of Health Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes Digestive Kidney Diseases)/ ; }, abstract = {Most mammals consume small and frequent meals. By contrast, pythons are ambush predators that exhibit extreme feeding and fasting patterns and provide a unique model for uncovering molecular mediators of the postprandial response[1-3]. Using untargeted metabolomics, we show that circulating levels of the metabolite para-tyramine-O-sulphate (pTOS) are increased more than 1,000-fold in pythons after a single meal. In pythons, pTOS production occurs in a microbiome-dependent manner via sequential decarboxylation and sulphation of dietary tyrosine. In both pythons and mice, pTOS administration activates a neural population in the ventromedial hypothalamus (VMH). In mice, these VMH neurons are required for the anorexigenic effects of pTOS. Chronic administration of pTOS to diet-induced obese male mice suppresses food intake and body weight. pTOS is also present in human blood, where its levels are increased after a meal. Together, these data uncover a conserved postprandial anorexigenic metabolite that links nutrient intake to energy balance.}, }
@article {pmid41849050, year = {2026}, author = {Cao, Y and Wu, X and Huang, Z and Xu, C and Ge, Z and Xie, Y and Wu, L and Qian, Y and Ding, B and Luo, H}, title = {Skin bacteriota ameliorates androgenetic alopecia via harmonizing skin immuno inflammatory balance.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41849050}, issn = {1678-4405}, support = {2023ZF011//Zhejiang Province Traditional Chinese Medicine Science and Technology Plan Project/ ; 2025R410B064//the Zhejiang Science and Technology Innovation Program/ ; 772213A13033//Zhejiang University Student Science and Technology Innovation Activity Plan/ ; }, abstract = {UNLABELLED: The human skin is the largest heterogeneous organ that protects the body from pathogens such as bacteria, fungi, mites, and viruses. The coexistence of skin microorganisms associated with the host helps maintain tissue integrity and immune homeostasis. This study aimed to investigate the effect of the skin microbiome on hair growth in androgenic alopecia (AGA) model mice. The dihydrotestosterone induced AGA model mice were engaged in this study. The ABF (Antibiotic-Free) and ABT (Antibiotic-Treated) mice were topically administrated with ddH2O and antibiotics, respectively. Seven days later, the three of mice in the ABF and ABT group were co-housed. Compared to ABF mice, ABT mice exhibited sparse hair, thinner skin, and fewer hair follicles, all of which has been improved in the Co-housed ABF/ABT mice. The translational expression of β-catenin and Wnt5a, as well as the mRNA levels of Vegfa, Fgfr, Igf1, and Lef1 decreased in ABT mice but recovered in ABF/ABT mice. Increased the expression of TLR4 and NF-κB, IL-6, and the mRNA levels of Il-17 levels in ABT mice compared to ABF mice indicated inflammation in dorsal skin. Cohousing notably affected Il-6, Il-17, Il-23, and Tnfα levels. The 16S rDNA sequencing results and the correlative analysis indicated that the relative abundance of Lactobacillus and Proteus might be the key genus influencing the immuno-inflammatory balance. Our findings suggest that restoring the dorsal skin bacteriota promotes hair growth in AGA model mice. This improvement is likely mediated by the modulation of the skin’s inflammatory microenvironment. Importance. This study highlights the critical role of skin bacteriota in modulating immuno-inflammatory balance in AGA, suggesting that restoration of bacteriota may contribute to the amelioration of DHT-induced hair loss by regulating TLR4/NF-κB pathways, which offers a novel insight for bacterial -based therapies.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01911-1.}, }
@article {pmid41853378, year = {2023}, author = {Zimmermann, P}, title = {Exploring the microbial landscape of the nasopharynx in children: a systematic review of studies using next generation sequencing.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1231271}, pmid = {41853378}, issn = {2813-4338}, abstract = {INTRODUCTION: The nasopharynx harbours a diverse and dynamic microbial community, which plays an important role in maintaining the health and homeostasis of the respiratory tract, as well as in immune system development. Understanding factors that influence the composition of the nasopharyngeal microbiome in children and its association with diseases is of particular importance, as children are at a heightened risk for respiratory infections and other adverse health outcomes.<br><br>OBJECTIVES: This review systematically summarises studies which investigated the nasopharyngeal microbiome in children, including its dynamics, stability over time, and the influence of intrinsic and extrinsic factors on its composition.<br><br>METHODS: MEDLINE was searched using the OVID interface. Original studies which investigated the nasopharyngeal microbiome using next generation sequencing in children were summarised.<br><br>RESULTS: The search identified 736 studies, of which 77 were included. The studies show that the nasopharyngeal microbiome in children is dynamic and influenced by many external factors. A high abundance of Haemophilus, Moraxella, and Streptococcus and a low abundance of Corynebacterium and Dolosigranlum are associated with adverse health outcomes such as respiratory tract infections, wheezing and asthma exacerbations. Factors which have been identified as risk factors for these adverse health outcomes, such as being born by Caesarean section, not being breast-fed, having siblings, day-care attendance, and antibiotic exposure have been shown to be associated with the aforementioned features in the nasopharyngeal microbiome.<br><br>CONCLUSION: The association between specific nasopharyngeal microbial profiles and adverse health outcomes highlights the potential of the nasopharyngeal microbiome as a marker for identifying children at risk for disease and even more importantly, as an avenue for targeted interventions and preventive strategies.}, }
@article {pmid41853380, year = {2023}, author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN}, title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1067019}, pmid = {41853380}, issn = {2813-4338}, abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.}, }
@article {pmid41853381, year = {2023}, author = {Li, L and Yan, Y and Wang, X and Hou, Y and Ding, L and Wang, Z and Song, Q and Ding, W and Zhang, X}, title = {Allicin modulates the intestinal microbiota to attenuate blood glucose and systemic inflammation in type 2 diabetic rats.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1102694}, pmid = {41853381}, issn = {2813-4338}, abstract = {INTRODUCTION: Allicin is a wide spectrum prebiotic for human health, but whether it can attenuate blood in diabetes patients is rarely reported. In this study, we built a rat model and investigated the effect of allicin on diabetes mellitus type 2 (T2DM). We found that allicin could effectively reduce blood glucose levels, regulate intestinal microbiota, reduce lipid and body weight accumulation, and systemic inflammation in T2DM rats.<br><br>METHODS: The rat model of type 2 diabetes was made by streptozotocin, and different doses of allicin were given orally by gavage. The intestinal contents of diabetes rats were sequenced and analyzed by 16S technology, and the clinical indicators of rats were detected for joint analysis.<br><br>RESULTS: Allicin can improve the intestinal flora of type 2 diabetes rats, enrich beneficial metabolites, reduce blood glucose, improve blood lipids, reduce systemic inflammation, and improve type 2 diabetes.<br><br>DISCUSSION: Intestinal microbiome analysis showed that allicin gavage significantly regulated the structure and main components of the intestinal microbiota in T2DM rats. Allicin increased the abundance of probiotic microbes, such as Lactobacillus, Clostridium and Akkermansia, while it reduced pathogenic microbes, such as Enterobacter, Erysipelatoclostridium and Colidextribacter. Allicin gavage increased the abundance of intestinal short-chain fatty acids, such as acetic acid and propionic acid. Correlation analysis showed that the increased gut microbes by allicin gavage were significantly associated with health physiological parameters but negatively related to serum inflammatory factors such as interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-a), and hypersensitive C-reactive protein (hs-CRP). In addition, our study also suggests that allicin may have prebiotic effects on chronic liver injury. This study shows that allicin can regulate various clinical symptoms of T2DM and is a potential therapeutic drug for T2DM.}, }
@article {pmid41853384, year = {2023}, author = {Walusimbi, B and Lawson, MAE and Nassuuna, J and Kateete, DP and Webb, EL and Grencis, RK and Elliott, AM}, title = {The effects of helminth infections on the human gut microbiome: a systematic review and meta-analysis.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1174034}, pmid = {41853384}, issn = {2813-4338}, abstract = {UNLABELLED: The gut microbiome is important in shaping human health. One key factor that has been proposed to affect the gut microbiome is helminth infection. Unravelling the association and/or interaction between helminth infections and the gut microbiome may reveal new insights into the mechanisms through which parasitic worms impact the prognosis of infections and diseases. While considerable work has gone into reviewing data on the effect of helminth infection on gut microbiome in animal studies, less attention has been given to this area of research in human studies. This study set out to address this through an exhaustive systematic review of literature. Articles were identified through EMBASE, MEDLINE, Web of Science and Science Direct following a registered protocol (PROSPERO). After assessing methodological quality (ICROMS) and publication bias, a random effects meta-analysis was performed to investigate the overall effect that intestinal parasites can have on the human gut microbiome using alpha- and beta-diversity metrics and adjusting for age, sex and antihelminthic treatment taken by individuals. A total of 19 out of 3466 articles were included in the final meta-analysis. Our results show that helminth infection increases the host bacterial diversity, as well as microbial richness. This work further contributes to the understanding of how the gut microbiome structure changes depends on whether one is infected with helminths or not. It also lays the foundation for future research aimed at establishing how these interactions could explain the disparity in phenotypes such as infection, disease and vaccine responses reported in different regions worldwide.<br><br>https://www.crd.york.ac.uk/prospero/, identifier CRD42020192182.}, }
@article {pmid41853385, year = {2023}, author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P}, title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1147082}, pmid = {41853385}, issn = {2813-4338}, abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.<br><br>OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).<br><br>METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.<br><br>RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.<br><br>CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.}, }
@article {pmid41853386, year = {2023}, author = {Goemann, HM and Ulrich, DEM and Peyton, BM and Gallegos-Graves, V and Mueller, RC}, title = {Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1310790}, pmid = {41853386}, issn = {2813-4338}, abstract = {Plants rely on a diverse rhizobiome to regulate nutrient acquisition and plant health. With increasing severity and frequency of droughts worldwide due to climate change, untangling the relationships between plants and their rhizobiomes is vital to maintaining agricultural productivity and protecting ecosystem diversity. While some plant physiological responses to drought are generally conserved, patterns of root exudation (release of small metabolites shown to influence microbes) and the consequential effects on the plant rhizobiome can differ widely across plant species under drought. To address this knowledge gap, we conducted a greenhouse study using blue grama (Bouteloua gracilis), a drought-tolerant C4 grass native to shortgrass prairie across North American plains, as a model organism to study the effect of increasing drought severity (ambient, mild drought, severe drought) on root exudation and the rhizobiome. Our previous results demonstrated physiological effects of increasing drought severity including an increase in belowground carbon allocation through root exudation and shifts in root exudate composition concurrent with the gradient of drought severity. This work is focused on the rhizobiome community structure using targeted sequencing and found that mild and severe drought resulted in unique shifts in the bacterial + archaeal and fungal communities relative to ambient, non-droughted controls. Specifically, using the change in relative abundance between ambient and drought conditions for each ZOTU as a surrogate for population-scale drought tolerance (e.g., as a response trait), we found that rhizobiome response to drought was non-randomly distributed across the phylogenies of both communities, suggesting that Planctomycetota, Thermoproteota (formerly Thaumarchaeota), and the Glomeromycota were the primary clades driving these changes. Correlation analyses indicated weak correlations between droughted community composition and a select few root exudate compounds previously implicated in plant drought responses including pyruvic acid, D-glucose, and myoinositol. This study demonstrates the variable impacts of drought severity on the composition of the blue grama rhizobiome and provides a platform for hypothesis generation for targeted functional studies of specific taxa involved in plant-microbe drought responses.}, }
@article {pmid41853387, year = {2023}, author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC}, title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1199766}, pmid = {41853387}, issn = {2813-4338}, abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.}, }
@article {pmid41853500, year = {2024}, author = {Wang, G and Menon, S and Wilsack, L and Rehak, R and Lou, L and Turbide, C and Auger, J and Tremblay, A and Mathieu, O and Binda, S and Tompkins, TA and Bruehlmann, S and Andrews, CN}, title = {Spatially and temporally precise microbiome profiling in the small intestine using the SIMBA capsule with X-ray tracking.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1321624}, pmid = {41853500}, issn = {2813-4338}, abstract = {INTRODUCTION: Few minimally invasive options for sampling the small intestinal (SI) luminal fluid exist to study the SI microbiota in health and disease. To address the lack of tools and methods to study GI regions that are difficult to access, Nimble Science developed a fully autonomous and passive sampling method, the Small Intestine MicroBiome Aspiration (SIMBA™) capsule, for convenient, high-quality, and reliable sampling to study the diet-microbiota interactions in the SI.<br><br>METHODS: The sealing efficacy and microbial DNA preservation capacity of the SIMBA capsules was first validated through in vitro simulation assays. Then, a clinical study was conducted with 20 healthy participants to validate the in vivo use of SIMBA capsules to reliably capture samples for SI microbiome analysis before and after an intervention (NCT04489329). Briefly, participants ingested the capsules at baseline and 7 days later, with a probiotic capsule containing a blend of L. rhamnosus R0011 and B. longum R0175. Following baseline SIMBA capsule ingestion, multiple low-dosage x-ray scans were performed to track the sampling location. Fecal samples corresponding with the baseline and intervention capsule were analyzed for comparison.<br><br>RESULTS: The SIMBA capsules' performance in vitro demonstrated the potential for contamination-free sampling with preservation of the microbial communities. Within the clinical study, the capsules performed safely and reliably for collection of SI content. X-ray tracking confirmed that 97.2% of the capsules completed sample collection in the SI regions before reaching the colon. Importantly, our data showed that the capsules sampled in the right area of the intestines and that baseline SIMBA microbiome profile is significantly different from fecal microbiome profile. SIMBA successfully detected a concurrent probiotic intervention in the small intestine, which was not detectable using stool samples.<br><br>DISCUSSIONS: The high accuracy of sampling location and sealing efficacy of the SIMBA capsules makes them potentially useful research tools in clinical trials for studying diet-microbiota interactions in health and disease, and perhaps eventually for the clinical diagnosis of GI tract conditions affecting the SI such as SIBO.}, }
@article {pmid41853502, year = {2024}, author = {Tarrant, I and Finlay, BB}, title = {The potential of live biotherapeutic products in allergic disease: current findings and future directions.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1418633}, pmid = {41853502}, issn = {2813-4338}, abstract = {With the global prevalence of allergic disease continuing to rise at an alarming rate, the need for effective and safe therapeutics is paramount. Given the critical role of the early-life microbiota on immune development, emerging research suggests the potential use of live biotherapeutic products (LBP) for the prevention and treatment of childhood allergy. However, findings are limited and inconsistent. Therefore, the present review critically evaluates the current animal and human data on the therapeutic value of LBPs in allergy, the underlying immunological mechanisms by which LBPs may mediate allergy susceptibility, limitations of the current research that need to be addressed, and future research directions. Accordingly, LBPs may protect against allergic disease through several immunological and physiological mechanisms during early-life, including regulation of Th1/Th2 balance, SCFA-induced activation of GPR41/43 and HDAC inhibition, and maturation of epithelial barrier integrity. Taken together, current findings indicate powerful immunomodulatory properties of LBPs on allergic immune response, with LBPs offering exciting potential as a novel therapeutic tool for childhood allergy. However, the efficacy of LBPs in allergy is complex and influenced by many population and methodological factors, resulting in varied therapeutic benefits. While research thus far has focused on traditional probiotic strains, greater investigation into microbial consortiums selected from the microbiota of non-allergic infants may provide greater promise as a therapeutic tool for allergic disease. Further investigation, particularly into long-term efficacy, strain-specific effects, optimal supplementation regimes, and use of multi-strain consortiums, is necessary before findings can be translated into clinical applications to tackle childhood allergic disease.}, }
@article {pmid41853503, year = {2024}, author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T}, title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1451735}, pmid = {41853503}, issn = {2813-4338}, abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.}, }
@article {pmid41853505, year = {2024}, author = {Rusling, MR and DeMar, JC and Chakraborty, N and Hoke, AV and Miller, SA and Rosenberger, JG and Batuure, AB and Wilder, DM and Sajja, VS and Long, JB and Hammamieh, R and Gautam, A}, title = {The effect of dietary omega-6 fatty acid enrichment in rodent models of military-relevant acute traumatic psychological stress and traumatic brain injury.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1430340}, pmid = {41853505}, issn = {2813-4338}, abstract = {INTRODUCTION: Sequelae from traumatic brain injuries (TBIs) and post-traumatic stress disorder (PTSD) are major career-limiting factors for combat soldiers. Overlap between TBI and PTSD symptoms alongside other common comorbidities complicate the diagnosis and treatment. Systems-level and high-throughput approaches are key in understanding the underlying biomolecular mechanisms and differentiating these conditions.<br><br>METHODS: The present study identifies dietary factors and proposes mechanisms behind psychological stress and TBI, using established preclinical animal models and a multi-omics approach. Here, we used microbiome characterizations of rats exposed to simulations of blast-induced TBI and underwater trauma (UWT)-induced psychological stress. We further studied the effect of dietary omega-6 versus omega-3 polyunsaturated fatty acid (n-6, n-3 PUFA) enrichment on the insult responses. The use of excess n-6 PUFA was chosen due to its high prevalence in the Western diet and pro-inflammatory nature. Prior to TBI or UWT, animals were maintained for 6 weeks and continued thereafter on either a standard diet or two customized chows imbalanced and diminished in omega-3 content. Corresponding shams were carried out for all groups. Fecal bacterial microbiome populations were assessed using 16S rRNA gene sequencing.<br><br>RESULTS: Physiologic outcome modeling identified that dietary status affected post-TBI lactate dehydrogenase (LDH) and triglyceride levels, with n-3 PUFA having a large attenuating influence. The UWT model showed similar trends, with diet significantly altering LDH, terminal corticosterone (14 days post-exposure), and a fear behavior susceptibility. Fecal microbiome alpha diversity was significantly reduced by high levels of n-3 PUFA. Likewise, beta diversity of the microbiome was significantly affected by both diet and time but not exposure to TBI or UWT. Compositionally, temporal effects on the microbiome were more likely to be observed with the diets. The most affected features fell within the Proteobacteria phyla, in which n-3 PUFA enrichment significantly reduced Alphaproteobacteria in the TBI model and increased Gammaproteobacteria in the UWT group.<br><br>DISCUSSION: All these observations can influence the vulnerability or resilience of the warfighter to blast-induced TBI and acute psychological stress. The microbiome mechanisms facilitate and provide a knowledge-driven unbiased panel of signatures to discriminate between the two insults and is an essential tool for designing precise care management.}, }
@article {pmid41853506, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1484878}, doi = {10.3389/frmbi.2024.1484878}, pmid = {41853506}, issn = {2813-4338}, abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].}, }
@article {pmid41853507, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1359580}, pmid = {41853507}, issn = {2813-4338}, abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.}, }
@article {pmid41853509, year = {2024}, author = {Fu, X and Shama, A and Norbäck, D and Chen, Q and Xia, Y and Zhang, X and Sun, Y}, title = {Exploring the role of indoor microbiome and environmental characteristics in rhinitis symptoms among university students.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1277177}, pmid = {41853509}, issn = {2813-4338}, abstract = {INTRODUCTION: Rhinitis is one of the most prevalent chronic respiratory diseases worldwide. There is emerging evidence suggesting that the indoor microbiome may contribute the onset and exacerbation of rhinitis symptoms, but comprehensive studies on this topic remain scarce.<br><br>METHODS: In this study, we assessed the microbiome assemblage of settled air dust collected in Petri dishes in 86 dormitory rooms of Shanxi University, China using 16s rRNA sequencing. A self-administered questionnaire, including questions about rhinitis symptoms and personal information, was completed by 357 students residing in these dormitories. Logistic and linear regression model was applied to examine the associations between environmental characteristics, indoor microbiome, and rhinitis.<br><br>RESULTS: The most abundant genera in the dormitories were Ralstonia (15.6%), Pelomonas (11.3%), Anoxybacillus (9.3%) and Ochrobactrum (6.2%). Taxa richness in the class of Actinobacteria and Fusobacteriia was negatively/protectively associated with rhinitis (p<0.05). Six bacterial genera, including those from Actinobacteria (Actinomyces), Fusobacteriia (Fusobacterium), and Bacteroidetes (Prevotella and Capnocytophaga), were negatively/protectively associated with rhinitis. Conversely, seven genera, predominantly from Alphaproteobacteria and Betaproteobacteria (Sphingomonas, Caulobacter, uncharacterized Caulobacteraceae and Comamonadaceae), were positively associated with rhinitis. Living in higher floor level and higher indoor PM2.5 concentrations were associated with a higher abundance of taxa potentially protective against rhinitis and a lower abundance of taxa potentially increasing the risk of rhinitis (P<0.01). However, having curtain indoor and higher indoor CO2 concentrations were associated with a lower abundance of taxa potentially protective against rhinitis and a higher abundance of taxa potentially increasing the risk of rhinitis (P<0.01).<br><br>DISCUSSION: This study enhances our understanding of the complex interactions between environmental characteristics, indoor microbiomes, and rhinitis, shedding light on potential strategies to manipulate indoor microbiome for disease prevention and control.}, }
@article {pmid41853510, year = {2024}, author = {Kim, H and Lee, K and Lee, JY and Kwon, BE and Kim, HJ and Park, H and Kim, T and Kwak, JG and Choi, JE and Hong, KH and Chun, J and Shin, C}, title = {Distinct Cutibacterium acnes subspecies defendens strains classified by multi-omics dissection alleviate inflammatory skin lesions of a rosacea-like mouse model.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1362408}, pmid = {41853510}, issn = {2813-4338}, abstract = {INTRODUCTION: Cutibacterium acnes (C. acnes) resides in various organs such as the skin, prostate, eye, nose, stomach, and intestine, indicating the possibility of extensive crosstalk between this bacterium and the human body. C. acnes strains are classified into three subspecies based on phylogenetics and distinguishable phenotypes. Among them, C. acnes subsp. defendens strains are characterized by anti-inflammatory features, raising expectations for their potential as future microbiome therapeutics. However, the heterogeneity of C. acnes subsp. defendens and its corresponding immunological functions have not been clearly addressed.<br><br>METHODS: The genetic diversity of the strains was assessed using single- and multi-locus sequence typing. Their immune-modulatory functions were evaluated in vitro using 2D and 3D assays with immune and epithelial cells. The anti-inflammatory effects were further confirmed in vivo using a rosacea-like mouse model. Comparative genomic and transcriptomic analyses were conducted to uncover mechanisms underlying the immunosuppressive activity of the strains.<br><br>RESULTS: We demonstrated that the newly isolated C. acnes subsp. defendens strains, exhibiting phenotypic heterogeneity, are distinctly clustered using single- and multi-locus sequence typing methods. These strains showed strong immune-regulatory functions in immune and epithelial cell-based 2D and 3D in vitro assays. Furthermore, their anti-inflammatory role was functionally confirmed in vivo using a rosacea-like mouse model, where they alleviated skin lesions characterized by hyperplasia and dermal inflammation. Comparative transcriptomics revealed that these strains may exert their immunosuppressive effects through the enhanced expression of acnecins and transcriptional variation in envelope stress regulators (specifically the two-component systems, CesSR homologs). Additionally, we propose that these C. acnes type II strains produce anti-inflammatory metabolites or peptides smaller than 3 kDa, which are associated with elevated pyrimidine and reduced L-arginine biosynthesis.<br><br>DISCUSSION: The newly isolated C. acnes subsp. defendens strains demonstrate significant anti-inflammatory properties both in vitro and in vivo, suggesting their potential as microbiome-based therapeutics. Their unique genomic and transcriptomic profiles, including the production of small bioactive compounds and specific transcriptomic patterns, underpin their immunosuppressive capabilities. These findings provide a foundation for developing novel treatments for inflammatory skin conditions, such as rosacea.}, }
@article {pmid41853511, year = {2024}, author = {Pitell, S and Woo, C and Trump, E and Haig, SJ}, title = {Balancing water conservation and health: do water-saving showerheads impact the microbes we breathe in during showering?.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1416055}, pmid = {41853511}, issn = {2813-4338}, abstract = {Low-flow showerheads offer consumers economic and water-saving benefits, yet their use may inadvertently affect the microbial content of produced water and water-associated aerosols. This study aimed to compare the abundance and microbial composition of bacteria in shower water and associated respirable aerosols produced by various low flow rate (1, 1.5, and 1.8 gpm) showerheads. Our findings indicate that the lowest-flow showerhead produces water with lower total microbial and opportunistic bacterial pathogen densities compared to higher low flow rate counterparts. However, microbiome analysis revealed that 1.8 gpm flow rate showerheads exhibit reduced abundance of Gram-negative organisms and common biofilm-forming organisms, suggesting potentially lower pathogenicity compared to 1 and 1.5 gpm low-flow showerheads. Additionally, the number of respirable aerosols produced by showerheads as well as the partitioning of certain microorganisms from the water to aerosol phases was negatively correlated with flow rate, suggesting that there may be increasing exposure potential to pathogenic bioaerosols when using a 1gpm showerhead compared to a 1.8 gpm showerhead. However, the 1.5 gpm showerhead seemed to balance microbial partitioning, aerosol generation, and water conservation. Moreover, the microbial composition of aerosols produced from shower water was more influenced by the age of the showerhead than the flow rate, highlighting the significance of biofilm formation on the microbial community. Overall, our findings underscore the importance of evaluating the microbial risk associated with low-flow showerheads using multiple metrics in both water and aerosols, and dynamically assessing this over time, to ensure accurate future risk assessment.}, }
@article {pmid41853512, year = {2024}, author = {Beilig, S and Pannekens, M and Voskuhl, L and Meckenstock, RU}, title = {Assessing anaerobic microbial degradation rates of crude light oil with reverse stable isotope labelling and community analysis.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1324967}, pmid = {41853512}, issn = {2813-4338}, abstract = {Oil reservoirs represent extreme environments where anaerobic degradation profoundly influences oil composition and quality. Despite the common observation of biodegraded oil, the microbial degradation rates remain largely unknown. To address this knowledge gap, we conducted microcosm incubations with light oil as carbon source, original formation water and sulfate as electron acceptor, closely mimicking in situ conditions to assess oil degradation rates. Samples were taken from a newly drilled oil well to exclude contamination with injection water and allochthonous microorganisms. At the end of the incubations, microbial community analyses with 16S rRNA gene amplicon sequencing revealed the most prominent phyla as Desulfobacterota, Thermotogota, Bacteroidota, Bacillota (formerly Firmicutes), and Synergistota, collectively accounting for up to 44% of relative abundance. Ion chromatography and reverse stable isotope labeling were used to monitor sulfate reduction and CO2 evolution respectively. We calculated an average degradation rate of 0.35 mmol CO2 per year corresponding to 15.2 mmol CO2/mol CH2(oil) per year. This resembles to approximately 200 years to degrade one gram of oil under the applied, presumably ideal conditions. Factoring in the available oil-water-contact (OWC) zone within the incubations yielded a degradation rate of 120 g CH2 m[-2] OWC per year, closely aligning with the modeled degradation rates typically observed in oil reservoirs. Moreover, our study highlighted the utility of the reverse stable isotope labeling (RSIL) approach for measuring complex substrate degradation at minute rates.}, }
@article {pmid41853514, year = {2024}, author = {Asumang, P and Ntumi, R and Dwomoh, F}, title = {Unveiling microbial dynamics: a review of health and immune enhancement in school settings.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1488702}, pmid = {41853514}, issn = {2813-4338}, abstract = {This review focuses on the role of microorganisms in promoting health and immune function within school environments. Microbes, including bacteria, viruses, fungi, and other microorganisms, constitute the human microbiome and play a crucial role in various bodily functions and immune system development. The complex interactions between microorganisms and the immune system in schools, where children spend a significant amount of time, are not fully understood. While schools have traditionally emphasized hygiene practices to prevent the spread of infectious diseases, recent research has highlighted the potential consequences of reduced microbial exposure during early life. The "hygiene hypothesis" suggests that limited exposure to microbes in infancy may increase the risk of allergies, asthma, and autoimmune diseases in adulthood. This paper explores the microbial diversity found in schools, the benefits of exposure to different microorganisms, and the implications of hygiene practices on immune system development. It also examines current research on microbial intervention strategies and their potential to influence overall health in schools. Understanding the role of microbes in school environments has implications for public health policies and educational practices, aiming to create healthier and more conducive learning environments for the younger generation. By comprehensively exploring this topic, this review contributes to a broader understanding of the significance of microbes in promoting health and immune function in school settings and its relevance to future health research.}, }
@article {pmid41853515, year = {2024}, author = {,  and Barberio, D}, title = {Navigating regulatory and analytical challenges in live biotherapeutic product development and manufacturing.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1441290}, pmid = {41853515}, issn = {2813-4338}, abstract = {The recent FDA approvals of Rebyota™ and Vowst™ represent landmark milestones within the burgeoning field of live microbiota-based products. Future microbiota-based treatment approaches also hold significant promise for treating patients with a myriad of diseases and disorders, yet substantial hurdles hinder their development and utilization. Foremost, existing regulatory frameworks governing live biotherapeutic product (LBP) manufacturing development have notable gaps, requiring comprehensive expansion and refinement. Along with regulatory challenges, hurdles remain in the optimization and validation of analytical methodologies essential for characterizing LBPs, including for microbial identification, potency, and bioburden. To address these challenges, Microbiome Therapeutics Innovation Group (MTIG) spearheaded collaborative efforts, engaging industry leaders and the FDA in discussions aimed at catalyzing improvements in LBP analytics and refining the current regulatory landscape. Extrapolating on feedback from these discussions, this review highlights challenges and identifies critical gaps. Specific recommendations for future regulatory guidance are proposed, as are recommendations for interactions that developers can take now with regulatory agencies to support the development of maturing guidance. Key analytical factors to consider in LBP development are reviewed, highlighting strengths and weaknesses of various methodologies. Collaboration among regulatory and government agencies, industry, and academia, facilitated by coalitions like MTIG, will be instrumental in ushering the microbiota-based therapeutics field into the next phase of approvals and advancements, ultimately benefiting patients.}, }
@article {pmid41853517, year = {2024}, author = {Dalman, MR and Simison, WB and Nielsen, D and Bhatta, S and Ramahi, N and Yee, C and Thapaliya, D and Kadariya, J and Cheatham, S and Olson, H and Smith, TC}, title = {Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1457940}, pmid = {41853517}, issn = {2813-4338}, abstract = {BACKGROUND: Staphylococcus aureus is a gram-positive bacterium commonly found in the nares and oropharynx of one in three individuals and has the potential to cause significant health problems. With antibiotic-resistant strains causing 11,000 deaths yearly and ~2% of the population nasally colonized with methicillin-resistant S. aureus, a search for predictive markers and associative relationships between carriage have been long-sought goals. Within our study, we leveraged monozygotic twin participants in concert with multi-site microbiome analyses to characterize the impacts of S. aureus on composition.<br><br>RESULTS: We recruited 147 monozygotic twin pairs and characterized three sites, i.e., the nares, oropharynx, and hand microbiomes, using 16S rRNA v3-v4 sequencing in addition to S. aureus carriage status. The prevalence of S. aureus was highest in the oropharynx followed by nares and hand with concordance between twin pairs highest in the nares, followed by oropharynx. The detection of S. aureus was statistically correlated with differences in microbiome composition across sites, as indicated by beta diversity and DESeq2 analyses. Microbiome composition was most similar in twins' nares that were S. aureus culture-positive concordant, whereas twins that were culture-negative concordant had the most similarity in the oropharynx. Of significance, Moraxella nonliquefacians and Capnocytophaga were inversely associated with S. aureus in the nares and oropharynx, respectively.<br><br>CONCLUSIONS: This improved understanding of S. aureus colonization in nares, oropharynx, and hand microbiomes in monozygotic twin pairs is a further step towards unraveling the degree to which the microbiome is influenced by host genetics and S. aureus carriage.}, }
@article {pmid41853520, year = {2024}, author = {Fu, X and Norbäck, D and Sun, Y}, title = {Editorial: Environmental microbiomes, metabolites, and respiratory diseases.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1388525}, doi = {10.3389/frmbi.2024.1388525}, pmid = {41853520}, issn = {2813-4338}, }
@article {pmid41853521, year = {2024}, author = {Curtis-Joseph, N and Peterson, R and Brown, CE and Beekman, C and Belenky, P}, title = {Mouse diet and vendor impact microbiome perturbation and recovery from early-life pulses of amoxicillin.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1432202}, pmid = {41853521}, issn = {2813-4338}, abstract = {The gut microbiome is a dynamic ecosystem shaped by various factors, including diet, sex, and environment. This system plays a crucial role in host health, such that perturbation in the form of antibiotics can lead to a vast array of negative outcomes. Accordingly, a growing body of work seeks to develop interventions to protect the microbiome during antibiotic exposure. While it is well established that antibiotics can disrupt the microbiome in the short term, how the impact of antibiotics is modulated by factors such as diet, sex, and environment is poorly understood. In this study, we analyzed how sex, diet and early life environment (vendor of origin) modulate the impact and recovery of the microbiome in mice treated with oral amoxicillin. Utilizing 16S rRNA gene sequencing and bioinformatic analyses, we looked at the microbiome response to antibiotics under high-sugar and high-fat (Western) and standard high-fiber mouse (Chow) diets in male and female C57BL/6 from Jackson Laboratory, and female mice from Charles River Laboratories. The microbiome composition of each set of mice had a distinct pre-antibiotic starting point, depending on vendor, sex, and diet. These differences were further exacerbated by antibiotic exposure and revealed that each group responded differently to this perturbation. In particular, we found that the Western diet microbiome had an exacerbated response to antibiotics with greater changes in alpha, and beta diversity, and microbial composition when compared to the antibiotic-treated Chow diet cohort. In particular, we detected blooms in Enterobacteriaceae, Streptococcaceae, and Peptostreptococcaceae that were not found in the Chow diet. The response to antibiotics on each diet also appeared to be vendor and sex dependent. Charles River female mice had less Bifidobacteriaceae, Clostridia_UCG.014, and Clostridiaceae compared to Jackson Laboratory females in a Western diet, while female mice had more Bacteroides, Bilophila, and Parasutterella compared to male mice. In a narrow sense, these findings underscore the importance of considering vendor source, diet, and sex when examining antibiotics' impact on mice. The broader implications suggest that we will likely need to utilize patient-specific microbiome-informed approaches in the development of human therapeutics to safeguard the microbiome during antibiotic exposure.}, }
@article {pmid41853522, year = {2024}, author = {Rusling, M and Karim, A and Kaye, A and Lee, CJ and Wegman Points, L and Mathis, V and Lampeter, T and Yuan, LL}, title = {Influences of Ruminococcus bromii and Peptostreptococcaceae on voluntary exercise behavior in a rodent model.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1389103}, pmid = {41853522}, issn = {2813-4338}, abstract = {INTRODUCTION: This study investigates the relationship between the gut microbiome and voluntary exercise, focusing on wheel running activity in a rat model. The gut microbiome plays a crucial role in host physiology, homeostasis, and behavior. Alterations in the gut microbiome have been linked to various pathological states and health conditions, including obesity.<br><br>METHODS: Given the strong association between physical inactivity and obesity development, our study aimed to identify microbiome factors associated with elevated levels of voluntary exercise. Male Sprague Dawley rats were used in the 4-week exercise paradigm in which voluntary wheel running behavior was monitored alongside weekly microbiome sampling from fecal pellets.<br><br>RESULTS: We observed individual differences in running activity among the cohort. Significant positive correlations in running distance were identified across the 4-week time course, suggesting that running activity ranking was largely preserved. Furthermore, earlier running activity emerged as a potential predictor for subsequent running behaviors. Analysis of gut microbiome revealed that alpha diversity was positively correlated with daily running distances, with significant differences in beta diversity observed between high and low running groups. Taxonomic analysis showed distinct abundance differences between running and sedentary conditions, particularly in the Ruminococcaceae and Peptostreptococcaceae families.<br><br>DISCUSSION: Our results suggest that the microbiome composition changes significantly early in exercise exposure, potentially influencing exercise behavior. Ruminococcaceae, particularly R. bromii, was identified as a significant contributor to exercise adaptation, while Peptostreptococcaceae was inversely related to running performance as well as alpha diversity. This study underscores the potential of the gut microbiome as a modulator of exercise behavior. Future research should focus on the biological mechanisms linking microbiome changes to exercise adaptation, with R. bromii and Peptostreptococcus as promising candidates for influencing exercise behaviors through future interventional studies.}, }
@article {pmid41853523, year = {2024}, author = {Kirsch, MR and Smith, SN and Becker, DJ and Watters, JL and Marske, KA and Siler, CD and Lanier, HC}, title = {Family shapes microbiome differences in Oklahoma salamanders.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1277645}, pmid = {41853523}, issn = {2813-4338}, abstract = {INTRODUCTION: Given the role of microbiomes in promoting host health and homeostasis, understanding the factors shaping skin microbial communities in wild vertebrates has become increasingly important in conservation. This goal is even more pressing for amphibians, for which the skin has multiple critical functions, and pathogens currently decimating populations are linked to significant changes in skin microbiomes. However, because microbiomes are also shaped by environmental and ecological influences, as well as by host phylogeny, it is important to quantify these contributions to microbiome structure in the presence of infection.<br><br>METHODS: To understand the joint influence of these diverse factors shaping microbiomes, we used 16S rRNA sequencing to characterize the skin microbial communities of six salamander species (families Plethodontidae and Salamandridae) found in Oklahoma and contrasted the effects of infection status, phylogeny, host ecology, and host environment (i.e., climate) on skin microbiomes.<br><br>RESULTS: Differences at the level of host family were the main factor influencing microbiome diversity; however, we did not detect a substantial phylogenetic signal. Instead, host ecology and environment were more important in driving microbiome differences among species and genera. Salamanders that tested positive for the skin fungal parasite Batrachochytrium dendrobatidis (Bd) also had slightly less diverse microbiomes than Bd-free animals, but no such differences were associated with the systemic pathogen ranavirus (RV).<br><br>DISCUSSION: Together, these results indicate a nuanced relationship between the number and type of microbes present on salamander skin and the factors influencing them. By developing a baseline assessment of the microbiome diversity and richness present on the skin of these focal species, this work also provides a foundation for monitoring and evaluating changes in skin microbiomes as populations continue to experience stressors and diseases.}, }
@article {pmid41853525, year = {2024}, author = {Gaber, M and Arnone, AA and Vidi, PA and Cook, KL}, title = {The microbiome: a link between obesity and breast cancer risk.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1394719}, pmid = {41853525}, issn = {2813-4338}, abstract = {Globally, breast cancer is the leading cause of cancer incidence and mortality among all female cancers. Hereditary factors only account for 5-10% of breast cancers, highlighting the importance of non-hereditary factors, such as obesity. The increasing prevalence of obesity underscores the need to understand its contribution to breast cancer risk. Multiple mechanisms may mediate pro-carcinogenic effects of obesity, including altered adipokine levels, local and systemic inflammation, disruption of insulin and insulin-like growth factor signaling, increased estrogen levels, and alterations of the microbiome. In this review, we focus on the link between gut microbiome alterations and breast cancer risk in the context of obesity. First, we discuss how obesity influences the gut microbiome. Next, we describe the effect of such microbiome alterations on breast carcinogenesis, highlighting underlying molecular mechanisms. Finally, we review preclinical data on the interactions between host and bacteria, current challenges to study the obesity-microbiome connection, and future perspectives in this field.}, }
@article {pmid41853527, year = {2024}, author = {Zorgani, A and Das, BC}, title = {Exploring the memory of the gut microbiome: a multifaceted perspective.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1363961}, pmid = {41853527}, issn = {2813-4338}, }
@article {pmid41853528, year = {2024}, author = {Kane, LP and Van Bonn, WG and Oliaro, FJ and Edwardson, CF and Smith, M and Pinnell, LJ}, title = {Transport from the wild rapidly alters the diversity and composition of skin microbial communities and antifungal taxa in spring peeper frogs.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1368538}, pmid = {41853528}, issn = {2813-4338}, abstract = {Amphibians are routinely collected from the wild and added into managed care and public display facilities; however, there is a gap in understanding how these practices might alter the diversity and composition of skin microbial communities on these animals. The aim of this study was to evaluate and compare skin microbial communities of spring peeper frogs (Pseudacris crucifer) from acquisition in the wild through the end of their quarantine period and identify microbial taxa with antifungal properties. From an original group of seventy-six frogs, cohorts of ten were swabbed when acquired in the wild, upon transport from the wild, and swabbed throughout a 9-week quarantine period while under managed care. An immediate loss of microbial richness and diversity was evident upon transfer of the frogs from their original environment and continued throughout subsequent sampling time-points during quarantine. Importantly, antifungal taxa comprised significantly more of the overall skin community after the frogs were moved from the wild, largely due to members of the family Moraxellaceae. Overall, our findings demonstrate that amphibian skin microbiome changes immediately on removal from the wild, and that these changes persist throughout quarantine while being housed under managed care. This may play a pivotal role in the development of dermatological disease and have implications in the health and immune function of amphibians.}, }
@article {pmid41853529, year = {2024}, author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM}, title = {Phage communities in household-related biofilms correlate with bacterial hosts.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1396560}, pmid = {41853529}, issn = {2813-4338}, abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.}, }
@article {pmid41853531, year = {2024}, author = {Smith, A and Ghori, NU and Foster, R and Nicol, MP and Barnett, T and Pickering, J and Whelan, A and Strunk, T and Wood, F and Raby, E and Fear, M and Weston, S and Campbell, AJ and Hoyne, GF and Bowen, AC}, title = {Optimisation of the sampling method for skin microbiome studies in healthy children: a pilot cohort study.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1446394}, pmid = {41853531}, issn = {2813-4338}, abstract = {INTRODUCTION: Recent interest in the diverse ecosystem of bacteria, fungi and viruses that make up the skin microbiome has led to numerous studies investigating the skin microbiome in healthy skin and in dermatological conditions. However, skin microbiome analysis is challenging due to relatively low numbers of skin microorganisms compared to mucosal sites, such as the respiratory or gastrointestinal tracts. Microbiome results are heavily influenced by sampling methods. Previous sampling methods include that of cotton swabs, tape stripping, patch sampling and punch biopsies. It is essential to have a standardised sampling method for microbiome studies to have comparable results between studies. Two non-invasive methods of sampling the skin microbiome; a skin scraping versus a flocked swab were chosen as methodologies likely to be efficient, effective, and easy to access for future skin microbiome studies in children. Here we compare the two sampling methods to describe the composition of the skin microbiome in healthy children.<br><br>METHOD: Samples were collected from six healthy children aged three to nine years from the skin overlying the cubital fossa, cheek and axilla using (i) flocked swabs and (ii) skin scrapings with a glass slide. Samples were collected from the left and right sides of the body at two separate time points, one week apart. Quantitative PCR of the gene encoding 16S ribosomal ribonucleic acid (rRNA) was performed to compare the bacterial load collected by each sampling method. Full-length 16S rRNA gene amplicon sequencing was performed to compare the relationship of sampling method and time with the diversity and ecology of bacteria between different body sites.<br><br>RESULTS: From six children, 78 flocked swabs and 78 skin scraping samples were collected, along with details of their overall health and skin care practices. qPCR results indicated higher total bacterial load from flocked swabs compared with skin scrapings. Flocked swabs and skin scraping methods had very similar bacterial compositional profiles. The skin microbiome was diverse between individuals and remained relatively stable within individuals over time.<br><br>DISCUSSION: Overall, results were similar between sample types, however bacterial DNA yield was higher for flocked swab samples (compared to skin scraping methods) and with a simpler protocol is the preferred sampling method for future studies.}, }
@article {pmid41853532, year = {2024}, author = {Wei, Y and Zhou, C}, title = {Bacteriophages: a double-edged sword in the gastrointestinal tract.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1450523}, pmid = {41853532}, issn = {2813-4338}, abstract = {The symbiotic relationship between the gut microbiome and the human body is a concept that has grown in popularity in recent years. Bacteriophages (phages) are components of the gut microbiota and their imbalance plays a role in the pathogenesis of numerous intestinal disorders. Meanwhile, as a new antimicrobial agent, phage therapy (PT) offers unique advantages when compared with antibiotics and brings a new dawn for treatment of multidrug-resistant bacteria in intestinal and extraintestinal disorders. In this review, we provide a brief introduction to the characterization of phages, particularly focusing on newly discovered phages. Additionally, we outline the involvement of gut phages in disease pathogenesis and discuss the status and challenges of utilizing phages as therapeutic targets for treatment of enteric infection.}, }
@article {pmid41853533, year = {2024}, author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z}, title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1384703}, pmid = {41853533}, issn = {2813-4338}, abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.<br><br>METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.<br><br>RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.<br><br>DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.}, }
@article {pmid41853538, year = {2024}, author = {Valeriano, VD and Lahtinen, E and Hwang, IC and Zhang, Y and Du, J and Schuppe-Koistinen, I}, title = {Vaginal dysbiosis and the potential of vaginal microbiome-directed therapeutics.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1363089}, pmid = {41853538}, issn = {2813-4338}, abstract = {A healthy vaginal microbiome (VMB) is dominated by Lactobacillus spp. and provides the first line of defense against invading pathogens. Vaginal dysbiosis, characterized by the loss of Lactobacillus dominance and increase of microbial diversity, has been linked to an increased risk of adverse genital tract diseases, including bacterial vaginosis, aerobic vaginitis, vulvovaginal candidiasis, sexually transmitted infections, and pregnancy complications such as preterm birth. Currently, antibiotics and antifungals are recommended first-line treatments with high cure rates, but they also can lead to high recurrence and resistance development. As an alternative, lactobacilli have been utilized to restore the vaginal microbiota. In this review article, we discuss vaginal dysbiosis in various gynecological infections and potential interventions based on Live Biotherapeutic Products (LBPs) with a focus on those that use intravaginal treatment modalities to modulate the VMB. Based on these, we provide insights on key factors to consider in designing phenotypic and genotypic screens for selecting bacterial strains for use as vaginally administered microbiome-directed therapeutics. Lastly, to highlight current progress within this field, we provide an overview of LBPs currently being developed with published clinical trial completion for recurrent BV, VVC, and UTI. We also discuss regulatory challenges in the drug development process to harmonize future research efforts in VMB therapy.}, }
@article {pmid41853539, year = {2024}, author = {Chandel, N and Gorremuchu, JP and Thakur, V}, title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1432646}, pmid = {41853539}, issn = {2813-4338}, abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.<br><br>METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.<br><br>RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.<br><br>DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.}, }
@article {pmid41853540, year = {2024}, author = {Kaye, A and Rusling, M and Dhopeshwarkar, A and Kumar, P and Wagment-Points, L and Mackie, K and Yuan, LL}, title = {Microbiome variations induced by delta9-tetrahydrocannabinol predict weight reduction in obese mice.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1412468}, pmid = {41853540}, issn = {2813-4338}, abstract = {INTRODUCTION: Obesity and high-fat diets induce consistent alterations in gut microbiota composition. Observations from epidemiological reviews and experiments also illustrate weight regulation effects of delta9-tetrahydrocannabinol (THC) with microbiome shifts. Therefore, we investigated the weight-loss potential of THC in obese mice models and to elucidate the contribution of specific gut microbiome changes in THC-induced weight loss.<br><br>METHODS: High-fat diet induced obese mice were treated with oral THC supplementation for two weeks and compared with controls. In addition to measuring weight, fecal samples were obtained at various timepoints, sequenced for bacterial 16s rRNA content and analyzed using QIIME2. Alpha and beta diversity were computed followed by linear mixed effects (LME) modeling of bacterial relative abundance relationship to THC treatment and weight change.<br><br>RESULTS: In both male and female mice, the THC group had significantly greater average weight loss than controls (-17.8% vs. -0.22%, p<0.001 and -13.8% vs. +2.9%, p<0.001 respectively). Male mice had 8 bacterial taxonomic features that were both significantly different in relative abundance change over time with THC and correlated with weight change. An LME model using three bacterial features explained 76% of the variance in weight change with 24% of variation explained by fixed effects of feature relative abundance alone. The model also accurately predicted weight change in a second male mouse cohort (R=0.64, R[2]=0.41, p=<0.001). Female mice had fewer significant predictive features and were difficult to model, but the male-produced 3-feature model still accurately predicted weight change in the females (R=0.66, R[2]=0.44, p<0.001).<br><br>CONCLUSION: Using a stepwise feature selection approach, our results indicate that sex-specific gut microbiome composition changes play some role in THC-induced weight loss. Additionally, we illustrated the concept of microbiome feature-based modeling to predict weight changes.}, }
@article {pmid41853542, year = {2024}, author = {Daharsh, L and Lohani, SC and Ramer-Tait, AE and Li, Q}, title = {Characterization of double humanized BLT-mice with stable engraftment of a human gut bacterial microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1404353}, pmid = {41853542}, issn = {2813-4338}, abstract = {Humanized mice with human-like immune systems are commonly used to study immune responses to human-specific pathogens. However, one limitation of using humanized mice is their native murine gut microbiota, which significantly differs from that in humans. Given the importance of the gut microbiome to human health, these differences may profoundly impact the ability to translate results from humanized mouse studies to humans. Further, there is a critical need for improved pre-clinical models to study the complex in vivo relationships of the gut microbiome, immune system, and human disease. We previously created double humanized mice with a functional human immune system and a stable, human-like gut microbiome. Here, we characterized the engrafted human gut bacterial microbiome in our double humanized mouse model generated by transplanting fecal material from healthy human donors into the gut of humanized mice. Analysis of bacterial microbiomes in fecal samples from double humanized mice revealed they had unique 16S rRNA gene profiles consistent with those of the individual human donor samples. Importantly, transplanted human-like gut microbiomes were stable in mice for the duration of the study, extending up to 14.5 weeks post-transplant. Microbiomes of double humanized mice also harbored predicted functional capacities that more closely resembled those of the human donors than humanized mice. In conclusion, our study highlights the successful engraftment of human fecal microbiota in BLT humanized mice and underscores the stability of this model, offering a valuable platform for investigating the intricate interplay among the human gut microbiome, immune system, and various diseases in vivo.}, }
@article {pmid41853546, year = {2024}, author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA}, title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1457537}, pmid = {41853546}, issn = {2813-4338}, abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.<br><br>METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.<br><br>RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.<br><br>CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.}, }
@article {pmid41853547, year = {2024}, author = {Giongo, A and Arnhold, J and Grunwald, D and Smalla, K and Braun-Kiewnick, A}, title = {Soil depths and microhabitats shape soil and root-associated bacterial and archaeal communities more than crop rotation in wheat.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1335791}, pmid = {41853547}, issn = {2813-4338}, abstract = {The plethora of microorganisms inhabiting the immediate vicinity of healthy root systems plays a pivotal role in facilitating optimal nutrient and water acquisition by plants. In this study, we investigated the soil microbial communities associated with wheat roots within distinct microhabitats, root-affected soil (RA), rhizosphere (RH), and rhizoplane (RP). These microhabitats were explored at five soil depths, and our investigation focused on wheat cultivated in a monoculture (WM) and wheat crop rotation (WR). Overall, there were significant differences in microbiota composition between WM and WR, although no difference in bacterial diversity was observed. Differentially abundant taxa between WM and WR were observed in all three microhabitats, emphasizing important insights on the localization of commonly associated bacteria to wheat roots. Comparing the microhabitats, RP exhibited the most dissimilar microbial composition between WM and WR. Taxa that were differentially abundant between WM and WR were observed in the three microhabitats. The high relative abundance of taxa belonging to the phylum Proteobacteria in the rhizoplane, such as Devosia, Pseudomonas, Shinella, and Sphingomonas, along with other genera, such as Pedobacter (Bacteroidota), Agromyces and Streptomyces (Actinobacteriota) highlight the recruitment of potentially beneficial bacterial taxa to the vicinity of the roots. Interestingly, these taxa were observed along the entire length of wheat roots, even at depths of up to 120 cm. The presence of specific taxa associated with wheat roots at all soil depths may be beneficial for coping with nutrient and water shortages, particularly under upcoming climate scenarios, where water may be a limiting factor for plant growth. This study provides valuable insights for designing management strategies to promote a diverse and healthy microbial community in wheat cropping systems, considering soil depth and microhabitats as key factors. Although, at this time, we cannot link specific bacterial taxa to yield reductions commonly observed in monocultural fields, we propose that some genera may enhance plant nutrient or water acquisition in rotation compared with monoculture. Advanced technologies, including functional analyses and culturomics, may further enhance our understanding of the ecological roles played by these microbes and their potential applications in sustainable agriculture.}, }
@article {pmid41853549, year = {2024}, author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R}, title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1408203}, pmid = {41853549}, issn = {2813-4338}, abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.}, }
@article {pmid41853551, year = {2024}, author = {Uzoigwe, CE}, title = {Gut eutrophication.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1481250}, pmid = {41853551}, issn = {2813-4338}, abstract = {"Classical eutrophication" occurs when raw unfixed nutrients enter an aquatic environment. This causes the deleterious proliferation in fauna most adept at exploiting this abundance of nutrition. The net effect is de-diversification. We propose an analogous process in the gut: "gut eutrophication". Evidence shows that consumption of processed food, high in unfixed disaccharides, causes an expansion of bacteria in the gut habitat with a metabolic proclivity for these nutrients. This is at the expense of microbiota with a predilection for complex macromolecule macronutrients. There is a loss of diversity and the effect is exacerbated by a sedentary lifestyle. Gut luminal low oxygen tension favors salubrious gut commensals. This effect is potentiated by exercise but thwarted by inactivity. Antibiotics cause an obvious gut dysbiosis. So too can diet in a more insidious manner. The transition in microbial composition, seen in "gut eutrophication", may be an aetiological component of metabolic disease-associated gut dysbiosis.}, }
@article {pmid41853553, year = {2024}, author = {Gupta, D and Sarkar, A and Pal, Y and Suthar, V and Chawade, A and Kushwaha, SK}, title = {Bovine reproductive tract and microbiome dynamics: current knowledge, challenges, and its potential to enhance fertility in dairy cows.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1473076}, pmid = {41853553}, issn = {2813-4338}, abstract = {The cattle production system focuses on maintaining an animal-based food supply with a lower number of cattle. However, the fecundity of dairy cows has declined worldwide. The reproductive tract microbiome is one of the important factors which can influence bovine fecundity. Therefore, reproductive tract microbiomes have been explored during the estrus cycle, artificial insemination, gestation, and postpartum to establish a link between the micro-communities and reproductive performance. These investigations suggested that microbial dysbiosis in the reproductive tract may be associated with declined fertility. However, there is a scarcity of comprehensive investigations to understand microbial diversity, abundance, shift, and host-microbiome interplay for bovine infertility cases such as repeat breeding syndrome (RBS). This review summarizes the occurrence and persistence of microbial taxa to gain a better understanding of reproductive performance and its implications. Further, we also discuss the possibilities of microbiome manipulation strategies to enhance bovine fecundity.}, }
@article {pmid41853555, year = {2024}, author = {Ferro, LE and Bittinger, K and Trudo, SP and Beane, KE and Polson, SW and Kim, JK and Trabulsi, JC}, title = {A short-term, randomized, controlled, feasibility study of the effects of different vegetables on the gut microbiota and microRNA expression in infants.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1342464}, pmid = {41853555}, issn = {2813-4338}, abstract = {The complementary diet influences the gastrointestinal (gut) microbiota composition and, in turn, host health and, potentially, microRNA (miRNA) expression. This study aimed to assess the feasibility of altering the gut microbial communities with short-term food introduction and to determine the effects of different vegetables on the gut microbiota and miRNA expression in infants. A total of 11 infants were randomized to one of the following intervention arms: control, broccoli, or carrot. The control group maintained the milk diet only, while the other groups consumed either a broccoli puree or a carrot puree on days 1-3 along with their milk diet (human milk or infant formula). Genomic DNA and total RNA were extracted from fecal samples to determine the microbiota composition and miRNA expression. Short-term feeding of both broccoli and carrots resulted in changes in the microbiota and miRNA expression. Compared to the control, a trend toward a decrease in Shannon index was observed in the carrot group on days 2 and 4. The carrot and broccoli groups differed by weighted UniFrac. Streptococcus was increased on day 4 in the carrot group compared to the control. The expression of two miRNAs (i.e., miR-217 and miR-590-5p) trended towards decrease in both the broccoli and carrot groups compared to the control, whereas increases in eight and two different miRNAs were observed in the carrot and broccoli groups, respectively. Vegetable interventions differentially impacted the gut microbiota and miRNA expression, which may be a mechanism by which total vegetable intake and variety are associated with reduced disease risk.}, }
@article {pmid41853558, year = {2024}, author = {Pannoni, SB and Holben, WE}, title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1274277}, pmid = {41853558}, issn = {2813-4338}, abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.}, }
@article {pmid41853703, year = {2024}, author = {Ellis, JR and Powell, EJ and Tomasovic, LM and Marcheskie, RL and Girish, V and Warman, A and Sivaloganathan, D}, title = {Changes in the Skin Microbiome Following Dermatological Procedures: A Scoping Review.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {4}, number = {2}, pages = {972-985}, pmid = {41853703}, issn = {2673-8007}, support = {T32 GM136577/GM/NIGMS NIH HHS/United States ; }, abstract = {The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence the skin microbiome, the effects of dermatological procedures have not been extensively studied. Here, we perform a scoping review to outline the studies investigating the impacts of dermatological interventions on the skin microbiome. Phototherapy emerged as the most studied intervention, encompassing UV phototherapy, light therapy, laser therapy, and photodynamic therapy. Chemical interventions, such as chemical peels, micropigmentation, and debridement, have comparatively limited studies describing their impacts on the skin microbiome. To date, no studies have been done on a wide variety of common dermatological procedures such as cryotherapy, skin grafts, and dermabrasion, which may have stronger likelihoods of affecting the skin microbiome. This underscores the need for further research on the influences of dermatological procedures, especially chemical and physical interventions, on the skin microbiome. More comprehensive pre-clinical and clinical studies are essential not only for understanding the long-term consequences of these procedures, but also for optimizing patient outcomes in dermatological care.}, }
@article {pmid41853869, year = {2026}, author = {Abedin, ZU and Shah, A and Mazhar, S and Khan, SM and Aamir, AB and Yousaf, S and Fnu, D and Mahato, RK and Ansari, A}, title = {Lactobacillus-Based Microbiome Therapy for Acne Vulgaris: A GRADE Systematic Review and Meta-Analysis of Randomized Controlled Trials.}, journal = {Journal of cosmetic dermatology}, volume = {25}, number = {3}, pages = {e70792}, pmid = {41853869}, issn = {1473-2165}, mesh = {Humans ; *Acne Vulgaris/therapy/microbiology ; *Probiotics/administration &amp; dosage/adverse effects/therapeutic use ; Randomized Controlled Trials as Topic ; *Lactobacillus ; Treatment Outcome ; Benzoyl Peroxide/therapeutic use/administration &amp; dosage ; *Microbiota ; Administration, Oral ; }, abstract = {BACKGROUND: Acne vulgaris is one of the most prevalent disorders affecting 9%-10% of the global population, representing as papules, pustules, and comedones, with a pathogenesis involving increased sebum production, C. acnes colonization, and inflammation. Conventional treatments like retinoids and antibiotics often cause side effects, thus diverting attention toward probiotics as an alternative therapy. Lactobacillus probiotics, having their immunomodulatory, anti-inflammatory, and antimicrobial properties, are useful in managing acne by reducing inflammation and oxidative stress with proved safety profile and the potential to reduce antibiotic reliance. This systematic review and meta-analysis evaluate the efficacy of Lactobacillus-based probiotics compared to placebo and benzoyl peroxide in reducing inflammatory lesions, non-inflammatory lesions, and total acne lesion counts. The findings aim to clarify their therapeutic role and provide evidence on their effectiveness and safety.<br><br>OBJECTIVES: This systematic review and meta-analysis investigated the effectiveness of oral and topical Lactobacillus-based probiotics or postbiotics, compared with placebo or benzoyl peroxide, in patients with acne vulgaris.<br><br>METHODS: A systematic review and meta-analysis of randomized controlled trials (RCTs) was conducted, including studies evaluating oral or topical Lactobacillus-based probiotic or postbiotic interventions in patients with acne vulgaris. Primary outcomes were changes in inflammatory lesion counts, while secondary outcomes included non-inflammatory and total lesion counts, skin hydration, and sebum concentration. All analyses were performed using random-effects models with 95% confidence intervals (CI), and heterogeneity was quantified using the I[2] statistic.<br><br>RESULTS: A total of five RCTs involving 332 participants were included. The pooled mean difference for non-inflammatory lesions was -1.39 (95% CI -5.10 to 2.32, p&#x2009;=&#x2009;0.46), for inflammatory lesions was -0.08 (95% CI -1.28 to 1.11, p&#x2009;=&#x2009;0.89), and for total lesion counts was -9.07 (95% CI -20.71 to 2.57, p&#x2009;=&#x2009;0.13). These results concluded that there was no significant reduction in lesion counts with Lactobacillus-based probiotics as compared to placebo or benzoyl peroxide. Heterogeneity was moderate to low across studies.<br><br>CONCLUSION: This meta-analysis indicates that Lactobacillus-based probiotics do not provide significant clinical benefits in reducing inflammatory lesions, non-inflammatory lesions, and total acne lesion counts in Acne vulgaris patients compared to placebo or benzoyl peroxide.}, }
@article {pmid41853881, year = {2026}, author = {Picariello, E and De Nicola, F}, title = {Unveiling the Hidden Drivers: How Vegetation Cover, Season and Forest Management Shape the Soil Microbial Community in Two Mediterranean Forest Ecosystems.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70255}, doi = {10.1111/1758-2229.70255}, pmid = {41853881}, issn = {1758-2229}, support = {//Fondo di Ricerca di Ateneo FRA 2023/ ; }, mesh = {*Soil Microbiology ; *Forests ; Seasons ; *Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/isolation &amp; purification/genetics ; Biodiversity ; Ecosystem ; Quercus/growth &amp; development ; *Microbiota ; Fagus/growth &amp; development ; Mediterranean Region ; Turkey ; Soil/chemistry ; }, abstract = {Soil provides essential ecosystem services and serves as a habitat for biodiversity, but it is often affected by disturbances from management practices and seasonal changes, which can alter its microbial communities. This study investigated the combined effects of dominant vegetation, forest management, and seasonal variation on soil microbial communities and enzyme activity over one year in turkey oak and beech forests managed as high forest or coppice. Results showed that the dominant vegetation type had a greater influence on microbial communities than seasonal changes. While forest management did not significantly affect microbial activity, it altered microbial community composition. In beech forests, bacterial communities (at the order level) showed relative abundances higher in soil under high forest with respect to coppice, whereas the fungal community showed orders most abundant under coppice management with respect to the high forest. Forest management changed the relative abundances of microbial communities, but it did not remarkably affect microbial community functions and, thus, the associated ecosystem services. Our results highlight that the forest type should be considered when evaluating forest management. This study offers new insights into the factors influencing the composition of soil microbial communities and their associated ecosystem functions.}, }
@article {pmid41853994, year = {2026}, author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C}, title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70245}, doi = {10.1111/1758-2229.70245}, pmid = {41853994}, issn = {1758-2229}, support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; }, mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; }, abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.}, }
@article {pmid41854082, year = {2026}, author = {Park, N and Lee, B and Jeon, HJ and Yeon Kim, J and Park, S and Kim, SE and Lee, DK and Lee, Y}, title = {Inulin-Butyrate Nanogel for Modulation of Gut Microbiome, Intestinal Barrier, and Regulatory T-Cells in Colitis.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e13252}, doi = {10.1002/smll.202513252}, pmid = {41854082}, issn = {1613-6829}, support = {//National Research Foundation of Korea/ ; RS-2023-00265981//Ministry of Health &amp; Welfare, Republic of Korea/ ; }, abstract = {Inflammatory bowel diseases (IBD) arise from a vicious cycle of intestinal barrier dysfunction, gut microbiome dysbiosis, and dysregulated immune responses. Current therapies predominantly suppress immunity but fail to address root causes or break this cycle. While inulin, a prebiotic, restores microbial diversity and enables colon-targeted drug delivery, they lack specificity for inflamed tissue. On the other hand, even though butyrate, a microbial metabolite, is a potent enhancer of intestinal barrier integrity and anti-inflammatory Treg cell differentiation, their clinical applications are limited by rapid systemic absorption, impractical dosing, and unpleasant odor. To address these limitations, we have developed an inulin-butyrate conjugate-based nanogel (IBN) which is capable of targeted modulation of gut microbiome, intestinal barrier, and immune systems in colitis. In dextran sodium sulfate (DSS)-induced colitis mice, IBN specifically accumulates in the inflamed colon and released high amounts of butyrate via gut microbial enzymes (inulinase/esterase). The inulin shell improved the gut microbiome, while the released butyrate enhances intestinal barrier functions and promotes Treg differentiation, yielding robust therapeutic activity. Taken together, IBN addresses the multifactorial nature of IBD, offering a biocompatible, transformative strategy to disrupt the disease cycle and restore gut homeostasis.}, }
@article {pmid41854140, year = {2026}, author = {Adamová, Z and Filová, M and Tisančinová, J and Chrostek, M and Slováček, R}, title = {Probiotics and synbiotics in perioperative care for colorectal surgery - a future component of the ERAS protocol?.}, journal = {Rozhledy v chirurgii : mesicnik Ceskoslovenske chirurgicke spolecnosti}, volume = {105}, number = {2}, pages = {75-79}, doi = {10.48095/ccrvch202675}, pmid = {41854140}, issn = {0035-9351}, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Synbiotics/administration &amp; dosage ; *Perioperative Care/methods ; *Postoperative Complications/prevention &amp; control ; Digestive System Surgical Procedures ; *Colorectal Surgery ; }, abstract = {INTRODUCTION: Colorectal surgery is associated with a high risk of postoperative complications, particularly infections. In recent years, the role of the microbiome in this context has been increasingly discussed. Probiotics and synbiotics are being investigated as potential tools for modulating the microbial environment and improving surgical outcomes.<br><br>AIM: This review article summarizes the available evidence from randomized con-trolled trials, meta-analyses, and systematic reviews evaluating the effects of probiotics and synbiotics on the incidence of complications and postoperative recovery in patients undergoing colorectal surgery. Current studies indicate that the administration of probiotics and synbiotics may reduce the risk of infectious complications, modulate systemic inflammatory responses, accelerate the restoration of bowel function, and shorten the duration of antibiotic therapy. Data regarding their impact on anastomotic leakage remain limited. The intervention appears to be well tolerated and safe.<br><br>CONCLUSION: Perioperative administration of probiotics or synbiotics represents a promising and cost-effective intervention in colorectal surgery. However, larger and more standardized trials are required to prove the effect, determine the optimal composition, dosage, and duration of therapy before routine clinical implementation.}, }
@article {pmid41854146, year = {2026}, author = {Guo, X and Zhao, J}, title = {Multidisciplinary advances in oral health management in patients with systemic lupus erythematosus: a comprehensive review.}, journal = {Quintessence international (Berlin, Germany : 1985)}, volume = {0}, number = {0}, pages = {0}, doi = {10.3290/j.qi.b6961709}, pmid = {41854146}, issn = {1936-7163}, abstract = {Systemic lupus erythematosus (SLE) is a complex chronic autoimmune disease that can affect multiple organ systems, including the skin, joints, kidneys and oral cavity. In recent years, there has been growing interest in the oral health of patients with SLE, with studies showing that the incidence of dental caries, periodontal disease, oral mucosal lesions and salivary dysfunction is significantly higher in patients with SLE than in the general population. Factors such as immune system abnormalities, long-term use of glucocorticoids and immunosuppressants, and dysbiosis of the oral microbiome all contribute to an increased oral disease burden in patients with SLE. Oral health problems affect not only patients' nutritional intake, social interactions and self-esteem but may also create an inflammatory feedback loop exacerbating the underlying systemic condition. A multidisciplinary management approach involving rheumatology, dentistry and psychological support - with more refined and individualised strategies for prevention, treatment and follow-up - is crucial for patients with SLE. This review distinguishes itself from prior syntheses by systematically integrating the pivotal role of nursing teams within the multidisciplinary framework, and proposing actionable, structured protocols for assessment, referral, and long-term follow-up. Future research should focus on exploring the interaction between the oral microbiome and immune response mechanisms and strive to develop more effective interventions and standardised diagnostic and treatment protocols to improve the oral health and overall quality of life of patients with SLE.}, }
@article {pmid41854347, year = {2026}, author = {Perry, EK and Hasnain, A and Cole, BJ and Carlson, HK and Deutschbauer, AM and Chiniquy, D}, title = {Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag023}, pmid = {41854347}, issn = {1574-6941}, abstract = {Rice paddies naturally host methane-oxidizing bacteria known as methanotrophs, due to the production of methane in flooded soils. Enhancing the activity of native methanotrophs could improve the sustainability of rice cultivation, but knowledge of how this could impact other members of the rice microbiome remains incomplete. To gain insight into which members of the rice microbiome might benefit from increased methanotrophic activity, we passaged 51 aerobic microbial enrichment cultures from rice rhizosphere and tissue samples in a chemically-defined medium with methane as the primary carbon source and electron donor. We profiled the cultures over time by 16S rRNA gene amplicon sequencing and sequenced the genomes of 44 isolates to gain functional insights. Taxa whose relative abundance increased during community growth on methane represented more than a dozen families, many of which are not known to utilize one-carbon substrates. Several of the enriched genera have not previously been linked to methane cycling in rice fields, and genomic analysis of the sequenced isolates revealed considerable variation in predicted carbon source utilization and nitrogen cycling capabilities. Together, these findings broaden the understanding of how aerobic methanotrophs may impact microbiome assembly and nutrient cycling in rice paddies.}, }
@article {pmid41854352, year = {2026}, author = {Joseph, J and Patnaik, SK and Abraham, D and Mathew, J and Alexander, J}, title = {Gut and oral microbiota characterized in systemic lupus erythematosus patients from India: A pilot study.}, journal = {Lupus}, volume = {}, number = {}, pages = {9612033261432163}, doi = {10.1177/09612033261432163}, pmid = {41854352}, issn = {1477-0962}, abstract = {Introduction: Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disorder influenced both intrinsically by immune cell alterations, genetic factors, and the microbiome, as well as extrinsically by environmental factors. Methods: In this pilot study, we investigated the role of various peripheral immune cells (CD3[+], CD4[+], CD8[+], CD4[+]/CD8[+], CD4-/CD8-, NK cells (CD16[+]CD56[+]), and CD19[+]) and the gut and salivary microbiota in patients with SLE, comparing these factors to healthy controls. Results and Discussion: Results showed significant alterations in the proportions of CD4[+] and CD8[+] T cells in SLE patients, with an inverse correlation between these subsets. Additionally, the CD4[+] ratio was found to be elevated in SLE. CD4[+] T cells were strongly correlated with double-negative T cells, while CD8[+] T cells correlated with NK cells. Metagenomic shotgun sequencing of fecal and salivary samples revealed a disruption in the microbiome, particularly the taxa Pasteurellaceae and Veillonella, which were altered in both the gut and oral microbiomes of SLE patients. These changes suggest that there may be overlap in the composition and function of these microbial populations across different body sites. Dysbiosis was observed in both the gut and oral microbiomes of individuals with SLE, distinguishing them from healthy controls. Conclusion: Our findings highlight specific microbiome alterations in SLE patients and suggest that microbiome composition could serve as a potential exploratory tool for diagnosing and prognosticating the disease in larger, adequately powered cohorts.}, }
@article {pmid41854449, year = {2026}, author = {Xing, N and Hu, J and Bao, G and Zhang, X and Huo, X and Wen, Y and Li, X and Tang, Y and Liu, W}, title = {Toxicity of Polystyrene Nanoplastics and Tributyl Phosphate to Rye under Freeze-Thaw Cycles: Implications for Crop Safety and Mechanistic Insights from Transcriptome and Root Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c14574}, pmid = {41854449}, issn = {1520-5118}, abstract = {Climate-driven freeze-thaw (FT) cycles amplify the combined toxicity of polystyrene nanoplastics (PS) and tributyl phosphate (TBP) in crops. TBP is a common plasticizer. Our multiomics study reveals that PS and TBP form complexes via van der Waals forces, enhancing PS uptake in rye roots. Coexposure induces severe oxidative stress (H2O2: 1.35-, 4.71-fold → 9.04-fold), suppresses photosynthesis, and activates antioxidant defenses, with FT conditions intensifying these effects. TBP restructures the root endophytic microbiome, enriching TBP-degrading bacteria (Acidovorax, Massilia). Transcriptomic analysis identifies jasmonic and abscisic acid (ABA) signaling pathways as central coordinators of plant defense through reactive oxygen species (ROS) scavenging and metabolic reprogramming. These findings demonstrate that FT cycles exacerbate NPs-plasticizer toxicity through three interconnected mechanisms: physicochemical complex formation, root microbiome remodeling, and hormonal signaling crosstalk. The study provides crucial mechanistic insights for assessing climate-pollution risks in cold-region agriculture, highlighting the need to consider pollutant interactions under dynamic environmental conditions.}, }
@article {pmid41854509, year = {2026}, author = {Jayamanna Mohottige, MW and Peel, E and Juhász, A and Nye-Wood, MG and Belov, K and Colgrave, ML and Hogg, CJ}, title = {Characterisation of pouch secretions from breeding Tasmanian devils.}, journal = {Reproduction (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/reprod/xaag024}, pmid = {41854509}, issn = {1741-7899}, abstract = {Tasmanian devils (Sarcophilus harrisii), like all marsupials, give birth to altricial young. Here we employ proteomic analysis to identify components of devil pouch secretions that may contribute to offspring survival and development. Proteins were extracted from five samples and analysed by liquid chromatography-tandem mass spectrometry. Peptide-level evidence revealed proteins involved in a diverse set of immune pathways, including those mediating iron-ion transport, defence responses to bacteria, innate immune responses, and antigen processing. A core set of 200 proteins was identified across at least three samples, 63 of which were associated with antimicrobial or immunoregulatory functions. These included immunoglobulins, components of complement and coagulation cascade, and antimicrobial proteins and peptides. These findings provide preliminary evidence that the Tasmanian devil's pouch secretions could be involved in microbiome restructuring during lactation through their immune protein content. Moreover, the data indicate that these proteins may act synergistically in pathways triggered by immune challenges or physiological stress.}, }
@article {pmid41854749, year = {2026}, author = {Balafif, F and Wardhana, DW and Nazwar, TA and Balafif, F and Panjaitan, C and Kholipah, AN and Mustofa, }, title = {Gut microbiota modulation as an adjuvant therapy to improve treatment response and survival in brain tumor patients: a systematic review.}, journal = {Neurosurgical review}, volume = {49}, number = {1}, pages = {}, pmid = {41854749}, issn = {1437-2320}, }
@article {pmid41855162, year = {2026}, author = {Armijos Briones, M and Ayala Aguirre, PE and Benitez Sellan, PL and Lanata-Flores, A and Marcillo-Toala, O and Rumbea, DA and Mera, RM and Del Brutto, OH}, title = {Study protocol: Dental and periodontal characteristics of older adults in Atahualpa, Ecuador within the Atahualpa Project cohort.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0337166}, pmid = {41855162}, issn = {1932-6203}, mesh = {Humans ; Ecuador/epidemiology ; Aged ; Male ; Cross-Sectional Studies ; Female ; Middle Aged ; *Oral Health ; *Periodontal Diseases/epidemiology ; Aged, 80 and over ; Gingival Crevicular Fluid ; Cohort Studies ; Cone-Beam Computed Tomography ; }, abstract = {This study protocol describes an observational, cross-sectional investigation of oral health in community-dwelling older adults from Atahualpa, a rural village in Ecuador, embedded within the long-standing Atahualpa Project cohort. Using a door-to-door survey approach, all registered residents aged ≥60 years (n = 410) will be invited to participate. Participants will attend twice weekly at the School of Dentistry of University through six coordinated stations: The first station will include a general oral diagnosis and the collection of general participant data using the unique Atahualpa project identifier. The second station will record the periodontal clinical examination according to the AAP/EFP 2018 clinical guidelines. In addition, subgingival biofilm sampling will be performed for 16S rRNA sequencing and gingival crevicular fluid for multiplex cytokine profiling. The third station will obtain high-resolution digital models through an intra-oral scanning (IOS) for dental morphometrics. The fourth station will record a cone-beam computed tomography (CBCT) to support periodontal charting, and complementary structural findings. The fifth station will indicate dental treatments: restorations, root canals, extractions, and prosthesis using computer-aided design and computer-aided manufacturing (CAD/CAM). Finally, the last station will perform an oral health education: oral health promotion and structured questionnaires such as the Geriatric Oral Health Assessment Index (GOHAI), the European Health Literacy Survey-16 (HLS-EU-Q16) (in its Spanish version) and the Short Health Literacy Screen (BHLS). Primary objectives are to quantify associations between periodontitis severity, microbial composition, and local inflammatory profiles with neurocognitive and neuroimaging outcomes already available in the cohort (total MoCA and a composite cerebral small vessel disease score), controlling. Therefore, this protocol addresses the research question of whether, in older adults residing in the Atahualpa community, greater periodontitis severity is associated with lower neurocognitive performance and a higher burden of cerebral small vessel disease on neuroimaging within the existing cohort. It also examines whether the composition of the subgingival microbiome and cytokine profiles in gingival crevicular fluid correlate with periodontal severity and are related to these cerebral outcomes. Furthermore, it describes three-dimensional dental morphology (including features derived from ASUDAS for comparison with published Pima frequencies) to clarify whether there is similarity between the two ethnic groups.}, }
@article {pmid41855263, year = {2026}, author = {Dutta, S and Mahen, KK and Massey, WJ and Varadharajan, V and Burrows, AC and Horak, AJ and Mrdjen, M and Mouannes, N and Orabi, D and Osborn, LJ and Grubb, T and Hohe, RC and Banerjee, R and Uppin, V and Laungani, D and Hamilton, GE and Ye, X and Sangwan, N and Dwidar, M and Hajjar, AM and Willard, B and Martin, M and Guetschow, E and Westcott, P and McMullen, MR and Nagy, LE and Wang, Z and Hazen, SL and Brown, JM}, title = {Gut microbe-derived N-acyl serinol lipids shape host postprandial metabolic homeostasis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {12}, pages = {e2517314123}, doi = {10.1073/pnas.2517314123}, pmid = {41855263}, issn = {1091-6490}, support = {R01 DK130227/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; RF1 NS133812/NS/NINDS NIH HHS/United States ; 24POST1178494//American Heart Association (AHA)/ ; N/A//Cleveland Clinic (CC)/ ; S10 OD030398/CD/ODCDC CDC HHS/United States ; R01 HL179780/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; *Postprandial Period/physiology ; *Homeostasis ; Animals ; Humans ; Mice ; Male ; *Lipids/chemistry ; Amides/metabolism ; Lipid Metabolism ; Mice, Inbred C57BL ; Bacteria/metabolism ; }, abstract = {Although strong evidence links the gut microbiome to metabolic disease, the mechanisms linking microbiota to hormonal and metabolic responses to food are not well understood. After a meal, gut bacteria produce a wide array of small molecule, protein, and lipid metabolites originating from bacterial sources. Attributing physiological function to select gut microbe-derived metabolites is critical to understanding diet-microbe-host interactions, and to developing microbiome-inspired therapies to improve human health. Here, we have investigated the role of a poorly annotated class of gut microbiome-derived lipids called N-acyl amides in postprandial metabolic physiology. Here, we show that both bacterial production and provision of exogenous N-acyl amides reorganize host hormone-driven metabolic transition after a meal. Moreover, N-acyl amides exert broad effects on the meal- and circadian-related reorganization of gene expression, metabolic hormones, and gut microbiome composition. Collectively, these results demonstrate that microbiota-derived N-acyl amides play a physiologic role in postprandial metabolic homeostasis in the host.}, }
@article {pmid41855730, year = {2026}, author = {Mudiyanselage, HH and Ali, A and Farooq, M and Ghaffar, A and Waduge, LW and Gomis, SM and Niu, YD and Abdul-Careem, MF}, title = {Probiotic-driven microbiota shifts confer the resistance to infectious bronchitis virus infection in poultry.}, journal = {Veterinary microbiology}, volume = {316}, number = {}, pages = {110986}, doi = {10.1016/j.vetmic.2026.110986}, pmid = {41855730}, issn = {1873-2542}, abstract = {Infectious bronchitis virus (IBV) is an economically significant viral infection in commercial broilers. Despite vaccination, outbreaks are still reported due to the emergence of new IBV variants. Probiotics, particularly strains of Lactobacillus, have been shown to help mitigate various disease outbreaks and exhibit strong immunomodulatory effects, especially in the respiratory tract. A study was conducted to understand the effect of a cocktail of Lactobacillus and a commercial probiotic on respiratory and gastrointestinal microbiome shifts in 6, 9 and 15 days post-infection (dpi) following IBV infection in commercial broilers. In general the virus-challenged group without any probiotics showed significantly higher (p = 0.0488) histopathological lesion scores compared to both probiotics treated groups prior to the IBV challenge. Cecum alpha diversity in Lactobacillus supplemented group prior to infection showed significantly higher (p < 0.05) diversity and evenness compared to the group supplemented with Lactobacillus only in all the considered time points, whereas the group supplemented with commercial probiotics prior to viral challenge showed significantly lower (p < 0.05) diversity compared to commercial probiotics only group at 15 dpi. Beta diversity analysis in cecum indicated both Lactobacillus supplemented and commercial probiotics supplemented prior to infection developed a significantly different (p < 0.05) and distinct microbial composition compared to all the other groups. According to differential abundance analysis, IBV infection was shown to favor the abundance of Lactobacillus in cecum. Commercial probiotics supplemented prior to the infection showed despite initial dysbiosis, dominant bacteria were able to get restored at 15 dpi in both cecum and trachea. Functional analysis in the cecum and trachea depicted that although Lactobacillus supplemented prior to infection showed more stress and proliferation in the initial time point, all the groups have more similar pathways at the later stage in the cecum but in the trachea, the group supplemented with Lactobacillus prior to infection was still showing transition to more colonization focused state. The study outcome adds to the understanding of respiratory and gastrointestinal microbiome shifts in a lengthier time period in probiotics supplemented broilers prior to IBV infection.}, }
@article {pmid41855966, year = {2026}, author = {Zhang, J and Ip, JC and Hamed, M and Lee, JS and Mo, J}, title = {A review on antibiotic use in tilapia farming: Pharmacokinetics, impacts, and potential health risks.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119582}, doi = {10.1016/j.marpolbul.2026.119582}, pmid = {41855966}, issn = {1879-3363}, abstract = {The rapid expansion of global aquaculture has propelled tilapia to become the third most widely farmed freshwater fish species worldwide, valued for its rapid growth, remarkable adaptability and economic value. However, the improper use of antibiotics, including misuse, overuse, and prophylactic application has posted multi-scale risks to health and ecological security, underscoring the urgent need for a comprehensive evaluation. This review aims to: (1) clarify the current status of antibiotic use in tilapia farming, covering major categories, administration methods, practical dose ranges, and international regulatory disparities, with emphasis on overuse and irrational drug combinations; (2) elucidate the pharmacokinetic behavior of antibiotics in tilapia (e.g., absorption, distribution, metabolism, and excretion), focusing on tissue-specific residue patterns and bioaccumulation; (3) systematically assess the direct toxicological impacts of antibiotics on tilapia, encompassing physiological disturbances, metabolic toxicity, immune suppression, gut microbiota dysbiosis and mechanisms of antimicrobial resistance induction; (4) reveal the ecological perturbations caused by antibiotics in aquaculture environments, including disruptions to microbial communities, degradation of essential ecological functions and the emergence and transmission of antibiotic resistance genes; (5) investigate the potential human health risks associated with food-chain bioaccumulation, including dietary exposure, allergic responses, gut microbiome imbalance, and promotion of resistant pathogens in humans. Overall, this review provides evidence to support rational antibiotic-use guidelines, improved residue monitoring and antimicrobial resistance surveillance, and the development of safer alternatives to promote sustainable aquaculture.}, }
@article {pmid41856032, year = {2026}, author = {Caetta, A and Aasen, D and Adamcyzk, P and Yuan, H and Zhou, Y and Roberts, D and Grindle, C and Schoem, S and Hughes, A}, title = {Characterizing the microbiome of the middle ear using 16S RNA sequencing in pediatric patients with and without middle ear effusions requiring ventilation tubes.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {204}, number = {}, pages = {112798}, doi = {10.1016/j.ijporl.2026.112798}, pmid = {41856032}, issn = {1872-8464}, }
@article {pmid41856106, year = {2026}, author = {Yuan, S and Zhu, H and Yu, M and Jia, H and Peng, S and Ma, Y}, title = {Discovery of human gut phage-encoded anti-CRISPR proteins unveils diverse mechanisms for phages to evade type II CRISPR immunity.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.017}, pmid = {41856106}, issn = {1934-6069}, abstract = {Phages encode diverse anti-CRISPR (Acr) proteins to counteract bacterial CRISPR-Cas systems. However, gut phage Acrs remain poorly characterized. Using an integrated bioinformatics and high-throughput functional screening approach, we identify 651 phage-encoded positive Acr candidates that target type II CRISPR systems, which predominate in the human gut. Among these, a subset of Acrs is verified through plasmid interference assays, with plaque assays confirming CRISPR-Cas inhibitory activity for 36 Acr candidates. Mechanistic characterization of five Acrs, including the Acr against subtype II-B systems (AcrIIB-1), reveals distinct inhibition strategies. Remarkably, 213 positive Acr candidates, designated here as GutAcraca, exhibit structural convergence by adopting similar folds and exhibit dual functionality: transcription regulation to support their production and inhibition of CRISPR-Cas systems. These GutAcraca are widely distributed across microbial species (detected in 26% of species). Our work uncovers the extensive diversity of phage-encoded Acrs in the human gut and highlights their potential as biotechnology tools.}, }
@article {pmid41856107, year = {2026}, author = {Potloane, D and Symul, L and Ngcapu, S and Lewis, L and France, M and Vermeren, L and Elsherbini, J and Chetty, C and Mafunda, NA and Polliah, AM and Mtshali, A and Kama, A and Magini, N and Mitchev, N and Mzobe, G and Khan, A and Demidkina, BC and Goldenberg, M and Xu, J and Rutt, L and Shirtliff, B and Cook, S and Murthy, M and Hussain, F and Passmore, JS and Jaspan, HB and Kullin, B and Happel, AU and Liebenberg, L and Relman, DA and Holmes, S and Kwon, DS and Ravel, J and Mitchell, CM}, title = {VIBRANT: A phase 1 randomized trial of multi-strain vaginal L. crispatus live biotherapeutic products in people with bacterial vaginosis.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.016}, pmid = {41856107}, issn = {1934-6069}, abstract = {Bacterial vaginosis (BV) is characterized by high microbial diversity. High recurrence rates following antibiotics may stem from poor recolonization by protective Lactobacillus species. This phase 1 randomized trial in the United States and South Africa evaluated two vaginally delivered live biotherapeutic products (LBPs) containing multiple Lactobacillus crispatus strains. After metronidazole treatment for BV, participants received either a placebo or 3 or 7 days of active LBPs. LBP strains were detected by metagenomics in 66.1% (47/71) of participants in the active arms in the first 5 weeks. Among those, nearly half (49%, 23/47) remained colonized at 12 weeks despite the short initial treatment course. Participants were most often colonized by one of three component strains, with no geographic differences in strain colonization observed. LBPs were safe, acceptable, and well tolerated, with no serious adverse events (AEs) reported. These results provide a foundation for the development of transformational interventions aimed at optimizing the vaginal microbiome.}, }
@article {pmid41856218, year = {2026}, author = {Wu, YH and Wang, LC}, title = {Establishment and utilization of striped catfish skin epithelial cell line to study host-pathogen interaction.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {111280}, doi = {10.1016/j.fsi.2026.111280}, pmid = {41856218}, issn = {1095-9947}, abstract = {The scaleless striped catfish (Pangasianodon hypophthalmus) is an economically important aquaculture species but is frequently infected by Aeromonas hydrophila (AH), causing substantial economic losses. Fish skin mucosa plays a protective role by initiating inflammatory responses to AH challenge. However, how the skin epithelial cells, the outermost defensive layer of skin tissue, respond and interact with AH remains unknown. This study aims to establish a skin epithelial cell line from striped catfish and investigate the response of skin epithelial cells under AH challenge. Skin epithelial cells were isolated and subcultured at optimal temperature and serum concentration, and epithelial properties were confirmed by the epithelial marker cytokeratin. The established skin epithelial cell line was inoculated with or without AH to evaluate survival and immune responses. We found cells survived at a tissue-damaging concentration of AH and showed an extremely higher immune response. Moreover, the presence of mucus and its microbiome may regulate AH-induced immune response, suggesting a complexity of skin-AH interaction in vivo. In conclusion, this study successfully established a striped catfish skin epithelial cell line and utilized it to characterize the outermost skin epithelial responses to AH in the presence of the mucus microbiome. By employing this cell line, new insights into epithelial-level immune interactions with pathogens were provided.}, }
@article {pmid41856288, year = {2026}, author = {Pudlo, NA and Pereira, GV and Schaus, SR and Yang, Q and Fuentes, JJ and Jin, C and Hein, R and Zhang, L and Terrapon, N and Lyssiotis, CA and Schmidt, TM and Hansson, GC and Luis, AS and Martens, EC}, title = {The butyrate-producing Gram-positive human gut bacterium, Hoskinsella mucinilytica, selectively targets host mucin N-acetylhexosamines.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {111371}, doi = {10.1016/j.jbc.2026.111371}, pmid = {41856288}, issn = {1083-351X}, abstract = {The personalized microbial communities (micobiota) that inhabit the distal guts of humans have evolved to process a variety of complex carbohydrates. Many gut bacteria depolymerize and ferment dietary fiber polysaccharides, mutualistically providing short-chain fatty-acids and other metabolites to their host. Some human gut bacteria have evolved to utilize components of host mucin glycoproteins-the major component of secreted mucus that protects the gut. Recent studies have implicated certain mucin-degrading bacteria in the development of intestinal inflammation, making identification of new gut bacteria that possess the ability to degrade mucins an important goal. We used gastric mucin to isolate a novel bacterium, Hoskinsella mucinilytica, that is largely restricted to using the N-acetylglucosamine and N-acetylgalactosamine sugars found in the O-linked glycans appended to secreted mucin. This butyrate-producing bacterium accesses these sugars from both polymeric gastric mucin and chemically released oligosaccharides. It also has a genome with correspondingly restricted carbohydrate-active enzyme content with only three demonstrated mucin-degrading glycoside hydrolase enzymes belonging to families GH31, 36 and 89. Surprisingly, strains with identical 16S rRNA V4 region to this isolate appear to be rare in the now numerous sequence-based microbiota surveys with only 30/7390 (0.41%) human subjects harboring detectable levels of this bacterium in their stool with an overall relative abundance ranging from 0.0004-0.013% when it is detected. This combination of low prevalence and low abundance suggests that this species could occupy an unknown niche for which access to mucin is important but otherwise renders it difficult to detect in stool-based microbiota surveys.}, }
@article {pmid41856524, year = {2026}, author = {Janssen, KP and Basic, M and Bolsega, S and Metwaly, A and Jokisch, F and von Gamm, S and Scheiber, J and Burkhardt, R and Liebisch, G and Neuhaus, K and Brunner, S and Clavel, T and Wortmann, E and Coleman, OI and Haller, D and Bleich, A and Krautbauer, S and Ecker, J}, title = {Extrinsic lipids are absorbed and accumulate in colorectal cancer.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336377}, pmid = {41856524}, issn = {1468-3288}, abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits increased levels of arachidonic acid-derived pro-inflammatory derivatives indicating an uptake of dietary polyunsaturated fatty acids (PUFAs).<br><br>OBJECTIVE: We aimed to investigate uptake of extrinsic fatty acids (FAs) in tumours and their relevance for CRC lipid metabolism and progression.<br><br>DESIGN: Total FAs were quantified using gas chromatography-mass spectrometry in non-diseased mucosa and tumour tissue from patients with CRC of a discovery cohort (n=152), validated in an independent cohort (n=28) and associated with clinical, genomic and microbiome data. The genetic mouse tumour model Apc[1638N] was used to track the flux of stable isotope-labelled FAs in tumours from the intestinal lumen. The relationship between FA uptake and tumour progression was investigated in 2D and 3D cell models.<br><br>RESULTS: Extrinsic long chain PUFAs, including arachidonic acid, accumulate in CRC, particularly in right-sided tumours, and in tumours of Apc[1638N] mice. The CRC-specific FA profiles were independent of sex, molecular subtypes, early-disease or late-disease onset. The absorption of FAs from the intestinal lumen in tumours was confirmed in specific pathogen-free Apc[1638N] mice. In the absence of the microbiome, in germ-free Apc[1638N] mice, fewer tumours were developed, and survival was increased. Inhibition of FA import or &#x3b2;-oxidation reduces cancer cell proliferation.<br><br>CONCLUSION: Extrinsic FAs accumulate in CRC, verifying a central role of arachidonic acid-derived inflammatory mediators, but also suggesting a relevance of dietary FAs for cancer cell proliferation. It will be intriguing to explore to what extent targeting this flux pathway together with the interrelated microbiome opens new therapeutic avenues for CRC in humans.}, }
@article {pmid41856839, year = {2026}, author = {Suchodolski, JS and Toresson, L}, title = {Microbiome Modulation in Veterinary Medicine: From Diet to Fecal Microbiota Transplantation.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cvsm.2026.01.009}, pmid = {41856839}, issn = {1878-1306}, abstract = {The intestinal microbiome plays a crucial role in host health. As intestinal dysbiosis can have different underlying causes, multimodal therapeutic approaches are often necessary. Dietary modulation potentially combined with fibers should be the first-line approaches in all patients with acute or chronic enteropathy and help modulate the microbiome. A subset of animals with chronic intestinal disease have marked dysbiosis that results in abnormal microbial function and reflects underlying mucosal pathology, which often persists in chronic inflammatory enteropathy. Fecal microbiota transplantation can be a useful adjunct treatment of chronic disorders, but in patients with severe dysbiosis, repeated treatments are likely needed.}, }
@article {pmid41843084, year = {2026}, author = {Madhusoodhanan, R and Raman, K and Akbar, R and Pambayan Ulagan, M and Mariadoss Arokia, VA and P, T}, title = {Modulating gut microbiota in type 2 diabetes mellitus: advances and challenges in precision medicine.}, journal = {Acta diabetologica}, volume = {}, number = {}, pages = {}, pmid = {41843084}, issn = {1432-5233}, }
@article {pmid41843114, year = {2026}, author = {Jabeen, M and Hameed, H and Razzaq, AA and Jamshaid, M and Shakeel, MA and Mushtaq, T}, title = {Dental caries beyond eradication: microbiome centered and equilibrium driven therapeutic strategies.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41843114}, issn = {1432-072X}, }
@article {pmid41843167, year = {2026}, author = {Shamsuzzaman, M and Dahal, RH and Kim, J}, title = {Probiotic and immune-modulatory capacities of three human gut-derived strains of Parabacteroides distasonis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41843167}, issn = {1432-072X}, mesh = {*Probiotics/pharmacology ; Humans ; Animals ; *Gastrointestinal Microbiome ; Mice ; RNA, Ribosomal, 16S/genetics ; *Bacteroidetes/genetics/isolation &amp; purification/classification/physiology/immunology ; Macrophages/immunology ; Cytokines/metabolism ; RAW 264.7 Cells ; Phylogeny ; Antioxidants/pharmacology ; Nitric Oxide/metabolism ; }, abstract = {The human gut microbiome harbors diverse beneficial bacteria with potential roles in supporting host health. Parabacteroides distasonis has recently attracted interest as a next-generation probiotic (NGP) candidate; however, functional evidence for human-derived strains remains limited. Here, three human gut-derived P. distasonis strains (B2-S-102, B2-Q-110, and Y3-G-102) were isolated from healthy individuals and characterized using comparative genomics and in vitro functional assays. Species-level identity was supported by 16S rRNA gene analysis and whole-genome relatedness metrics (ANI > 97% and dDDH > 70%), consistent with established species delineation thresholds. Under controlled laboratory conditions, the strains showed tolerance to acidic pH (pH 2.0), bile salts (0.3%), and simulated gastric and intestinal fluids. Functionally, the strains exhibited measurable antioxidant activity (35.03 ± 7.76% to 51.22 ± 5.60% DPPH inhibition) and α-amylase inhibitory activity (51.03 ± 32.12% to 69.23 ± 4.26%) in vitro. Cell-free supernatants inhibited albumin denaturation (47.65 ± 3.56% to 65.26 ± 4.15%), while live bacteria reduced nitric oxide production and pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ, and IL-1β) in LPS-stimulated RAW 264.7 macrophages (p < 0.05). The strains also displayed in vitro growth-inhibitory activity against Escherichia coli, Acinetobacter baumannii, and Salmonella enteritidis. Genome mining identified multiple biosynthetic gene clusters, indicating genetic potential for secondary metabolite production; however, expression and metabolite identity were not experimentally validated. No haemolytic activity was observed, supporting a favorable preliminary safety profile. Overall, these findings provide preliminary in vitro evidence supporting the potential of human-derived P. distasonis strains as NGP candidates for further evaluation.}, }
@article {pmid41843355, year = {2026}, author = {Alum, EU and Nwachoko, N and Tufail, T and Govindarajan, RK and Alum, BN and Nwuruku, OA and Aja, PM}, title = {Gut Microbiota Resilience and Environmental Stressors: A Hidden Key to Lifespan Optimization?.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41843355}, issn = {1867-1314}, abstract = {Gut microbiota resilience, the capacity of intestinal microbial communities to resist, adapt, and recover from perturbations has emerged as a critical determinant of human health and longevity. Environmental stressors such as antibiotics, pollutants, poor diet, infections, and psychosocial stress challenge this resilience, often leading to dysbiosis (a sustained disruption of microbial community structure and/or function), impaired metabolism, chronic inflammation, and increased disease susceptibility across the lifespan. While dysbiosis has been extensively studied, the resilience dimension remains underexplored, particularly in the context of cumulative and repeated stress exposures. This narrative review explores microbial resilience, identifying environmental disruptors, and their manifestation at life stages, highlighting its hidden yet crucial role in optimizing lifespan. We critically evaluate the consequences of reduced resilience for chronic disease, frailty, and therapeutic response, while emphasizing the protective roles of diversity, functional redundancy, and host-microbe feedback loops. Translational strategies including dietary modulation, microbial therapeutics, behavioral interventions, and precision tools such as multi-omics and biosensors, are assessed for their potential to strengthen resilience and promote healthy aging. By reframing gut microbiota resilience as both a biological property and a public health target, this work advances a novel perspective: that fostering resilience may mitigate environmental insults, personalize interventions, and extend healthspan.}, }
@article {pmid41843611, year = {2026}, author = {Zhang, WX and Du, J and Dong, L and Zhang, SS and Song, G and Ao, L and Wang, Y and Ma, L and Sun, W and Ma, J and Tian, X and Qu, B and Long, T and Chen, L and Huang, Z and Qiao, J and Zhang, Y and Li, J and Lu, X and Cui, F and Ren, X and Lu, QB}, title = {Comprehensive profiling of skin microbiome diversity and major determinants in a multi-regional Chinese population.}, journal = {Cell reports}, volume = {45}, number = {3}, pages = {117097}, doi = {10.1016/j.celrep.2026.117097}, pmid = {41843611}, issn = {2211-1247}, abstract = {The human skin microbiome is essential for health and is shaped by both host and environmental factors. To establish a nationwide baseline, we profile the skin microbiome of 1,029 Chinese individuals across three body sites (hand, axilla, and foot), four geographic regions, and four ethnic groups using 16S rRNA gene sequencing. Within each skin site, we identify two cutotypes, one of which is consistently dominated by Staphylococcus. Microbial diversity and community composition vary across body sites, geography, ethnicity, gender, and age, with geographic location emerging as the strongest source of variation and enabling accurate classification by Random Forest models. Notably, Han and minority populations within the same region exhibit greater similarity than the same ethnic group across different regions. Aging-related shifts differ by both body site and geography, reflecting interactions between physiological and environmental influences. This population-scale study provides a comprehensive reference for the Chinese skin microbiome and reveals how host and environmental factors jointly structure skin microbial communities.}, }
@article {pmid41843697, year = {2026}, author = {Dilrukshi, N and Kottahachchi, J and Dissanayake, T and Muneeswaran, K and Fernando, N}, title = {Group B Streptococcus and Vaginal Microbiome Dynamics in Pregnancy.}, journal = {Medical principles and practice : international journal of the Kuwait University, Health Science Centre}, volume = {}, number = {}, pages = {1-23}, doi = {10.1159/000551477}, pmid = {41843697}, issn = {1423-0151}, abstract = {OBJECTIVE: This study aims to compare the vaginal microbiome of Group B Streptococcus (GBS) positive and negative pregnant women in selected tertiary care hospitals in Sri Lanka.<br><br>METHOD: Fifteen GBS-positive and fifteen GBS-negative women were included in the study. The composition of vaginal microbiome was profiled by sequencing 16S rRNA V3-V4 region. Microbiome diversity and variation were evaluated.<br><br>RESULTS: Alpha diversity measured by Shannon diversity and Chao1 index differed significantly between GBS-positive and GBS-negative groups (Chao1 p=0.0003, Shannon p=0.0003), while beta diversity Pairwise Permutational Multivariate Analysis of Variance (PERMANOVA) p=0.435) showed no significant difference, indicating similar overall bacterial compositions. Gardnerella and Prevotella were more abundant in GBS-positive group, while majority of the GBS-negative group was dominated by Lactobacillus (87.9%). Lactobacillus iners was the most abundant species in both groups. Lactobacillus gallinarum, reported for the first time in Sri Lanka, was the second most common Lactobacillus species. Linear Discriminant Analysis effect size (LEfSe) identified no taxa enriched in GBS-negative group, whereas GBS-positive group showed significantly higher relative abundance with several taxa with Bifidobacterium showed the highest linear discriminant analysis (LDA) score (4.459). Methylocystis, though of low biological relevance, was significantly abundant in GBS-positive group (p=0.025).<br><br>CONCLUSIONS: Lactobacillus spp. were reduced in GBS-positive women, with higher abundance of other bacterial taxa suggesting that disruption of a Lactobacillus dominant vaginal microbiome may facilitate GBS colonization and potentially increase the risk of neonatal infection. &#x2003;.}, }
@article {pmid41843749, year = {2026}, author = {Ribeiro, MM and Liu, C and Xu, JF and Liang, S and Goldman, GH}, title = {Pseudomonas aeruginosa adaptation and persistence in the aspergilloma microbiome revealed by integrated multi-omics.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkag063}, pmid = {41843749}, issn = {2160-1836}, abstract = {Chronic pulmonary aspergillosis involves the formation of a fungal ball (aspergilloma) in lung cavities. Pseudomonas aeruginosa commonly co-colonizes these lesions; however, the in vivo mechanisms underlying its persistence are unknown. Using a multi-omics approach on resected aspergillomas, we defined the genomic, transcriptional, and metabolic adaptations of P. aeruginosa within this polymicrobial niche. We reconstructed high-quality P. aeruginosa genomes and identified a conserved core genome, along with accessory genes for secondary metabolism, virulence, and antimicrobial resistance. Phylogenomics revealed heterogeneous evolutionary paths among co-colonizing strains. Metatranscriptomics showed stark physiological heterogeneity, from metabolically aggressive to stress-adapted states. High expression of phenazine, quorum-sensing (PQS), siderophore, and secretion-system operons was corroborated by metabolomic detection of phenazine-1-carboxylic acid and 2-heptylquinolin-4(1H)-one, confirming active bacterial antagonism in vivo. Concurrent Aspergillus fumigatus transcriptomics revealed the activation of oxidative stress responses, secondary metabolism (e.g., fumagillin), and iron scavenging, demonstrating reciprocal competition. Host transcriptomics revealed patient-specific immune signatures that correlated with the metabolic activity of the co-colonizers. This work provides an integrated systems-level analysis of the tri-kingdom aspergilloma ecosystem. P. aeruginosa persistence is driven by genomic plasticity and context-dependent expression of competitive pathways, shaped within a chronic inflammatory environment. These findings redefine aspergillomas as active polymicrobial consortia, establishing a framework for targeting resilient microbial communities in chronic lung disease.}, }
@article {pmid41844212, year = {2026}, author = {O'Connell, KA and Celdran-Bonafonte, D}, title = {Beyond Comfort: A Review of the Critical Role of Bedding Selection in Rodent Welfare, Microenvironment, and Research Reproducibility.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {}, number = {}, pages = {1-13}, doi = {10.30802/AALAS-JAALAS-25-182}, pmid = {41844212}, issn = {2769-6677}, abstract = {This review addresses the critical but often underappreciated influence of bedding selection on rodent welfare, cage microenvironment, occupational health, and research outcomes in biomedical studies. Although contact bedding is widely preferred by mice and rats and is the current industry standard, there is considerable variation in bedding type, volume, sterility, and manufacturer practices, with no established universal protocols. We synthesize over 150 publications, evaluating corncob, wood, and cellulose-based beddings with respect to their physical attributes, absorbency, ammonia management, dust and contaminant control, and support of species-typical behaviors. The review highlights methodological challenges and inconsistent results across studies, with absorbency and ammonia accumulation particularly affected by bedding mass, volume, and microbial contamination, rather than material type alone. Occupational health risks, including ergonomic strain and allergen exposure, are impacted by bedding handling frequency and composition. Animal health is generally not strongly influenced by bedding type, although pine shavings and certain corncob products present toxicity and reproductive risks in some studies. Bedding also has documented impacts on hepatic enzyme induction, neurobehavioral development, pain sensitivity assays, and gut microbiome composition, posing substantial risks for experimental confounding and compromised reproducibility. Based on the evidence, cellulose bedding is recommended for minimizing negative outcomes, but the complexity and variability inherent in bedding selection necessitate careful documentation and transparent reporting. We advocate for standardized detail in publications to ensure comparability and rigor across rodent-based research.}, }
@article {pmid41844223, year = {2026}, author = {Graziano, M and Garbini, GL and Devigili, A and Pinzoni, L and Quagliariello, A and Bosi, E and Gasparini, C and Fondi, M and Martino, ME}, title = {From microbiome to sperm motility traits: an inside-out perspective.}, journal = {Biology letters}, volume = {22}, number = {3}, pages = {}, doi = {10.1098/rsbl.2025.0759}, pmid = {41844223}, issn = {1744-957X}, support = {//Italian Ministry of University and Research/ ; //University of Padova/ ; }, mesh = {Animals ; Male ; *Poecilia/microbiology/physiology ; *Sperm Motility/physiology ; *Microbiota ; Skin/microbiology ; Spermatozoa/physiology ; Bacteria/classification ; }, abstract = {Growing interest in the relationship between microbiome composition and host biology has revealed the many ways host-associated microbes influence physiology, ecology and evolution. However, microbial communities associated with reproductive organs-and their roles in reproduction-remain poorly understood. Here, we characterized the skin- and ejaculate-associated microbiomes in an internally fertilizing fish and tested whether microbial diversity and specific bacterial taxa correlate with sperm motility traits key for reproductive success. We used the guppy (Poecilia reticulata), a well-established model in ecology and evolutionary biology with well-characterized reproductive physiology. In guppies, sperm velocity is a validated predictor of male reproductive performance, making them a powerful system for exploring microbiome-fertility interactions. Our analyses reveal a correlation between skin microbiome diversity and sperm performance. Notably, increased skin microbiome total richness is associated with reduced sperm velocity, whereas no significant associations were detected for ejaculate-associated microbiomes. We also identified bacterial taxa across both tissues that were positively or negatively linked with sperm performance. These findings suggest that, while the ejaculate-associated microbiome may directly influence sperm traits, the skin microbiome could serve as a proxy for reproductive potential by reflecting systemic physiological and immunological states associated with fertility.}, }
@article {pmid41844930, year = {2026}, author = {Kumari, N and Pal, G and Chawak, K and Arbi, SH and Anand, S}, title = {Current trends and updates on the emerging role of fecal microbiota transplantation in the treatment of neurodegenerative diseases.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {4}, pages = {}, pmid = {41844930}, issn = {1572-9699}, mesh = {*Fecal Microbiota Transplantation/trends/methods ; Humans ; *Neurodegenerative Diseases/therapy/microbiology ; Gastrointestinal Microbiome ; Animals ; Feces/microbiology ; }, abstract = {Fecal microbiota consists of a consortium of bacterial populations that reside in the human body, particularly in the gastrointestinal system, and are crucial to numerous physiological processes. Due to its promising clinical potential and acceptable safety profile, FMT has been the subject of numerous investigations as a possible therapeutic method for curing diverse disorders. Neurodegenerative diseases (NDs) are one among them and warrant immediate attention. There is a lack of efficient treatments for many ailments, and despite decades of research, we still don't fully understand their mechanisms and causes. The lack of advancement has prompted the research community to focus more on investigating novel or different elements that may impact the etiology or management of these disorders. The gut-brain axis, which embraces the two-way communication between the gut and brain via immunological, neurological, endocrine, and metabolic pathways, is one such element. Since NDs are frequently linked to aberrant gut microbiome compositions, it is not surprising that altering the gut microbiome can be a promising strategy in the treatment and management of neurological disorders. Fecal microbiota transplantation (FMT) is a technique employed for modulating microbiome composition and is becoming more and more common. FMT or recolonizing the ''diseased'' gut with a normal microbiome is one way to restore a dysbiotic gut. Traditionally used to treat Clostridium difficile-linked infections, FMT has lately been investigated as a probable treatment strategy for NDs. This review aims to systematically tap the current trends and updates on the employment of FMT in neurodegenerative research, whether as a treatment regimen or to look into the role of the microbiota in pathogenesis.}, }
@article {pmid41844942, year = {2026}, author = {Thu, MS and Le, HBC and Duc, NP and Mai, VH and Walker, N and Hirankarn, N}, title = {Impact of microbiome-modulating strategies in cancer patients receiving immunotherapy (MSIT): A systematic review and meta-analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44743-7}, pmid = {41844942}, issn = {2045-2322}, support = {N42A680423//National Research Council of Thailand/ ; }, abstract = {The gut microbiota influences immune checkpoint inhibitors (ICIs) efficacy. Microbiome-modulating strategies (MMSs), including probiotics, synbiotics, and faecal microbiota transplantation (FMT), have emerged as promising adjuncts, but their clinical impact remains uncertain. We systematically reviewed PubMed, Embase, and CENTRAL to February 2025 for clinical cohorts evaluating MMS in cancer patients receiving ICIs. Thirty-six studies (25 trials/cohorts; n = 2,746) were included. Meta-analyses, and subgroup analyses were performed for efficacy along with microbiome shifts and safety. MMS plus ICIs achieved a pooled objective response rate (ORR) of 40% (95% CI: 31%-49%; I[2] = 63.4%; p = 0.0003; 95% PI: 15%-72%). Descriptive proportions showed ORR of 45% (95% CI: 32%-58%; I[2] = 72.5%; p = 0.0058) for probiotics and 33% (95% CI: 22%-48%; I[2] = 60.7%; p = 0.0064) for FMT; however, these findings are non-comparative and confounded by study differences. Exploratory subgroup signals were noted for probiotics in NSCLC (ORR 55%; 95%CI: 45%-64%; I[2] = 0%; p = 0.3683) and FMT in melanoma (ORR 39%; 95% CI: 15%-69%; I[2] = 72.5%; p = 0.0262). Dual ICI regimens showed the highest point estimate for ORR (43%; 95% CI: 17%-73%; I[2] = 68.5%; p = 0.0747) but increased toxicity. Microbiome analyses revealed enrichment of short-chain fatty acid-producing taxa and Bifidobacterium spp. among responders. Based on a limited pooled sample size (n = 143), MMS-related adverse events were mostly grade 1-2 (42%; 95% CI: 14%-77%, I[2] = 53.8%, p = 0.0210), with rare severe events (1%). Overall, MMS show promising, though preliminary, hypothesis-generating signals for modulating ICI response. Given high heterogeneity and reliance on early-phase, single-arm trials, the findings underscore urgent need for large, biomarker-driven randomized controlled trials to define optimal interventions and cautiously integrate microbiome modulation into immuno-oncology care.}, }
@article {pmid41845058, year = {2026}, author = {Doan, T and Yan, D and Arzika, AM and Abdou, A and Maliki, R and Aichatou, B and Bello, IM and Beidi, D and Galo, N and Harouna, N and Karamba, AM and Mahamadou, S and Abarchi, M and Ibrahim, A and Zhong, L and Chen, C and Liu, Y and Yu, D and Abraham, T and Cheng, AS and Peterson, B and Oldenburg, CE and Porco, TC and Arnold, BF and Hinterwirth, A and Lebas, E and O'Brien, KS and Lietman, TM}, title = {Mass azithromycin distribution and antibiotic resistance in the gut and nasopharynx: a cluster-randomized trial.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41845058}, issn = {1546-170X}, abstract = {Repeated semiannual azithromycin mass drug administration (MDA) to children has been shown to reduce all-cause childhood mortality. However, antibiotic resistance is a major public health concern as the program is being implemented in sub-Saharan Africa. In the double-blind, cluster-randomized, placebo-controlled trial (AVENIR) in Niger, we evaluated the impact of azithromycin MDA targeting different age groups on mortality and on the gut and nasopharyngeal microbiome and resistome of children in participating communities. A total of 3,000 communities were randomized in a 1:1:1 allocation to 3 arms: 2 years of semiannual MDA of (1: child-azithromycin) azithromycin to 1-59-month olds, (2: infant-azithromycin) azithromycin to 1-11-month olds and placebo to 12-59-month olds or (3: placebo) placebo to 1-59-month olds. Mortality (co-primary endpoint) and safety data have previously been published. Here we report on resistance (the co-primary endpoint). One hundred fifty communities (50 per arm) were selected for this analysis. A total of 4,382 rectal and 4,402 nasopharyngeal samples were included. The co-primary outcomes included changes in gut and nasopharynx macrolide AMR. The trial met its primary AMR endpoint for the gut but not for the nasopharynx. The gut macrolide AMR burden in fold change between arms was highest in child-azithromycin compared with placebo (1.16, 95% confidence interval (CI): 1.06-1.28; P < 0.01), followed by child-azithromycin compared with infant-azithromycin (1.13, 95% CI: 1.02-1.23; P = 0.01), and infant-azithromycin compared with placebo (1.04×, 95% CI: 0.94-1.15×; P = 0.66). There were no statistically significant differences in macrolide AMR selection fold change in the nasopharynx between arms: 2.14 (95% CI: 0.93-4.99) for child-azithromycin versus placebo, 2.08 (95% CI: 0.93-4.69) for infant-azithromycin versus placebo, and 1.03 (95% CI: 0.46-2.30) for child-azithromycin versus infant-azithromycin. Close monitoring of AMR should be an essential component of MDA for childhood mortality. ClinicalTrials.gov registration: NCT04224987.}, }
@article {pmid41845406, year = {2026}, author = {Zong, Y and Kong, J and Yang, F and Wang, M and Wang, J and Wang, Q}, title = {Guominkang formula alleviates airway inflammation in HDM-induced asthma mice by regulating Wnt/β-Catenin pathway.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {41845406}, issn = {1749-8546}, support = {No. 82174243//the General program of National Natural Science Foundation of China/ ; No. 7242227//the General project of Beijing Natural Science Foundation/ ; No.zyyzdxk-2023251//the High level Key Discipline of National Administration of Traditional Chinese Medicine - Traditional Chinese constitutional medicine/ ; No.2023-JYB-JBZD-009//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: The Guominkang formula (GMK), formulated according to the principle of "treatment based on constitution differentiation," comprises Prunus mume (Siebold) Siebold &amp; Zucc. (Wumei), Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk. (Fangfeng), Ganoderma lucidum (Curtis) P. Karst. (Lingzhi), and Periostracum Cicadae (Chantui). Clinically, GMK has been shown to modulate allergic constitution, effectively treating allergic asthma (AA) and various other allergic conditions, with a favorable safety profile and substantial therapeutic benefits. However, the precise mechanisms underlying its immune-modulatory effects, particularly in the context of AA, remain inadequately defined.<br><br>AIMS: This study aimed to investigate the therapeutic effects and underlying mechanisms of GMK in a mouse model of AA.<br><br>METHODS: The components of GMK were analyzed via LC-MS/MS. AA was induced in female mice through nasal instillation of house dust mites (HDM). Therapeutic efficacy was assessed through histopathological examination of lung tissue, measurement of airway hyperresponsiveness (AHR), and analysis of inflammatory cell infiltration, including eosinophils, neutrophils, macrophages, and subsets of T cells (Th1, Th2, Th17, and Treg). Serum levels of total IgE, HDM-specific IgE (HDM-sIgE), and cytokines (IL-1&#x3b2;, IL-4, IL-5, IL-6, IL-10, IL-13, IL-17, and IFN-&#x3b3;) were quantified. Additionally, gut microbiome composition and differences between experimental groups were analyzed. Lung tissue transcriptomics identified differentially expressed genes (DEGs) and related signaling pathways. Western blot analysis was performed to evaluate protein expression levels of the Wnt/&#x3b2;-Catenin signaling pathways, contributing to the understanding of GMK's anti-asthma effects. Molecular docking studies were conducted to explore the binding interactions between GMK and&#xa0;the Wnt3a protein.<br><br>RESULTS: Fourteen compounds were identified in GMK. The formula exhibited significant therapeutic effects in an AA mouse model, evidenced by a reduction in Th2 and Th17 cell populations, restoration of the Th1/Th2 and Th17/Treg immune balance, alleviation of eosinophilic airway inflammation, and a decrease in total IgE and HDM-sIgE levels in serum. GMK also downregulated the expression of IL-1&#x3b2;, IL-4, IL-5, IL-6, IL-10, IL-13, and IL-17, while upregulating IFN-&#x3b3; expression. Among the various doses, the medium dose proved most effective in mitigating airway inflammation, reducing airway remodeling, and decreasing AHR. Microbiome analysis revealed that GMK treatment reversed the reduced abundance of Firmicutes and Dubosiella in asthma mice, while increasing the abundance of Bacteroidetes and Norank_f_Muribaculaceae. Transcriptomic analysis demonstrated that, compared to asthma mice, DEGs in the lung tissue of GMK-treated mice were primarily enriched in the Wnt and related pathways. Furthermore, GMK modulated the Wnt/&#x3b2;-catenin signaling pathway to treat AA. Molecular docking studies confirmed predicted strong binding interactions between multiple bioactive compounds in GMK and the Wnt3a protein.<br><br>CONCLUSIONS: GMK regulates Th immune balance by modulating the Wnt/&#x3b2;-catenin signaling pathway, thereby reducing airway inflammation in HDM-induced asthma mice. Targeting the Wnt/&#x3b2;-catenin signaling pathway in the lungs may offer a novel therapeutic approach for allergic asthma treatment.}, }
@article {pmid41845494, year = {2026}, author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P}, title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02363-3}, pmid = {41845494}, issn = {2049-2618}, support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.<br><br>RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.<br><br>CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.}, }
@article {pmid41845517, year = {2026}, author = {Lin, L and Popova, M and Tapio, I and Guan, LL and Seifert, J}, title = {Harnessing the early-life gut microbiome for sustainable ruminant production.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00549-6}, pmid = {41845517}, issn = {2524-4671}, }
@article {pmid41845563, year = {2026}, author = {Liu, S and Schlicht, K and Beckmann, A and Hartmann, K and Wang, W and Kruse, L and Wietzke-Braun, P and Hollstein, T and Becker, U and Ziegenbruch, U and Baumgartner, F and Diederich, W and Laudes, A and Muchaier, J and Stobbe, M and Homeister, L and Remy, S and Dornstauder, N and Vogel, M and Schindler, C and Türk, K and Geisler, C and Rohmann, N and Laudes, M}, title = {Parasutterella excrementihominis is associated with attenuated metabolic improvements during obesity therapy in humans.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644687}, doi = {10.1080/19490976.2026.2644687}, pmid = {41845563}, issn = {1949-0984}, mesh = {Humans ; *Obesity/microbiology/therapy/metabolism ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Cross-Sectional Studies ; Weight Loss ; Insulin Resistance ; C-Reactive Protein/metabolism ; Diabetes Mellitus, Type 2/microbiology/metabolism ; }, abstract = {Alterations in the composition and function of the gut microbiome are important in obesity and type 2 diabetes development. Using our cross-sectional FoCus cohort, we recently found Parasutterella species were increased in human obesity and type 2 diabetes and linked to abnormalities in triglyceride metabolism and L-cysteine homeostasis, the latter being important for beta-cell function. To gain further insights, we now quantified gut Parasutterella excrementihominis by qPCR in n = 215 human subjects during an interdisciplinary non-surgical obesity therapy program consisting of an initial weight-reduction phase (weeks 1-12) followed by a weight-maintenance phase (weeks 13-26). P. excrementihominis abundance was significantly reduced during the weight reduction phase. While baseline abundance levels did not predict the success of weight-reduction, they were inversely associated with C-reactive-protein improvements. Interestingly, the decrease in P. excrementihominis abundance during the weight reduction phase was positively correlated with improvements in insulin sensitivity throughout the overall obesity intervention. Regarding the weight maintenance phase, a re-increase of P. excrementihominis abundance was significantly associated with weight regain. In summary, our data suggest that P. excrementihominis attenuates metabolic and inflammatory improvements in obese human subjects under therapy and highlight a potential role of this bacterial species in metabolic adaptation during weight loss interventions.}, }
@article {pmid41845564, year = {2026}, author = {Zhang, Y and Wang, DD}, title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644682}, doi = {10.1080/19490976.2026.2644682}, pmid = {41845564}, issn = {1949-0984}, mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Proteomics ; Multiomics ; }, abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.}, }
@article {pmid41845903, year = {2026}, author = {Cao, H and Sun, J and Lv, Y and Ye, J and Wang, Y and Jiang, H}, title = {Targeting the gut-kidney axis to improve kidney transplantation prognosis: from mechanisms to clinical intervention strategies.}, journal = {Renal failure}, volume = {48}, number = {1}, pages = {2642487}, doi = {10.1080/0886022X.2026.2642487}, pmid = {41845903}, issn = {1525-6049}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/immunology ; *Graft Rejection/prevention &amp; control/immunology ; Prognosis ; Fecal Microbiota Transplantation ; *Kidney/immunology ; *Kidney Failure, Chronic/surgery/immunology ; Intestinal Mucosa/immunology ; Immune Tolerance ; }, abstract = {Kidney transplantation is an important treatment for end-stage renal disease, but lifelong immunosuppression is needed to prevent immune rejection, but the immunosuppressive therapy increases the risk of post-transplant complications. Therefore, how to improve the long-term survival of transplanted kidneys and reduce rejection has become a hot spot in current research. Recently, the 'gut-kidney axis' has received widespread attention as an important pathway for immune regulation. It refers to the fact that changes in either side of the gastrointestinal tract and kidney will affect the other side through energy metabolism, immuno-inflammation, intestinal mucosa, intestinal flora, among others, up and including to adverse consequences, which can be mutually causative. With the theory of 'gut-kidney axis', more and more studies have found that intestinal immune cells and microbiota play an important role in maintaining immune homeostasis and regulating the immune microenvironment of renal transplant recipients. Some studies have found that intestinal immune cells and microbiota not only influence the systemic immune status, but also may regulate the immune response of transplanted kidneys through metabolites and inflammatory mediators. In this review, we summarize the potential mechanisms of intestinal immune cells and microbiota in immune tolerance and rejection after renal transplantation based on the theory of 'gut-kidney axis'. In addition, we highlight microbiome modulation strategies, particularly dietary interventions and fecal microbiota transplantation, as emerging approaches with potential to improve transplant outcomes. A deeper understanding of the mechanism of action of the gut-kidney axis will provide new ideas and therapeutic targets for immunomodulation after renal transplantation.}, }
@article {pmid41845908, year = {2026}, author = {Yao, R and Qian, F and Zhao, H and Shen, X and Zhu, Y and Wang, L}, title = {Microbiome Landscapes in Squamous Cell Carcinoma Tissue Microenvironments: A Comparative Analysis.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {3}, pages = {e70406}, doi = {10.1002/iid3.70406}, pmid = {41845908}, issn = {2050-4527}, support = {2022MS009//Basic scientific research project of Naval Medical University/ ; XTCX-KJ-2023-44//Shanghai Collaborative Innovation Project/ ; }, mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; *Tumor Microenvironment ; *Microbiota/genetics ; Female ; Male ; Middle Aged ; }, abstract = {INTRODUCTION: Squamous cell carcinoma (SCC) is one of the most prevalent human cancers. While anatomically distinct, SCCs exhibit diverse similarities in etiology and molecular. The extent to which different SCCs share microbial landscapes within the tumor tissue microenvironment remains unclear.<br><br>METHODS: We analyzed RNA sequencing data from 419 SCC samples across five anatomical sites: cutaneous (CuSCC), esophageal (ESCC), lung (LSCC), head and neck (HNSCC), and cervical (CeSCC). Differential microbial abundance between tumor and adjacent normal tissue was assessed using multivariable linear models implemented in MaAsLin2. For each anatomical site, an independent external validation cohort was included (totaling 156 samples) to validate key microbial findings using the area under the receiver operating characteristic curve (AUROC).<br><br>RESULTS: The five SCC cohorts shared 28 shared core bacterial genera, with Staphylococcus was widespread and had the highest relative abundance (mean 13.74%) in all cohorts. ESCC, HNSCC, and LSCC exhibited more similar dysregulated microbiota, with Clostridioides showing the most significant up-regulation in tumor relative to adjacent tissue (the mean model coefficient value, coef = 3.26). Notably, Bradyrhizobium (CeSCC, CuSCC, LSCC, mean coef&#x2009;=&#x2009;-2.58), Massilia (in CeSCC, ESCC, HNSCC, mean coef&#x2009;=&#x2009;-1.99), Providencia (in CeSCC, HNSCC, LSCC, mean coef = 0.93), and Ralstonia (in CuSCC, ESCC, HNSCC, mean coef&#x2009;=&#x2009;-0.52) displayed significant differential expression across multiple cohorts, as confirmed in the validation cohorts (AUROC&#x2009;>&#x2009;0.6).<br><br>CONCLUSIONS: Despite the absence of a common dysbiotic microbiota among SCCs due to anatomical differences, potential similarities in adjacent sites suggest a unified disease perspective and may pave the way for novel preventive and therapeutic strategies.}, }
@article {pmid41846072, year = {2026}, author = {Oladokun, S and Grenier, B and Oakley, B and Bortoluzzi, C and Ramkumar, M}, title = {Gut check: Exploring tools, techniques, and future directions in microbiome research.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106713}, doi = {10.1016/j.psj.2026.106713}, pmid = {41846072}, issn = {1525-3171}, abstract = {Poultry microbial communities are now recognized as key contributors to host nutrition, immune function, disease resilience, and overall health and performance, driving growing interest in this research field. This symposium brought together leading experts to discuss the latest advancements in analytical tools and technologies for investigating the poultry microbiome. Presentations highlighted current progress in microbiome profiling techniques, next-generation sequencing technologies, advanced data analysis methods such as machine learning, and the integration of cutting-edge approaches in microbiome research. A roundtable discussion further engaged participants in identifying key challenges in the field, including method standardization, reproducibility, and data interpretation, while emphasizing emerging opportunities to translate microbiome insights into practical strategies for disease control, antibiotic alternatives, and sustainable poultry production. The knowledge shared in this symposium is highly relevant to poultry researchers and the industry, as they work to enhance bird health, welfare, and productivity.}, }
@article {pmid41846103, year = {2026}, author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J}, title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1872}, number = {5}, pages = {168216}, doi = {10.1016/j.bbadis.2026.168216}, pmid = {41846103}, issn = {1879-260X}, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.<br><br>METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15&#xa0;mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10&#xa0;mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.<br><br>RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.<br><br>CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.}, }
@article {pmid41846126, year = {2026}, author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE}, title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141760}, doi = {10.1016/j.jhazmat.2026.141760}, pmid = {41846126}, issn = {1873-3336}, abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.}, }
@article {pmid41846268, year = {2026}, author = {Stengele, K and Stauber, L and Thoenen, L and Janse van Rensburg, H and D'Adda, V and Schlaeppi, K}, title = {Benzoxazinoid-mediated microbiome feedbacks enhance Arabidopsis growth and defence.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71098}, pmid = {41846268}, issn = {1469-8137}, support = {189249//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //University of Bern Interfaculty Research Collaboration "One Health"/ ; }, abstract = {Plants modulate their surrounding microbiome via root exudates and such conditioned soil microbiomes feed back on the performance of the next generation of plants. How plants perceive altered soil microbiomes and modulate their performance in response to such microbiome feedbacks, however, remains largely unknown. As tool to condition contrasting microbiomes in soil, we made use of two maize lines, which differ in their ability to exude benzoxazinoids (BXs). Based on these differentially conditioned soil microbiomes we have established a model system with Arabidopsis thaliana (Arabidopsis) to investigate the mechanisms of microbiome feedbacks. Arabidopsis plants responding to the BX-conditioned soil microbiome grew better and were developmentally more advanced. Further, these plants harboured differential root bacterial communities, showed enhanced defence signatures in transcriptomes of their shoots, and they were more resistant to the fungal pathogen Botrytis cinerea. Intriguingly, Arabidopsis responded with both improved growth and enhanced defence to the BX-conditioned soil microbiome, and we found that this simultaneous increase of growth and defence was mediated by priming of the defences. Further advancing our basic understanding of how plants respond to soil microbiomes and mediate their feedbacks is particularly important for the goal to improve crops so they can benefit from their soil microbiome.}, }
@article {pmid41846281, year = {2026}, author = {Clarke, C and Banasik, M and Juodeikis, R and Warren, MJ and Pickersgill, RW}, title = {Evolutionarily divergent DUF4465 domains have a common vitamin B12-binding function.}, journal = {FEBS open bio}, volume = {}, number = {}, pages = {}, doi = {10.1002/2211-5463.70231}, pmid = {41846281}, issn = {2211-5463}, support = {Grant BB/X001946/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The DUF4465 family (DUF, domain of unknown function) contains more than 1000 members distributed across eight bacterial clades with species from diverse microenvironments including various gut microbiomes, hydrothermal vents, and soil. In the gut commensal Bacteroides thetaiotaomicron (B. theta), DUF4465 containing proteins act as high-affinity B12-binding proteins that scavenge this cofactor to ensure bacterial survival. Such B12 capture is essential for bacteria that have lost the ability to synthesize B12 de novo. This raises the question of whether B12-binding is ubiquitous across this family of proteins. Here, we show that B12-binding is a recurrent function of eight distantly related members of the DUF4465 family. It is reasonable to conclude that B12-binding is a common function of most DUF4465 proteins. These results establish DUF4465 as a structurally conserved family of augmented β-jellyroll B12-binding proteins with widespread roles in microbial competition for this essential cofactor. Impact statement DUF4465 defines a widespread, structurally conserved bacterial cobalamin-binding domain and provides a promising scaffold for protein-based B12 capture and purification.}, }
@article {pmid41846394, year = {2026}, author = {Müller, T and Kohlhepp, W}, title = {Advances in the pharmacological management of early motor manifestations of Parkinson's disease (PD).}, journal = {Expert review of neurotherapeutics}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/14737175.2026.2645845}, pmid = {41846394}, issn = {1744-8360}, abstract = {INTRODUCTION: Parkinson's disease (PD) is a heterogeneous, chronic neurodegenerative disorder. Once the diagnosis is made, symptomatic dopamine substituting therapy is initiated.<br><br>AREAS COVERED: This narrative review discusses exemplary past and recent failed attempts.<br><br>EXPERT OPINION: The diagnosis of PD at the onset of motor symptoms is already late in terms of disease progression. An easy-to apply, reliable, sensitive diagnostic biomarker for predictive screening is currently outstanding. Nevertheless, the ability to delay progression and/or cure of the disease is currently the greatest unmet need. Chronic neurodegenerative processes arise from various distinct yet interconnected metabolic and pathological cascade sequences that work together. The translation of promising treatments concepts for beneficial disease modification has failed once they were tested in levodopa-naive patients. Microbiome alteration with short fatty acids or acetyl-DL-leucine supplementation, only enhance levodopa efficacy, But do not modify disease progression in a benefical way. Presently, there is also a lack of real innovation in terms of dopamine substitution.}, }
@article {pmid41846613, year = {2026}, author = {Mura, JD and Kaundal, A and Vashisth, T and Nimmakayala, P}, title = {Editorial: Isolation, identification, characterization, and utilization of beneficial microbes for crop improvement.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1792485}, doi = {10.3389/fpls.2026.1792485}, pmid = {41846613}, issn = {1664-462X}, }
@article {pmid41846864, year = {2026}, author = {Váradi, M and Magyar, B and Széles, &#xc1; and Korda, S and Németh, B and Simon, B and Reis, H and Oláh, C and Horváth, O and Dér, B and Nyirády, P and Szarvas, T}, title = {Prognostic and predictive factors of immune checkpoint inhibitor therapy in urinary bladder cancer.}, journal = {Pathology oncology research : POR}, volume = {32}, number = {}, pages = {1612333}, pmid = {41846864}, issn = {1532-2807}, mesh = {Humans ; *Urinary Bladder Neoplasms/drug therapy/pathology/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; Prognosis ; *Biomarkers, Tumor ; Immunotherapy/methods ; B7-H1 Antigen ; }, abstract = {Immune checkpoint inhibitor (ICI) therapy has become a firmly integrated component of the systemic treatment repertoire for locally advanced and metastatic urothelial bladder cancer (UBC). Over the past decade, multiple ICIs have demonstrated meaningful clinical activity, and their indications have expanded across treatment lines, including second-line therapy after platinum, first-line therapy for cisplatin-ineligible disease, avelumab maintenance following chemotherapy, and, more recently, combination strategies such as pembrolizumab plus enfortumab vedotin. Despite these advances, patient responses to ICIs remain highly heterogeneous. While a subset of patients achieves substantial tumor regression and long-term survival, a considerable proportion derives little or no benefit. The rapidly evolving therapeutic landscape - encompassing antibody-drug conjugates, targeted agents, and perioperative ICI approvals - further emphasizes the need to identify which patients are most likely to respond to immunotherapy. Given the marked variability in therapeutic sensitivity and the increasing availability of alternative effective treatments, accurate prediction of ICI efficacy is becoming increasingly crucial for personalized treatment selection. In this review, we provide a comprehensive overview of currently established and emerging biomarkers of ICI response in UBC, including PD-L1 immunohistochemistry, serum inflammatory markers, tumor mutational burden, histology and molecular subtypes, gene expression patterns and microbiome features. We discuss their strengths, limitations, and potential translational relevance, highlighting ongoing challenges and future directions.}, }
@article {pmid41846867, year = {2025}, author = {Hu, C and Wang, S and Gao, Z and Qing, M and Tan, L and Yang, L and Li, F}, title = {Curcumin in oral health: mechanisms, clinical evidence, and delivery strategies.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1661443}, pmid = {41846867}, issn = {1663-9812}, abstract = {Curcumin, a polyphenolic compound derived from the turmeric rhizome (Curcuma longa), has attracted significant interest in dentistry and oral medicine because of its multifaceted therapeutic properties. In particular, curcumin exhibits potent anti-inflammatory, antioxidant, and antimicrobial activities that are relevant to a wide spectrum of oral diseases. We conducted a narrative search of PubMed (2000-2025) using iterative keyword combinations related to curcumin and oral diseases/mechanisms, screened reference lists, and selected studies on the basis of their relevance to oral pathobiology, delivery systems, and clinical/translational outcomes. This narrative review summarized the current knowledge concerning the molecular mechanisms of curcumin and its clinical applications in oral health. We outlined how curcumin modulates key inflammatory pathways and oxidative stress responses, and how it exerts broad-spectrum antimicrobial effects against oral pathogens. We detailed the efficacy of curcumin in specific oral conditions, including periodontal diseases, dental caries, recurrent aphthous stomatitis, oral lichen planus, oral submucous fibrosis, oral candidiasis, radiation/chemotherapy-induced oral mucositis, and oral cancers. In each context, we highlighted evidence from in vitro studies, animal models, and clinical trials, and noted the benefits of curcumin, such as reduced inflammation, enhanced healing, microbial inhibition, and in some cases outcomes comparable to those of standard therapies. Across conditions, curcumin shows adjunctive benefit: In periodontal disease, it reduces plaque and gingival inflammation comparable to chlorhexidine and improves probing outcomes when added to scaling and root planing; in recurrent aphthous stomatitis, it reduces pain and ulcer size with steroid-like efficacy; in radiotherapy/chemotherapy-induced oral mucositis, it delays onset and decreases severity; in oral candidiasis, it decreases fungal burden and enhances photodynamic therapy; and in oral squamous cell carcinoma early clinical studies show modulation of inflammatory cytokines and the oral microbiome. Various delivery systems developed to overcome the poor bioavailability of curcumin-from mouthwashes and gels to nanocarriers and mucoadhesive formulations-are reviewed. Although many studies reported promising results with minimal toxicity or side effects, there were study limitations such as small sample sizes, variability in formulations, and the pharmacokinetic properties of curcumin. Overall, the reviewed data support the role of curcumin as a safe, formulation-dependent adjunct-not a stand-alone therapy-in oral medicine.}, }
@article {pmid41846893, year = {2026}, author = {Bautista, J and Cortiñas Sardi, P and Paguay-Caisabanda, I and Gancino-Guevara, K and López-Cortés, A}, title = {Integrating microbiome insights into cervical cancer.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1766052}, pmid = {41846893}, issn = {2296-858X}, abstract = {Cervical cancer is largely preventable, yet it continues to cause substantial morbidity and mortality worldwide, particularly in regions with limited access to human papillomavirus (HPV) vaccination and screening. Persistent infection with high-risk HPV genotypes, especially HPV-16 and HPV-18, represents the primary initiating event in cervical carcinogenesis. However, viral infection alone does not fully explain why only a subset of infected individuals develop high-grade lesions or invasive disease. Recent longitudinal and mechanistic studies indicate that the cervicovaginal microbiome plays an important modulatory role by influencing epithelial barrier integrity, local immune responses, and inflammatory homeostasis. This review synthesizes current evidence from multi-omics and translational studies linking cervicovaginal microbial composition and function to HPV persistence, cervical intraepithelial neoplasia (CIN), and cervical cancer progression. Communities dominated by Lactobacillus crispatus are frequently associated with antiviral conditions and mucosal stability, whereas anaerobe-enriched microbial profiles, commonly referred to as community state type IV (CST IV), are associated with chronic inflammation, metabolic dysregulation, and increased lesion severity. Microbial metabolites and inflammatory mediators may interact with HPV oncogene activity and host epigenetic regulation, supporting a microbiome-metabolome-epigenome axis in cervical carcinogenesis. The review also discusses emerging clinical implications, including microbiome-based biomarkers and microbiota-targeted interventions. While early studies suggest potential benefits of probiotics and postbiotics for HPV clearance and immune modulation, current evidence remains limited. Methodological heterogeneity, low-biomass sampling, and population variability continue to restrict causal inference and clinical translation. Addressing these challenges will be essential for integrating microbiome-informed strategies into cervical cancer prevention and management.}, }
@article {pmid41846999, year = {2026}, author = {Mechan-Llontop, ME and Nauta, KM and Gates, DR and Wang, X and Cooper, J and Burton, NO}, title = {Bacterial pyruvate metabolism regulates host insulin sensitivity in C. elegans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.04.709558}, pmid = {41846999}, issn = {2692-8205}, abstract = {Two different individuals can consume an identical diet but experience different physiological outcomes. While there are many potential mechanistic reasons for this, one increasingly recognized reason is that differences in an animal's microbiome can lead to differences in the processing of dietary nutrients. Thus, though a diet might start out the same, how it is experienced by a host is dependent on their microbiome. While exciting, mechanistic studies of diet-microbiome-host effects are often limited by the lack of high throughput laboratory techniques to identify and define interactions between dietary metabolites, microbial metabolism, and host biology. We hypothesized that the model organism Caenorhabditis elegans is an advantageous animal model for rapidly identifying and genetically dissecting interactions between dietary nutrients, microbial metabolism, and host physiology. Here, we used an established model of the effects of dietary glucose on insulin resistant mutant animals (daf-2 /IR mutants) to study how differences in bacterial metabolism influence the consequences of dietary sugars on animal physiology. We found that the effect of dietary sugars on daf-2 mutant physiology is dependent on how the microbiome metabolizes dietary sugars. We found dietary sugar suppresses multiple daf-2 mutant phenotypes in the presence of some bacteria but has no effect in the presence of others. To determine how bacteria mediate the effects of dietary sugars on host physiology we screened 5,000 transposon mutations in the canonical C. elegans dietary bacteria, E. coli OP50 for effects on animal insulin signaling. From this, we found that the effects of exogenous sugars on the phenotype of daf-2 mutant animals is dependent on the function of pyruvate dehydrogenase in bacteria and that the loss of bacterial pyruvate dehydrogenase genes (ex. aceE) is sufficient to mimic the effects of dietary sugars on dauer formation, longevity, and gene expression in insulin signaling deficient animals. Collectively, our findings further support the growing body of evidence that the effects of dietary nutrients on animal physiology can be influenced by the gut microbiome. In addition, these studies demonstrate the advantages of the C. elegans model system for studying 3-way diet-microbiome-host interactions that are difficult to dissect in other model systems.}, }
@article {pmid41847005, year = {2026}, author = {Azamar, KMM and Rajesh, K and Downing, B and Javith, M and Yamhure, I and Porras, AM}, title = {Comparative Genomic and Functional Profiling of ECM-Targeting Enzymes in Bacteroides , a Key Genus of the Human Gut Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.04.709643}, pmid = {41847005}, issn = {2692-8205}, abstract = {UNLABELLED: Purpose The human extracellular matrix (ECM) provides essential cues for intestinal homeostasis. While most studies focus on ECM degradation by host cells, our prior work suggests that commensal gut microbes may also contribute to these remodeling processes. Here, we continue exploring this novel dimension of host-microbe interactions by profiling the proteolytic diversity and substrate-specific activity of ECM-targeting enzymes across species of Bacteroides, a dominant and metabolically versatile gut genus.<br><br>METHODS: We curated a custom ECM-specific enzyme database from the BRENDA repository and used it to perform comparative genomic analyses across 11 Bacteroides species, mapping the diversity and abundance of candidate ECM-degrading proteases and carbohydrate active enzymes (CAZymes). Functional activity was evaluated via in vitro degradation assays using purified substrates. Family-specific protease inhibitors were used to confirm the major catalytic classes involved.<br><br>RESULTS: ECM-targeting CAZymes and proteases were broadly encoded across all 11 genomes, with gene counts positively correlated with genome size and GAG-associated genes comprising the largest substrate category. Experimental degradation assays revealed species- and substrate-specific activity patterns, including elastin degradation restricted to a subset of species, a capacity previously undocumented in intestinal Bacteroides . Genomic predictions showed limited concordance with measured enzymatic activity, suggesting context-dependent regulation of ECM-degrading enzymes. Inhibitor experiments confirmed that collagen degradation is driven primarily by metalloproteases and secondarily by serine proteases across representative species.<br><br>CONCLUSIONS: Our findings position commensal Bacteroides as a rich, yet underappreciated, source of ECM-degrading enzymes. This work underscores the need to consider microbiota as key modulators of host tissue homeostasis and potential targets for therapeutic modulation.<br><br>BIOGRAPHY: Dr. Ana Maria Porras is an Assistant Professor of Biomedical Engineering at the University of Florida, where she leads the Tissue-Microbe Interactions lab. Her group leverages cell and tissue engineering, bioinformatics, and statistical modeling to understand how microorganisms regulate human extracellular matrix remodeling. Her work centers primarily on the gut microbiome, cardiovascular health, and tropical infectious diseases. Dr. Porras is also a science artist, and a science communicator, particularly in interested in evidence-based, culturally informed, and multilingual practices to improve public engagement with science. She is the co-founder and Senior Advisor of the Latinx in Biomedical Engineering community, and the recipient of multiple awards, including the UF Excellence Award for Assistant Professors, the NSF Faculty Early Career Development (CAREER) Award, the NIH Maximizing Investigators Research Award (MIRA), the AAAS Early Career Award for Public Engagement with Science, and and the Rising Star Award from the Academy of Science, Engineering, and Medicine of Florida. Prior to arriving in Florida, Dr. Porras was a Presidential Postdoctoral Fellow at Cornell University. She holds a B.S. in biomedical engineering from the University of Texas at Austin, and a Ph.D. from the University of Wisconsin-Madison, where she was an American Heart Association Predoctoral Fellow.}, }
@article {pmid41847008, year = {2026}, author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR}, title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.06.710096}, pmid = {41847008}, issn = {2692-8205}, abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA) , which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.}, }
@article {pmid41847165, year = {2026}, author = {Khanna, S}, title = {Specialty grand challenge in gastrointestinal infections.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {5}, number = {}, pages = {1808344}, pmid = {41847165}, issn = {2813-1169}, }
@article {pmid41847176, year = {2026}, author = {Gu, Z and Zhang, M and Shen, F and Chen, J and Gu, Y and Gong, Y and Xue, Q and Zhou, H and Liu, Y and Shao, S and Zhang, Y and Bai, J and Hua, K and Zhou, G and Ding, J}, title = {The Role of Bacterial Outer Membrane Vesicles in Tumor Development: Facts, Potential Applications and Future Perspectives.}, journal = {International journal of nanomedicine}, volume = {21}, number = {}, pages = {582600}, pmid = {41847176}, issn = {1178-2013}, mesh = {Humans ; *Neoplasms/therapy/pathology/immunology ; *Bacterial Outer Membrane/chemistry/metabolism ; Animals ; Tumor Microenvironment ; Antineoplastic Agents ; Epithelial-Mesenchymal Transition ; }, abstract = {Bacterial outer membrane vesicles (OMVs), nanosized lipid bilayer particles released by both Gram-negative and Gram-positive bacteria, are emerging as crucial mediators of host-microbe interactions in cancer biology. This review synthesizes current evidence on how OMVs modulate tumor initiation, progression, and therapeutic responses through multifaceted mechanisms aligned with the 14 hallmarks of cancer. Studies demonstrate that OMVs can either promote or inhibit neoplastic processes depending on their bacterial origin and cargo composition. Tumor-promoting OMVs enhance proliferative signaling, drive epithelial-mesenchymal transition, facilitate metastatic dissemination via barrier disruption and angiogenesis, and weaken antitumor immunity. Conversely, other OMVs exert antineoplastic effects by triggering intrinsic apoptosis, cell-cycle arrest, immunogenic cell death, and remodeling of the tumor immune microenvironment. Pre-clinical studies further highlight the translational potential of engineered OMVs as precision nano-vaccines, immunotherapeutic agents, and adjuvants that synergize with immune checkpoint blockade, chemotherapy, or photothermal therapy while minimizing systemic toxicity. Future directions could focus on mapping of OMV cargo-pathway-phenotype networks by multidisciplinary methods, programmable vesicle design using synthetic biology, and real-time microbiome-OMV monitoring in early-phase clinical trials to enable individualized onco-therapeutics. Collectively, OMVs represent a versatile platform to bidirectionally regulate oncogenesis and therapeutic responses. Exploiting their molecular plasticity through rational engineering and precision medicine frameworks would bring transformative potential for cancer prevention, diagnosis, and treatment.}, }
@article {pmid41847216, year = {2026}, author = {Shi, H and Huang, L and Zhang, JH and Shen, C and Zhang, N and Lv, C and Shao, L and Li, M and Sun, Z and Shi, L and Yu, G and Chen, Y}, title = {Gut Microbiota Regulates Brain-Bone Axis to Influence Osteoporosis Pathogenesis and Treatment.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1178}, pmid = {41847216}, issn = {2639-5274}, abstract = {Osteoporosis is a systemic skeletal disorder characterized by reduced bone mass, impaired microarchitecture, and increased fracture risk, primarily resulting from dysregulated bone remodeling. Increasing evidence highlights a close interaction between bone metabolism and the gut microbiota. Alterations in bone mineral density can influence gut microbial composition. Conversely, microbial dysbiosis disrupts bone homeostasis through multiple pathways, including microbial metabolites, immune regulation, and neuroendocrine signaling. Short-chain fatty acids suppress osteoclast differentiation and enhance intestinal calcium absorption, while gut dysbiosis promotes bone loss by impairing intestinal barrier integrity and increasing proinflammatory cytokines such as tumor necrosis factor-α and interleukin-6. The gut-brain-bone axis represents an important regulatory network linking the central nervous system, gut-derived signals, and skeletal remodeling. Chronic stress and neurodegenerative conditions activate the hypothalamic-pituitary-adrenal axis and bone-derived extracellular vesicle signaling, thereby favoring bone resorption. Estrogen deficiency further disrupts the receptor activator of nuclear factor κΒ ligand/osteoprotegerin signaling pathway and alters gut microbial composition, contributing to postmenopausal bone loss. Therapeutic strategies targeting this axis, including probiotics, prebiotics, fecal microbiota transplantation, dietary fiber supplementation, and pharmacological or natural compounds, show potential in restoring microbial balance and improving bone metabolism. Future studies integrating multiomics approaches and well-designed clinical trials are needed to clarify microbiome-bone interactions and support the development of targeted interventions for osteoporosis.}, }
@article {pmid41847367, year = {2026}, author = {Park, S and Yang, J and Lee, SH and Jeong, J and Jang, JY and Barrila, J and Yang, JY}, title = {Cross-cohort meta-analysis reveals conserved gut microbiome signatures of insomnia.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100577}, pmid = {41847367}, issn = {2666-5174}, abstract = {Insomnia is a prevalent sleep disorder associated with broad metabolic, immune, and neuropsychiatric consequences, yet its association with the gut microbiome remains difficult to define across individuals. Here, we performed a cross-cohort meta-analysis of five publicly available human fecal 16S rRNA case-control datasets to identify conserved microbiome features associated with insomnia. All raw sequencing data were reprocessed using a unified analytical workflow, generating a harmonized cohort of 468 individuals while controlling for cohort-specific effects. Across cohorts, insomnia was associated with directionally consistent differences in gut microbiome structure, including a statistically significant increase in Shannon diversity (p = 0.003) and a significant group effect after covariate adjustment. Integrating four complementary statistical approaches, we identified a core set of eight gut taxa that were consistently associated with insomnia across analyses. Functional prediction and integrative filtering indicated that insomnia-related microbial changes extended beyond taxonomy, with coordinated shifts in metabolic potential encompassing pathways previously linked to host immune and neurobiological processes, thereby suggesting relevance to biological systems implicated in sleep regulation. Notably, these functional alterations were concentrated within a limited subset of taxa rather than broadly distributed across the community. Among them, the Burkholderia-Caballeronia-Paraburkholderia complex emerged as a dominant functional contributor. Independent correlation analyses validated key taxon-function relationships and reinforced a model of focused, pathway-specific microbiome remodeling. Together, these findings demonstrate that insomnia is associated with a reproducible gut microbiome signature characterized by targeted functional remodeling driven by specific microbial taxa. This study provides a cross-cohort framework for investigating microbiome-mediated metabolic and immune contexts relevant to sleep regulation.}, }
@article {pmid41847441, year = {2026}, author = {Yu, Z and Cai, S and Shen, Z and Chen, G and Chen, Y and Liu, Y and Zhong, X}, title = {Bibliometric analysis of the trends in research on the link between gut microbiota and pancreatic cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1623945}, pmid = {41847441}, issn = {2235-2988}, mesh = {*Pancreatic Neoplasms/microbiology/etiology ; *Gastrointestinal Microbiome ; Humans ; *Bibliometrics ; *Biomedical Research/trends ; }, abstract = {BACKGROUND: Pancreatic cancer (PC) is a highly prevalent and aggressive malignancy of the digestive system, characterized by notably low survival rates. Recently, the influence of gut microbiota (GM) on the development and progression of PC has gained more attention. While the only existing bibliometric study has explored the association of GM in PC, it has failed to adequately reflect the latest trends and hotspots in this field due to research timeframes and methodologies.<br><br>METHODS: Publications from January 1, 2000 to November 18, 2023 were collected from the Web of Science Core Collection (WoSCC) and screened based on specific criteria. Various software tools, including VOSviewer, Scimago Graphica, R, Pajek64 and Cite Space, were employed in this bibliometric study to visualize research trends and hot spots concerning the relationship between GM and PC.<br><br>RESULTS: This study analyzed 763 publications, including 397 articles and 366 reviews, on the relationship between GM and PC. The number of Publications has steadily increased since 2013, with China and the USA leading in contribution. The journal Cancers published the most papers (37), while Gut had the highest average citations (136.83). The most productive institution was SUTMD Anderson Cancer Center, and the top 3 authors were Michaud, Dominique S. McAllister, Florencia, and Miller, George. Keyword analysis revealed that "Gut Microbiota", "Pancreatic Cancer", "Cancer", "Sequence", "Microbiome" and "Tumor Microbiome" are the most frequent terms, highlighting key research trends.<br><br>CONCLUSIONS: Over the past two decades, interest in the relationship between GM and PC has significantly increased. The comprehensive bibliometric analysis offers an in-depth evaluation of the prevailing research trends and advancements regarding the relationship between GM and PC. It indicates that current research hotspots mainly focus on "sequencing", "microbiomes" and "tumor microbiomes".}, }
@article {pmid41847555, year = {2026}, author = {Tyborski, N and Koehler, T and Steiner, FA and Tung, SY and Wild, AJ and Pausch, J and Lueders, T}, title = {Breeding effects on the root-associated microbiome of Zea mays L. are linked to plant-induced variation in soil water potentials.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag033}, pmid = {41847555}, issn = {2730-6151}, abstract = {Modern crop varieties may exert reduced influence on their microbiome compared to their progenitors, as plant-microbe interactions were not targeted during breeding. Moreover, formerly beneficial microbiome functions might no longer be relevant in modern agricultural ecosystems. We hypothesised that such patterns could become particularly evident under drought, since drought-tolerance has not been a primary breeding target. To test this, we grew six maize landraces (released before 1945) and six modern varieties (released from 2010 onwards) in a field under ambient and 60% reduced precipitation. The experiment was repeated over two years, differing in amounts and temporal distributions of precipitation. We assessed the composition of root-associated prokaryotic communities during grain filling by 16S rRNA gene metabarcoding. Intra-variety dispersion in microbiome composition relative to plant biomass-based dispersion was higher in modern varieties, suggesting breeding may have affected plant control over microbiomes. Besides that, shifts in microbiome composition between landraces and modern varieties were driven mainly by the plants' impact on soil water potentials. Consequently, the taxa that increased in relative abundance during soil drying, mainly Actinomycetota, were similar between landraces and modern varieties. Exploring microbiome-mediated alleviation of drought effects, therefore, appears promising also for applications in modern agricultural ecosystems. Specifically, filamentous Streptomyces spp. potentially contributed to soil aggregate stability, which should be further investigated in the context of drought mitigation. The reduced plant control over microbiome composition of modern varieties suggested by dispersion analysis likely has functional implications beyond microbiome adaptation to drought and should be considered in future assessments of breeding.}, }
@article {pmid41847618, year = {2026}, author = {You, Y and Cui, Y and Zheng, K and Yang, H and Yu, C and Wang, Q and Chen, Y and Ma, X}, title = {Oral microbiome diversity shapes the association between leisure-time physical activity and cognitive function among older adults.}, journal = {iScience}, volume = {29}, number = {3}, pages = {115086}, pmid = {41847618}, issn = {2589-0042}, abstract = {Regular leisure-time physical activity and the composition of the oral microbiome may influence late-life cognition, but their combined effects are unclear. We studied 575 US adults aged 60-69 years from a nationally representative survey with oral microbiome sequencing, self-reported leisure-time physical activity, and four standard cognitive tests of memory, verbal fluency, and processing speed. Higher weekly physical activity and meeting current guideline levels were associated with better memory and processing speed scores after multivariable adjustment. Greater oral microbiome diversity, including higher richness and evenness, was also related to better processing speed. Among participants who met activity guidelines, those with intermediate to high Shannon diversity and a specific community composition profile showed the most favorable verbal fluency and processing speed. These findings suggest that maintaining both regular physical activity and a diverse oral microbiome may jointly support cognitive function in later life and promote healthy aging.}, }
@article {pmid41847619, year = {2026}, author = {Mousavi, SM and Roayaei Ardakani, M and Galehdari, H and Dorostghoal, M}, title = {Integrated multi-omics profiling of gut microbiome and metabolome in ulcerative colitis insights from the Iranian population.}, journal = {iScience}, volume = {29}, number = {3}, pages = {114721}, pmid = {41847619}, issn = {2589-0042}, abstract = {Ulcerative colitis is a chronic inflammatory disorder of the gastrointestinal tract associated with substantial alterations in gut microbial composition and metabolic function. This study investigated intestinal dysbiosis in affected individuals using microbial profiling, genetic analysis, metabolomic assessment, and pathway modeling. Patients showed reduced microbial diversity, loss of beneficial species such as Faecalibacterium and Roseburia, and increased abundance of inflammatory taxa, including Escherichia coli and Fusobacterium, alongside a marked decrease in the Firmicutes-to-Bacteroidetes ratio. Levels of key short-chain fatty acids, particularly butyrate, and protective metabolites such as indole-3-propionic acid were diminished, whereas pro-inflammatory metabolites, including sphingosine, were elevated. Pathway analysis indicated disruptions in tryptophan metabolism and short-chain fatty acid biosynthesis, and species-metabolite networks highlighted antagonistic relationships between inflammatory bacteria and protective metabolites. These findings reveal extensive structural and functional dysbiosis and underscore the potential of microbiome-based therapeutic strategies for managing ulcerative colitis.}, }
@article {pmid41847847, year = {2026}, author = {Glowacki, RWP and Till, JM and Brock, OD and Makarov, V and Engelhart, MJ and Ahern, PP}, title = {Strain-level antigen variation facilitates immune evasion in Bacteroides thetaiotaomicron.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {215}, number = {3}, pages = {}, doi = {10.1093/jimmun/vkaf333}, pmid = {41847847}, issn = {1550-6606}, support = {LRP0000016021/NH/NIH HHS/United States ; LRP0000045724/NH/NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Immune Evasion/immunology ; *Bacteroides thetaiotaomicron/immunology/genetics ; *CD4-Positive T-Lymphocytes/immunology ; Mice, Transgenic ; *Antigens, Bacterial/immunology/genetics ; *Antigenic Variation/immunology ; Receptors, Antigen, T-Cell/immunology/genetics ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/immunology ; Epitopes, T-Lymphocyte/immunology ; }, abstract = {The T cell receptor (TCR) repertoire of intestinal CD4+ T cells is enriched for specificity towards microbiome-encoded epitopes shared among many microbiome members, providing broad microbial reactivity from a limited pool of cells. These cells actively coordinate mutualistic host-microbiome interactions, yet many epitopes are shared between gut symbionts and closely related pathobionts and pathogens. Given the disparate impacts of these agents on host health, intestinal CD4+ T cells must maintain strain-level discriminatory power to ensure protective immunity while preventing inappropriate responses against symbionts. However, to date, the mechanisms by which this occurs have remained enigmatic. To interrogate this, we leveraged BθOM mice that express a transgenic TCR specific for a BT4295-encoded epitope in B. thetaiotaomicron. While many B. thetaiotaomicron strains potently activated BθOM CD4+ T cells in vitro, strain dnLKV9 escaped recognition. Bioinformatic analyses uncovered two BT4295 homologs in B. thetaiotaomicron-dnLKV9, with each homolog harboring sequence modifications relative to strain VPI-5482, specifically, a premature stop codon, and a T548S substitution within the epitope. Reconstruction of these variants in B. thetaiotaomicron-VPI-5482ΔBT4295 conferred evasion from BθOM CD4+ T cells in vitro to this otherwise permissive strain. Adoptive transfer of BθOM CD4+ T cells to gnotobiotic RAG1-/- colonized with B. thetaiotaomicron harboring these variant BT4295 forms verified the sufficiency of these antigen modifications for evasion of BθOM CD4+ T cells. Collectively, these data uncover the existence of strain-level immune evasion in B. thetaiotaomicron and reveal a mechanism whereby strains evade recognition by CD4+ T cells, facilitating strain-level discrimination in responsiveness to the microbiome.}, }
@article {pmid41847896, year = {2026}, author = {Kirti, P and Eghtesady, P and Garand, M}, title = {AxioParse: streamlining Axiom Microbiome assay data processing and dataset generation.}, journal = {BioTechniques}, volume = {78}, number = {1-12}, pages = {93-97}, doi = {10.1080/07366205.2026.2644218}, pmid = {41847896}, issn = {1940-9818}, mesh = {*Microbiota/genetics ; *Software ; *Computational Biology/methods ; Bacteria/genetics/classification ; Humans ; }, abstract = {The Applied Biosystems Axiom Microbiome Array enables high-throughput detection of bacteria, archaea, viruses, protozoa, and fungi across multiple samples. However, its native software outputs are not compatible with common downstream analysis tools, requiring preprocessing. We identified a lack of open-source pipelines tailored to these outputs. To address this gap, we developed AxioParse, a Python-based pipeline built with the Dagster orchestration framework that automates data cleaning, taxonomic mapping, and formatting for downstream analysis. AxioParse reduces manual processing and generates datasets compatible with platforms such as QIIME2 and R, improving reproducibility and facilitating broader use of the Axiom Microbiome Array in microbiome research (https://github.com/Eghtesady-Lab-Bioinformatics/axioparse).}, }
@article {pmid41847967, year = {2026}, author = {Huang, C and Sáez-Sandino, T and Zhou, G and Zhou, L and Kong, T and Fu, Y and Chen, H and Zhu, Y and Qiu, S and Xue, K and Fan, C and Cao, L and Wu, C and He, Y and Zhou, X}, title = {Warming-Induced Carbon Vulnerability in Permafrost Forests: A Shift in Q10 From Continuous to Discontinuous Zones.}, journal = {Global change biology}, volume = {32}, number = {3}, pages = {e70787}, doi = {10.1111/gcb.70787}, pmid = {41847967}, issn = {1365-2486}, support = {32241032//National Natural Science Foundation of China/ ; 32271713//National Natural Science Foundation of China/ ; ZD2021C002//Natural Science Key Foundation of Heilongjiang Province/ ; }, mesh = {*Permafrost/chemistry ; *Forests ; *Soil Microbiology ; *Carbon/metabolism/analysis ; Microbiota ; *Global Warming ; Temperature ; *Climate Change ; }, abstract = {Permafrost forests harbor vast, climate-sensitive carbon (C) reservoirs whose vulnerability largely depends on temperature sensitivity of microbial respiration (Q10). However, substantial uncertainties persist in predicting Q10 patterns due to complex interactions among multiple ecological factors. Here, we conducted a standardized field survey with controlled incubations across a regional gradient from continuous permafrost (CP) and discontinuous permafrost (Dis-CP, including sporadic and isolated ones) in the Greater Khingan Mountains to quantify Q10 values and identify their main ecological controls. We found that the Q10 values were significantly higher in CP than Dis-CP forests, indicating a stronger microbial respiratory response to warming in the coldest permafrost regions. Statistical analysis revealed that the soil microbiome was the most important factor explaining Q10 values in CP forest (47.8%), whereas a distinct set of factors (plant production, fine texture, substrate quality, and mean annual ground temperature) explained the largest proportion (63.2%) of Q10 variation in Dis-CP forests. Our findings suggest that warming-induced permafrost degradation is likely to shift the dominant controls for Q10 from microbial community to abiotic and plant-related factors, while enhancing greenhouse gas emissions from permafrost soils.}, }
@article {pmid41848094, year = {2026}, author = {Huang, Y and Liao, Y and Yang, Z and Fu, X}, title = {Beneath the Surface: Root Metabolites Driving Shoot Agronomic Traits in Tea Plant (Camellia sinensis L.).}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c12265}, pmid = {41848094}, issn = {1520-5118}, abstract = {While tea quality traits are largely attributed to leaf-derived metabolites, the role of roots in determining tea (Camellia sinensis L.) productivity and quality has been relatively understudied. Tea roots are central to nitrogen assimilation, carbohydrate storage, and phytohormone biosynthesis, thereby influencing shoot development and environmental responses. Although recent efforts have focused on identifying key genes coordinating quality, yield, and stress resilience, the long lifespan of tea plants limits the practicality of genetic replacement in mature plantations. This review instead emphasizes agronomic and environmental regulation of root metabolites as an alternative approach for enhancing plant performance. Based on the findings (including multiomics studies) about root metabolites and their effects on aboveground traits, we propose a rhizosphere-to-canopy optimization framework incorporating microbiome modulation, nutrient management, and precision agronomy. Root-centered interventions represent a promising, sustainable approach to enhance tea quality, yield, and stress tolerance without replacing established cultivars.}, }
@article {pmid41848103, year = {2026}, author = {Leal, M and Beukes, J and Alcock, S and Thompson, U and Norris, SA}, title = {Antibiotic overuse as a modifiable early-life risk factor for non-communicable diseases in sub-Saharan Africa.}, journal = {Global health action}, volume = {19}, number = {1}, pages = {2646042}, doi = {10.1080/16549716.2026.2646042}, pmid = {41848103}, issn = {1654-9880}, mesh = {Humans ; Africa South of the Sahara/epidemiology ; *Noncommunicable Diseases/epidemiology/prevention &amp; control ; *Anti-Bacterial Agents/adverse effects/therapeutic use/administration &amp; dosage ; Risk Factors ; Infant ; Child, Preschool ; Infant, Newborn ; *Prescription Drug Overuse ; }, abstract = {Early-life antibiotic overuse is a public health concern. In low- and middle-income countries, consumption has surged by 76% since 2000. This trend is particularly acute in sub-Saharan Africa (SSA), where antimicrobial resistance contributes to 255,000 deaths annually and infant antibiotic exposure is widespread in the first two years of life. While a substantial body of research associates antibiotic-induced microbiome disruption with metabolic and immune dysregulation, with large cohorts reporting ~20% higher odds of childhood obesity and asthma, these observational findings do not establish causality and derive largely from high-income settings. This potential pathway remains a policy blind spot within most non-communicable disease (NCD) prevention frameworks. By synthesising biological, epidemiological and implementation evidence, this paper considers early-life antibiotic exposure as a potentially modifiable determinant of lifelong health and outlines a pragmatic research and policy agenda to integrate antibiotic-aware prevention into NCD prevention efforts and routine child health platforms in resource-limited SSA settings.}, }
@article {pmid41848207, year = {2026}, author = {Pearson, AC and Barreñada, O and Brieño-Enríquez, MA}, title = {Could the naked mole-rat become the new standard for studying human gut health and probiotics?[†].}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.70049}, pmid = {41848207}, issn = {1096-9896}, support = {1R01HD116853-01A1//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; //Magee-Womens Research Institute/ ; /NH/NIH HHS/United States ; }, abstract = {The naked mole-rat (NMR; Heterocephalus glaber) is a subterranean rodent native to the arid regions of the Horn of Africa. The NMR is the longest-lived rodent and is known for its distinctive physiological and social traits. This species has become a notable model organism for studying aging, cancer biology, behavioral ecology, and reproduction. Recently, NMRs have gained attention because their gastrointestinal tract features an exceptionally strong intestinal barrier, a large number of goblet cells, a thicker mucin layer, and reduced gut permeability. The NMR gut microbiome, similar to that observed in human centenarians, is highly diverse and characterized by a high microbial load. In fact, Hart et al (2026) demonstrated that spontaneous infection with Citrobacter braakii in the NMR causes clinical symptoms and histopathological changes that are very similar to those observed in human colitis. If left untreated, the disease can progress and become fatal. However, probiotic treatment can reverse the clinical and histopathological phenotypes. These findings indicate that, in addition to serving as a powerful model for aging, cancer, and reproduction, the NMR may also serve as a powerful tool for studying human diseases such as gut dysbiosis, gut barrier dysfunction, and colitis. © 2026 The Pathological Society of Great Britain and Ireland.}, }
@article {pmid41848406, year = {2026}, author = {Gajski, G and Szewczyk-Roszczenko, O and Roszczenko, P and Vassetzky, Y and Sjakste, N}, title = {Friends and foes: impact of bacteria on genome stability.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/1040841X.2026.2641726}, pmid = {41848406}, issn = {1549-7828}, abstract = {Bacteria, present in normal conditions in the microbiome or during infections, exert profound effects on genome stability, with both genotoxic and genoprotective consequences. Certain pathogenic bacteria, such as Escherichia coli (colibactin-producing strains), Helicobacter pylori, Fusobacterium nucleatum, and Campylobacter jejuni, induce DNA damage and are implicated in cancer development through direct toxin production, chronic inflammation, immune modulation, and disruption of host cell signaling. Genotoxins such as colibactin, the cytolethal distending toxin, and the typhoid toxin induce DNA double-strand breaks, chromosomal instability, and impair DNA repair pathways, contributing to carcinogenesis. These effects occur upon gastrointestinal, urogenital, systemic (sepsis), and neurological (meningitis) infections, in both humans and animals. Conversely, commensal and probiotic bacteria, notably Lactobacillus and Bifidobacterium species, play a protective role by reducing oxidative DNA damage, modulating immune responses, and enhancing DNA repair. Their beneficial actions are partly mediated by metabolites such as short-chain fatty acids (e.g. butyrate), which influence gene regulation, apoptosis, and mucosal health. Probiotic bacteria can mitigate the genotoxic effects of dietary and bacterial toxins, offering a potential preventive strategy against genome instability and cancer. This review highlights the dualistic nature of bacterial influence on host genome integrity and underscores the importance of maintaining microbial balance.}, }
@article {pmid41848410, year = {2026}, author = {Mercer, SD and Elias, A and Taylor, G and Briggs, GS and Bell, M and McBain, AJ and O'Neill, CA}, title = {Ultraviolet radiation reshapes the metabolome of skin commensal bacteria, influencing AhR signaling and barrier function.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0238525}, doi = {10.1128/aem.02385-25}, pmid = {41848410}, issn = {1098-5336}, abstract = {Ultraviolet radiation (UVR) is an environmental stressor to the skin and its associated microbiota. Many commensal bacteria produce tryptophan-derived metabolites that modulate epidermal barrier function through aryl hydrocarbon receptor (AhR) signaling. However, the effects of UVR on these metabolic outputs and the subsequent effects on skin barrier function remain unclear. This study examined these interactions. Individual skin commensal bacteria were irradiated with 37.5 mJ/cm[2] or 150 mJ/cm[2] of solar-simulated radiation (SSR). Cell-free supernatants (CFSNs) were collected and analyzed for tryptophan metabolites (using LC-MS), untargeted metabolites (using GC-MS), and AhR agonist activity (via a reporter assay). The effects on barrier function were assessed by measuring transepithelial electrical resistance (TEER) of CFSN-treated keratinocyte cultures. Time-course expression of tryptophan-related genes after irradiation was measured by qPCR. Unirradiated bacterial metabolomes were species-specific. Following irradiation, the abundance of metabolites generated by the indole pathway generally increased after 37.5 mJ but decreased following 150 mJ. Untargeted analyses revealed several decreases in amino and organic acid production after high-dose SSR, while 37.5 mJ resulted in fewer changes. Low-dose SSR upregulated genes involved in tryptophan metabolism (ipdC, ALDH) and synthesis (trpE). AhR agonism increased in 8/11 organisms following irradiation, statistically correlating with increased levels of indole-pathway metabolites (indole-3-acetamide, tryptophol, indole-3-carboxaldehyde, and tryptamine). Keratinocytes treated with irradiated Staphylococcus hominis, Micrococcus luteus, and Staphylococcus capitis CFSNs showed enhanced TEER, concurrent with increased AhR activation; inhibition of the AhR removed this effect. UVR significantly alters the metabolomes of skin commensal bacteria, with knock-on effects for AhR signaling and barrier integrity, potentially influencing the skin's response to UVR.IMPORTANCEThe skin and its commensal bacteria are regularly exposed to ultraviolet radiation (UVR). Many skin bacteria generate tryptophan-derived metabolites that influence host physiology through activation of the aryl hydrocarbon receptor (AhR), a key regulator of barrier integrity and stress responses. However, the impact of UVR on the metabolic activity of skin commensals and the downstream consequences for epidermal barrier function remains poorly understood. Here, we show that UVR significantly alters the metabolic outputs of diverse skin commensals, shifting production of indole-pathway metabolites and modulating AhR agonist activity. These changes translated into measurable effects on keratinocyte barrier function, including enhanced transepithelial electrical resistance following UVR exposure. Our findings reveal a previously underappreciated role for bacterial photometabolism in shaping epidermal barrier regulation and host responses to UVR.}, }
@article {pmid41848650, year = {2026}, author = {Thorpe, AC and Busi, SB and Warren, J and Newbold, LK and Taylor, JD and Walsh, K and Read, DS}, title = {River Microbiomes as Sentinels of National-Scale Freshwater Ecosystems.}, journal = {Global change biology}, volume = {32}, number = {3}, pages = {e70809}, pmid = {41848650}, issn = {1365-2486}, support = {SC220034//Environment Agency/ ; NE/X015947/1//Natural Environment Research Council/ ; NE/Z000106/1//Natural Environment Research Council/ ; BB/X011089/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Rivers/microbiology/chemistry ; *Microbiota ; RNA, Ribosomal, 16S/genetics/analysis ; *Ecosystem ; Biofilms ; *Bacteria/classification/genetics ; *Environmental Monitoring/methods ; }, abstract = {Freshwaters face increasing pressures from chemical, hydrological and climatic changes, yet tools for assessing their condition remain limited. River biofilms, composed of diverse microbial communities, integrate environmental signals over space and time, making them sensitive indicators of river health. Using 16S rRNA gene sequencing of more than 1600 biofilms collected across a national river network, we quantified bacterial diversity and community composition and applied network analysis to identify ecologically cohesive sub-communities with keystone taxa underpinning community stability. Alkalinity, dissolved oxygen, nitrate-nitrogen and temperature were among the principal gradients shaping community composition. Threshold indicator analyses identified taxa with breakpoints along these gradients, revealing interpretable ecological thresholds. Our results demonstrate the potential for microbiome-based monitoring frameworks that could complement existing biotic indices, enabling early detection of ecological changes and supporting the integration of genomic indicators into routine ecosystem assessment. This scalable approach offers a powerful strategy for managing freshwaters under accelerating anthropogenic pressures.}, }
@article {pmid41848939, year = {2026}, author = {Liu, W and Bo, X and Cao, Y and Xiao, J and Zhang, R and Liu, H and Chen, D and Geng, Y and Ouyang, P and Huang, X}, title = {Dose-dependent effect of Bacillus subtilis on aquaculture pond ecosystems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41848939}, issn = {1573-0972}, support = {NO: 2025ZNSFSC0275//Natural Science Foundation Project of Sichuan Province Science and Technology Department/ ; }, }
@article {pmid41849207, year = {2026}, author = {El-Malah, SS and Alhaj Sulaiman, A and Jabbar, KA and Prator, CA and Gratalo, D and Goldfarb, D and Mahmoud, KA}, title = {Effect of nucleic acid concentration method on Severe Acute Respiratory Syndrome Coronavirus 2 detection sensitivity in aircraft wastewater.}, journal = {Journal of medical microbiology}, volume = {75}, number = {3}, pages = {}, pmid = {41849207}, issn = {1473-5644}, mesh = {*SARS-CoV-2/isolation &amp; purification/genetics ; *Wastewater/virology ; *Aircraft ; *COVID-19/diagnosis/virology ; Humans ; *RNA, Viral/isolation &amp; purification/genetics/analysis ; Sensitivity and Specificity ; *COVID-19 Nucleic Acid Testing/methods ; }, abstract = {Introduction. Global interconnectedness and rapid urbanization intensify the spread of infectious diseases, underscoring the critical need for effective and scalable surveillance. Wastewater-based epidemiology (WBE) has proven to be a practical and cost-effective approach for monitoring community-level pathogen prevalence, such as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).Hypothesis/Gap Statement. Despite WBE's success in municipal settings, its application to aircraft wastewater remains underexplored. This matrix presents unique analytical challenges due to its high particulate matter, concentrated inhibitory components and variable composition, creating a significant gap in surveillance capabilities.Aim. This study aimed to evaluate and directly compare the performance of two distinct virus concentration techniques - PEG precipitation and Nanotrap[®] Microbiome Particles (NMPs) - for the detection and molecular characterization of SARS-CoV-2 in aircraft wastewater collected from Hamad International Airport.Methodology. Aircraft wastewater samples underwent thermal inactivation and concentration using both the PEG and NMP methods. The resulting extracted RNA was analysed by Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) targeting SARS-CoV-2 genes. All positive samples were subsequently analysed using next-generation sequencing to identify circulating viral variants.Results. The NMPs method detected SARS-CoV-2 RNA in 66.7% of samples, significantly exceeding the 20.8% detection rate achieved with PEG. NMPs also consistently yielded lower cycle threshold (Ct) values, indicating superior viral RNA recovery efficiency. Molecular analysis of positive samples successfully revealed circulating Omicron sublineages (XBB and XBB.1.16), demonstrating the efficacy of aircraft WBE for genomic surveillance.Conclusion. Although PEG precipitation is a cost-effective alternative, its high false-negative rate (72.2%) severely compromises its reliability for surveillance in this matrix. In stark contrast, NMPs proved to be highly sensitive and efficient, making it demonstrably better suited for rapid, large-scale screening. Future strategies could focus on standardized, automated protocols based on high-efficiency methods to enhance early warning and genomic surveillance of emerging pathogens in aviation settings.}, }
@article {pmid41849477, year = {2026}, author = {Cardoso, PHM and Moreno, AM and Nadal, NV and Martins, ML and Balian, SC}, title = {Ornamental coral pests and parasites: a biosecurity alert for aquarium trade.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e303418}, doi = {10.1590/1519-6984.303418}, pmid = {41849477}, issn = {1678-4375}, mesh = {Animals ; *Anthozoa/parasitology ; *Biosecurity ; Coral Reefs ; Pest Control, Biological/methods ; }, abstract = {Aquarium corals have emerged as a relevant sector not only from an economic perspective but also as a tool for ex situ conservation. However, coral pests and parasites, such as flatworms Prosthiostomum acroporae, nudibranchs Phestilla spp., parasitic copepods Tegastes acroporanus, epizoic acoelomorphs Waminoa spp., and histophagous ciliates Philaster spp., pose significant biological and economic risks in captive systems. This review synthesizes current knowledge on major pest groups affecting ornamental corals, emphasizing their life cycles, host specificity, and control strategies. Chemical treatments (e.g., levamisole, praziquantel, KCl, milbemycin, amoxicillin) show partial efficacy, yet many are limited to adult stages and risk disrupting coral microbiota. Biological control using compatible fish and invertebrates offers promise but remains underutilized. Emerging approaches, including probiotics and microbiome engineering, represent future directions for enhancing coral resilience. The aquarium environment acts as a sentinel model, often anticipating disease outbreaks later observed in wild reefs. Simple and low-cost measures, such as quarantining corals for 4 to 6 weeks, conducting visual inspections under adequate lighting, applying preventative baths, removing egg masses, and maintaining stable water quality parameters, are effective and affordable practices for reducing outbreaks in captive environments. In an era of climate change and increasing demand for captive-bred corals, integrating science-based management with aquarist practices is essential. Preventive measures, rapid diagnostics, and biotechnological innovation will be key to ensuring coral health and advancing the aquarium hobby as a tool for marine conservation.}, }
@article {pmid41849696, year = {2026}, author = {Surber, J and Lork, M and Morsy, Y and Scharl, M and Engeler, DS and Langenauer, J and Hefermehl, LJ and Ebner, A and Kaufmann, B and Hunziker, M and Eberli, D and Bieri, U and Poyet, C}, title = {Exploring the Gut-Prostate Axis: Microbial Signatures Linked to Prostate Volume and Bladder Function.}, journal = {The Prostate}, volume = {}, number = {}, pages = {}, doi = {10.1002/pros.70160}, pmid = {41849696}, issn = {1097-0045}, support = {KFS-5308-02-2021-R//Swiss Cancer Research Foundation/ ; }, abstract = {BACKGROUND: Benign prostatic hyperplasia (BPH) is a common urologic condition in aging men, often linked to systemic inflammation and metabolic dysfunction. Emerging evidence suggests that the gut microbiome may contribute to prostate health and disease. Here we aim to explore potential associations between gut microbiota composition and clinical parameters, such as prostate volume (PV) and residual bladder volume (RBV).<br><br>METHODS: This cross-sectional study analyzed stool samples from 28 patients undergoing transurethral surgery. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Patients were stratified into groups based on PV (&#x2009;&#x2264;&#x2009;40&#x2009;mL vs. >&#x2009;40&#x2009;mL) and RBV (&#x2009;&#x2264;&#x2009;100&#x2009;mL vs. >&#x2009;100&#x2009;mL). &#x3b1;-diversity (Chao1 and Shannon indices) and &#x3b2;-diversity (Jaccard distance) were calculated. Linear discriminant analysis effect size (LEfSe) was used to identify differentially abundant taxa between groups.<br><br>RESULTS: No significant differences in gut microbial &#x3b1;- or &#x3b2;-diversity were observed between groups stratified by PV or RBV. Nevertheless, several specific bacterial taxa showed significant variation between groups. Methanobrevibacter smithii was markedly less abundant in patients with PV&#x2009;>&#x2009;40&#x2009;mL (p&#x2009;<&#x2009;0.01). Similarly, patients with high RBV (&#x2009;&#x2265;&#x2009;100&#x2009;mL) exhibited distinct gut microbial profiles compared to those with lower RBV, characterized by a reduced abundance of Collinsella and an increased abundance of Gastranaerophilales (both p&#x2009;<&#x2009;0.01).<br><br>CONCLUSION: Our findings suggest that while overall gut microbial diversity may remain stable, specific taxa are associated with prostate and bladder phenotypes, supporting the concept of a gut-prostate axis. Future research should focus on longitudinal studies to investigate how gut (and urinary) microbiota evolve alongside BPH and/or LUTS over time, with the goal of determining whether microbial signatures could serve as early indicators for symptomatic BPH.}, }
@article {pmid41849700, year = {2026}, author = {Schultz, H and Paulo, DGS and Meriño-Cabrera, Y and de Andrade, RJ and Santos, ILB and Rodrigues, MCNG and Mariano, GA and Lima, MG and de Oliveira, HJR and Oliveira, MGA}, title = {Synthetic Peptide Inhibition of Trypsin-Like Proteases in Spodoptera frugiperda (Lepidoptera: Noctuidae): Evaluating the Influence of Gut Microbiota.}, journal = {Archives of insect biochemistry and physiology}, volume = {121}, number = {3}, pages = {e70145}, pmid = {41849700}, issn = {1520-6327}, support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de Ensino Superior/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; pesquisa do Estado de Minas Gerais/ ; }, mesh = {Animals ; *Spodoptera/growth &amp; development/enzymology/microbiology/drug effects ; *Gastrointestinal Microbiome/drug effects ; Larva/growth &amp; development/drug effects/enzymology/microbiology ; *Peptides/pharmacology ; *Insect Proteins/antagonists &amp; inhibitors/metabolism ; *Protease Inhibitors/pharmacology ; Serine Endopeptidases ; }, abstract = {Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae) is a major agricultural pest whose control has been increasingly challenged by resistance to conventional insecticides. Synthetic protease inhibitors represent promising alternatives; however, the potential modulation of their efficacy by gut microbiota remains poorly understood. Here, we evaluated two rationally designed synthetic tripeptides, GORE1 and GORE2, as inhibitors of trypsin-like digestive proteases and investigated whether gut microbiota disruption alters their inhibitory performance in S. frugiperda. Enzymatic assays revealed competitive inhibition patterns, with Ki values of 1.41 mM for GORE1 and 0.49 mM for GORE2. Most treatments increased apparent KM values, indicating reduced substrate affinity, whereas GORE2 consistently showed lower KM values. Despite stronger in vitro affinity (lower Ki), GORE2 did not produce greater biological impairment than GORE1. Microbiota imbalance induced by antibiotic treatment did not significantly alter larval survival or enzymatic inhibition patterns but modulated specific developmental responses, particularly prolonged larval development and reduced body mass under GORE1 exposure. Nutritional indices (ECI and ECD) were significantly reduced in peptide-treated larvae, supporting impaired protein metabolism. These findings demonstrate that synthetic peptides effectively inhibit trypsin-like proteases in S. frugiperda and negatively affect larval nutritional performance. Although microbiota disruption did not modify survival or primary enzymatic inhibition, microbiota-mediated compensatory mechanisms cannot be excluded. Future integrative studies combining microbiome profiling and metabolic analyses will be essential to resolve host-enzyme-microbiota interactions under digestive inhibition.}, }
@article {pmid41849703, year = {2026}, author = {Tabone, M and Carreras-Presas, CM and Cenzato, N and Del Fabbro, M and Soltero, RG}, title = {Impact of Clear Aligners on the Oral Microbiome: A Systematic Review of Current Evidence.}, journal = {Clinical and experimental dental research}, volume = {12}, number = {2}, pages = {e70265}, doi = {10.1002/cre2.70265}, pmid = {41849703}, issn = {2057-4347}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; *Malocclusion/therapy/microbiology ; }, abstract = {OBJECTIVES: Oral malocclusion affects a large portion of the population, impacting both function and aesthetics. Recent advances in orthodontics offer a variety of treatment options, including traditional fixed appliances (FA) and, more recently, clear aligners (CA). This systematic review aims to synthesize and critically evaluate current evidence on oral microbiological changes during orthodontic treatment, with a focus on CA.<br><br>MATERIALS AND METHODS: A comprehensive literature search was conducted using PubMed, Medline, Cochrane Library, Embase, and Scopus. Keywords included: ("Bacteria" OR "Microbio*") AND ("Orthodontic aligners" OR "Invisalign"). The review was registered in PROSPERO (CRD420240628072), and the final search was completed on October 15, 2024. Two reviewers independently screened studies, extracted data, and assessed risk of bias. Primary outcomes included changes in oropharyngeal microbiota (salivary, lingual, gingival, and pharyngeal) and functional diversity (e.g., alpha and beta diversity, metabolic pathways).<br><br>RESULTS: Twelve studies met inclusion criteria. Findings revealed that CA use leads to time-dependent shifts in the oral microbiome, with notable changes in beta diversity within 24&#x2009;h. Over periods from 1 to 12 months, CA users exhibited more favorable oral health outcomes compared to FA users, including lower plaque index (PI), reduced gingival inflammation (GI), and decreased probing pocket depth (PPD). These improvements are likely to be due to the easier hygiene maintenance of CA.<br><br>CONCLUSION: Clear aligners appear to promote better oral microbiological balance and periodontal health than FA, likely due to easier hygiene maintenance and reduced plaque accumulation, with consistently lower levels of Streptococcus mutans observed in subjects undergoing CA therapy.}, }
@article {pmid41849813, year = {2026}, author = {Rashik, RA and Guanella, O and Mao, W and Gallant, ND}, title = {Biomechanical design principles of intestine-on-chip models: past, present and future directions.}, journal = {Biomedical materials (Bristol, England)}, volume = {}, number = {}, pages = {}, doi = {10.1088/1748-605X/ae5437}, pmid = {41849813}, issn = {1748-605X}, abstract = {Human intestine is a complex organ that performs critical roles in nutrient absorption, immune regulation, and host-microbiome interactions. Traditional 2D and 3D in vitro models, while useful for some applications, fall short in replicating the dynamic and multifaceted environment of the small intestine. In recent years, Intestine-on-Chip (IoC) technologies have emerged as promising platforms that integrate microfluidics, biomechanical cues, and tissue engineering to better simulate intestinal structure and function. This review provides a comprehensive overview of IoC devices, covering their underlying principles, historical development, design elements, and key functional capabilities, with special emphasis on the incorporation of mechanical strain and peristalsis-like motion. We also discuss the limitations of current models, including application of constant uniaxial strain, scale constraints, material challenges, biological complexity, and lack of standardization as well as prospective directions for advancing this field. By addressing these gaps, next-generation IoC systems can pave the way for more predictive disease models, advanced drug testing platforms, and personalized medicine applications.}, }
@article {pmid41850056, year = {2026}, author = {Van Hoeck, V and Spaepen, R and Somers, I and Abdelqader, A and Forier, B and Mahasneh, Z}, title = {N-acetylated chito-oligosaccharides and xylanase improve intestinal health and production performance in laying hens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106698}, doi = {10.1016/j.psj.2026.106698}, pmid = {41850056}, issn = {1525-3171}, abstract = {Synergistic feed additives that target the gut-immune axis offer a promising strategy to enhance health, nutrient utilization, and productivity. N-acetylated chito-oligosaccharides (NACOS) provide stimbiotic, antimicrobial, and immunomodulatory benefits, while xylanase improves non-starch polysaccharide degradation, nutrient availability, and microbial fermentation. This study evaluated a novel dual-action strategy combining NACOS, xylanase, or their combination (CXNRGY) on production performance, nutrient utilization, jejunal histomorphology, systemic immune status, and the cecal microbial community in laying hens. Forty HiSex White laying hens were randomly assigned to four dietary groups and fed either a control diet (CD) or the CD supplemented with NACOS (50 g/t), Xylanase (45,000 U/kg), or CXNRGY at the same respective doses. Dietary supplementation improved production metrics: egg weight was highest in the CXNRGY group compared with control and NACOS (P < 0.001), while egg mass increased in Xylanase, NACOS and CXNRGY groups compared to control in the second phase (P < 0.001). Xylanase and CXNRGY achieved the lowest FCR compared with NACOS and the control group. Haugh unit and albumen height were elevated in NACOS and Xylanase treatments (P < 0.05), whereas CXNRGY maximized shell thickness and breaking strength (P < 0.001). Nutrient utilization of crude fat, organic matter, and apparent metabolizable energy (AME) was significantly improved by NACOS, while Xylanase and CXNRGY further enhanced fiber and protein utilization. NACOS produced the greatest improvements in jejunal morphology (P < 0.05) and, along with Xylanase and CXNRGY, reduced serum IL-1α, TNF-α, and IL-10 (P < 0.05), while IL-1β and IL-6 were unaffected (P > 0.05). Notably, CXNRGY altered the cecal microbiota by increasing the relative abundance of Lachnospiraceae, Ruminococcaceae, Subdoligranulum, Prevotellaceae and Clostridia, while decreasing Bacteroidaceae and Negativicutes, indicating a synergistic effect on microbial community structure. Xylanase enhances nutrient utilization and prebiotic availability, while NACOS strengthens gut barrier integrity and modulates immune responses. These results indicate that combining NACOS with xylanase provides a synergistic, antibiotic-free nutritional strategy that enhances gut health, immunity, egg quality, and overall performance in laying hens.}, }
@article {pmid41850059, year = {2026}, author = {Wang, W and Liu, S and Zhang, S and Li, Y and Zuo, J}, title = {The promise of pectic oligosaccharides as a novel sustainable additive in poultry production: A systematic review.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106704}, doi = {10.1016/j.psj.2026.106704}, pmid = {41850059}, issn = {1525-3171}, abstract = {The prohibition of antibiotic growth promoters in animal feeds due to their well-known hazards has driven the accelerated research and development of novel practicable alternatives, among which functional oligosaccharides are characterized as one of the most promising candidates because of their stability, safety and excellent biological activities. Pectic oligosaccharides (POS) are an emerging class of functional oligosaccharides obtained through physicochemical or biological degradation (especially the enzymolysis) of pectins (a crucial kind of plant cell wall components). The preparation of POS is economically feasible, which not only overcomes the anti-nutritional impacts of native pectins in plant ingredients, but also obtains other benefits for poultry, because the prepared POS possess numerous functions, such as optimizing gut microbiome via both prebiotic and non-prebiotic actions, regulating lipid metabolism and immune responses, as well as exerting antioxidant and antitumor properties. Noticeably, the above functions of POS that depend largely on their structure have been primarily validated in laboratory animals or in vitro models, while the related researches in poultry or other farm animals are relatively few. The present review systematically discusses the preparation methods of POS, their biological activities and underlying mechanisms that may benefit poultry growth and health, as well as their structure-activity relationships. We also summarize the currently limited evidences on the positive roles (such as improvements of production performance along with intestinal and genital health) of POS in poultry nutrition, thus supporting the promise of POS as a novel sustainable additive in poultry diets. Since the application of POS in feeds is still underexplored, future studies deserve to be conducted to elucidate the definite mechanisms together with the structure-effect and dose-effect relationships of POS, as well as the synergy between POS and other additives (e.g. probiotics) in poultry nutrition. Such research efforts are anticipated to further extend the role of POS as a cost-efficient and sustainable additive in advancing poultry production.}, }
@article {pmid41850170, year = {2026}, author = {Ren, L and Zhu, Y and Chen, H and He, D and Li, B and Song, X and Yang, Y and Wu, QL}, title = {Thermal stress drives coastal microbiome transitions from phototrophic carbon fixation to energy-conserving chemotrophy.}, journal = {Water research}, volume = {297}, number = {}, pages = {125760}, doi = {10.1016/j.watres.2026.125760}, pmid = {41850170}, issn = {1879-2448}, abstract = {Localized thermal discharge offers a natural analog for extreme warming, providing unique insights into how thermal stress shape microbial metabolism in coastal ecosystems. By examining taxonomic and functional dynamics across a pronounced thermal gradient (30-36°C), we identified a distinct transition near 33°C, marked by a systematic decline in phototrophic cyanobacteria (e.g., Synechococcus) and concurrent downregulation of genes involved in oxygenic photosynthesis and the Calvin-Benson-Bassham (CBB) cycle in subtropical Daya Bay. This phototrophic collapse coincided with enrichment of chemoautotrophic (Rhodobacteraceae, Halieaceae) and heterotrophic (SAR11 Ia) lineages, alongside upregulation of energy-efficient chemolithoautotrophic pathways (Wood-Ljungdahl and HP/HB cycle). This metabolic transition near 33°C was reinforced by enhanced energy-generating metabolism (glycolysis, TCA cycle, β-oxidation), dissimilatory nitrogen/sulfur reduction (DNRA: narH/nirB/nirD; DSR: aprA/aprB), and thiosulfate oxidation (SOX: soxY/soxZ/soxD), accelerating nutrient cycling. Microbial adaptation was further reinforced by the upregulation of thermal stress-response genes, including hspR, hspQ, rpoH, and cytochrome oxidases. Collectively, local seawater warming induces a survival strategy prioritizing energy conservation and chemotrophy over phototrophic carbon fixation, reprogramming ecosystem function at the expense of primary production and carbon sequestration while accelerating nitrogen/sulfur turnover. This metabolic transition underscores microbial plasticity but signals vulnerability in critical coastal blue carbon sinks under thermal stress.}, }
@article {pmid41850177, year = {2026}, author = {Zhang, J and Huang, J and Li, Y and Wu, X and Guo, F}, title = {The Actinobacteria-to-Proteobacteria (A/P) Ratio: A Novel Oral Microbial Marker for Metabolic Syndrome.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109499}, doi = {10.1016/j.identj.2026.109499}, pmid = {41850177}, issn = {1875-595X}, abstract = {INTRODUCTION AND AIMS: Oral microbial biomarkers for metabolic syndrome (MetS), in contrast to its well-characterized relationship with the gut microbiome, have not been well defined. This study aims to systematically identify composite oral microbial indices by analyzing a large-scale cohort.<br><br>METHODS: We analyzed oral rinse samples from 3911 U.S. individuals (aged &#x2265; 14 years), integrating 16S rRNA sequencing with metabolic phenotyping. We used principal coordinates analysis and permutational multivariate analysis of variance to assess &#x3b2;-diversity separation, linear discriminant analysis effect size analysis to identify microbial signatures, multivariable-adjusted logistic regression with restricted cubic splines (RCS) to evaluate MetS associations, Cox proportional hazards models to analyze all-cause mortality in the MetS population, and stratified analyses to test for effect modification by age, BMI and medication use.<br><br>RESULTS: MetS participants exhibited higher BMI and were older than non-MetS controls (P < .001). Oral microbiome &#x3b2;-diversity diverged significantly in MetS despite stable &#x3b1;-diversity, marked by enrichment of Actinobacteria and depletion of Proteobacteria (P < .001). In adjusted models, the highest tertile of Actinobacteria was associated with 42% higher odds of MetS (aOR = 1.42, 95% CI: 1.06-1.91), whereas the highest tertile of Proteobacteria was associated with 42% lower odds (aOR = 0.58, 95% CI: 0.43-0.79). Capturing this dysbiotic shift, the composite Actinobacteria-to-Proteobacteria (A/P) ratio demonstrated a superior predictive value than either phylum alone (aOR = 1.58, 95% CI: 1.08-2.30). RCS analysis demonstrated a linear association of the A/P ratio with MetS and all-cause mortality among individuals with MetS. Kaplan-Meier analysis confirmed significantly reduced survival in the high-A/P ratio group (P < .001).<br><br>CONCLUSIONS: This study provides the first population-level evidence that an elevated the A/P ratio is independently associated with MetS, suggesting its potential as a novel oral microbiomarker.<br><br>CLINICAL RELEVANCE: These findings provide a non-invasive tool to assess metabolic status and lay a foundation for future research into targeted oral microbial interventions for MetS.}, }
@article {pmid41850235, year = {2026}, author = {Chen, L and Brustad, N and Thorsen, J and Wang, T and Ali, M and Kyvsgaard, JN and Lovric, M and Ebrahimi, P and Luo, Y and Pedersen, CT and Prince, N and Kelly, RS and Schoos, AM and Vahman, N and Rasmussen, MA and Brix, S and Litonjua, AA and Weiss, ST and Wheelock, CE and Lasky-Su, J and Bønnelykke, K and Stokholm, J and Chawes, B}, title = {Maternal 12-HETE is associated with childhood asthma and the responses to prenatal omega-3 supplementation.}, journal = {Cell reports. Medicine}, volume = {7}, number = {3}, pages = {102689}, doi = {10.1016/j.xcrm.2026.102689}, pmid = {41850235}, issn = {2666-3791}, mesh = {Humans ; Female ; Pregnancy ; *Asthma/blood ; *Fatty Acids, Omega-3/administration &amp; dosage/therapeutic use/pharmacology ; *Dietary Supplements ; *12-Hydroxy-5,8,10,14-eicosatetraenoic Acid/blood ; Adult ; Male ; Child ; Prenatal Exposure Delayed Effects ; Respiratory Tract Infections ; Infant ; }, abstract = {A recent mouse study has shown that deficiency in 12-hydroxyeicosatetraenoic acid (12-HETE) affects neonatal alveolar macrophage imprinting and associates with increased respiratory morbidity, but this has not been investigated in humans. Utilizing data from two mother-child cohorts, COPSAC2010 and VDAART, we demonstrate that undetectable maternal plasma 12-HETE during pregnancy associates with increased risk of childhood asthma and respiratory infections alongside an altered infant airway microbiota structure and airway immune profile. Further, we observed an interaction between maternal 12-HETE levels and maternal N-3 long-chain polyunsaturated fatty acid (n-3 LCPUFA) supplementation in a randomized clinical trial in COPSAC2010 and maternal dietary n-3 LCPUFA intake in VDAART in relation to offspring respiratory morbidity; higher prenatal n-3 LCPUFA exposure reduced asthma and respiratory infection among mothers with detectable 12-HETE levels. These findings identify maternal 12-HETE as a potential biomarker for risk of offspring respiratory morbidity and suggest that maternal 12-HETE status may determine responsiveness to prenatal n-3 LCPUFA supplementation.}, }
@article {pmid41850377, year = {2026}, author = {Shan, Y and Zheng, M and Zhao, Y and Sha, S and Bian, C}, title = {Synbiotics regulate gut microbiota-derived indole-3-acetic acid production to modulate the intestinal barrier and improve antibiotic-associated diarrhea.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28138}, pmid = {41850377}, issn = {1525-3198}, abstract = {Given the global risks associated with antibiotic overuse, antibiotic-associated diarrhea (AAD) has become a widespread public health concern worldwide. Human milk oligosaccharides (HMOs) and Bifidobacteria are often used to prepare synbiotics to enhance their health effects. However, the synergistic effect of this combination in alleviating AAD remains unclear. In this study, lincomycin was used to establish a mouse model of AAD, and the effects of the 3-fucosyllactose (3-FL) +6'-sialyllactose (6'-SL), as well as the Bifidobacterium bifidum, were evaluated. Further analyses examined the impact of HMOs plus probiotics on the gut microbiota and its associated metabolites. In addition, the roles and underlying mechanisms of specific metabolites in AAD were investigated. The results indicate that HMOs plus probiotics significantly ameliorate diarrheal symptoms in mice with AAD. This effect is reflected by increased body weight, markedly reduced diarrhea scores and fecal water content, significantly elevated aquaporin-3 (AQP3) expression, and substantially decreased levels of the inflammatory mediators tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β). Moreover, the combination of HMOs and probiotics demonstrated superior efficacy compared with either intervention alone. Integrated microbiome-metabolomics analysis revealed that HMOs plus probiotics significantly enriched Lactobacillus, a change that was potentially associated with increased levels of the gut metabolite indole-3-acetic acid (IAA). IAA plays a crucial role in intestinal barrier repair by promoting Muc2 expression and thereby enhancing the intestinal chemical barrier. Concurrently, IAA contributes to the restoration of the mechanical barrier by regulating claudin-1 protein expression. Furthermore, the effects of IAA were significantly attenuated following intervention with aryl hydrocarbon receptor (AhR) inhibitors, indicating that IAA exerts its actions via activation of AhR. In summary, this study suggests that HMOs plus probiotics may alleviate AAD by promoting IAA production via the gut microbiota, thereby activating the IAA/AhR/Muc2/claudin-1 axis. This research provides novel insights into microbiota-based interventions targeting intestinal health.}, }
@article {pmid41850701, year = {2026}, author = {Tursi, A}, title = {Optimal use of rifaximin in diverticular disease of the colon: use less for use better.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338723}, pmid = {41850701}, issn = {1468-3288}, }
@article {pmid41850876, year = {2026}, author = {Regmi, H and Dritsoulas, A and Kamali, S and Stelinski, LL and Diepenbrock, LM and Duncan, L}, title = {Edge effects, tree cover and soil properties linked to the distribution of Diaprepes abbreviatus in a Florida citrus orchard.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70723}, pmid = {41850876}, issn = {1526-4998}, support = {CRDF22-013//Citrus Research and Development Foundation, Inc./ ; }, abstract = {BACKGROUND: Diaprepes root weevil (DRW, Diaprepes abbreviatus) is a major economic pest of citrus trees in Florida and the Caribbean Basin. To identify potential drivers of local patterns of weevil abundance and tree condition, we measured relationships between DRW and edaphic properties in a Florida orchard in which half the trees were initially protected from herbivores by individual protective covers (IPCs) of fabric mesh. Weevils were monitored for 2 years in 94 plots arranged in a grid pattern. Soil samples were processed for physicochemical properties, and DNA from soil organisms was subjected to metabarcoding for ITS2 rDNA, 16S rDNA, and COI mtDNA.<br><br>RESULTS: Weevils aggregated each summer along plot boundaries adjacent to a natural area of alternate hosts, consistent with an edge-biased distribution reflecting seasonal weevil migration. Fourteen months after the covers were removed, 93% of 484 prokaryote species (dominated by Bacilli, Actinobacteria, Alphaproteobacteria, and Cyanobacteria) that were most closely associated with IPC use were less abundant beneath the trees that were formerly covered than under previously uncovered trees. Soil moisture, Paenibacillus spp. diversity, and IPCs were associated with DRW patterns and tree condition including mortality.<br><br>CONCLUSIONS: Early season, edge-biased distribution of DRW should be exploited for monitoring and management efficacy. The relationship here between tree mortality and microbiome species deficits associated with IPCs supports the need for research to resolve the role of tree covers in potential trophic cascades that affect plant health. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid41851036, year = {2026}, author = {Siddique, F and Wei, J and Guan, M and Xu, R and Xiong, LT and Zhao, Y and Zeng, Q and Cui, ZN}, title = {A Novel Thiazolidin-2-Cyanamide Derivative Suppresses Bacterial Blight by Targeting the Type III Secretion System and Reassembling a Protective Rice Leaf Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c17706}, pmid = {41851036}, issn = {1520-5118}, abstract = {Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial leaf blight, relies on a type III secretion system (T3SS) for virulence. Using chemical inhibitors to suppress T3SS without affecting bacterial growth is a novel strategy that minimizes disturbance of the innate leaf microbiome. (Z)-N-(3-(5-(2-nitrophenyl) furan-2-carbonyl) thiazolidin-2-ylidene) cyanamide (II-2) is a chemical inhibitor of T3SS in Xoo and an effective control alternative. This study evaluated whether II-2 treatment and Xoo infection alter the leaf microbiome. Using 16S rRNA gene sequencing, Xoo infection markedly reshaped the leaf microbiome, shifting the dominance from Proteobacteria to Pseudomonadales and Xanthomonadales. II-2 influenced bacterial communities in both healthy and Xoo-infected leaves, with low-dose treatment enriching Gram-negative taxa in diseased leaves, whereas the high dose enriched Sphingomonas in healthy leaves. In healthy plants, higher II-2 doses preserved microbial stability, suggesting minimal ecological disturbance. II-2 exhibited no toxicity in silkworms or earthworms, functioning as a T3SS-targeting, microbiome-compatible antivirulence agent.}, }
@article {pmid41851065, year = {2026}, author = {Fagundes, RR and Colgan, SP}, title = {Feeding microbes to feed the Gut: inulin reprograms intestinal epithelial metabolism and proliferation through HIF1α.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644684}, doi = {10.1080/19490976.2026.2644684}, pmid = {41851065}, issn = {1949-0984}, mesh = {*Inulin/metabolism ; *Intestinal Mucosa/metabolism/drug effects/microbiology ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Prebiotics/administration &amp; dosage ; Cell Proliferation/drug effects ; Animals ; Fermentation ; Epithelial Cells/metabolism ; }, abstract = {Indigestible dietary fibers shape intestinal mucosal physiology, yet the mechanisms linking fiber-derived microbial activity to epithelial remodeling remain incompletely understood. In their recent study, Ribeiro Castro et al. revealed that the prebiotic inulin induces reprogramming of intestinal epithelial metabolism and proliferation through microbiota-dependent hypoxia and epithelial HIF1α activation. In this commentary, we discuss their findings and highlight the emerging concept that microbial fermentation and oxygen concentrations act as structured physiological signals that guide intestinal epithelial differentiation and crypt-villus dynamics. We further explore how these findings intersect with prior work on SCFA metabolism, butyrate-mediated ISC inhibition, and fructose-driven epithelial growth, and we discuss open questions regarding downstream HIF1α programs, niche accessibility, and immune‒epithelial crosstalk. Understanding how HIF1α calibrates this balance will be essential for safely leveraging prebiotics and microbiome-targeted interventions that promote mucosal health.}, }
@article {pmid41851098, year = {2026}, author = {Asiloglu, R and Kuno, H and Fujino, M and Bodur, S and Aycan, M and Ishizuka, H and Kazama, S and Iwasaki, S and Murase, J and Harada, N and Arai, M and Ikazaki, K}, title = {Predator-mediated local convergence fosters global microbial community divergence.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41851098}, issn = {2041-1723}, support = {JP22K14804//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K01654//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP25K02147//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Microbiota/physiology/genetics ; *Bacteria/genetics/classification ; Ecosystem ; Soil Microbiology ; Animals ; Predatory Behavior ; }, abstract = {Understanding how microbial communities assemble is central to predicting ecosystem function. Although predators strongly influence bacterial communities through predation, the role of microbial predators in modulating global microbial divergence and convergence patterns remains largely neglected. Here, we integrated global-scale amplicon sequencing data, controlled field experiments, and reconstructions of natural and synthetic communities to examine predator-mediated community assembly mechanisms. We show that bacterivorous protists exert dual, scale-dependent effects on microbial communities: promoting local convergence by suppressing dominant bacterial taxa, while generating global divergence through species-specific predation effects. We find that predator identity and prey susceptibility jointly determine convergence outcomes. Communities dominated by predator-resistant taxa exhibit reduced convergence under predation pressure, revealing a predictable trait-based filtering mechanism. This work establishes bacterivorous protists as key, context-dependent agents of biogeography and suggests new opportunities for microbiome engineering, where targeted use of protists may steer microbial communities toward functional configurations that enhance soil health and ecosystem resilience.}, }
@article {pmid41851313, year = {2026}, author = {Nguyen, HTL and Hoang, HT and Le, DP and Duong, TQ and Vuong, NTH and Truong, MT and Nguyen, HT and Nguyen, AH and Pham, TD and Nguyen, ATV}, title = {Bacillus spore probiotics for alleviating functional constipation in children: a randomized, double-blind, placebo-controlled trial.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {41851313}, issn = {2730-664X}, abstract = {BACKGROUND: Functional constipation is common in children and often responds poorly to standard treatments. This study evaluated the efficacy and mechanisms of multi-strain Bacillus spore probiotics, which tolerate gastrointestinal conditions, in paediatric functional constipation.<br><br>METHODS: We conducted a randomized, double-blind, placebo-controlled trial (ClinicalTrials.gov NCT06154525, 4/12/2023) in preschool children (24-60 months) with functional constipation in Vietnam. A total of 111 participants were randomly assigned (1:1:1) to receive placebo or two multi-strain Bacillus spore probiotics (LiveSpo Kids or Preg-Mom, &#x2265;3 billion CFU/5&#x2009;mL registered; each tested at 3.7 billion CFU/5&#x2009;mL) for 28 days. Primary outcomes were changes in functional constipation (main focus), anorexia, and underweight risk at day 28. Secondary outcomes included serum cytokines, stool IgA, and gut microbiota; stool samples from 10 healthy children provided a reference microbiota profile.<br><br>RESULTS: Both probiotic groups show significant improvements at day 28. Percentages of children with constipation decrease 3.7-fold in Kids and 5.1-fold in PregMom (p&#x2009;<&#x2009;0.0001). Absolute Risk Reductions (ARR) are 52.38% (95%CI: 35.45%-77.26%) and 59.97% (95%CI: 44.48%-84.68%) in Kids and PregMom vs Placebo. Kids and PregMom groups improve anorexia (ARR: 24.40% (95%CI: 3.09%-49.44%) and 25.98% (95%CI: 4.69%-51.25%)) and underweight risk (ARR: 7.87% (95%CI: 0%-23.80%) and 19.30% (95%CI: 1.70%-37.50%)) vs. Placebo. Probiotics reduce serum IL-6 and IL-23, increase IL-10 and stool IgA, and shift the gut microbiota toward a composition more closely resembling healthy children, enriching beneficial species while reducing harmful ones.<br><br>CONCLUSIONS: Multi-strain Bacillus spore probiotics alleviate functional constipation, improve immune markers, and modulate gut microbiota in children, supporting their potential as effective microbiome-targeted interventions.}, }
@article {pmid41851530, year = {2026}, author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E}, title = {Advances and opportunities in measuring dietary intake: from omics to AI.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {41851530}, issn = {2522-5812}, abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.}, }
@article {pmid41851757, year = {2026}, author = {Zhang, Y and Zhang, B and Pang, W and Gu, W and Wang, X and Yuan, H and Fang, S and Zhang, J and Li, X and Xing, X and Ji, X and Liu, T and Wei, F and Zhang, C and Wang, S}, title = {The interplay between Peptostreptococcus and Fusobacterium as novel signatures in colorectal cancer recurrence.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02378-w}, pmid = {41851757}, issn = {2049-2618}, support = {TJWJ2023QN040//Tianjin Health Technology Project/ ; No. 25JCYBJC01130//Natural Science Foundation of Tianjin/ ; 25ZXWQSY00010//Tianjin Municipal Public Health Program/ ; 23JCZXJC00390-J230038//Beijing-Tianjin-Hebei Basic Research Cooperation Project/ ; 2024ZD0521200-2024ZD0521203//National Science and Technology Major Project/ ; 82473806//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: After resection surgery, recurrence occurs in more than 30% of colorectal cancer (CRC) patients. Previous studies have highlighted the role of the gut microbiota in CRC initiation and progression; however, the microbial features associated with recurrence remain not completely understood. In particular, integrated multi-omics biomarkers, the interactions between microorganisms, as well as those between microbes and the host, and their relevance to recurrence risk require further investigation.<br><br>RESULTS: In this study, 120 tumor mucosal samples collected during surgery from CRC patients underwent 16S rRNA gene sequencing and LC-MS metabolomic profiling. Recurrence status was determined through postoperative follow-up. Compared to the relatively minor variations in mucosal microbial and metabolomic signatures across different tumor node metastasis (TNM) stages, recurrent patients exhibited a distinct landscape. Machine learning analysis identified an integrated signature comprising five bacterial genera (Peptostreptococcus, Fusobacterium, Bacteroides, Porphyromonas, and Prevotella) and five metabolites (alanylglutamic acid, putrescine, arginine, histidine, and sebacic acid), which demonstrated strong discriminatory performance between recurrent and non-recurrent patients (AUC&#x2009;=&#x2009;0.89). By integrating 10 biomarkers, a comprehensive risk score for patient stratification was derived. After adjusting for TNM stage, patients classified as high-risk had a significantly shorter recurrence-free survival (adjusted HR&#x2009;=&#x2009;1.59, 95% CI 1.35-1.88, P&#x2009;<&#x2009;0.0001). The microbial biomarkers Fusobacterium and Peptostreptococcus displayed positive correlation and were observed to co-aggregate and form dense dual-species biofilms. Further cellular and murine experiments revealed that P. anaerobius significantly enhanced the adhesion of F. nucleatum to tumor cells and its colonization of colonic mucosa. KEGG pathway analysis of differential metabolites identified enrichment of arginine and proline metabolism pathways in the recurrence group. Concurrently, arginine was found to disrupt F. nucleatum-P. anaerobius co-aggregation, while its metabolite putrescine significantly promoted dual-species biofilm formation.<br><br>CONCLUSION: Our study identified integrated microbial and metabolic features associated with CRC recurrence and proposes an exploratory risk stratification framework. Furthermore, a previously unrecognized link between pathobionts and metabolites relevant to recurrence was reported, which requires further validation in a larger independent cohort. Video Abstract.}, }
@article {pmid41851770, year = {2026}, author = {Okuyama, K and Naruse, T and Matsushita, Y and Fujimoto, J and Yanamoto, S and Lei, YL and Hu, J}, title = {Precision immunotherapy for head and neck cancer: therapeutic combinations, biomarker strategies, and translational challenges.}, journal = {Molecular cancer}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12943-026-02609-6}, pmid = {41851770}, issn = {1476-4598}, abstract = {Immune checkpoint inhibitors (ICIs) have fundamentally altered the therapeutic paradigm for head and neck squamous cell carcinoma (HNSCC); however, durable clinical benefit remains limited to biologically defined patient populations. These clinical limitations necessitate a shift away from empirical monotherapy toward precision-guided combination strategies that actively reprogram immune resistance. In this review, we integrate contemporary clinical and translational evidence regarding ICI-based combinations with radiotherapy (RT), chemotherapy, and emerging non-cytotoxic sensitization approaches, with particular emphasis on neoadjuvant and perioperative treatment settings. Central to these strategies is the dynamic remodeling of the tumor immune microenvironment (TIME), rather than simple amplification of immune activation. Recent studies demonstrate that immune-sensitizing interventions - including RT-induced immunogenic cell death, innate immune pathway activation, metabolic and microbiome modulation, and bioengineered drug delivery systems-can convert immunologically inert tumors into immune-interrogable tissues by restoring antigen presentation, spatial immune organization, and effector T-cell competence. Concurrently, integrative biomarker frameworks-encompassing PD-L1 expression, tumor mutational burden, tertiary lymphoid structures, tissue-resident memory T cells, and immune spatial organization-are redefining approaches to patient stratification and therapeutic sequencing. Despite compelling mechanistic rationale, clinical translation remains hindered by inadequate biomarker integration, heterogeneous clinical trial design, and discordance between biological endpoints and survival outcomes. Collectively, these advances delineate a transition from empiric combination therapy toward immune-centric precision immuno-oncology in HNSCC, underscoring the necessity for biomarker-driven trial design, longitudinal immune monitoring, and multidisciplinary collaboration to translate mechanistic synergy into durable clinical benefit.}, }
@article {pmid41851901, year = {2026}, author = {Zhao, Y and Zhai, S and Wang, P and Yang, W and Liu, X and Dai, Y and Li, C and Liu, F and Yang, N and Yan, W}, title = {Host genomic regulation of ileal Bradyrhizobium abundance modulates eating speed and fat metabolism in birds: a causal mechanism study.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41851901}, issn = {1674-9782}, support = {SYND-QDJF-04//China Agricultural University Sanya Research Institute/ ; 325RC806//Hainan Provincial Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Eating speed is a key eating behavior trait that influences energy intake and fat deposition, yet its regulation by host genetics and gut microbiota remains poorly understood in birds.<br><br>RESULTS: We systematically investigated the interplay among host genetics, gut microbiota, eating speed, and fat deposition in chickens. Phenotypic analyses revealed a positive association between eating speed and abdominal fat, and Mendelian randomization (MR) analysis identified a bidirectional feedback loop in which fat deposition promotes faster eating, which in turn exacerbates fat accumulation. Microbiome and MR analyses highlighted the ileal genus Bradyrhizobium as a causal regulator of both eating speed and fat deposition, with higher abundance reducing abdominal fat, triglyceride levels, and inflammatory markers. Microbiome genome-wide association studies (mGWAS) further identified host genetic variants and candidate genes, including convergent signals at RECK, influencing Bradyrhizobium abundance. Mediation analyses indicated that Bradyrhizobium modulates eating speed partially through its effects on abdominal fat, emphasizing a host-microbe-behavior feedback axis.<br><br>CONCLUSIONS: Our findings reveal a complex interplay among host genetics, gut microbes, and eating behavior, providing mechanistic insights and potential targets for precision interventions to optimize growth and metabolic health in poultry.}, }
@article {pmid41852017, year = {2026}, author = {Kumar, S and Swati,  and Salila, S and Raj, A and Gupta, P and Sharad, N}, title = {HPV in Pregnancy: Implications for Screening, Vaccination, and Maternal-Fetal Health.}, journal = {Journal of pregnancy}, volume = {2026}, number = {1}, pages = {e1466858}, pmid = {41852017}, issn = {2090-2735}, mesh = {Humans ; Female ; Pregnancy ; *Papillomavirus Infections/diagnosis/prevention &amp; control/epidemiology/complications ; *Pregnancy Complications, Infectious/diagnosis/prevention &amp; control/epidemiology/virology ; Papillomavirus Vaccines/administration &amp; dosage ; Vaccination ; Pregnancy Outcome ; Mass Screening ; Infectious Disease Transmission, Vertical/prevention &amp; control ; }, abstract = {Human papillomavirus (HPV) infection is the most common sexually transmitted infection worldwide. It is highly prevalent among women of reproductive age. During pregnancy, hormonal changes and immunological modulation may promote viral persistence, thus likely increasing the risk of adverse maternal and neonatal outcomes. However, the clinical significance of HPV infection in pregnancy remains incompletely understood. This qualitative thematic analysis is aimed at evaluating the epidemiological and clinical impact of HPV during pregnancy, focusing on pathophysiological mechanisms, diagnostic challenges, obstetric and perinatal outcomes, and gaps in clinical management. A comprehensive literature search of PubMed and Scopus was conducted for peer-reviewed original studies published in the last 10 years in English. The review followed PRISMA 2020 guidelines. Of 1667 records initially identified, 34 studies met the inclusion criteria and were included in the qualitative synthesis. Study quality was assessed using the Newcastle-Ottawa Scale. Given the heterogeneity of study designs and outcomes, a thematic narrative synthesis was performed. Four major themes emerged: (1) pregnancy-related immunological, hormonal, and microbiome changes that facilitate HPV persistence; (2) diagnostic challenges arising from physiological cervical changes that affect cytology and colposcopy accuracy; (3) associations between maternal HPV infection and adverse outcomes such as preterm birth, premature rupture of membranes, miscarriage, low birth weight, and vertical transmission; and (4) disparities in screening and vaccination policies between high-income countries and low- and middle-income countries. While HPV is not directly teratogenic, evidence suggests it may indirectly compromise placental function and the integrity of the cervix. In conclusion, HPV infection during pregnancy is a clinically relevant concern with potential implications for both maternal and fetal health. Standardized screening strategies, improved vaccination coverage, and longitudinal studies are needed to guide evidence-based clinical practice and policy development.}, }
@article {pmid41852383, year = {2025}, author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M}, title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1672438}, pmid = {41852383}, issn = {2813-4338}, abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.}, }
@article {pmid41852385, year = {2025}, author = {Ataei, P and Kalantari, H and Bodnar, TS and Turner, RJ}, title = {The gut-brain connection: microbes' influence on mental health and psychological disorders.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1701608}, pmid = {41852385}, issn = {2813-4338}, abstract = {The human gut microbiome has emerged as a pivotal modulator of brain function and mental health, acting through intricate bidirectional communication along the gut-brain axis. Mounting evidence suggests that microbial communities influence neurodevelopment, neurotransmission, and behavior via pathways involving the vagus nerve, immune signaling, and microbiota-derived metabolites such as short-chain fatty acids and neurotransmitter precursors. This review critically examines the mechanistic underpinnings of microbiota-brain communication and evaluates current findings linking dysbiosis to psychiatric conditions, including depression, anxiety, schizophrenia, autism spectrum disorder, and bipolar disorder. In addition, it assesses the therapeutic potential of microbiome-targeted interventions-such as probiotics, fecal microbiota transplantation (FMT), and precision dietary modulation-in ameliorating neuropsychiatric symptoms. While the field holds considerable promise, limitations, including correlational study designs, small sample sizes, and a lack of standardized methodologies, underscore the need for rigorous, large-scale clinical trials. A deeper understanding of host-microbe interactions may catalyze a paradigm shift in psychiatric treatment, paving the way for novel, personalized microbiome-based therapeutics.}, }
@article {pmid41852386, year = {2025}, author = {Zhu, B and McHale, SS and Van Scoyk, M and Riddick, G and Wu, PY and Chou, CF and Tossas, KY and Chen, CY and Winn, RA}, title = {Microbial hallmarks of the respiratory tract in lung cancer: a meta-analysis.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1589686}, pmid = {41852386}, issn = {2813-4338}, abstract = {INTRODUCTION: Lung cancer is a leading cause of cancer-related deaths and has been associated with the microbiota of the human respiratory tract. However, the optimal sample type for studying the role of microbiota in lung cancer and the microbial hallmarks of lung cancer patients remain unclear.<br><br>METHODS: In this study, we downloaded 16S rRNA sequencing data of 1,105 high-quality samples from 13 BioProjects, including lung tissues, bronchoalveolar lavage (BAL) fluids, and saliva, and performed a meta-analysis.<br><br>RESULTS: Our results revealed that the BAL microbiota, dominated by taxa such as Sphingomonas and Pseudomonas, which are not typically abundant in the oral microbiota, served as hallmarks of individuals without lung cancer. In contrast, BAL samples from lung cancer patients showed higher relative abundances of oral-associated taxa, e.g., Streptococcus and Prevotella, with increased rates of dominance by these taxa in the BAL microbiota of lung cancer patients. Additionally, beta diversity analysis revealed significant compositional differences between the BAL microbiota of healthy individuals and those with lung cancer. Furthermore, while compositional differences were observed in the oral microbiota between healthy participants and lung cancer patients, as well as between microbiota from lung tumors and normal adjacent tissues, these differences were less pronounced than those observed in the BAL samples between healthy individuals and lung cancer patients. Cross-site correlations indicated limited associations between the relative abundances of taxa in the oral, BAL, and lung tissue microbiota, implying that differences in lower respiratory microbiota may not be directly driven by upper respiratory tract microbiota.<br><br>DISCUSSION: These findings highlight distinct microbial patterns linked to lung cancer in the respiratory tract. More pronounced differences were observed in the BAL microbiota between healthy individuals and lung cancer patients, with the predominance of taxa, typically not abundant in the oral microbiota, serving as hallmarks of health.}, }
@article {pmid41852388, year = {2025}, author = {Roques, S and Koning, L and Bossers, A and van Gastelen, S and Schokker, D and Zaccaria, E and Šebek, L and Kar, SK}, title = {Farm conditions shape microbial communities and their association with methane intensity in dairy cattle: insights from the rumen microbiome at the community level.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1540197}, pmid = {41852388}, issn = {2813-4338}, abstract = {Rumen microbial communities are known to drive methane (CH4) production, but their dynamics in variable "real-world" farming environments are less understood. This research aims to identify specific microbial taxa linked to CH4 emission in commercial dairy farms by employing 16S rRNA gene sequencing, thereby providing a more ecologically relevant understanding of CH4 production in real-world settings.Rumen fluid samples were collected from 212 cows across seventeen Dutch dairy farms. Methane production was measured from these dairy cows using the GreenFeed system and expressed as CH4 intensity (g fat- and protein-corrected milk yield[-1]). Rumen microbiota was analyzed using 16S rRNA gene amplicon sequencing. Analysis was performed to assess association between microbial taxa and CH4 intensity, using data from individual cattle across the dairy farm. We observed that diet and lactation stage influenced CH4 intensity, consistent with previous studies. Results showed higher CH4 intensity in cows during late lactation, and feeding type, particularly fresh grass intake, strongly influenced rumen microbiota. However, after classifying low and high CH4 emitting cows, only limited differences in microbiota composition could be measured. Few taxa, like Lachnospiraceae, were common across both groups, while Ruminoccocaceae and Rikenellaceae were more abundant in low emitters, and Oscillospiraceae in high emitters. Methanobrevibacter differentiated CH4 emission groups, but archaeal methanogen abundance may not accurately reflect CH4 variation due to methodological limitations, including reliance on relative abundance, limited taxonomic resolution, and primer bias. Using a bacterial-biased 16S rRNA approach, we observed a limited number of consistent bacterial taxa associated with CH4 intensity highlights the challenges of studying dairy farms under practical conditions, where variability in diet, genetics, and management practices complicates the identification of specific rumen microbes associated with CH4 emission. Even with control over key variables, the inherent variability of on-farm conditions impeded the detection of stable microbial patterns. In conclusion, our study clearly indicates that understanding CH4 emissions from dairy cattle in real-world settings fundamentally requires a broader ecological perspective where rumen microbes are recognized as key determinants influencing microbiota signals within multi-factorial farm settings.}, }
@article {pmid41852389, year = {2025}, author = {Gaiser, L and Beblo-Vranesevic, K and Van Houdt, R and Fahrion, J and Gillet de Chalonge, L and Bunchek, JM and Zabel, P and Schubert, D and Rettberg, P}, title = {The EDEN ISS mobile test facility microbiome changes by cleaning and continued use.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1608732}, pmid = {41852389}, issn = {2813-4338}, abstract = {INTRODUCTION: Bioregenerative life support systems (BLSS) utilizing plants and/or microorganisms to provide the crew of a spacecraft with food, clean water, breathable air, and other amenities are likely to form key components of future long-distance spaceflight missions. Extensive testing and validation of such technologies are necessary before they can be implemented. EDEN ISS was a platform in Antarctica that tested various plant cultivation technologies for a BLSS. To ensure the continued operation of a BLSS, it is vital that plants remain healthy, which necessitates the monitoring of the plant production facility microbiome to ensure that pathogens are detected early and countermeasures can be engaged.<br><br>METHODS: Swab surface samples collected in the EDEN ISS Mobile Test Facility (MTF) during different campaigns were used to estimate the bioburden of the various surfaces via viable count. Isolates obtained from the cultivation of the surface samples were identified via partial 16S rRNA gene sequencing. Additionally, 16S amplicon sequencing was performed on DNA extracted directly from the swab samples to characterize the microbiome.<br><br>RESULTS AND DISCUSSION: The results revealed that the bioburden of the different sampling positions was not significantly reduced by cleaning, indicating that the employed cleaning regime was unsuited in its current form to adequately lower the bioburden. Identification of the isolates, as well as the full microbiome, revealed mostly environmental genera. However, in both cases, genera containing plant as well as human pathogens, like Pseudomonas and Acinetobacter, were identified and accounted for up to 16.1% of all reads for a sampling condition in the case of Pseudomonas. The two sets of sequencing data had little overlap, with Rhodococcus and Microbacterium being the only genera shared between all sampling conditions and sequencing approaches, and emphasized different aspects of the MTF microbiome, highlighting the advantages of using a combined approach to obtain a more complete picture of the microbiome composition.}, }
@article {pmid41852390, year = {2025}, author = {Adawi, M}, title = {The role of gut microbiota in autoimmune disease progression and therapy: a comprehensive synthesis.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1553243}, pmid = {41852390}, issn = {2813-4338}, abstract = {Autoimmune diseases arise from the immune system's dysregulated attack on the body's own tissues, influenced by a complex interplay of genetics, environment, and the microbiome. This comprehensive review and meta-analysis examines the dynamic relationship between gut microbiota and autoimmune diseases, highlighting their role in disease onset, progression, and potential therapeutic interventions. Emerging evidence underscores the bidirectional interactions between microbiota and immune pathways, particularly through mechanisms like mucosal immune modulation and regulatory T-cell activity. Microbiota dysbiosis, characterized by altered diversity and function, is consistently associated with autoimmune conditions such as rheumatoid arthritis, multiple sclerosis, and type 1 diabetes. The review identifies critical microbiota-driven factors, including antigenic mimicry and inflammatory signaling pathways that disrupt immune tolerance and exacerbate autoimmunity. Meta-analysis findings reveal a consistent reduction in microbial diversity across autoimmune diseases, emphasizing the role of specific taxa and their metabolites in influencing disease severity and immune responses. Therapeutic strategies, such as probiotics, prebiotics, and microbiome-targeted interventions, offer promising avenues to restore microbiome balance and mitigate autoimmune inflammation. Despite significant advances, challenges in methodology, limited longitudinal studies, and heterogeneity in results highlight the need for standardized research protocols and larger, well-controlled clinical trials. Future studies should prioritize personalized approaches to microbiome modulation, integrating dietary, genetic, and environmental factors to improve disease management and prevention. This work consolidates current knowledge, providing a framework for future research and clinical applications in the field of microbiome-autoimmune interactions.}, }
@article {pmid41852391, year = {2025}, author = {Kamassa, HE and Katawa, G and Isawumi, A and Olwal, C and Gbewonyo, WS and Quashie, PK and Bediako, Y}, title = {Understanding the role of oral and vaginal microbiomes in HPV-related cervical, head, and neck cancers: knowledge gaps and feasibility in Sub-Saharan Africa.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1576394}, pmid = {41852391}, issn = {2813-4338}, abstract = {Microbiome dysbiosis, characterized by an imbalance in the composition of microbial communities, has emerged as a potential risk factor for the development of cervical, head, and neck cancers. While previous studies have predominantly focused on high-income countries, there is a significant gap in understanding the relationship between microbiome alterations and cancer development in sub-Saharan Africa. Considering the unique socio-economic and environmental factors in this region, investigating the role of vaginal and oral microbiota in the progression of these cancers is crucial. This review explores the involvement of microbial dysbiosis in cervical, head, and neck cancers, particularly how it influences Human Papillomavirus-driven immune evasion, and highlights the importance of microbiota profiling in sub-Saharan Africa. The implications of these insights for cancer prevention and treatment strategies in this population are also discussed.}, }
@article {pmid41852393, year = {2025}, author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B}, title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1592023}, pmid = {41852393}, issn = {2813-4338}, abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.<br><br>METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.<br><br>RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (&#x3b1;-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (&#x3b2;-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (&#x3b1;-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.<br><br>DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.}, }
@article {pmid41852395, year = {2025}, author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C}, title = {Interplay between host genetics and gut microbiome composition in the Japanese population.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1635907}, pmid = {41852395}, issn = {2813-4338}, abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.<br><br>METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.<br><br>RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p &#x2264; 5&#xd7;10[-8]). However, none of these associations surpassed the stringent significance threshold of p &#x2264; 2.75&#xd7;10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.<br><br>CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.}, }
@article {pmid41852396, year = {2025}, author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K}, title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1688681}, pmid = {41852396}, issn = {2813-4338}, abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.<br><br>RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[&#x2122;] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[&#xae;] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.<br><br>CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.}, }
@article {pmid41852398, year = {2025}, author = {Burrill, HM and Magnoli, SM and Bever, JD}, title = {Soil microbiome composition is highly responsive to precipitation and plant composition manipulations in a field biodiversity experiment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1460319}, pmid = {41852398}, issn = {2813-4338}, abstract = {INTRODUCTION: Climate change and plant biodiversity loss have large impacts on terrestrial ecosystem function, with the soil microbiome being primary mediators of these effects. The soil microbiome is a complex system, consisting of multiple functional groups with contrasting life histories. Most studies of climate forces and plant biodiversity effects on microbiome consider the perturbations and the microbial functional groups in isolation preventing us from understanding the full picture of the relative and differential impacts of perturbations on microbial functional groups.<br><br>METHODS: We measured changes in multiple microbial communities with different functionality, including plant mutualists and pathogens, after three growing seasons in a full-factorial experiment manipulating precipitation (50%, 150% of ambient), plant diversity, and plant composition. Using amplicon sequencing to characterize the response of fungi, arbuscular mycorrhizal fungi, bacteria and oomycetes, and we found that composition of all microbial groups differentiated strongly between precipitation treatments.<br><br>RESULTS: Oomycete and bacterial diversity increased with 150% precipitation, while AM and saprotroph fungal diversity decreased. Microbial differentiation in response to plant family and plant species composition was stronger after the third growing season than observed after year one. However, microbial response to plant species richness was weaker in year three. Microbiome response to plant composition was largely independent of the response to precipitation, except for oomycetes, which had greater response to plant composition in high precipitation.<br><br>DISCUSSION: These findings build upon prior findings that these microbial community members differentially respond to plant community compositional treatments, by measuring the response over 3 years and with the addition of precipitation treatments. We find that both changes in climate and plant composition can drive major differences in soil microbiome composition, which can feed back on plant community structure and alter ecosystem function.}, }
@article {pmid41852400, year = {2025}, author = {Fischer, A and Singh, JP and Van Hamme, J and Bottos, E and Fraser, LH}, title = {Investigating impacts from topsoil stockpile height on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1607677}, pmid = {41852400}, issn = {2813-4338}, abstract = {Mining activities are often severely disruptive to the landscape, and a significant barrier to reclamation following mining operations is the lack of quality topsoil. This project addresses knowledge gaps in the industry by exploring the compositional nature of topsoil stockpiles and their ability to facilitate post-mining revegetation after long-term storage. To do this, we conducted a microbial profiling of two topsoil stockpiles in the interior of British Columbia, Canada. Both stockpiles show depleted soil quality and significant changes compared to reference soils. Notably, there were declines in microbial diversity and significant shifts in community structure with increasing stockpile depths in one of the stockpiles. These results highlight the influence of topsoil-stockpile height on microbial communities in the soil, which ultimately influences the success of restoration. This research can help the industry to optimize restoration and expedite recovery in their mine-closure practices and provides insights into the general structure of the microbiome existing across a gradient in severely disturbed mining soils.}, }
@article {pmid41852401, year = {2025}, author = {Abegaz, F and Abedini, D and Dong, L and Westerhuis, JA and van Eeuwijk, F and Bouwmeester, H and Smilde, AK}, title = {Analysis of microbiome high-dimensional experimental design data using generalized linear models and ANOVA simultaneous component analysis.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1584516}, pmid = {41852401}, issn = {2813-4338}, abstract = {In microbiome studies, addressing the unique characteristics of sequence data-such as compositionality, zero inflation, overdispersion, high dimensionality, and non-normality-is crucial for accurate analysis. In addition, integrating experimental design elements into microbiome data analysis is important for understanding how factors such as treatment, time, and interactions affect microbial abundance. To achieve these objectives, we developed a new method that combines generalized linear models (GLMs) with ANOVA simultaneous component analysis (ASCA), which we term GLM-ASCA. This method aims to improve microbiome analysis by providing a more comprehensive understanding of differential abundance patterns in response to experimental conditions. GLM-ASCA models the unique characteristics of microbiome sequence data with GLMs and uses ASCA to effectively separate the effects of different experimental factors on microbial abundance. We evaluated GLM-ASCA using simulated data and subsequently applied it to real data to analyze the effect of nitrogen deficiency on root microbiome recruitment in tomato. Simulation studies demonstrated the effectiveness of GLM-ASCA in analyzing microbiome data in complex experimental designs, and the real-data application revealed valuable insights into the dynamics of microbial communities under nitrogen starvation, including the identification of beneficial bacterial species that promote tomato (Solanum lycopersicum) growth and health through nitrogen fixation.}, }
@article {pmid41852402, year = {2025}, author = {Forehand, CR and Smith, SN and Nielsen, F and Bauer, B and Watters, JL and Moody, RW and Becker, DJ and Lanier, H and Marske, K and Siler, C}, title = {Comparative assessment of Texas horned lizard (Phrynosoma cornutum) gut microbiome diversity and composition throughout transition from captivity to wild.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1601442}, pmid = {41852402}, issn = {2813-4338}, abstract = {Microbiomes play a key role in the health of animal hosts. To improve conservation translocation programs like headstarting, it is necessary to consider how the structure of these programs impact the host-associated microbiome. Bringing animals into captivity introduces novel diets and environments; however, the extent to which these factors contribute to the structure of the host's gut microbiome remains poorly understood. Additionally, it is unclear if periods of captivity leave a lasting signature on the host-associated gut microbiome, which could impact individual health and fitness in the long-term. In this study, we repeatedly sampled the gut microbiome of a cohort of headstart Texas horned lizards (Phrynosoma cornutum) throughout their transition from captivity to the wild. We also collected samples of extrinsic microbial communities present in their captive and wild diet and environment. Finally, we sampled the gut microbiome of wild resident lizards to serve as a baseline comparison. Using 16S rRNA microbial inventories, we examined differences in microbial community composition and diversity between pre-release headstart, post-release headstart, and resident lizards of the wild population. Additionally, we assessed the contribution of environmental and dietary microbial communities to the assembly of P. cornutum gut microbiomes in captivity and the wild. Our results suggest captive P. cornutum harbor gut microbiomes that are distinct from their wild counterparts. However, within two-months post-release, the headstart gut microbiome restructures to be indistinguishable from the wild resident microbiome. Microbiomes associated with the captive diet and environment are distinct in beta diversity, but not alpha diversity, from those in the wild. Our results provide important insights into host-associated microbiome dynamics associated with transition from captivity to the wild and can be used to inform conservation translocation practices.}, }
@article {pmid41852403, year = {2025}, author = {Helal, M and Bari, VK}, title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1549166}, pmid = {41852403}, issn = {2813-4338}, abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.}, }
@article {pmid41852404, year = {2025}, author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y}, title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1531991}, pmid = {41852404}, issn = {2813-4338}, abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.<br><br>METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.<br><br>RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.<br><br>CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.}, }
@article {pmid41852407, year = {2025}, author = {Reddy B S, Y and Doraiswamy, C and Singh, D and Surendra, N and Damle, A and Dutta, M and Rajkumar, S and Potterf, B and Roy, A and Cheviti, B and Dadd, T and Arnold, D and Paterson, S and Sachdev, M and Van-Der Logt, P and Nair, N and Chandra, N}, title = {Microbial dysbiosis in melasma through community profiling.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1505565}, pmid = {41852407}, issn = {2813-4338}, abstract = {BACKGROUND: The complex ecosystem on skin comprising tens of thousands of microorganisms plays an important role in health and disease. The last decade in particular has witnessed a surge in microbiome research, which has been elucidating the role of the microbiota in numerous skin pathologies. Of relevance to the current study, are recent evidences implicating the microbiome in skin pigmentary conditions. Melasma is one such refractory, hyperpigmentary condition with a poorly understood pathogenesis. The present study was carried out to characterize the nature of microbial dysbiosis and its impact on microbial community structure in melasma subjects.<br><br>RESULTS: The clinical assessment of melasma carried out using biophysical, biochemical and biomarker-based measures confirmed significant changes in melasma lesions, most notably, those linked to redox, inflammation and barrier properties. A deep characterization of the skin microbiome in melasma from human face, indicated significant differences between lesional and peri-lesional areas. Of the 377 genera identified through an agglomeration of all OTUs at the Genus level through 16S rRNA sequencing, 344 were common, while 12 were unique to lesional and 21 unique in peri-lesional areas. A significant decrease was observed in alpha diversity in melasma lesion as compared to peri-lesion areas, with an accompanying decrease in number of interconnections among them. The differences in the microbiome also appeared to correlate with several clinical parameters, notably with the melasma severity measured through modified MASI (mMASI) scoring. The observed changes in both host and microbiome, point to a potential role for the latter in melasma pathogenesis.<br><br>CONCLUSIONS: Our study indicates that there are significant differences in the microbiome between lesional and peri-lesional areas of melasma subjects, with associated changes in microbial community structures. Additionally, the observed changes were seen to correlate with measured clinical parameters. These findings provide the opportunity to further probe the nature of host and microbiome links that may underlie the phenotypic manifestation, as well as provide effective routes for managing this recalcitrant disorder.}, }
@article {pmid41852409, year = {2025}, author = {Bailey, A and Leuther, KK and Robinson, LA}, title = {The microbiome and lung cancer: microbial effects on host immune responses and treatment outcomes.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1606551}, pmid = {41852409}, issn = {2813-4338}, abstract = {The human microbiome plays a critical role in shaping physiological processes, immune system function, metabolism, and disease development. Recent research has highlighted the microbiome's profound cancer impact, particularly on lung cancer. This review explores how microbial communities in lung and gut influence tumor progression, immune responses, and treatment outcomes as well as describing the interactions between the microbiome and the host immune system in modulating the efficacy of cancer therapies. Emerging evidence from preclinical and clinical studies investigating the role of the lung and gut microbiome in lung cancer focus on alterations in the microbiota that influence the tumor microenvironment, modulate immune responses, and potentially enhance/hinder treatment effectiveness such as chemotherapy, targeted therapies, and immunotherapy. Microbial diversity plays a significant role in immune regulation, and specific microbial species may activate/suppress immune cells such as T-cells, dendritic cells, and macrophages. Furthermore, this review examines the therapeutic implications of microbiome modulation, including the use of probiotics, antibiotics, and fecal microbiota transplantation in enhancing cancer therapies. Alterations in the lung and gut microbiome and their interaction in the recently described gut-lung axis with its bidirectional communication significantly influence the tumor microenvironment and systemic immune responses. These findings suggest that microbial diversity can regulate immune functions, with specific species capable of activating or suppressing immune cell activity. Furthermore, microbiome-targeted interventions show potential in improving the effectiveness of treatments including chemotherapy, targeted therapies, and immunotherapy, underscoring the importance of the microbiome as a key factor in lung cancer pathogenesis and treatment.}, }
@article {pmid41852412, year = {2025}, author = {Craft, AK and Karapareddy, S and Anche, VC and Janga, MR and Soyinka, O and Sanathanam, SK and Nyaku, ST and Sharma, GC and Senwo, Z and Sripathi, VR}, title = {Effects of biopolymers, cork, and Rhizobium tropici-derived extracellular polymeric substances on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1614472}, pmid = {41852412}, issn = {2813-4338}, abstract = {INTRODUCTION: Soil microorganisms play a crucial role in plant development, while biopolymers, such as cork and Extracellular Polymeric Substances/Exopolysaccharides (EPS), can enhance soil health. However, these amendments may affect DNA extraction and microbial analysis, necessitating the validation of the extraction method before conducting next-generation sequencing (NGS).<br><br>METHODS: This study evaluated 48 soil samples from Decatur, Alabama (Silt loam) that underwent four treatments: unamended soil (soil.control), soil with cork (soil.cork), soil with EPS (soil.EPS), and soil with both cork and EPS (soil.cork.EPS). Samples were collected at four time intervals (0-, 24-, 48-, and 72-hours post-treatment), with three biological replicates for each treatment. The FastDNA Spin Kit proved the most effective among the six DNA extraction methods tested.<br><br>RESULTS AND DISCUSSION: Amplicon sequencing of the 16S rRNA gene identified 62,996 amplicon sequence variants (ASVs), with 513 ASVs shared across all time points and 467 ASVs shared among the different treatments. The microbial community was primarily composed of Actinobacteria, Proteobacteria, and Acidobacteria, with Actinobacteria being the most abundant phylum. Actinobacteria, Alphaproteobacteria, Bacilli, and Betaproteobacteria contributed to microbial diversity at the class level. Notable families such as Bacillaceae, Gaiellaceae, Micromonosporaceae, and Streptomycetaceae showed treatment-dependent variations. Core microbiome analysis revealed Bacillus and Gaiella as the dominant genera, which play vital roles in soil ecosystem stability and nutrient cycling. These microbes contribute to carbon sequestration, nitrogen fixation, and phosphorus solubilization, improving soil fertility and plant-microbe interactions. These findings offer valuable insights into microbial dynamics in amended soils, providing information that can improve soil quality and agricultural productivity.}, }
@article {pmid41852413, year = {2025}, author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH}, title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1707779}, pmid = {41852413}, issn = {2813-4338}, abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.}, }
@article {pmid41852414, year = {2025}, author = {Oliver, L and Malagón, M and Ramió-Pujol, S and Sánchez-Vizcaino, M and Sánchez-Algans, R and Lacosta, E and Saéz-Zafra, M and Serra-Pagès, M and Aldeguer, X and Garcia-Gil, J and Oduber, S}, title = {Categorizing and characterizing intestinal dysbiosis: evaluating stool microbial test clinical utility.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1512257}, pmid = {41852414}, issn = {2813-4338}, abstract = {BACKGROUND: Interest in the intestinal microbiota has surged in recent years, leading to the development of various microbiota tests utilizing stool analysis. This study aimed to assess the clinical utility of the TestUrGut.<br><br>RESULTS: The abundances of different microbial markers analyzed correlated with various factors and symptoms. While no age differences were observed, an increase in A. muciniphila abundance was noted in women compared to men. Body mass index significantly influenced the abundance of A. muciniphila and M. smithii. Additionally, variations in the abundances of A. muciniphila and M. smithii, as well as a greater presence of Firmicutes or Bacteroidetes based on stool patterns, were linked to diarrhea or constipation. The dysbiosis index was validated, distinguishing between temporary and pathological dysbiosis.<br><br>CONCLUSIONS: This study revealed significant relationships between the intestinal microbiota and digestive tract symptoms. Microbial markers have emerged as robust indicators of the overall state of the intestinal microbiota, demonstrating that variations are closely associated with patients' clinical symptoms.}, }
@article {pmid41852415, year = {2025}, author = {Hinsu, A and Dai, X and Dadousis, C and Hay, M and Fosso, B and Crotta, M and Pandit, R and Guitian, J and Tomley, F and Koringa, P and Joshi, C and Blake, D and Psifidi, A}, title = {Unveiling host-genetic drivers of caecal microbial communities in chickens through genome-wide association studies.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1539923}, pmid = {41852415}, issn = {2813-4338}, abstract = {Enteric microbiota plays a crucial role in the health and productivity of poultry, including influences on nutrient absorption, immune function, and pathogen resistance. In this study, we conducted a genome-wide association study (GWAS) to identify host genetic variants associated with selected bacterial genera found in chickens. We used high-density 600K SNP Affymetrix DNA arrays for genotyping, alongside 16S rRNA gene sequencing to profile caecal microbiota from the same individual chickens. A commercial broiler line (Cobb400, n = 300) and an indigenous (Kadaknath, n = 300) chicken breed from India were investigated, allowing for a comprehensive cross-ecotype analysis. Our analysis identified several host-genetic markers and candidate genes associated with the presence and abundance of specific bacterial genera with known pathogenic or commensal roles, and with specific caecal Enterotypes. Whole-genome sequencing data were then used to further investigate candidate regions around significantly associated variants from the high-density DNA array. Of note, we found markers nearby the genes coding for classical complement activation component C1q, ephrin receptors, and other immunity and inflammatory responses as well as genes coding for products associated with vitamin and co-factor metabolism. The results underscore the impact that host genetics has on the regulation of the gut microbiota and highlights potential pathways through which host genetic variation influences host-bacterial crosstalk and potentially modulates microbial community structure. These findings contribute to the growing understanding of the genetic basis of host-microbiota interactions and offer new avenues for improving poultry health and productivity through selective breeding strategies targeting the microbiome.}, }
@article {pmid41852417, year = {2025}, author = {Rius-Sansalvador, B and Bars-Cortina, D and Khannous-Lleiffe, O and Garcia-Serrano, A and Guinó, E and Saus, E and Gabaldón, T and Moreno, V and Obón-Santacana, M}, title = {Stability of oral and fecal microbiome at room temperature: impact on diversity.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1334775}, pmid = {41852417}, issn = {2813-4338}, abstract = {INTRODUCTION: When collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing are not always feasible. It is essential to study the impact of temporary room temperature (RT) storage on microbiome diversity.<br><br>METHODS: We conducted a pilot study to validate a sampling protocol based on the viability of 16S rRNA gene sequencing in microbiome samples. Fecal and oral samples from five participants were collected and preserved under different conditions: a) 70% ethanol; b) FIT tube for stool; and c) chlorhexidine solution for oral wash. Four aliquots per sample were stored at RT and frozen at days 0, 5, 10, and 15.<br><br>RESULTS: Alpha diversity showed a maximum average decrease of 0.3%, 1.6%, and 1.7% after 5 days for oral, stool in ethanol, and stool in FIT samples, respectively. The relative abundances of the main phyla and orders remained stable throughout the 15 days.<br><br>DISCUSSION: Microbiome diversity appears remarkably resilient. Fecal and oral samples stored at RT in 70% ethanol, chlorhexidine, and FIT tubes exhibited minimal changes over 15 days. These results support the feasibility of large-scale microbiome studies with delayed sample processing.}, }
@article {pmid41852421, year = {2025}, author = {Schweikhard, J and Pauly, A and Dierkes, PW and Zoelzer, F}, title = {From leaves to microbes: How diet and season shape the fecal microbiome of captive Coquerel´s Sifakas (Propithecus coquereli).}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1680152}, pmid = {41852421}, issn = {2813-4338}, abstract = {The community of microorganisms occurring in the animal gut, known as the gut microbiota, is closely connected to host health. It is essential for metabolic processes, digestion, and defense against pathogens. Knowledge about the composition of an intact gut microbiota, along with its natural fluctuations and diversity, is a crucial aspect of proper husbandry and breeding of animals in human care. In this study, we analyzed the fecal microbiota of the critically endangered Coquerel's sifaka (Propithecus coquereli), with a special focus on seasonal effects and the impact of dietary variations. As a tropical species, European winters may influence microbiota diversity or composition, highlighting the importance of this assessment. Ninety-seven fecal samples collected from all individuals housed in European zoos revealed high microbial diversity and variation. Some of the core taxa present in every sample included Lachnospiraceae, Erysipelotrichaceae, Clostridiaceae, and Bacillaceae. Microbial α-diversity showed no decline in winter, indicating no seasonal effect caused by dietary changes. However, results suggest compositional differences between seasons, indicated by significant differences in β-diversity. These findings confirm the importance of longitudinal studies to fill knowledge gaps between sampling intervals and to characterize microbiota oscillations throughout the year.}, }
@article {pmid41852422, year = {2025}, author = {Balacco, DL and Bardhan, A and Ibrahim, H and Kuehne, SA and Grant, MM and Hirschfeld, J and Heagerty, AHM and Chapple, IL}, title = {Optimisation of cutaneous microbiota sampling methodology.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1559981}, pmid = {41852422}, issn = {2813-4338}, abstract = {INTRODUCTION: The cutaneous microbiome plays an essential role in guarding against invasive pathogens and maintaining healthy skin homeostasis. Several studies have demonstrated the importance of a healthy skin microbiome through its alteration in several diseases. Differing skin characteristics across the body (temperature, pH, humidity) create distinct ecological niches inhabited by diverse microbial communities. The study of cutaneous microbiota is further complicated by numerous variables at all stages of investigation, including study design, skin sampling method, sample storage, sample processing, sequencing, and data analysis. Utilisation of standardised approaches is critical for reproducibility and comparison between skin microbiome studies. However, there is a notable lack of standardisation of sampling methodologies in the literature. Studies have employed differing sampling strategies and conditions which may affect microbiota characterisation.<br><br>METHODS: Antecubital fossa was sampled from sixteen individuals using sterile dry cotton swabs or eSwabs. Sterile phosphate buffered saline, or 0.9% sterile saline were used as moistening solutions. Samples were then either stored at room temperature for 30 minutes or stored at -80&#xb0;C for at least 24 hours before processing. Cutaneous microbiome was identified using 16S sequencing.<br><br>RESULTS: Comparative analysis determined whether the type of swab (cotton/eSwab), moistening solution (saline solution/phosphate buffered saline), duration of swabbing (30 sec/1 min), and sample storage temperature (room temperature/-80&#xb0;C) affect sampling and identification of skin microbial communities. Comparison of the total DNA yield extracted using different conditions showed that while moistening solution, duration of swabbing, and storage conditions did not affect the total DNA amount, using eSwabs yielded higher biomass.<br><br>DISCUSSION: Sampling approaches are critical for the success of sequencing. The conditions investigated in this study did not influence microbiome profiling allowing consistent sampling of the microbiota. However, data clustering was affected more by individual subject than by the conditions investigated, suggesting the importance of recognizing inter-individual variability as an important factor in real-life skin microbiome studies.}, }
@article {pmid41852423, year = {2025}, author = {Yang, R and Hammamieh, R}, title = {Editorial: Gut microbiota modulation to mitigate stress-induced functional changes.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1731851}, doi = {10.3389/frmbi.2025.1731851}, pmid = {41852423}, issn = {2813-4338}, }
@article {pmid41852425, year = {2025}, author = {Yoosefzadeh Najafabadi, M and Khalaf, EM and Mysara, M and El-Baz, AM}, title = {Editorial: Harnessing machine learning to decode plant-microbiome dynamics for sustainable agriculture.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1602938}, pmid = {41852425}, issn = {2813-4338}, }
@article {pmid41852426, year = {2025}, author = {Flynn, CM and Blackburn, LM and Yuan, Q}, title = {Probiotic supplementation prevents stress-impaired spatial learning and enhances the effects of environmental enrichment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1454909}, pmid = {41852426}, issn = {2813-4338}, abstract = {Probiotics are live microorganisms that offer health benefits, influencing the microbiota-gut-brain axis. Probiotics can improve cognitive functions, including learning and memory, by modulating the gut microbiota, reducing inflammation, and producing neuroactive substances. This study examined the effects of probiotic supplementation prior to chronic stress or enrichment (EE) treatment on cognitive function and brain physiology. Rats received probiotics or control diet starting at 6 months of age for 3 months. They were then randomly assigned to unpredictable stress, or EE for 6 weeks, with a home cage control group on a control diet included. Results showed that probiotic supplementation prevented spatial memory impairments induced by chronic stress and enhanced learning when combined with EE. These behavioral improvements were linked to increased gut microbiome diversity. Higher levels of the microglia marker Iba-1 were found in the stressed group compared to the EE group in the locus coeruleus, which probiotic reversed. Differences in blood-brain-barrier integrity were observed between the stress and EE groups, as indicated by albumin levels. Higher levels of tyrosine hydroxylase were observed in the hippocampus of the EE groups. The interaction of probiotic supplementation, chronic stress, and environmental EE offers a promising area for enhancing cognitive function and brain health.}, }
@article {pmid41852427, year = {2025}, author = {Al-Kuwari, A and Al-Karbi, H and Al-Khuzaei, A and Baroudi, D and Bendriss, G}, title = {Beyond antibiotics: leveraging microbiome diversity to combat antimicrobial resistance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1618175}, pmid = {41852427}, issn = {2813-4338}, abstract = {The best way to fight harmful microbes may not lie in new antibiotics, but rather in leveraging the power of microbes themselves. Antimicrobial resistance (AMR) is a growing global concern, where the overuse of antibiotics has led to the emergence of resistant strains. This paper explores the potential of increasing diversity in gut microbiomes as natural approaches to fight AMR. The promotion microbial diversity is proposed as a promising strategy to reduce dependency on antibiotics by fostering a resilient microbial community. Strategies are discussed to address the loss of diversity caused by antibiotics including diet, probiotics, fecal transplants (FMT) and fermentation of animal/plant products. Preliminary findings from an experiment with camel milk fermentation suggest that fermentation can increase microbial diversity, potentially affecting resistance to common antibiotics such as tetracycline, streptomycin, penicillin, and chloramphenicol, and enhancing microbiome resilience, allowing it to naturally resist pathogens without additional antibiotic use. The results highlight both the benefits and potential risks fermented products. Additionally, FMT, naturally occurring in the animal world, is a promising method to restore microbiome balance and mitigating the impact of AMR. A mechanistic model is discussed to underscore the importance of maintaining microbial balance as an effective strategy for mitigating AMR and promoting long-term health. Further research are needed to better understand the mechanisms behind these changes and their implications for public health. This perspective paper calls for a shift in the approach to AMR, advocating for microbiome-based solutions as a sustainable alternative to traditional pharmaceutical interventions.}, }
@article {pmid41852428, year = {2025}, author = {Asefa, Z and Belay, A and Welelaw, E and Haile, M}, title = {Postbiotics and their biotherapeutic potential for chronic disease and their feature perspective: a review.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1489339}, pmid = {41852428}, issn = {2813-4338}, abstract = {Postbiotics, which are bioactive compounds derived from the metabolic processes of probiotics, are gaining recognition as a promising alternative for managing chronic diseases without the need for live microorganisms, positioning them as a valuable strategy in biotherapeutics that offers both curative and preventive techniques in modern medicine. This paper provides a comprehensive review of the potential health benefits of postbiotics, particularly concerning noncommunicable diseases like diabetes, cancer, obesity and cardiovascular conditions, which present significant global health challenges. We explore the various mechanisms by which postbiotics exert their beneficial effects, including immune modulation to enhance the body's immune response and reduce inflammation, as well as improving gut barrier function to maintain gut integrity and prevent increased intestinal permeability. Additionally, the antioxidant properties of postbiotics play a critical role in neutralizing oxidative stress, which is linked to the progression of chronic diseases. Despite the encouraging insights into their health benefits, we highlight the urgent need for further research to clarify the specific roles of different postbiotic components. A deeper understanding of these mechanisms is essential for developing targeted preventive healthcare applications, and by advancing this knowledge, we aim to create innovative strategies that could significantly enhance health outcomes for at-risk populations. Ultimately, integrating postbiotics into health interventions has the potential to improve preventive care and contribute to the overall well-being of affected individuals and communities.}, }
@article {pmid41852429, year = {2025}, author = {Cuperus, T and Kool, J and Boverhoff, D and van der Ark, K and Opsteegh, M and Fuentes, S}, title = {Prevotella as the main driver for the association between dairy farming and human gut microbiome composition.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1612922}, pmid = {41852429}, issn = {2813-4338}, abstract = {The human gut microbiota is shaped by a multitude of environmental factors, including contact with animals. To investigate the association between occupational exposure to cattle and the gut microbiome, a cross-sectional study was performed on 65 individuals working and/or living on Dutch dairy cattle farms in comparison to controls. The gut microbiome of the participants was assessed by 16S rRNA gene amplicon sequencing of stool samples. A lower alpha diversity and divergent microbiome composition was observed, driven largely by a greater Prevotella abundance in dairy farm participants when compared to controls. Prevotella was also associated with contact frequency with the dairy cattle, with participants with more frequent contact showing higher abundance. The results of this study show occupational contact with cattle is associated with gut microbiome composition, which is of relevance because of the importance of the microbiome for human health.}, }
@article {pmid41852430, year = {2025}, author = {da Cruz, RS and Suguru, S and Paiva, SPC and Nwugwo, I and Kallakury, B and Weinberg, BA and Cook, KL and de Assis, S}, title = {Obesity reprograms the normal pancreas and pancreatic cancer microbiome in mice and humans.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1543144}, pmid = {41852430}, issn = {2813-4338}, abstract = {INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive form of pancreatic cancer, with overall 5-year survival rates of about 8%. Obesity (and underlying metabolic dysfunction) is estimated to account for up to 50% of all PDACs. Microbial communities can be modulated by obesity and exert biological effects on tissues they colonize as well as distant sites. Recent studies showed that tumors, including PDAC, harbor a microbiome that is able to regulate cancer outcomes such as tumor progression, response to therapy and overall survival. Yet, it is not understood whether patient's characteristics impact this relationship.<br><br>METHODS: We examined the influence of obesity (defined by body weight in mice or body mass index [BMI] in humans) on the normal and cancerous pancreas microbiome in mice and humans using 16S sequencing.<br><br>RESULTS: Overall, we observed that diet-induced obesity accelerated PDAC progression in the KC mouse model of PDAC. We also detected an obesity-induced decrease in the microbial abundance of the normal or cancerous pancreas. Obesity modified the bacterial community composition in the normal pancreas and PDAC of both mice and humans. Further, obese animals and humans each had a distinctive pancreatic microbiome signature with specific bacterial phylum, genus and species compared to controls. Notably, both the normal mouse pancreas and human PDAC showed an obesity-induced decrease in Pseudomonadota phylum. We also found that the presence of cancer by itself reduced microbial diversity in both the pancreas as well the intestinal microbiota. This reduction in microbial richness was further exacerbated by obesity. Finally, we observed that obesity increased inflammatory cytokines and altered the tumor immune infiltrate in humans and mice.<br><br>DISCUSSION: Further investigation of obesity-driven microbial differences in the pancreas could provide important insights for personalized treatments for PDAC patients.}, }
@article {pmid41852431, year = {2025}, author = {Antoni, D and Rump, M and Gerdts, G}, title = {Olivine and dissolved alkalinity trigger different bacterial community shifts in water and oyster gills: insights from a mesocosm experiment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1659695}, pmid = {41852431}, issn = {2813-4338}, abstract = {Ocean Alkalinity Enhancement (OAE) is a proposed marine carbon dioxide removal strategy that increases seawater buffering capacity and CO2 uptake through the addition of alkaline substances. While OAE shows promise as a climate mitigation tool, its ecological implications remain poorly understood, particularly regarding microbial communities. This paper provides a risk assessment of two different OAE strategies: alkalization with olivine and alkalization with addition of dissolved sodium hydroxide (NaOH). With a mesocosm experiment designed to simulate coastal OAE application, European flat oysters (Ostrea edulis) were chronically exposed to alkalinity-enhanced seawater at two concentrations (250 and 500 µmol·L[-][1]) derived either from olivine weathering or addition with NaOH. The bacterial community composition of both alkalization types was assessed with amplicon sequencing of the 16S rRNA gene and ecotoxicological impacts were compared to a non-alkalized control. The sampling strategy included samples of the treated waters and the gill microbiome of Ostrea edulis. Our results show that the alkalization type was the primary driver of microbial shifts in the bacterial community of the water samples. Olivine treatments caused distinct taxonomic changes, including an increase in Gammaproteobacteria and Flavobacteriales and a marked decline in Alphaproteobacteria and SAR11 clade. Olivine-treated waters showed reduced richness and evenness. In contrast, dissolved alkalinity treatments produced minimal changes compared to untreated controls. The analysis of the oyster gill microbiome detected a response that was stronger influenced by alkalinity concentration than by alkalization type. Notably, high-alkalinity olivine treatments favored potentially pathogenic Vibrios. Together, these findings highlight that OAE method selection significantly influences bacterial community composition in both marine and host-associated microbiomes. In our experiment, olivine-based OAE posed a greater environmental risk than dissolved OAE. Our study provides insights on the impact of different OAE scenarios, representing a first step toward future field trials and applications.}, }
@article {pmid41852433, year = {2025}, author = {Delamare-Deboutteville, J and Mahmuddin, M and Gan, HM and Rodde, C and Khor, L and Verner-Jeffreys, D and Mohan, CV and Benzie, JAH}, title = {Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT).}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1567816}, pmid = {41852433}, issn = {2813-4338}, abstract = {INTRODUCTION: Tilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry's reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential for identifying the characteristics that constitute a healthy microbial community.<br><br>METHODS: In this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia. We compared them to those reared in earthen ponds on another farm in Malaysia.<br><br>RESULTS: A total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species. Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%). At the same time, other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples exhibited notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition.<br><br>DISCUSSION: These results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of practical microbiome monitoring strategies, such as early-warning tools for farm health, and inform targeted interventions to improve aquaculture performance.}, }
@article {pmid41852434, year = {2025}, author = {Chen, XD}, title = {Understanding of the effect of microbiome on human health: a chemical process engineering perspective.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1605814}, pmid = {41852434}, issn = {2813-4338}, abstract = {Aspects about the straightforward linking of gut health or the gut microbiota with existing diseases are critically explored. While there is a popular notion that gut health directly influences overall health and can cause or alleviate diseases, the mechanisms behind these effects are not fully understood. Chemical process engineering (CPE) concepts bring new insights into the effects of human microbiome, which may clarify the fundamental influences. The discussions presented here suggest the future directions of research, which need to be pursued for the benefit of human health.}, }
@article {pmid41852436, year = {2025}, author = {Kollath, DR and McAulay, K and Higgins Keppler, EA and Reilly, KS and Sakata, KK and Barker, BM and Grys, TE}, title = {Active fungal infections alter the respiratory microbiome profiles of Mayo Clinic Arizona patients.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1699912}, pmid = {41852436}, issn = {2813-4338}, abstract = {INTRODUCTION: The function of the respiratory microbiome during an active infection is not well characterized. Studies from the gut microbiome suggest a diverse community can aid in modulating the immune system to control infectious pathogens.<br><br>METHODS: To determine if there are microbial community compositional changes in the human lung during an infection, we conducted an analysis of both the 16S rDNA and the Internal Transcribed Spacer (ITS) region of DNA from bronchoalveolar lavage fluid (BALF) of patients from Mayo Clinic Arizona. In addition to general classification, we assessed differences in the lung microbiome of patients with different infections including coccidioidomycosis, a common fungal pneumonia in Arizona.<br><br>RESULTS: We observed patterns of dysbiosis in the lung microbiome during active fungal infection. Patients with active coccidioidomycosis infections had an overabundance of Malassezia, Epicoccum, and Penicillium species in the fungal communities and bacteria in the classes Bacilli, Bacteroidia, Clostridia, and Gammaproteobacteria. Patients with disseminated coccidioidomycosis showed evidence of extreme dysbiosis in the lung microbiome with a significant overabundance of Malassezia and Bacilli. We also observed differences in the fungal communities of patients with an active Candida albicans infection, with an overabundance of the genera Candida and Nakaseomyces. Additionally, we observed a decrease in diversity in the lung fungal communities in patients with an active Coccidioides or Candida infection but no difference in the bacterial community.<br><br>DISCUSSION: These compositional changes in the lung microbiome during an active Coccidioides spp. infection associated with shifts in the fungal community. This is the first study to examine how these fungal pathogens affect the lung microbial community of humans.}, }
@article {pmid41852437, year = {2025}, author = {Ment, D and Mishra, S}, title = {The integral role of the Black Soldier fly, Hermetia illucens L., microbiota in its life history.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1517715}, pmid = {41852437}, issn = {2813-4338}, abstract = {The Black Soldier fly (BSF), Hermetia illucens, exhibits versatile bioconversion abilities and effectively transforms various waste materials into a nutritious biomass suitable for consumption. The degradation ability of BSF larvae has been attributed to their gut microbiota. Therefore, this review explores the role of the BSF microbiota throughout the BSF life stages in the bioconversion, focusing on the BSF larvae and its microbiota. We reflect on the microbiota's contribution to life cycle aspects, growth, reproduction, immune response, and waste breakdown. The key points discussed include the gut microbiota in organic waste bioconversion by BSF larvae, the role of microbiota in BSF oviposition and growth throughout its life history, and microbiota's role in immunity with a specific focus on antimicrobial peptides. Where knowledge gaps were identified for BSF, we provide examples of closely related dipteran insects or insects with well-studied microbiota functioning. The significant role of the BSF gut microbiota is enabling its versatile waste degradation while conferring protection against pathogens and xenobiotic compounds. As such, we discuss the future perspectives that microbiome engineering may offer for BSF.}, }
@article {pmid41852438, year = {2025}, author = {Machado, JLP and Schaan, AP and Mamede, I and Fernandes, GR}, title = {Gut microbiota and type 2 diabetes associations: a meta-analysis of 16S studies and their methodological challenges.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1506387}, pmid = {41852438}, issn = {2813-4338}, abstract = {Diabetes mellitus is a prevalent chronic non-communicable disease, and recent studies have explored the link between gut microbiota and its development. Despite some evidence suggesting an association, the influence of gut microbiota on type 2 diabetes (T2D) remains unclear. A systematic search of PubMed (January 2016- December 2023) using the keywords "16S" and "diabetes" or "DM2" or "T2DM" or "T2D" and "gut microbiota" and "diabetes" or "DM2" or "T2DM" or "T2D". The studies included compared gut microbiome diversity between diabetic and non-diabetic adults using 16S rRNA sequencing, excluding children, interventions, and type 1 diabetes. Alpha diversity indices and bacterial mean abundance were analyzed, with statistical assessments using a random-effects model and I[2] for heterogeneity. Thirteen studies met the criteria, with the Shannon index being the most commonly used measure. Results showed significant heterogeneity (I[2] > 75%) and no notable differences between diabetic and non-diabetic groups. Other indices, such as Chao1 and phylogenetic whole tree, similarly showed no consistent differences. Taxonomic analysis also failed to find phyla consistently correlated with T2D, with variability across studies. The relationship between gut microbiota and diabetes remains uncertain due to technical and biological factors that are often overlooked. The inconsistencies across studies highlight the low reproducibility common in microbiota research.}, }
@article {pmid41852439, year = {2025}, author = {Turner, F and Williams, M and Gregoretti, S and Bielamowicz, D and Roach, K and Gehner, L and Kunnatha, A and Phillips, S and Hagel, R and Harshman, R and Vargo, E and Dutton, SBB and Kovacs, J and Larimore, J}, title = {Gut microbiota diversity is altered in a sex-dependent manner in Shank3B heterozygote mice.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1628819}, pmid = {41852439}, issn = {2813-4338}, abstract = {The gut-brain axis is a dynamic interface that has been implicated in the pathogenesis and severity of various neurodevelopmental disorders such as schizophrenia (SZ) and autism spectrum disorders (ASD). Also implicated in ASD and SZ, SHANK3B is a critical gene for postsynaptic protein scaffolding at excitatory synapses. Shank3B knockout mice not only exhibit ASD-like behaviors but demonstrate altered gastrointestinal epithelium morphology and fecal microbiota composition. Utilizing Shank3B heterozygote mice to better reflect the clinical presentation of ASD, we sequenced the gut microbiome from the small intestine of 12-week-old wild type Shank3B[+/+] or Shank3B[+/-] mice in a sex-dependent manner, analyzing bacterial phyla, classes, orders, families, genera, and species. Firmicutes emerged as the dominant phylum in Shank3B[+/-] mice and Bacilli as the dominant class, with Lactobacillales as the dominant order. The dominant family is Lactobacillaceae. The Shank3B[+/-] males but not the Shank3B[+/-] females show an increase in Staphylococcaceae and Erysipelotricaceae. Our results indicate increased biodiversity in Shank3B[+/-] males and reduced biodiversity in Shank3B[+/-] females compared to wild-type controls. Altogether, this data reveals sex-specific microbial signatures that may contribute to the pathogenesis of ASD thus providing potential therapeutics that target gut microbiota in neurodevelopmental disorders.}, }
@article {pmid41852440, year = {2025}, author = {Maloney, AL and Crawford, T and Hurlbut, J and Martinez, M and Mulhern, TJ and Wiellette, EL and Vedula, EM and Vijayakumar, V}, title = {A multi-strain human skin microbiome model provides a testbed for disease modeling.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1473292}, pmid = {41852440}, issn = {2813-4338}, abstract = {The skin microbiome plays a critical role at the interface between the human epidermis and the environment, providing colonization resistance against pathogenic strains, training host immunity, and supporting epithelial turnover. Inversely, dysbiotic skin microbiome states are associated with skin disease, particularly inflammatory conditions such as atopic dermatitis and psoriasis. Current evaluation of human host and microbiome interactions relies on post hoc studies after disease onset. This limits the ability to evaluate the causal roles of host and microbe during disease progression. One approach to characterizing microbial and host biology in a controlled and reproducible context is to derive in vitro models of sufficient complexity and stability to support perturbation and response. Current tools for studying these processes are focused on testing antagonistic or synergistic relations between two or more strains for short (hours to days) culture durations, thereby precluding studies of relevant complexity and chronic disease states. Here, we present an in vitro model of the human skin microbiome comprising a six strain consortium colonizing primary human keratinocyte-derived tissue in Air-Liquid Interface for up to 7 days. We evaluated readouts of tissue health including histology, gene expression, and transepithelial electrical resistance (TEER), as well as relative strain abundance to characterize microbiome stability over time. Skin cells formed a complex tissue structure over two weeks and maintained stable or increasing TEER after 7 days of co-culture with the microbial consortium. Up to five of the six strains were viable on the skin tissue surface on day 7 as validated by custom qPCR assays, demonstrating a robust and stable testbed for microbiome studies. A remarkable feature of this model is the persistence of Cutibacterium acnes in an aerobic tissue culture environment, since C. acnes growth is typically demonstrated under anaerobic conditions, suggesting that the skin tissue model is conducive to more natural growth states of native skin strains. The addition of cytokines representative of atopic dermatitis elicited a marked decrease in tissue barrier by day 7 compared to healthy controls, irrespective of the microbiome presence. Furthermore, an alteration in relative strain abundance was observed in diseased model tissues, demonstrating capability to study the impact of disease states on the microbiome and vice versa. We envision this model system as a test bed to evaluate the influence of commensals on host biology, the influence of external environment on microbiome stability, and chronic diseases impacted by dysbiosis.}, }
@article {pmid41852441, year = {2025}, author = {Stres, B}, title = {Editorial: Defining a healthy microbiome.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1652331}, doi = {10.3389/frmbi.2025.1652331}, pmid = {41852441}, issn = {2813-4338}, }
@article {pmid41852442, year = {2025}, author = {Yang, S and Yuan, T and Duan, T and Zhu, H and Zhang, X and Zhang, H and Jiang, J and Yang, J and Hu, L and Yu, Y and Zhang, L and Yuan, Z}, title = {Integrated omics analysis of PGPR and AMF effects on soil microbiota and root metabolites in Isatis indigotica.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1709335}, pmid = {41852442}, issn = {2813-4338}, abstract = {INTRODUCTION: The intensive use of chemical fertilizers and pesticides in modern agriculture has led to severe soil degradation and environmental pollution, which threatens the long-term production of crops. Plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) are promising biofertilizers which can boost plant growth and improve soil quality. However, the combined effects of these factors on medicinal plants such as Isatis indigotica remain unclear.<br><br>METHODS: This study isolated and identified six plant growth-promoting rhizobacteria (PGPR) strains (Acinetobacter sp. and Bacillus albus) from the rhizosphere of Isatis indigotica. A pot experiment was conducted with control, PGPR inoculation and AMF+PGPR co-inoculation treatments to assess the effects of these treatments on the growth of Isatis indigotica and its soil physicochemical properties. High-throughput sequencing was used to analyse the structure of the rhizosphere microbial community, while non-targeted metabolomics was employed to profile root metabolites. Finally, a redundancy analysis (RDA) was performed to reveal the correlations between the key microbial taxa and the differential metabolites.<br><br>RESULTS: All six of the isolated PGPR strains exhibited multiple capacities that promote plant growth. The pot experiment demonstrated that both PGPR inoculation and AMF+PGPR co-inoculation significantly increased the height and root length of Isatis indigotica compared to the control, while also enhancing the soil's SOC, TN and AP content. Analysis of the microbial community revealed that the inoculation treatments enriched the rhizosphere microbiome with beneficial taxa such as Proteobacteria and Ascomycota. Metabolomic analysis revealed that inoculation treatments significantly increased the concentrations of key bioactive compounds, such as flavonoids, lipids and amino acids. Furthermore, the RDA revealed a strong correlation between the accumulation of various root metabolites (e.g., benzenesulfonic acids, carbohydrates and fatty acids) and dominant microbial genera (e.g., Acinetobacter, Paenibacillus and Botryotrichum).<br><br>CONCLUSIONS: PGPR and AMF improve the uptake of nutrients and the synthesis of secondary metabolites in Isatis indigotica by altering the structure of the rhizosphere microbiome and root metabolomes. These findings support the use of PGPR and AMF as biofertilizers for sustainably cultivating medicinal plants.}, }
@article {pmid41852443, year = {2025}, author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F}, title = {Position statement of the Microbiota International Clinical Society.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1657750}, pmid = {41852443}, issn = {2813-4338}, }
@article {pmid41852445, year = {2025}, author = {Costa, LT}, title = {Editorial: Gut microbiota and its importance on human health - the need for reliable measurements to assess the microbial gut function and its correlated pathologies.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1657144}, doi = {10.3389/frmbi.2025.1657144}, pmid = {41852445}, issn = {2813-4338}, }
@article {pmid41852446, year = {2025}, author = {Shuai, W and Hegarty, B and Mahnert, A and Hartmann, EM}, title = {Editorial: Interactions between natural and built environment microbiomes in a One Health context.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1608228}, pmid = {41852446}, issn = {2813-4338}, }
@article {pmid41852447, year = {2025}, author = {Sieler, MJ and Al-Samarrie, CE and Kasschau, KD and Kent, ML and Sharpton, TJ}, title = {Modeling the zebrafish gut microbiome's resistance and sensitivity to climate change and parasite infection.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1605168}, pmid = {41852447}, issn = {2813-4338}, abstract = {INTRODUCTION: As climate change increases global water temperatures, ecologists expect intestinal helminth infection ranges to expand and increase the health burden on aquatic organisms. However, the gut microbiome can interact with these parasites to influence infection outcomes, raising the possibility that its response to increasing temperatures may help buffer against increased infection burden or worsen infection outcomes (e.g., inflammatory bowel disease). To evaluate this hypothesis, we sought to determine if the microbiome is resistant or resilient to the stressors of increased water temperature, helminth exposure, and their combination, and whether this variation linked to infection outcomes.<br><br>METHODS: We leveraged the zebrafish (Danio rerio) model organism to measure how these variables relate to the temporal dynamics of the gut microbiome. In particular, we exposed adult zebrafish to Pseudocapillaria tomentosa, parasitic capillarid with a direct life cycle, across three different water temperatures (28&#xb0;C, 32&#xb0;C, 35&#xb0;C), and analyzed fecal microbiome samples at five time points across 42 days.<br><br>RESULTS: Our findings show that parasite exposure and water temperature independently alter gut-microbiome diversity. Moreover, water temperature moderates the association between parasite infection and the gut microbiome. Consistent with this observation, yet counter to prevailing expectations, we find that increasing water temperature reduces P. tomentosa infection worm development and overall abundance in zebrafish. The decline in worm burden at 35&#xb0;C may be due to either direct thermal inhibition of P. tomentosa development or temperature-mediated interactions with the host microbiome and immune response.<br><br>DISCUSSION: Overall, our results indicate that water temperature alters the contextual landscape of the gut microbiome and shapes its response to an intestinal parasite in zebrafish. To our knowledge, this represents the first report of elevated temperature constraining nematode development in a fish host, underscoring that climate change may impose unanticipated, context-dependent impacts on vertebrate gut microbiomes and health outcomes.}, }
@article {pmid41852522, year = {2026}, author = {Luo, Y and Cao, J and Li, B and Wang, J and Geng, T and Luo, Z and Xie, J}, title = {Global landscape analysis of clinical trials on gut microbiota modulation therapies for irritable bowel syndrome.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1737537}, pmid = {41852522}, issn = {2296-858X}, abstract = {OBJECTIVE: Systematically analyze the global landscape of interventional clinical trials on gut microbiota modulation (GMM) therapies for irritable bowel syndrome (IBS).<br><br>METHODS: Searched the Trialtrove database (1998-July 2025) with the key term combination "(Disease is Autoimmune/Inflammation: Irritable Bowel Syndrome) AND (Mechanism of Action: Microbiome modulator)", included 305 interventional trials (excluded 15 observational studies). Descriptive analysis was done via SPSS 26.0, adhering to TITAN Guidelines 2025.<br><br>RESULTS: Asia was the most active region; trials peaked in 2021, with Phase II (44.3%) and IV (33.3%) dominant. Probiotics led (single-strain: Lactobacillus/Bifidobacterium; multi-strain: Lactobacillus&#x202f;+&#x202f;Bifidobacterium), followed by fecal microbiota transplantation (FMT). IBS-D (49.6%) was the main subtype (IBS-C: 26.1%); probiotics were the most frequently studied for both, FMT for IBS-D, and prebiotics for IBS-C.<br><br>CONCLUSION: GMM therapies for IBS are relatively mature. Personalized therapies are necessary; multiomics and emerging therapies (e.g., Akkermansia muciniphila) will promote IBS precision medicine.}, }
@article {pmid41852664, year = {2026}, author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H}, title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748638}, pmid = {41852664}, issn = {2235-2988}, mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.}, }
@article {pmid41852665, year = {2026}, author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L}, title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1728182}, pmid = {41852665}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; }, abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.<br><br>METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.<br><br>RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.<br><br>CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.}, }
@article {pmid41852693, year = {2026}, author = {Topcu, I and Bernal, JS and Antony-Babu, S}, title = {Maize leaf endosphere microbiome was affected by domestication and shows patterns consistent with microbial dysbiosis.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1735358}, pmid = {41852693}, issn = {2813-4338}, abstract = {BACKGROUND: Whether domestication, post-domestication spread, and breeding affected the maize leaf endosphere microbiota is poorly understood despite the well-known effects of those processes on the crop's genetics and responses to the environment. We examined the leaf endosphere microbial communities associated with three plant groups (Zea mays): teosintes, maize landraces, and maize elite inbreds. The teosintes group included Balsas (Z. mays parviglumis) and perennial (Zea diploperennis) teosinte, and each maize (Z. mays mays) group included genotypes from Mexico and USA. We used 16S-V4 region amplicon sequencing of the leaf endophytic microbiota to infer how the microbial communities of inbred maize may have been shaped by the crop's evolution, and whether they were affected by: (i) the transition from a perennial life history to an annual life history in the teosintes; (ii) domestication of maize from Balsas teosinte; (iii) northward spread of landrace maize from Mexico to the US; and (iii) breeding of landrace maizes to produce elite inbreds.<br><br>RESULTS: The leaf endophytic microbial community differed among the plant groups and genotypes, and was affected by domestication, as indicated by a decline in bacterial diversity and changes in microbial community structure between wild (teosinte) and domesticated (maize) Zea. While the microbial community structure was stringent and regulated in the teosintes, it was variable in the maize landraces and inbreds, as evidenced by greater distances to centroid based on Euclidean dissimilarity metric. This pattern was suggestive of microbial dysbiosis in the leaf endosphere associated with domestication and is consistent with predictions of the Anna Karenina principle. This finding marks the first evidence of dysbiosis associated with domestication. FAPROTAX predictions suggested that the teosintes may harbor microbial communities enriched in taxa associated with cellulolytic, chitinolytic, and nitrate respiration functions, while the maizes showed higher fermentation and nitrate reduction functions.<br><br>CONCLUSIONS: Our results showed that the leaf endosphere microbial community structures in maize are consistent with alterations associated with dysbiosis. Our findings enhanced our understanding of the effects of anthropogenic processes including crop domestication, spread, and breeding on the leaf endosphere of elite maize cultivars, and may guide the development of evolutionarily-and ecologically sustainable biofertilizers and biocontrol agents.}, }
@article {pmid41852694, year = {2026}, author = {Jablonska, S and Kula, A and Putonti, C}, title = {Shared taxa but distinct communities: within-individual comparisons of oral, nasal, and urinary microbiomes in asymptomatic "healthy" females.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1691965}, pmid = {41852694}, issn = {2813-4338}, abstract = {Although microbial community compositions vary throughout the healthy human body, some taxa can be found to reside in multiple anatomical sites. Moreover, some microbiota that have been found to be interconnected, e.g., the gastrointestinal tract and the oral cavity, the female urinary tract and the vagina, the nose (specifically the nares) and the skin. Previously, the urinary microbiome has only been compared to proximal sites; however, several species that inhabit the asymptomatic female urinary tract are also found in distant communities, e.g., Streptococcus mitis, also found in the oral cavity, and Staphylococcus epidermidis, also found in the nares. This prompted our investigation of communities of the oral cavity, nares, and urinary tract, collected from the same individual. In this study, we profiled the oral, nasal, and urinary microbiomes of 26 self-identified "healthy" female participants using 16S rRNA amplicon sequencing. The urinary microbiome was found to be distinct from the oral and nasal communities. Nevertheless, Actinomyces, Corynebacterium, Escherichia + Shigella, Lawsonella, Staphylococcus, and Streptococcus were found to be present within communities of all three anatomical sites. Genera predominant within the oral and nasal communities were often low-abundant taxa within the urinary microbiome. To date, comparisons of the urinary microbiome to microbiomes of other anatomical sites is limited. The distinction between the urinary microbiome and that of the more distant oral and nasal site highlights the role that the environment plays in shaping these communities.}, }
@article {pmid41852735, year = {2026}, author = {Wang, P and Xie, J and Xiang, F and Xiong, S and Li, Y and Xia, B and Lin, L and Peng, Q}, title = {Hepato-ocular crosstalk: Bile acids bridging pathogenesis and therapy.}, journal = {iScience}, volume = {29}, number = {3}, pages = {115118}, pmid = {41852735}, issn = {2589-0042}, abstract = {Bile acids, the major metabolites of cholesterol, function as pleiotropic signaling molecules beyond their classical role in lipid digestion. Increasing evidence indicates that dysregulated bile acid metabolism represents a shared molecular basis linking hepatic dysfunction with ocular pathology. Aberrations in bile acid synthesis, transport, and signaling lead to bile acid imbalance, which drives ocular injury through direct cytotoxicity, disruption of retinal and lens homeostasis mediated by FXR and TGR5 signaling, and immune activation along the gut-liver-eye axis. These mechanisms are implicated across a spectrum of conditions, ranging from inborn metabolic disorders to acquired cholestatic diseases. This review further highlights the translational potential of targeting bile acid homeostasis. We summarize emerging therapeutic strategies, including bile acid-based interventions, targeted drug delivery, and microbiome modulation, that aim to restore systemic bile acid balance. Collectively, we propose reconstruction of systemic bile acid homeostasis as a unifying therapeutic framework for hepato-ocular comorbidities.}, }
@article {pmid41852793, year = {2026}, author = {Razzak, E and Friesch, M and Gocal, J and Balagtas, M and Schmitt, D and Brown, N}, title = {Association between antibiotic history and revision risk in arthroplasty outcomes.}, journal = {Journal of clinical orthopaedics and trauma}, volume = {75}, number = {}, pages = {103397}, pmid = {41852793}, issn = {0976-5662}, abstract = {BACKGROUND: Recent evidence has shown a connection between the gut microbiome (GM) and joint health, with changes in the microbial community (dysbiosis) leading to joint degeneration, prosthesis loosening, and joint infection. A leading cause of dysbiosis is excessive antibiotic use. However, the relationship between antibiotics and post-operative joint recovery is largely unexplored. This study aims to investigate whether a history of antibiotic use is associated with a higher odds of revision following primary total knee arthroplasty (TKA) or total hip arthroplasty (THA.).<br><br>METHODS: This retrospective study analyzed the records of patients who underwent a primary TKA or THA from January 2014 to January 2024&#xa0;at a quaternary-care medical center. Demographic information, comorbidities, lifetime antibiotic prescriptions excluding perioperative prophylaxis, post-operative infection status, and reoperation data were collected. Controlling for age, sex, BMI, race, prior prosthetic joint infections, and Charlson Comorbidity Index, a multivariable logistic regression analysis was conducted.<br><br>RESULTS: A total of 2457 patients were analyzed. Among patients undergoing TKA, any history of antibiotics was associated with revision (OR 2.04, 95% CI 1.19-3.58, p&#xa0;=&#xa0;0.011). The THA cohort had similar odds of revision (OR 2.51, 95% CI 1.25-5.18, p&#xa0;=&#xa0;0.011). In a model limited to revisions caused by infection, antibiotic use on a binary scale was not a significant predictor (OR 1.63, 95% CI 0.735-3.70 p&#xa0;=&#xa0;0.232). However, on a continuous scale, the odds of revision increased by 1% for each additional antibiotic taken for infection-related revisions (OR 1.01, 95% CI 1.000-1.03&#xa0;P&#xa0;=&#xa0;0.046).<br><br>CONCLUSIONS: Our study demonstrates that antibiotic use is associated with higher odds of revision following TKA and THA. These preliminary findings contextualize the gut-joint axis, adding a unique variable to this relationship. Future studies may build on this hypothesis-generating information to further understand the interplay between the GM and joint health.}, }
@article {pmid41852811, year = {2022}, author = {Marsh, AJ and Azcarate-Peril, MA and Aljumaah, MR and Neville, J and Perrin, MT and Dean, LL and Wheeler, MD and Hines, IN and Pawlak, R}, title = {Fatty acid profile driven by maternal diet is associated with the composition of human milk microbiota.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1041752}, pmid = {41852811}, issn = {2813-4338}, abstract = {Little is known regarding the impact of diet on the breast milk microbiome. We hypothesized that vegan, vegetarian, and omnivore diets would impact the human milk microbiota. We also aimed to explore associations between human milk fatty acid concentrations and microbial composition. A cross-sectional microbiome diversity analysis of human milk samples (N = 72) was performed using 16S rRNA amplicon sequencing. Human milk microbial diversity was not associated with diet type. However, analysis of microbiome in relation to fatty acid profiles revealed significant differences in the overall composition of the human milk microbiota between high (> 0.7% of total fat) and low (< 0.7%) trans-fatty acid groups (TF) (p = 0.039, pairwise PERMANOVA p = 0.035), high (> 40%) versus low (< 40%) saturated fatty acids (UniFrac p = 0.083, PERMANOVA p = 0.094), and high (>60%) versus low (<60%) unsaturated fatty acids (UF) (UniFrac p = 0.094, PERMANOVA p = 0.093). 84% of samples from omnivore mothers were in the high TF group compared to only 12% of samples from vegans. Gut-associated species (Faecalibacterium, Blautia, Roseburia and Subdoligranulum) and Lactobacillus were characteristic of both high UF and TF groups, but not the low-fat groups. Functional analysis revealed 2,4-dichlorophenol 6-monooxygenase was differentially abundant in the high UF group. Although microbiome diversity did not differ by diet type, TF breast milk content differed by diet group, highlighting the relationship between maternal diet and the microbial profile of human milk.}, }
@article {pmid41852812, year = {2022}, author = {McDaneld, TG and Workman, AM and Chitko-McKown, CG and Kuehn, LA and Dickey, A and Bennett, GL}, title = {Detection of Mycoplasma bovirhinis and bovine coronavirus in an outbreak of bovine respiratory disease in nursing beef calves.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1051241}, pmid = {41852812}, issn = {2813-4338}, abstract = {INTRODUCTION: Respiratory disease incidence is intimately associated with an animal's commensal bacteria populations (microbiome), as microbes that are involved with morbidity and mortality are commonly found in animals with no sign of disease. In addition, viral pathogens affect the immune system and appear to play an integral role in the overall incidence of bovine respiratory disease (BRD); so, an understanding of the interaction of the bacterial and viral pathogens in the upper respiratory tract (URT) may help us to understand the impact of these pathogens on development of BRD. For this research, the overall goal was to characterize bacterial and viral populations in the URT of nursing beef calves at initial vaccination and at the time of a BRD outbreak.<br><br>METHODS: Nasal swabs from the URT were collected at initial vaccination (average 45 days of age) and again at the time of the BRD outbreak (average 126 days of age). DNA and RNA were extracted from nasal swabs to evaluate bacterial and viral populations in the URT. Whole blood was also collected at the time of the BRD outbreak for determination of complete blood counts. To evaluate the microbiome, hypervariable regions 1 through 3 along the 16S ribosomal RNA (rRNA) gene were amplified by PCR and sequenced using next-generation sequencing (Illumina MiSeq) for identification of the bacterial taxa present. To evaluate the viral pathogens, multiplex reverse transcription real-time polymerase chain reaction and next-generation sequencing (Illumina NextSeq) was completed.<br><br>RESULTS: Overall, evaluation of these samples revealed that at the time of the BRD outbreak, all calves were nasally shedding bovine coronavirus and a large percentage had a coinfection with Mycoplasma sp., with Mycoplasma bovirhinis being the predominant species. Neither bovine coronavirus nor Mycoplasma sp. were present at high abundance at the earlier timepoint of initial vaccination. When comparing bacterial population diversity between the two sampling timepoints, alpha diversity was significantly greater at initial vaccination compared to the BRD outbreak (P-value <0.001). Values of leukocytes at the time of the BRD outbreak were also identified to be significantly different between calves with normal or elevated rectal temperatures (P-value <0.05).<br><br>DISCUSSION: Analysis of the respiratory microflora in the URT during initial vaccination and a BRD outbreak will provide insight into the distribution of bacterial and viral populations in nursing beef calves.}, }
@article {pmid41852813, year = {2022}, author = {Cervantes, K and Heerema, RJ and Randall, JJ}, title = {The core microbiome of Carya illinoinensis (pecan) seedlings of different maternal pecan cultivars from the same orchard.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1003112}, pmid = {41852813}, issn = {2813-4338}, abstract = {Carya illinoinensis (pecan) produce a high valued and desired nut crop; with production expanding worldwide. Important attributes of pecans and their ability to adapt to different environments aside from their native regions are currently being investigated. Microbial communities are known to play an important role in crop productivity and overall plant health. Studies in other plant species have shown that the plant microbiome may be influenced by both the environmental conditions and genetics of the plant. Microbiota research in pecan is in its early stages and here we report insights into the core microbiome of seedlings derived from five pecan cultivars located in an orchard from Las Cruces, New Mexico. Seeds from open-pollinated pecan cultivars ('Burkett', 'Mandan', 'Pawnee', 'Western', and 'Wichita') were collected and grown in a quarantine greenhouse under highly regulated conditions. DNA from the resulting seedlings were used for next generation sequencing (MiSeq) for 16S and ITS and microbiome analyses revealed significant differences in microbial composition and relative abundance (bacterial and fungal) between seedling organs, with roots having the highest alpha diversity followed by stems and leaves. Bacterial family Chitinophagaceae was identified to be most relatively abundant in the roots of seedlings compared to the bacterial families Rhizobiaceae and Moraxellaceae, which were found to be most relatively abundant in the stems and leaves, respectively. Analyses also indicated that there were several families (bacterial families: Rhizobiaceae, Enterobacteriaceae, Chitinophagaceae, Burkholderiaceae, Sphingomonadaceae, Pseudomonadaceae, Moraxellaceae, Microscillaceae, Rubritaleaceae, Caulobacteraceae; fungal families: Serendipitaceae, Nectriaceae, Ophiostomataceae, Hypocreaceae, Aspergillaceae, and Cephalothecaceae) that were found in all seedlings and these constitute a core microbiome for pecan. There were also differences in microbial composition (bacterial and fungal) between seedlings from different maternal pecan cultivars and these differences are proposed to constitute a signature microbiome for the maternal cultivar. As pecan trees continues to extend to other growing regions it is important to understand the role that these microbes play in pecan. By establishing the core microbiome of pecans, the selection of microbes for breeding and improving pecan production will become a possibility.}, }
@article {pmid41852815, year = {2022}, author = {van Belkum, A and Lisotto, P and Pirovano, W and Mongiat, S and Zorgani, A and Gempeler, M and Bongoni, R and Klaassens, E}, title = {Being friendly to the skin microbiome: Experimental assessment.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1077151}, pmid = {41852815}, issn = {2813-4338}, abstract = {Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically "microbiome friendly" while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.}, }
@article {pmid41852816, year = {2022}, author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R}, title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1097124}, pmid = {41852816}, issn = {2813-4338}, abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.}, }
@article {pmid41852819, year = {2022}, author = {Bakus, C and Budge, KL and Feigenblum, N and Figueroa, M and Francis, AP}, title = {The impact of contraceptives on the vaginal microbiome in the non-pregnant state.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1055472}, pmid = {41852819}, issn = {2813-4338}, abstract = {The vaginal microbiome exists in a dynamic state and its disruption, by diminution of Lactobacillus concentrations, can induce a state of microbial imbalance with significant health consequences, such as increased risk of sexually transmitted infection (STI) acquisition, preterm labor, and low birth weight babies. This delicate balance of microbes can be affected by many processes such as mechanical practices (i.e. douching) and hormonal changes: physiologic (i.e. menstrual cycle, menopause, puberty), pathologic (i.e. PCOS), and exogenous (i.e. contraceptives). Contraceptives fall into mechanical and hormonal categories, both of which prevent unintended pregnancy. The mechanical contraceptives of spermicides, diaphragms, and cervical caps alter the vaginal ecosystem, with spermicides being linked to an increased risk of vaginal dysbiosis. The impacts of Copper T intrauterine devices (Cu-IUDs) and hormonal contraceptives on the vaginal microbiome are contradictory. A better understanding and consensus of how contraceptive methods affect the vaginal microbiome is needed.}, }
@article {pmid41852820, year = {2022}, author = {Ajeeb, TT and Gonzalez, E and Solomons, NW and Koski, KG}, title = {Human milk microbial species are associated with mild growth deficits during early infancy among Guatemalan mother-infant dyads.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1008467}, pmid = {41852820}, issn = {2813-4338}, abstract = {Growth faltering is common in Guatemalan indigenous communities, but the possibility that it may be related to milk microbial composition has not been explored. For this cross-sectional study, unrelated mother-infant dyads (n = 64) from eight communities in the remote Western Highlands of Guatemala were recruited. Milk samples and infant length-for-age and weight-for-age Z-scores were collected at two stages of lactation: early (6-46 days postpartum, n = 29) or late (109-184 days postpartum, n = 35). Within each stage of lactation, infants were subdivided into mildly underweight [weight-for-age Z-score (WAZ) < -1 SD] or normal weight (WAZ ≥ -1 SD) and mildly stunted [length-for-age Z-score (LAZ) < -1.5 SD] or non-stunted (LAZ ≥ -1.5 SD). 16S ribosomal RNA gene sequencing was used to identify milk microbial communities, and DESeq2 was used to compare the differential abundance (DA) of human milk microbiota at the species level for WAZ and LAZ subgroups at each stage of lactation. A total of 503 ESVs annotated as 256 putative species across the 64 human milk samples were identified. Alpha diversity did not differ, but beta-diversity redundancy analysis identified four distinct clusters among the four WAZ (p = 0.004) and LAZ subgroups (p = 0.001). DA identified 15 different taxa in the WAZ and 11 in the LAZ groups in early lactation and 8 in the WAZ and 19 in the LAZ groups in late lactation. Mothers' milk had more DA taxa of oropharyngeal and environmental bacteria with opportunistic activities in the LAZ < -1.5 SD infants, whereas the LAZ ≥ -1.5 SD had DA taxa with potential probiotic and antimicrobial inhibitory activity against pathogens. In particular, milk microbial communities of infants not classified as underweight or stunted had more beneficial species including Lactococcus_lactis. These findings suggest the potential associations between the milk microbiome at the species level with infant growth prior to 6 months of age. These data provide important evidence of the associations between the human milk microbiome and the growth of breastfed infants.}, }
@article {pmid41852824, year = {2022}, author = {Văcărean-Trandafir, IC and Amărandi, RM and Ivanov, IC and Iacob, &#x15e; and Muşină, AM and Bărgăoanu, ER and Dimofte, MG}, title = {The impact of cefuroxime prophylaxis on human intestinal microbiota in surgical oncological patients.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1092771}, pmid = {41852824}, issn = {2813-4338}, abstract = {INTRODUCTION: The intestinal microbiota is vital to human health, and has a profound influence on several biological processes including inflammation and pathogen resistance. Antibiotic intake greatly impacts bacterial diversity, can increase antibiotic resistance and impair the equilibrium between bacterial species. The key to grasping post-antibiotic effects on the gut microbiota rests on the implementation of a suitable procedure to isolate microbial DNA and a meticulous consideration of experimental sequencing artefacts.<br><br>METHODS: We herein report the bacterial community dynamics of a cohort of 128 surgical oncology patients before and after the intravenous administration of cefuroxime, an antibiotic routinely used in surgical antibioprophylaxis with proven efficiency against both gram-positive and gram-negative bacteria. In our study, we analyzed patient fecal samples collected through rectal examination before and 7 days post cefuroxime treatment by employing a high-throughput sequencing assay which targets the V3-V4 region of the 16S rRNA gene. A first challenge in applying the study design was to extract an appropriate amount of DNA characteristic to the sampled microbiota, which implied the use of both mechanical (ceramic beads) and chemical (proteinase K, lysozyme and lysostaphin) lysis.<br><br>RESULTS: Gut microbiota richness and composition was significantly different between the two groups, but most differences were determined by additional perioperative procedures, rather than antibioprophylaxis. Intestinal microbiota composition was not significantly changed one week post cefuroxime treatment when compared to pre-treatment condition for patients without mechanical bowel preparation, but some loss in taxonomic variety could be observed.<br><br>DISCUSSION: Taken together, cefuroxime does not promote short-term dysbiosis in surgical patients without any additional perioperative procedures.}, }
@article {pmid41852852, year = {2026}, author = {Gusareva, ES and Vettath, VK and Gaultier, NE and Sadovoy, AV and Dacanay, JGA and Schuster, SC}, title = {Dermatophagoides pteronyssinus in ambient air bioaerosols.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {3}, pages = {100667}, pmid = {41852852}, issn = {2772-8293}, abstract = {BACKGROUND: House dust mite (HDM) sensitization is a leading cause of allergic rhinitis and asthma worldwide, with Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Blomia tropicalis being the primary allergenic species typically associated with indoor environments. Even effective multicomponent interventions creating an HDM-free indoor environment are often insufficient to prevent allergy, as HDM exposure may also occur outdoors.<br><br>OBJECTIVE: To assess the potential for outdoor HDM exposure, we applied air biomass sequencing and metagenomic techniques to detect HDM DNA in both indoor and outdoor bioaerosols, offering an alternative to conventional dust sampling methods.<br><br>METHODS: We used 2 data sets in this study: (1) a global data set comprising 1,171 outdoor air samples collected across 33 countries in open air environments and (2) a data set of indoor (n = 161) and outdoor (n = 156) air samples collected across 156 apartments from 106 locations in Singapore. All air samples were collected by drawing 24,000 to 36,000 L of air using SASS3100 air samplers; all samples were processed identically. Species-level taxonomic classification was performed using Kaiju software aligned to the National Center for Biotechnology Information nonredundant database, with a minimum threshold of 40 reads per taxon.<br><br>RESULTS: Analysis of 1,171 global outdoor air samples revealed D pteronyssinus as the most prevalent HDM species; it was detected in 208 samples, with abundance increasing from temperate toward equatorial regions. In Singaporean households, D pteronyssinus was found in 58.4% of indoor samples and 21.2% of nearby outdoor samples, with high median DNA read counts outdoors suggesting that exposure to HDM is not limited to domestic environments. B tropicalis and D farinae were also detected in Singapore, albeit at lower frequencies.<br><br>CONCLUSION: Our findings highlight the need to expand environmental allergen surveillance beyond household dust to include ambient and outdoor air, particularly in tropical climates.}, }
@article {pmid41852858, year = {2026}, author = {Tume, R and Cruz, M and Sandoval, V and Iglesias-Vejar, L and Sanz-Lamora, H and Pérez-Martí, A and Torres-Oteros, D and Cubedo-Cullere, M and Carmona-Pontaque, F and Martínez-Huélamo, M and Marrero, PF and Haro, D and Canudas, S and Andres-Lacueva, C and Relat, J and Meroño, T}, title = {Modulation of the gut microbiome-adipose tissue AXIS by maqui supplementation improved insulin resistance and lipid metabolism in mice under a high-fat diet.}, journal = {Food chemistry. Molecular sciences}, volume = {12}, number = {}, pages = {100383}, pmid = {41852858}, issn = {2666-5662}, abstract = {To assess the impact of maqui (Aristotelia chilensis) supplementation on the gut microbiome-adipose tissue axis, and to associate it with gene expression changes in white adipose tissue (WAT) in mice fed a high-fat diet. Our hypothesis is that the gut microbiome-adipose tissue axis will be involved in Maqui's effect on WAT browning. Twenty-nine 4-week-old C57BL/6 J mice were randomly assigned to a high-fat diet (HFD, n = 15) or HFD + Maqui (n = 14) for 16 weeks. Plasma samples were analyzed using an UPLC-QTRAP exposome-based metabolomics method. Gut microbiome was studied by fecal 16S rRNA gene sequencing. Gene expression in WAT was assessed by real-time PCR. Data were analyzed by multivariate methods and integrated through multiomics analyses. Maqui supplementation induced an increase in Lactobacillus, Lactococcus and Bifidobacterum and a reduction in Desulfovibrium, and Acetatifactor. Out of 19 metabolites altered by maqui supplementation, 9 were derived from gut bacterial fermentation of anthocyanins. Increases in L. gasseri and L. johnsonii in the gut were associated to increased production of phenyllactic acid, 4-O-methylgallic acid, and 3-(3'-hydroxyphenyl)-γ-valerolactone. Integrative analysis revealed a concerted role of Lactobacillus spp. and its ability to ferment maqui polyphenols, along with increased expression of Chrebpb, Pgc1a and Ucp1 in WAT. Enrichment of Lactobacillus gasseri and johnsonii and exposure to 2-hydroxybenzoic acid derived from polyphenols fermentation are evidences of the involvment of the gut-microbiome-adipose tissue axis in WAT browning induced by maqui.}, }
@article {pmid41852978, year = {2026}, author = {Tamhane, V and Shah, N and Khadilkar, AV and Khadilkar, VV and Gondhalekar, K and Patwardhan, V and Gupta, A and Bhanushali, SP and Shouche, Y and Muralidharan, S}, title = {Influence of the Gut Microbiome on Body Composition and Metabolic Risk in Indian Children with Type 1 Diabetes Mellitus (T1dm).}, journal = {Journal of pharmacy &amp; bioallied sciences}, volume = {18}, number = {Suppl 1}, pages = {S57-S61}, pmid = {41852978}, issn = {0976-4879}, abstract = {INTRODUCTION: The study aims to explore the gut flora presentation among Type 1 DM children with and without metabolic risks (MR) at a tertiary care center.<br><br>MATERIALS AND METHODS: A cross-sectional, observational study was conducted on children with T1DM (n = 68, mean-age = 12.9 years, disease-duration = 5.5 years, average HbA1c = 9.8%) divided into two groups based on with (n = 35) and without (n = 33) metabolic risk factors. Clinical-history, anthropometry, biochemical investigations, and body composition analysis was performed. Stool samples were collected; DNA extraction and targeted 16srRNA gene amplicon sequencing was performed.<br><br>RESULTS: Significant differences were observed in the relative abundance of gut microbiome at the family and genera level in children with metabolic risk as compared to without metabolic risk.<br><br>CONCLUSION: Gut microbiome significantly differs in children with or without MR among T1DM cases.}, }
@article {pmid41853081, year = {2026}, author = {Peter, J and Pritz, A and Hiebler, M and Mahmoudi, M and Fuchshuber, J and Mörkl, S and Holasek, S and Humer, E and Unterrainer, HF}, title = {Metabolomic and gut microbial biomarkers of smoking cessation treatment in long-term drug therapy: a study protocol for a randomized controlled trial.}, journal = {Frontiers in psychiatry}, volume = {17}, number = {}, pages = {1677235}, pmid = {41853081}, issn = {1664-0640}, abstract = {THEORETICAL FRAMEWORK: Cigarette smoking is the leading preventable cause of death worldwide, with nicotine dependence notably common among individuals with Substance Use Disorders (SUD). Smoking exacerbates both physical and mental health issues, further complicating the treatment of SUD. Current therapeutic approaches for SUD often prove inadequate, indicating a need for new strategies. Recent advancements in metabolomics and gut microbiome research have provided valuable insights into the biological mechanisms underlying addiction, warranting further investigation.<br><br>OBJECTIVES: This study aims to investigate the therapeutic potential of smoking cessation for individuals with SUD, using a Cognitive-Behavioral Therapy (CBT) six-week group intervention within a therapeutic community. The research specifically explores the psychobehavioral, metabolic, and gut microbiome domains. It is hypothesized that smoking cessation will improve emotional regulation self-efficacy and reduce substance craving, mediated by changes in metabolic and microbiome profiles linked to brain systems of affect and reward.<br><br>METHODS: A randomized controlled trial (N&#xa0;=&#xa0;100) will be conducted, examining outcomes such as clinical relapse rates as well as microbial and metabolic markers, investigating pathways of short-chain fatty acids, oxidative stress and inflammation, lipid, tryptophan, and one-carbon metabolism. Participants will undergo a CBT smoking cessation intervention, with pre- and post-assessments, compared to a control group receiving treatment as usual. Metabolomic and microbiome analyses will be conducted using blood and stool samples, alongside psychological assessments via questionnaires. Covariate analyses will be undertaken to control for metabolic and gut microbial effects of long-term psychiatric medications (antidepressants, mood stabilizers, antipsychotics, and opioid substitutions) present in the sample. Behavioral assessments will be conducted at a 3-month follow-up. The study is registered at clinicaltrials.gov under NCT06803706.<br><br>LEVEL OF ORIGINALITY: This research will enhance our understanding of the complex interplay between smoking and mental health, offering potential for more effective treatment strategies for SUD. The current study's focus on connections between metabolic and gut microbiome pathways with affect and reward is expected to yield valuable insights into addiction mechanisms and improve diagnostic and therapeutic practices.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT06803706?cond=metabolomic%20and%20microbial%20biomarkers%20in%20smoking%20cessation&amp;rank=1, identifier NCT06803706.}, }
@article {pmid41853095, year = {2026}, author = {Aamery, A and Ba Wazir, H and Amer, MS and Omer, EEA}, title = {Small Intestinal Fungal Overgrowth Mimicking a Surgical Abdomen and Presenting as Bowel Obstruction: A Case Report and Literature Review.}, journal = {Cureus}, volume = {18}, number = {3}, pages = {e105283}, pmid = {41853095}, issn = {2168-8184}, abstract = {Small intestinal fungal overgrowth (SIFO) is defined by an abnormal proliferation of fungal organisms, most commonly Candida species, within the small intestine. Fungal infections, particularly candidiasis, are recognized causes of gastrointestinal (GI) symptoms, especially in patients with underlying conditions, such as malignancy or diabetes mellitus (DM), and in those exposed to immunosuppressive therapies, corticosteroids, or prolonged antibiotic use. SIFO is an underrecognized cause of GI symptoms, including bloating, diarrhea, and malabsorption. In rare cases, excessive fungal colonization can lead to mechanical bowel obstruction. This case report describes a patient with advanced retroviral infection who developed small bowel obstruction secondary to SIFO, underscoring the diagnostic challenges, therapeutic approaches, and the critical importance of early recognition and management.}, }
@article {pmid41853273, year = {2026}, author = {Huang, XT and Feng, H and Tan, Y and Wang, Q and Wei, JM and Huang, ZD and Wang, XT and Lu, HJ}, title = {Effectiveness of Streptococcus salivarius probiotics on alleviating radiation-induced oral mucositis via inflammatory and microecological modulation: a prospective pragmatic interventional study in nasopharyngeal carcinoma.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745549}, pmid = {41853273}, issn = {1664-3224}, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; Male ; *Stomatitis/etiology/therapy/microbiology ; Female ; Middle Aged ; *Nasopharyngeal Carcinoma/radiotherapy/therapy ; Prospective Studies ; *Streptococcus salivarius ; *Nasopharyngeal Neoplasms/radiotherapy/therapy ; Adult ; *Radiation Injuries/therapy/etiology ; Aged ; Chemoradiotherapy/adverse effects ; Microbiota ; Treatment Outcome ; }, abstract = {BACKGROUND: Radiation-induced oral mucositis (OM) is a prevalent and debilitating complication of head and neck radiotherapy, yet its severity varies markedly between patients. Emerging evidence suggests that this heterogeneity is influenced by the pre-existing oral microbiome and host inflammatory tone.<br><br>METHODS: This prospective, pragmatic interventional study grouped nasopharyngeal carcinoma (NPC) patients receiving chemoradiotherapy by probiotic exposure: no probiotic, Streptococcus salivarius K12 (SsK12), or Streptococcus salivarius M18 (SsM18). Weekly oral assessments were used to characterize the onset, duration, and severity of OM. Group-based trajectory modeling (GBTM) was used to identify OM trajectories. Univariate, multivariate, and mediation analyses were used to explore associated factors and potential relationships.<br><br>RESULTS: Among 69 evaluable patients, OM occurred in 95.7%, with severe OM (SOM) in 42.4%. Compared with non-probiotic group, SsM18 significantly delayed OM onset (p = 0.014), reduced SOM duration (p = 0.019), and shortened total OM duration (p = 0.031), outperforming SsK12. GBTM identified two distinct OM trajectories: 'Rapid-Onset, Severe' group and 'Late-Onset, Mild' group. Multivariate analysis revealed that elevated log-transformed Interleukin-6 levels (odds ratio [OR] = 4.20, p = 0.020), and high Beck Oral Assessment Scale (BOAS) score (OR = 3.06, p = 0.044) as independent predictors of 'Rapid-Onset, Severe' trajectory. The Teeth subdomain of BOAS was identified as an independent predictor for earlier OM onset (p = 0.042). Mediation analysis suggested that the association between a higher Teeth subdomain score and OM was partially mediated by IL-6 elevation (proportion mediated: 30-50%).<br><br>CONCLUSIONS: Radiotherapy-induced OM was associated with baseline oral health and inflammatory status. SsM18 supplementation was associated with improved OM-related outcomes, suggesting a potential role for precision probiotic strategies.<br><br>CLINICAL TRIAL INFORMATION: https://www.chictr.org.cn/, identifier ChiCTR2600118357.}, }
@article {pmid41853278, year = {2026}, author = {Li, C and Zhu, L and Wang, Y and Zhao, L and Lin, X and Sun, Z and Yan, T and Wang, Y and Piao, J and Jin, A}, title = {Spatiotemporal control of immunogenic cell death: rewiring tumor-immune dialogues for next-generation immunotherapy.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1784935}, pmid = {41853278}, issn = {1664-3224}, mesh = {Humans ; *Immunogenic Cell Death/immunology ; *Neoplasms/immunology/therapy/metabolism/pathology ; *Immunotherapy/methods ; Animals ; Alarmins/metabolism/immunology ; Tumor Microenvironment/immunology ; Dendritic Cells/immunology ; }, abstract = {Immunogenic cell death (ICD) is a regulated cell death process distinguished by its ability to stimulate an adaptive immune response. This occurs through the emission of damage-associated molecular patterns (DAMPs), such as calreticulin (CRT), adenosine triphosphate (ATP), High Mobility Group Box 1 (HMGB1), type I interferons (IFN-α/β), and heat shock proteins(HSPs). Collectively, these signals promote dendritic cells (DCs) maturation, facilitate antigen cross-presentation, and trigger cytotoxic T lymphocytes (CTLs) activation. This cascade of immunostimulatory events is critical for converting immunologically "cold" tumors into "hot" ones. This review systematically explains the molecular mechanism of ICD, focusing on the space-time regulation of DAMPs emission and their role in remodeling the tumor immune environment. We also list a variety of ICD inducers, including conventional chemotherapeutic drugs, targeted drugs, nanotechnology-driven systems, physical means, and tumor-lytic viruses. The core theme is the synergistic potential of ICD with immune checkpoint inhibitors(ICIs), chimeric antigen receptor T cells (CAR-T cells)therapy, and microbiome regulation, supported by emerging preclinical and clinical evidence. We also discuss some current challenges, such as the heterogeneity of tumors released by DAMPs and immune escape mechanisms, and explore the development of biomarkers for patient stratification. In the future, we have emphasized some promising research directions, including artificial intelligence-assisted drug design, spatially differentiated metometric technology, and engineered immune cell therapy to achieve precise space-time-induced immune cell death. This review presents the mechanistic insights and transformative research directions for positioning ICD as a central pillar in the future landscape of immuno-oncology.}, }
@article {pmid41853332, year = {2023}, author = {Naylor, D and Naasko, K and Smith, M and Couvillion, S and Nicora, C and Trejo, J and Fransen, S and Danczak, R and McClure, R and Hofmockel, KS and Jansson, JK}, title = {Interactive effects of depth and differential irrigation on soil microbiome composition and functioning.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1078024}, pmid = {41853332}, issn = {2813-4338}, abstract = {Two factors that are well-known to influence soil microbiomes are the depth of the soil as well as the level of moisture. Previous works have demonstrated that climate change will increase the incidence of drought in soils, but it is unknown how fluctuations in moisture availability affect soil microbiome composition and functioning down the depth profile. Here, we investigated soil and wheatgrass rhizosphere microbiomes in a single common field setting under four different levels of irrigation (100%, 75%, 50%, and 25%) and three depths (0-5 cm, 5-15 cm, and 15-25 cm from the surface). We demonstrated that there is a significant interactive effect between depth and irrigation, where changes in soil moisture more strongly affect soil microbiomes at the surface layer than at deeper layers. This was true for not only microbiome community composition and diversity metrics, but also for functional profiles (transcriptomic and metabolomic datasets). Meanwhile, in rhizosphere communities the influence of irrigation was similar across the different depths. However, for the 'Alkar' wheatgrass cultivar, the rhizosphere microbial communities responded more strongly to changes in irrigation level than did the communities for the 'Jose' cultivar rhizosphere. The lessened response of deeper soil microbiomes to changes in irrigation may be due to higher incidence of slow-growing, stress-resistant microbes. These results demonstrate that the soil microbiome response to moisture content is depth-dependent. As such, it will be optimal for soil microbiome studies to incorporate deeper as well as surface soils, to get a more accurate picture of the soil microbiome response to stress.}, }
@article {pmid41853336, year = {2023}, author = {Gonçalves-Nobre, JG and Gaspar, I and Alpuim Costa, D}, title = {Anthracyclines and trastuzumab associated cardiotoxicity: is the gut microbiota a friend or foe? - a mini-review.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1217820}, pmid = {41853336}, issn = {2813-4338}, abstract = {Breast cancer (BC) is one of the most prevalent cancers worldwide. Fortunately, BC treatment has taken a huge turn in the last few years. Despite these advances, one of the main issues related to systemic treatment remains the management of its side effects, including cardiotoxicity. In this regard, we highlight the irreversible dose-dependent cardiotoxicity of anthracyclines related to oxidative stress and the reversible cardiotoxicity with trastuzumab, whose mechanism is still poorly understood. Moreover, the combination of anthracyclines and trastuzumab further exacerbate the myocardial damage. More recently, altered gut microbiota composition has been linked to the long-term effects of cancer therapy, including the potential connection between treatment-related microbial changes and cardiotoxicity. Bacteroides spp., Coriobacteriaceae_UGC-002, and Dubosiella have already been reported as bacterial species with deleterious effects on the myocardium, mainly due to the promotion of inflammation. On the other hand, Alloprevotella, Rickenellaceae_RC9, Raoultella planticola, Klebsiella pneumoniae, and Escherichia coli BW25113 can induce cardioprotection, predominantly by increasing anti-inflammatory cytokines, promoting intestinal barrier integrity and early metabolization of doxorubicin. Herein, we explore the role of gut microbiota in the development of cardiotoxicity, as well as future perspectives to decrease the risk of cardiotoxicity associated with BC treatment.}, }
@article {pmid41853341, year = {2023}, author = {Hay, MC and Hinsu, AT and Koringa, PG and Pandit, RJ and Liu, PY and Parekh, MJ and Jakhesara, SJ and Dai, X and Crotta, M and Fosso, B and Limon, G and Guitian, J and Tomley, FM and Xia, D and Psifidi, A and Joshi, CG and Blake, DP}, title = {Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1301609}, pmid = {41853341}, issn = {2813-4338}, abstract = {Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.}, }
@article {pmid41853344, year = {2023}, author = {Yao, H and Zhang, Z and Wu, N and Wang, M and Wu, Q and Wu, H and Zhao, D}, title = {Comparative analysis of intestinal flora at different overwintering periods in wild relict gulls (Larus relictus): first evidence from Northern China.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1218281}, pmid = {41853344}, issn = {2813-4338}, abstract = {The migratory bird's gut microbiome composition and function change during the overwintering period, helping the host to adapt to different environments. Our study investigated the gut microbiome of migratory relict gulls (Larus relictus) in the early and late wintering stages from their overwintering grounds in Tianjin, China. We collected 24 and 29 fecal samples at the early and late stages, respectively, and analyzed the samples using high-throughput sequencing technology to find the relationship between diet, living environment, and gut microbiome of migratory birds. The results showed that the diversity and abundance of microbial communities (alpha diversity) increased during the overwintering period and significantly differed between both groups (beta diversity). Based on the gut microbial taxonomic composition, the relative abundance of Firmicutes decreased during the overwintering period, and Proteobacteria increased significantly. Furthermore, Catellicoccus and Breznakia were the main genera in both the early and late stages. Prediction of KEGG functions based on the PICRUSt2 method showed that changes in the gut microbiome resulted in an increased abundance of bacteria associated with amino acid metabolism, metabolism of cofactors and vitamins, energy metabolism, and environmental adaptation in the late stage. Differences in diet and environment at different stages during the overwintering period may have led to the differentiation of microbial communities, and their adaptive mechanisms need to be further investigated. This is the first in-depth study of the gut microbial composition of L. relictus during the overwintering period in northern China. These findings may contribute to the protection of migratory birds.}, }
@article {pmid41853346, year = {2023}, author = {Barfod, KK and Lui, JC and Hansen, SSK and Sengupta, S and Zachariassen, LSF and Hansen, AK and Sørli, JB}, title = {The impact of bacterial exposure in early life on lung surfactant gene expression, function and respiratory rate in germ-free mice.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1085508}, pmid = {41853346}, issn = {2813-4338}, abstract = {Early-life changes to lung and gut microbiota have been linked to alterations in immune responses that may lead to pulmonary diseases later in life. Associations between early-life microbiota, germ-free status, lung gene expression, lung development and function are not well described. In this study, we compare early-life lung gene transcription under germ-free and different perinatal microbial exposures, and analyze with a predetermined focus on lung capacity and lung surfactant. We also analyze the later-in-life physiological measures of breathing patterns and lung surfactant function between the germ-free, gnotophoric and gnotobiotic offspring. To achieve this, we kept pregnant BALB/c germ-free mice in separate germ-free isolators until exposure to either A: no exposure (GF), B: Bifidobacterium animalis ssp. Lactis (BI04) or C: full cecum content harvested from other female SPF mice (Cecum). Subsequently, perinatally exposed offspring were used for the analyses. Lung tissue transcriptomics analysis was done at postnatal day 10 (PNday10) at the first phase of lung alveolar development. Head-out plethysmography for breathing pattern analysis was performed on the siblings at PNday23 followed by lung surfactant collection. The function of the collected lung surfactant was then analyzed ex vivo using the constrained drop surfactometer. Our results show that lung transcriptomics had differentially expressed genes related to surfactant turnover between groups and sex at PNday10. They also show that the GF and BI04 animals had lower respiratory rate than Cecum mice, or compared to age-matched specific pathogen-free (SPF) reference animals. We also see changes in lung surfactant function ex vivo. The overall conclusions are that 10-day-old GF mice do not have a markedly different lung gene transcription compared to gnotophoric or gnotobiotic mice, but genes related to surfactant metabolism are among the few differentially expressed genes. We show here for the first time that early-life microbiome status correlates with early-life surfactant-gene transcription and to later-in-life lung surfactant function and associated respiratory-rate changes in mice.}, }
@article {pmid41853347, year = {2023}, author = {Busi, SB and Peter, H and Brandani, J and Kohler, TJ and Fodelianakis, S and Pramateftaki, P and Bourquin, M and Michoud, G and Ezzat, L and Lane, S and Wilmes, P and Battin, TJ}, title = {Cross-domain interactions confer stability to benthic biofilms in proglacial streams.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1280809}, pmid = {41853347}, issn = {2813-4338}, abstract = {Cross-domain interactions are an integral part of the success of biofilms in natural environments but remain poorly understood. Here, we describe cross-domain interactions in stream biofilms draining proglacial floodplains in the Swiss Alps. These streams, as a consequence of the retreat of glaciers, are characterised by multiple environmental gradients and perturbations (e.g., changes in channel geomorphology, discharge) that depend on the time since deglaciation. We evaluate co-occurrence of bacteria and eukaryotic communities along streams and show that key community members have disproportionate effects on the stability of community networks. The topology of the networks, here quantified as the arrangement of the constituent nodes formed by specific taxa, was independent of stream type and their apparent environmental stability. However, network stability against fragmentation was higher in the streams draining proglacial terrain that was more recently deglaciated. We find that bacteria, eukaryotic photoautotrophs, and fungi are central to the stability of these networks, which fragment upon the removal of both pro- and eukaryotic taxa. Key taxa are not always abundant, suggesting an underlying functional component to their contributions. Thus, we show that there is a key role played by individual taxa in determining microbial community stability of glacier-fed streams.}, }
@article {pmid41853349, year = {2023}, author = {English, MK and Langdon, CJ and Schubiger, CB and Mueller, RS}, title = {Dominant bacterial taxa drive microbiome differences of juvenile Pacific oysters of the same age and variable sizes.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1071186}, pmid = {41853349}, issn = {2813-4338}, abstract = {Oyster aquaculture is a growing industry that depends on production of fast-growing, healthy larvae and juveniles (spat) to be sold to farmers. Despite nearly identical genetics and environmental conditions in the early life stages of oysters, larvae and spat sizes can vary drastically. As the microbiome can influence the health and size of marine invertebrates, we analyzed the microbiomes of differently-sized juvenile Pacific oyster (Crassostrea gigas) spat of the same age to examine the relationship of their microbiomes with size variation. We used 16S sequencing of 128 animals (n = 60 large, n = 68 small) to characterize the microbiomes of each size class, comparing alpha diversity, beta diversity, and differentially abundant taxa between size classes. We observed that small spat had higher alpha diversity using measures that considered only richness, but there was no difference in alpha diversity between the two size classes using measures that incorporate compositional metrics. Additionally, large and small spat had distinct microbiomes, the separation of which was driven by more dominant bacterial taxa. Taxa that were differentially abundant in large oysters were also more abundant overall, and many appear to have roles in nutrient absorption and energy acquisition. The results of this study provide insight into how the microbiome of C. gigas may affect the early development of the animal, which can inform hatchery and nursery practices.}, }
@article {pmid41853350, year = {2023}, author = {Oliveira, RS and Pinto, OHB and Quirino, BF and de Freitas, MAM and Thompson, FL and Thompson, C and Kruger, RH}, title = {Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1206961}, pmid = {41853350}, issn = {2813-4338}, abstract = {The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge's microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group's abundance in GARS sponges. The workflow consisted of MAG's quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host's survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.}, }
@article {pmid41853351, year = {2023}, author = {Song, JS and Kim, JOR and Yoon, SM and Kwon, MJ and Ki, CS}, title = {The association between gut microbiome and hypertension varies according to enterotypes: a Korean study.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1072059}, pmid = {41853351}, issn = {2813-4338}, abstract = {INTRODUCTION: Several animal and clinical studies have reported that the state of the human gut microbiome is associated with hypertension. In this study, we investigated the association between the gut microbiome and hypertension in a Korean population from an enterotypic perspective.<br><br>METHODS: A total of 623 participants were enrolled from a healthcare center and classified into four enterotypes, Bacteroides1- (Bac1), Bacteroides2- (Bac2), Prevotella- (Pre), and Ruminococcus enterotype-like-composition (Rum).<br><br>RESULTS: When comparing the four enterotypes, clinical characteristics related to obesity, metabolic syndrome, and blood pressure were significantly associated with th e enterotypes, showing unfavorable associations with the Bac2 group and the opposite for the Rum group. Similarly, the prevalence of hypertension was highest in the Bac2 group and lowest in the Rum group. When analyzing the association between gut microbiota and blood pressure for each enterotype, gut microbial features of lower diversity, depletion of important short chain fatty acid-producing taxa, such as Faecalibacterium, Blautia, Anaerostipes, and enrichment of lipopolysaccharide -producing taxa, such as Megamonas, were found only in the dysbiotic Bac2 group.<br><br>DISCUSSION: From an enterotype perspective, this study on a large Korean cohort shows that low-diversity Bacteroides2-enterotype-like composition is associated with hypertension, while the reverse is true for high-diversity Ruminococcus-enterotype-like composition and, to a limited degree, Bacteroides1-enterotype-like composition. In addition, we suggest that the effect of gut microbiota-mediated risk of hypertension could be modulated by altering the gut microbiome via diet. Dietary intervention trials promoting a balanced Korean diet instead of a more Western alternative may provide more definitive evidence for the involvement and role of the gut microbiome in relation to blood pressure.}, }
@article {pmid41853352, year = {2023}, author = {Guduk, E and Hall, MB and Zanton, GI and Steinberger, AJ and Weimer, PJ and Suen, G and Weigel, KA}, title = {Characterization of rumen microbiota in lactating Holstein cows fed molasses versus corn grain at two levels of rumen-degradable protein.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1204988}, pmid = {41853352}, issn = {2813-4338}, abstract = {We evaluated the influence of diets differing in non-fiber carbohydrates and rumen-degradable protein (RDP) levels on changes in the ruminal bacterial populations in lactating Holstein cows. In all, 12 ruminally cannulated cows were assigned to diets with high or low RDP levels. Within each RDP level, molasses was substituted for corn grain at a concentration of 0%, 5.25%, or 10.5% of diet dry matter in a replicated 3 × 3 Latin square design with 28-day periods. Liquid and solid rumen digesta fractions collected at the end of each period underwent 16S rRNA gene sequencing to identify operational taxonomic units and were analyzed for short-chain fatty acids. Protein degradability affected 6 bacterial genera, whereas carbohydrate alteration impacted 13 genera (p < 0.05). Of the 30 genera with the highest relative abundance, 26 differed by digesta fraction (p < 0.05), with Bacteroidetes genera showing a greater abundance in solids and Firmicutes genera demonstrating a greater prevalence in liquids. Regarding relative abundances, with increasing molasses, Succiniclasticum decreased in liquid (p < 0.05), and CF231, YRC22, Clostridium, Desulfovibrio, BF311, and Oscillospira increased in solids (p < 0.05). In contrast, at higher RDP levels, Succiniclasticum increased while YRC22 and Pseudobutyrivibrio decreased in solids (p < 0.05). Genera with abundances found to be correlated with fermentation products in the liquid included Shuttleworthia, Treponema, Lachnospira, and Schwartzia, which typically have lower relative abundances, showing strong positive correlations with molar proportions (mol%) of propionate, butyrate, and valerate (p < 0.05), and negative correlations with pH and acetate mol% (p < 0.05). Fibrobacter was positively correlated with lactate mol% (p < 0.05). Butyrate mol% exhibited a quadratic increase as molasses increased (p = 0.017), and lactate mol% rose with increased RDP levels (p = 0.042). No treatment effects were detected for pH propionate and valerate mol%; however, we observed a tendency (p = 0.075) for a quadratic effect of molasses treatment on the mol% of acetate. These findings substantiate the pivotal role of diet in shaping rumen microbiota and metabolism, elucidating a nuanced relationship between dietary components, bacterial community structure, and metabolic output. This offers a more detailed understanding of rumen function and the potential for high-precision dietary management in lactating cows.}, }
@article {pmid41853354, year = {2023}, author = {de Muinck, EJ and Trosvik, P and Nguyen, N and Fashing, PJ and Stigum, VM and Robinson, N and Hermansen, JU and Munthe-Kaas, MC and Baumbusch, LO}, title = {Reduced abundance of Faecalibacterium prausnitzii in the gut microbiota of children diagnosed with cancer, a pilot study.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1151889}, pmid = {41853354}, issn = {2813-4338}, abstract = {BACKGROUND: There is an increasing awareness of the importance of the gut microbiome in disease progression and the maintenance of human health. However, links between the microbiome and cancer onset remain relatively unexplored. This is especially the case for childhood cancers, which although rare, are the predominant cause of death among children in Western countries.<br><br>METHODS: Fecal samples were collected from patients, before the onset of treatment, by the Norwegian Childhood Cancer Biobank in Oslo and from children attending kindergartens in Oslo, Norway. Using 16S rRNA gene amplicon sequencing, we compared the gut microbiome compositions of the children diagnosed with cancer with children attending kindergarten.<br><br>RESULTS: We observed significant differences in the relative abundances of several taxa, including a striking depletion of Faecalibacterium prausnitzii, an important taxa linked to gut health maintenance.<br><br>CONCLUSIONS: Our observations provide evidence that the gut microbiome may play an important role in physiological changes associated with the onset of childhood cancer. However, further studies should be designed in order to validate our findings. Furthermore, these results suggest that variations in the microbial community could potentially be used as an early indicator of childhood cancer.}, }
@article {pmid41853355, year = {2023}, author = {Bassis, CM and Bullock, KA and Sack, DE and Saund, K and Pirani, A and Snitkin, ES and Alaniz, VI and Quint, EH and Bell, JD and Young, VB}, title = {Vaginal microbiota of adolescents and their mothers: A preliminary study of vertical transmission and persistence.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1129394}, pmid = {41853355}, issn = {2813-4338}, abstract = {INTRODUCTION: Factors that influence vaginal microbiota composition, including its source, are not well understood.<br><br>METHODS: To determine if vaginal microbiota transmission from mother to daughter at birth could possibly influence the human vaginal microbiota composition in adolescence, we conducted a preliminary study to investigate the relationship between the vaginal microbiota of 13 adolescents (ages 15-21) and their mothers and the daughter's birth mode.<br><br>RESULTS AND DISCUSSION: Based on analysis of bacterial 16S rRNA gene sequences, the vaginal microbiotas of mother/daughter pairs were more similar to each other if the daughter was born by vaginal delivery rather than by C-section. Specifically, within pair &#x3b2;-diversity, measured by the Yue and Clayton &#x3b8; (&#x3b8;YC) distance metric, was significantly lower if the daughter was born by vaginal delivery. Additionally, genome sequences from an important member of the vaginal microbiota, Lactobacillus crispatus, isolated from one mother/daughter pair in which the daughter was born by vaginal delivery, were highly similar based on recombination-filtered single nucleotide polymorphisms (SNPs). Both community-level analysis and isolate genome sequence analysis are consistent with birth-mode dependent transmission and persistence of at least some members of the vaginal microbiota.}, }
@article {pmid41853357, year = {2023}, author = {Ma, S and Zhang, Y and Li, Z and Guo, M and Liu, B and Wang, Z and Cui, Y and Wang, C and Li, D and Shi, Y}, title = {Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1272625}, pmid = {41853357}, issn = {2813-4338}, abstract = {Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4[+] and CD8[+]) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level.}, }
@article {pmid41853358, year = {2023}, author = {Whitaker, BK and Heiniger, RW and Hawkes, CV}, title = {Foliar fungal communities in agroecosystems depend on crop identity and neighboring vegetation.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1216462}, pmid = {41853358}, issn = {2813-4338}, abstract = {Agricultural intensification causes plant diversity loss and environmental homogenization, which may result in changes to plant-microbiome interactions mediating plant growth and stress tolerance. We hypothesized that foliar fungal microbiomes would depend on plant traits and environmental filters, constrained by neighboring vegetation expected to serve as a fungal source. Thus, we sampled foliar fungi from four crops (three annual and one perennial), four sites per crop, and three varieties per annual crop, across a 500-km expanse in North Carolina, USA and tested the role of host traits, environmental traits, and vegetative landcover on foliar fungal community structure. Crop species and site were major determinants of community structure, primarily due to differences in plant size and growing season. Site consistently explained 10× more variation in community structure than host variety across the annual crops. Finally, reduced natural vegetative cover surrounding farms was correlated with decreased fungal richness and more homogeneous microbiome assembly. Based on these results, we posit that foliar fungal assembly in crops results from host and environmental filters acting on inputs from the nearby vegetation. Future efforts at agricultural microbiome management must therefore consider landscape management and will require an improved understanding of how agricultural intensification alters microbial source pools.}, }
@article {pmid41853360, year = {2023}, author = {Chen, L and Ding, H and Chen, X and Wang, J and Hu, Y and Chen, H and Liu, Y}, title = {Cultivation modes impacting root microbiomes and metabolites in medicinal orchid Dendrobium denneanum.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1287336}, pmid = {41853360}, issn = {2813-4338}, abstract = {INTRODUCTION: The plant microbiome is the second genome of plants and is important for plant growth and health. Dendrobium is an epiphytic herbal plant of the family Orchidaceae that is often found attached to tree trunks or rocks and exhibits different cultivation modes. Microbiological and metabolite studies of Dendrobium denneanum Kerr (D. denneanum) in different cultivation modes can reveal important relationships between Dendrobium spp., their microbiomes, and their pharmacological substances, which is important for sustainable agricultural development and human health, particularly in the study of medicinal plants.<br><br>METHODS: In this study, three cultivation modes, living tree epiphytic (LT), stone epiphytic (SE), and pot cultivation (PO) of D. denneanum in the same environment were selected, and the metabolites were using ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Subsequently, differential metabolites were screened, the rhizosphere and root endosphere microorganisms were sequenced via high-throughput sequencing, and the 16S rRNA gene/ITS sequences were obtained.<br><br>RESULTS: The main microbial taxa in the rhizosphere and root endosphere of&#xa0;D. denneanum included bacteria belonging to Proteobacteria, Actinobacteria, and Actinobacteria, and the fungi Basidiomycota and Ascomycota, whose abundances varied in different cultivation modes. Soil properties affect the composition of D. denneanum metabolites and root microbiome, among which, soil total phosphorus (TP) and pH in particular are important factors for soil microorganisms. Studies of root microbial communities have shown that root endosphere fungi are similar to rhizosphere fungi with microbial enrichment occurring from the external environment to the internal structures. Root microbial communities and metabolites correlation analyses revealed significant correlations between rhizosphere microbes, as well as endophytes and metabolites. For example, the rhizosphere bacterium genus Occallatibacter and root endosphere fungus Clonostachys showed a significant negative correlation with the pharmacodynamic substance gigantol in D. denneanum (P<0.05).<br><br>CONCLUSION: This study elucidates the effects of different cultivation modes on D. denneanum from the perspective of microorganisms and metabolites, and investigates the effects of root microorganisms on metabolites. The findings enhance the current understanding of root microorganisms in orchid plants and provide a theoretical basis for the cultivation of Dendrobium spp., represented here by D. denneanum.}, }
@article {pmid41853361, year = {2023}, author = {Njoku, EN and Mottawea, W and Hassan, H and Hammami, R}, title = {Prebiotic capacity of novel bioengineered wheat arabinoxylans in a batch culture model of the human gut microbiota.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1156797}, pmid = {41853361}, issn = {2813-4338}, abstract = {Arabinoxylan (AX) is an essential component of dietary fiber with potential prebiotic properties. However, owing to its complex structure, fermentation of AX by gut microbes is structure dependent. In this study, we evaluated the effect of bioengineered wheat AX on the metabolism and composition of gut microbiota using an in vitro fermentation model. We compared the effect of bioengineered AX with that of untreated AX and a control. Structurally modified AX did not significantly alter gut microbiome composition within 48 h of treatment; however, it enhanced the abundance of health-promoting bacterial taxa, such as Bacteroides, Bifidobacterium, Anaerofustis, and Eubacterium. Furthermore, the bioengineered AX significantly increased the level of acetate produced over 24 h. The amount of microbiota-generated butyrate was significantly increased 24 h after adding α-L-arabinofuranosidase-treated AX. AX treated with the α-L-arabinofuranosidase B25 enzyme induced higher levels of production of total short-chain fatty acids by the microbiota from four donors. The results of this study provide evidence that enzymatic structural modification of AX has the potential to modulate gut microbiome composition and metabolic activities.}, }
@article {pmid41853362, year = {2023}, author = {Morgan, PA and Parbie, PK and Ntiamoah, DO and Boadu, AA and Asare, P and Lamptey, INK and Gorman, CN and Afreh, E and Asante-Poku, A and Otchere, ID and Aboagye, SY and Yeboah-Manu, D}, title = {Gut microbiome variation in pulmonary TB patients with diabetes or HIV comorbidities.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1123064}, pmid = {41853362}, issn = {2813-4338}, abstract = {BACKGROUND: The gut microbiota is known to play a critical role in shaping the host immunity, and metabolism and influences the onset and progression of both communicable and non-communicable diseases. This study assessed the gut microbiome of tuberculosis (TB) cases with diabetes mellitus (DM) or HIV comorbidities before anti-TB therapy and after the intensive phase anti-TB therapy.<br><br>METHODS: Ninety cases comprising 60 TB-only, 23 TB-DM, 7 TB-HIV were recruited, among which 35 TB-only, 10 TB-DM, 5 TB-HIV were also sampled after 2 months of anti-TB treatment. Total gut microbiome was detected by 16S rRNA gene sequencing of DNA extracted from collected stool specimen. The taxonomic and functional diversity of the different groups were compared in addition to changes that could occur after 2 months antibiotics use.<br><br>RESULTS: Compared to the healthy controls, the gut microbiome of all the TB cohorts was characterized by a significant decreased alpha diversity and significant compositional changes. All the three TB cohorts were enriched with inflammatory related microorganisms of the genera Escherichia-shigella, Streptococcus, Enterococcus and Erysipelatoclostridium with depletion in beneficial taxa of the genera Faecalibacterium, Bifidobacterium and Clostridium. In pairwise comparison with the healthy controls, the TB-only cohort were enriched with Streptococcus and Erysipelatoclostridium, the TB-DM enriched with Bacteroides, and TB-HIV enriched with Escherichia-shigella, Dialister and Erysipelatoclostridium. After the intensive phase anti-TB therapy, there was general enrichment of the genera Erysipelotrichaceae_UCG 003, Veillonella and Fusobacterium.<br><br>CONCLUSION: Our findings show a dysbiotic gut microbiome and associated upregulation of inflammation related microorganism in gut microbiome of TB individuals with or without comorbidity.}, }
@article {pmid41853363, year = {2023}, author = {Zheng, S and Chen, H and Yang, H and Zheng, X and Fu, T and Qiu, X and Wang, M}, title = {Differential enrichment of bacteria and phages in the vaginal microbiomes in PCOS and obesity: shotgun sequencing analysis.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1229723}, pmid = {41853363}, issn = {2813-4338}, abstract = {INTRODUCTION: Previous research has linked vaginal bacteria to polycystic ovary syndrome (PCOS) and obesity in women, yet the specific disparities in vaginal microbiota between these conditions remain unclear.<br><br>METHODS: In this study, we aimed to elucidate the contribution of dysregulated vaginal microbiota to PCOS and obesity by analyzing the vaginal microbiota in reproductive-aged women with and without PCOS, as well as obese and non-obese women, using shotgun sequencing.<br><br>RESULTS: Swab specimens were collected from four groups of subjects: PCOS and obese, PCOS and non-obese, non-PCOS and obese, and non-PCOS and non-obese. A total of 333 bacteria and 24 viruses/phages were identified to the species level. Clustering analysis revealed that non-PCOS and non-obese individuals exhibit a similar "healthy" vaginal microbiome, while both obesity and PCOS were associated with microbial dysbiosis. Significant differences in abundance were observed for 26 bacterial species and 6 phages/viruses between groups. Notably, pathobionts such as Streptococcus pyogenes, Leptospira santarosai, Citrobacter amalonaticus, Listeria ivanovii, and Clostridium perfringens were significantly less abundant or absent in the non-PCOS and non-obese group. Furthermore, the abundance of Lactobacillus, Pseudomonas bacteria, and their corresponding phages exhibited positive correlations. Lactobacillus bacteria, lactobacillus phage, and pseudomonas phage/virus were identified as indicators of a healthy vaginal microbiome. Importantly, the differentially enriched bacteria in the PCOS and obesity groups were distinct.<br><br>DISCUSSION: This study confirms that PCOS and obesity are associated with differing enrichment of bacteria and viruses/phages, with both conditions linked to microbial dysbiosis. Moreover, our findings suggest that vaginal phage diversity is associated with a healthy vaginal microbiota, while dysbiosis is associated with a decrease in phages alongside increased bacterial diversity.}, }
@article {pmid41853364, year = {2023}, author = {Smith, ML and O'Neill, CA and Dickinson, MR and Chavan, B and McBain, AJ}, title = {Exploring associations between skin, the dermal microbiome, and ultraviolet radiation: advancing possibilities for next-generation sunscreens.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1102315}, pmid = {41853364}, issn = {2813-4338}, abstract = {Recent studies have provided strong evidence of a functional link between the microbiota of the skin and overall host health. While sunscreens offer protection against acute and chronic dermatological damage by reflecting, absorbing and scattering ultraviolet radiation, their impact on the skin microbiota is poorly understood. The use of sunscreens may affect the skin microbiota directly or indirectly through mechanisms associated with UV protection, and conversely, the microbiota could mediate or alleviate UV-induced skin damage. Here we consider opportunities for the development of improved sunscreens including formulas that work in tandem with skin commensal microorganisms or which minimise direct effects on the skin microbiota.}, }
@article {pmid41853366, year = {2023}, author = {Scaturro, M and Del Chierico, F and Motro, Y and Chaldoupi, A and Flountzi, A and Moran-Gilad, J and Girolamo, A and Koutsiomani, T and Krogulska, B and Lindsay, D and Matuszewska, R and Papageorgiou, G and Pancer, K and Panoussis, N and Rota, MC and Uldum, SA and Velonakis, E and Chaput, DL and Ricci, ML}, title = {Premise plumbing bacterial communities in four European cities and their association with Legionella.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1170824}, pmid = {41853366}, issn = {2813-4338}, abstract = {INTRODUCTION: Legionella species are Gram negative, facultative, intracellular bacteria found in natural and engineered water systems. Understanding the bacterial interactions underlying the success of Legionella in aquatic environments could be beneficial for control.<br><br>MATERIALS AND METHODS: We aimed to profile, by 16S rRNA gene amplicon sequencing (V3-V4), the bacterial communities in premise plumbing systems of buildings in four European cities (Copenhagen, Warsaw, Rome, Athens), and identify positive and negative associations of specific community members to culturable Legionella.<br><br>RESULTS: The coarse taxonomic composition was similar across the four cities, but Copenhagen and Warsaw had richer, more diverse communities than Athens and Rome, with a greater number of city-specific amplicon sequence variants (ASVs). The cities had statistically significant differences in bacterial communities at the ASV level, with relatively few shared ASVs. Out of 5,128 ASVs, 73 were classified as Legionella, and one or more of these were detected in most samples from each city (88.1% overall). Interestingly, the relative abundance of Legionella ASVs did not correlate with Legionella culture status. Overall, 44.2% of samples were Legionella culture positive: 71.4% in Warsaw, 62.2% in Athens, 22.2% in Rome, and 15.2% in Copenhagen. 54 specific ASVs and 42 genera had significant positive or negative associations with culturable Legionella. Negative associations included Staphylococcus, Pseudomonas, and Acinetobacter. Positive associations included several Nitrospira ASVs and one classified as Nitrosomodaceae oc32, ASVs in the amoeba-associated genera Craurococcus-Caldovatus and Reyranella, and the predatory genus Bdellovibrio.<br><br>DISCUSSION: Some of these associations are well supported by laboratory studies, but others are the opposite of what was expected. This highlights the difficulties in translating pure culture results to in complex real-life scenarios. However, these positive and negative associations held across the four cities, across multiple buildings and plumbing compartments. This is important because developing better control measures, including probiotic approaches, will require an understanding of ecological relationships that can be generalised across different engineered water systems.}, }
@article {pmid41853367, year = {2023}, author = {Smith, SN and Watters, JL and Siler, CD}, title = {Host ecology drives frog skin microbiome diversity across ecotone in South-Central North America.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1286985}, pmid = {41853367}, issn = {2813-4338}, abstract = {Anurans (frogs and toads) are an ecologically diverse group of vertebrate organisms that display a myriad of reproductive modes and life history traits. To persist in such an expansive array of habitats, these organisms have evolved specialized skin that is used for respiration while also protecting against moisture loss, pathogens, and environmental contaminants. Anuran skin is also colonized by communities of symbiotic microorganisms, and these skin microbiota serve critical roles in numerous processes associated with anuran host health and persistence such as pathogen resistance and immunity. However, gaps remain in our understanding of the environmental and evolutionary processes that shape frog skin microbial communities. Here, we combined existing anuran disease data with 16S rRNA skin microbial inventories to elucidate the roles that geographic location, host evolutionary history, host ecology, and pathogen presence play in the microbial community assemblage of five co-distributed frog host species in Oklahoma. These focal species possess distinct ecological preferences: aquatic, semi-aquatic, and arboreal, and our results indicate that host ecology is the primary driver of frog skin microbial community structure. Additionally, compositional differences were observed among select host species based on geographic location, but this was not consistent among all five frog species. We did not find evidence of phylogenetic signal among our samples and results from the Classification and Regression Tree Analysis revealed that the presence of the amphibian pathogen Batrachochytrium dendrobatidis and the severity of infection were not drivers of skin microbiome differences among our focal host species. Results from this comparative study contribute to our growing understanding of the environmental and host-associated drivers of skin microbial community assemblage and represents one of the first studies on landscape-level variation in skin microbial communities among North American frogs.}, }
@article {pmid41853368, year = {2023}, author = {Paulo, LS and Msema Bwire, G and Klipstein-Grobusch, K and Kamuhabwa, A and Kwesigabo, G and Chillo, P and Asselbergs, FW and Lenters, VC}, title = {Urbanization gradient, diet, and gut microbiota in Sub-Saharan Africa: a systematic review.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1208166}, pmid = {41853368}, issn = {2813-4338}, abstract = {INTRODUCTION: As Sub-Saharan Africa (SSA) undergoes rapid urbanization changes in diet and lifestyle have contributed to a rise in non-communicable diseases (NCDs) across the region. Changes in gut microbiota which play an important role in human health may be an underlying driving factor. While evidence suggests that the gut microbiota differs between the extreme levels of economic development (least vs highly developed), it is not well-established which factors along the urbanization gradient are most influential, especially for SSA. This systematic review analyzed published articles from SSA countries that examined the differences in the composition and diversity of gut microbiota along the urbanization gradient. The findings of this review have important implications for understanding the impact of urbanization on human health in the SSA.<br><br>METHODS: Peer-reviewed articles that examined the link between the urbanization gradient, dietary patterns, and gut microbiota using culture-independent techniques were included in the review.<br><br>RESULTS: A total of 3,265 studies were identified and screened. Eighty-nine (89) studies underwent full-text review, and 23 studies were extracted and included for final analysis. Among these studies, it was observed that hunter-gatherers had high alpha diversity (within-person variation) and beta diversity (between-person variation) in their gut microbiota compared to rural and urban residents in SSA. However, there were inconsistent differences between rural and urban at the individual taxa levels, potentially due to limited statistical power and large variability in the study techniques and designs. Similarly, there were no clear differences in the relative abundance of genera across the urbanization gradient. Additionally, both diet and intestinal parasites were associated with the composition and diversity of the gut microbiota.<br><br>CONCLUSION: The review revealed there are variations in both alpha and beta diversity of the gut microbiota across the urbanization gradient with a higher diversity observed in rural areas. However, we did not observe significant differences in the relative abundance at phyla or genus levels consistently across the urbanization gradient. Moreover, our findings suggest that the mode of subsistence, diet, and intestinal parasites play a role in shaping the composition and diversity of the gut microbiota in SSA.<br><br>https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42021251006, identifier CRD42021251006.}, }
@article {pmid41853369, year = {2023}, author = {Weir, TL}, title = {Grand challenges: Actualizing the potential of the gut microbiome to address global nutrition challenges.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1146827}, pmid = {41853369}, issn = {2813-4338}, }
@article {pmid41853370, year = {2023}, author = {Berryman, MA and Triplett, EW and Ludvigsson, J}, title = {Human leukocyte antigen-dependent colonization of Lactobacillus in the early-life gut.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1192773}, pmid = {41853370}, issn = {2813-4338}, abstract = {To determine the importance of Lactobacillus in shaping the human gut microbiome, the microbial composition of stools from 1,602 children between the ages of 0.3 months and 37.2 months was analyzed in a general population cohort in the All Babies in Southeast Sweden study. Lactobacillus colonized only 32% of the total pediatric population at an average relative abundance of 0.29%. Lactobacillus was age-dependent, decreasing in prevalence and relative abundance over time. The main determining factor for Lactobacillus colonization was whether the individual was actively breastfeeding. Following cessation of breastfeeding, Lactobacillus prevalence rapidly declined. However, within the actively breastfeeding cohort, 45.6% of the population remained uncolonized by Lactobacillus. The presence versus absence of Lactobacillus was determined to be human leukocyte antigen (HLA) dependent. Individuals with HLA DR15-DQ6.2 were 3.4 times more likely to be colonized by Lactobacillus than those without the haplotype, and those with HLA DR5-DQ7 were more likely to have zero Lactobacillus despite actively breastfeeding. These results suggest that HLA genetics should be considered when designing Lactobacillus-based probiotics.}, }
@article {pmid41853371, year = {2023}, author = {Campbell, PM and Willmott, T and Humphreys, GJ and Piscoran, O and Chea, H and Summers, AM and Konkel, JE and Knight, CG and Augustine, T and McBain, AJ}, title = {Transplantation impacts on the oral microbiome of kidney recipients and donors.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1258290}, pmid = {41853371}, issn = {2813-4338}, abstract = {INTRODUCTION: Chronic kidney disease (CKD) may affect the human microbiome via increased concentrations of uremic toxins such as urea and creatinine.<br><br>METHODS: We have profiled the oral microbiota in patients with CKD before and one week after kidney transplantation. Living kidney donors were also longitudinally tracked over a similar period, allowing direct comparison between a group undergoing transplant surgery alone (donors) (n=13) and a group additionally undergoing the introduction of immunosuppressive agents and the resolution of CKD (recipients) (n=45).<br><br>RESULTS: Transplantation was associated with a similar pattern of decreasing alpha diversity in the oral microbiome in recipients and donors via Kruskal-Wallis testing, within one week of transplantation. Amplicon sequence variants (ASVs) associated with Haemophilus parainfluenzae, Aggregatibacteria segnis, Peptostreptococcus and Actinobacillus were significantly decreased in recipients within a week of transplantation.<br><br>DISCUSSION: A reduction in ASVs in these genera could influence the risk of bacterial endocarditis, a rare but high-mortality kidney transplantation complication. A range of factors may drive the observed changes in oral microbiome including both factors associated with surgery itself and the decreases in salivary urea, administration of macrolide antibiotic immunosuppressants, and disruption to immune function that characterise kidney transplant.}, }
@article {pmid41853372, year = {2023}, author = {Dehinsilu, J and Sergaki, C and Amos, G and Fontana, V and Pirmohamed, M}, title = {The interplay between the microbiome and colonic immune system in checkpoint inhibitor therapy.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1061193}, pmid = {41853372}, issn = {2813-4338}, abstract = {The advent of immune checkpoint inhibitor therapy was a significant step in the development of treatments for cancer. It is, however, a double-edged sword. Immune related adverse events are the result of unleashing brakes on the immune system and affect many patients undergoing checkpoint inhibitor therapy, often being debilitating and occasionally lethal. It has been shown both in mice and in humans that the presence of certain families, genera and species of bacteria are associated with improved responses to checkpoint inhibitor therapy, whereas in their absence the response to therapy is often poor. Recent studies have demonstrated that immune related adverse events to checkpoint inhibitor therapy can be perturbed and perhaps predicted based on the composition and functional capacity of the gut microbiota and parts of the immune system. In the case of colitis associated with immune checkpoint inhibitor therapy, one interesting avenue of investigation is based on the activity of secretory immunoglobulin A (SIgA). Produced by plasma cells, IgA is present in high concentrations at the gut mucosa and is involved in both the maturation and maintenance of the microbiota as well as the development of IBD. Here we summarise the current literature surrounding the interplay between the gut microbiota and response to CPI therapy. Additionally, we overview the colonic immune system, paying particular attention to IgA, as a key component of the microbiota-immune system interaction.}, }
@article {pmid41853373, year = {2023}, author = {Marsh, A and Azcarate-Peril, MA and Aljumaah, M and Neville, J and Perrin, MT and Dean, LL and Wheeler, MD and Hines, IN and Pawlak, R}, title = {Corrigendum: Fatty acid profile driven by maternal diet is associated with the composition of human milk microbiota.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1143303}, doi = {10.3389/frmbi.2023.1143303}, pmid = {41853373}, issn = {2813-4338}, abstract = {[This corrects the article DOI: 10.3389/frmbi.2022.1041752.].}, }
@article {pmid41853374, year = {2023}, author = {Gudka, R and Nyinoh, IW}, title = {Fecal microbial transplantation as a novel therapeutic for autism spectrum disorders: a review of the current literature.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1222089}, pmid = {41853374}, issn = {2813-4338}, abstract = {BACKGROUND: Autism spectrum disorders (ASDs) are complex neurobiological conditions with poor long-term outcomes and limited treatment options. The microbiota-gut-brain axis indicates a pathway by which the gut microbiota links to ASDs. Fecal microbial transplantation (FMT), whereby the gut microbiota is replaced with that of a healthy individual, shows promise for the treatment of neurobiological conditions. This review examines the current evidence for the use of FMT as a therapeutic for ASD.<br><br>DISCUSSION: ASDs and their associated gastrointestinal symptoms are improved with FMT, potentially due to the engraftment of features of a healthy gut. Longer treatment regimens that include daily maintenance doses appear to be the most effective long-term therapeutic option, with benefits persisting 2 years post-intervention. Evidence is mixed regarding the use of preparatory treatments. Considering the sex bias in ASD research, small sample sizes and the lack of placebo control arms, randomized controlled trials would be of benefit to the evidence base regarding the use of FMT as a therapeutic option for ASD.<br><br>CONCLUSION: FMT is a promising new therapeutic for ASD, but the evidence base is in its infancy.}, }
@article {pmid41853376, year = {2023}, author = {Favela, A and Bohn, MO and Kent, AD}, title = {Application of plant extended phenotypes to manage the agricultural microbiome belowground.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1157681}, pmid = {41853376}, issn = {2813-4338}, abstract = {Plants have a surprising capacity to alter their environmental conditions to create adequate niches for survival and stress tolerance. This process of environmental transformation, commonly referred to as "extended phenotypes" or "niche construction", has historically been studied in the domain of ecology, but this is a process that is pervasive across the plant kingdom. Furthermore, research is beginning to show that plants' extended phenotypes shape the assembly and function of closely associated microbial communities. Incorporation and understanding the role that plant-extended phenotypes play in agriculture may offer novel, bioinspired methods to manage our arable soil microbiomes. Here, we review the challenges agriculture faces, the plant extended phenotypes we know to shape the microbiome, and the potential utilization of this knowledge to improve the environmental impact of agriculture. Understanding how plant extended phenotypes shape microbial communities could be a key to creating a sustainable future with both plants and microbiomes in consideration.}, }
@article {pmid41835236, year = {2026}, author = {Ariyan, M and Mikryukov, V and Khalil, H and Gohar, D and Hosseyni Moghaddam, MS and Drenkhan, R and Tedersoo, L}, title = {Impact of plant species, mycorrhizal type, and leaf traits on foliar fungal communities (in a common garden experiment).}, journal = {IMA fungus}, volume = {17}, number = {}, pages = {e173358}, pmid = {41835236}, issn = {2210-6340}, abstract = {Foliar fungal communities are essential components of the plant microbiome, playing a vital role in maintaining plant health and influencing ecosystem dynamics. Despite increasing interest in plant-microbe associations, the drivers shaping foliar fungal community composition remain poorly understood, including the roles of host phylogeny, functional traits, and belowground mycorrhizal symbiosis. We used the MycoPhylo experimental field, in which plant species are planted in a replicated, phylogenetically diverse design, to investigate the influence of host plant identity, mycorrhizal type, and leaf functional traits on foliar fungal assemblages. We examined foliar fungal communities across 158 plots representing 110 distinct plant species using a metabarcoding approach. The resulting operational taxonomic units (OTUs) were dominated by Dothideomycetes (44.5%), Tremellomycetes (12.7%), and Taphrinomycetes (9.0%). Functional guild analysis revealed that plant pathogens and saprotrophs were the most abundant ecological groups. Foliar fungal alpha diversity and community composition were significantly influenced by plant growth form and mycorrhizal association. Although plant deciduousness did not affect fungal richness, it significantly affected fungal community composition. The measured leaf traits (hairiness and thickness) showed the least influence on fungal richness. Mantel tests revealed weak, guild-dependent relationships between host phylogenetic distance and foliar fungal community dissimilarity. Moreover, plant phylogenetic eigenvectors accounted for up to 25.8% of the variation in fungal richness. These findings indicate that host phylogeny and plant traits contribute to-but do not solely determine-the structure of foliar fungal assemblages under field conditions.}, }
@article {pmid41835377, year = {2026}, author = {Alsanie, SA}, title = {Integrated omics approaches with non-thermal food fortification: pathways to personalized nutrition solutions.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1778056}, pmid = {41835377}, issn = {2296-861X}, abstract = {The integration of multi-omics technologies with non-thermal food processing represents a paradigm shift from population-based to precision nutrition interventions. This review synthesizes current advances in genomics, transcriptomics, proteomics, metabolomics, and microbiomics alongside emerging non-thermal technologies, including high-pressure processing, pulsed electric fields, cold plasma, ultrasound, and supercritical fluid extraction, to enable the development of personalized fortified foods. Non-thermal processing offers distinct advantages by preserving heat-sensitive nutrients, enhancing bioavailability through matrix modification, and supporting innovative encapsulation systems that overcome limitations of conventional thermal methods. Multi-omics approaches provide insights into genetic polymorphisms, metabolic phenotypes, and microbiome profiles that influence nutrient metabolism, thereby informing targeted fortification strategies for individuals and subpopulations. We examine nutrient-gene interactions, the impact of non-thermal processing on food matrices and fortificant stability, and the integration of complex omics datasets through systems biology. Key challenges include industrial scalability, harmonization of omics data interpretation, regulatory frameworks for personalized products, equitable access, and genetic data privacy. Emerging opportunities involve artificial intelligence for predictive modeling, biosensor-based monitoring, blockchain-enabled traceability, and convergence with precision medicine. This review provides a comprehensive framework to guide researchers, food technologists, healthcare professionals, and policymakers in advancing omics-guided, non-thermally processed fortified foods as innovative strategies for addressing malnutrition, preventing chronic disease, and promoting optimized health across diverse populations.}, }
@article {pmid41836174, year = {2026}, author = {Lewis, N and Schätzle, S and Cardone, F and Erpenbeck, D and Wörheide, G and Vargas, S}, title = {Species-specific community structure in the microbiomes and eukaryotic communities associated with Mediterranean golf ball sponges.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20452}, pmid = {41836174}, issn = {2167-8359}, mesh = {*Porifera/microbiology ; Animals ; *Microbiota/genetics ; Phylogeny ; Species Specificity ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; *Eukaryota/genetics/classification ; }, abstract = {BACKGROUND: Sponges harbor complex and diverse microbiomes that contribute to the host's fitness and, ultimately, the health of the ecosystems sponges inhabit.<br><br>METHODS: Using high-throughput 16S and 18S rRNA amplicon sequencing, we explore the prokaryotic and eukaryotic communities associated with three sympatric Mediterranean demosponges, namely Tethya aurantium, Tethya meloni, and Tethya citrina.<br><br>RESULTS: We found species-specific prokaryotic and eukaryotic communities despite the close sympatry of the three Mediterranean Tethya species studied. This offers further support for the phylogenetic nature of the sponge microbiome, where microbial communities reflect the evolutionary ancestry of their host species. These patterns are both present in the eukaryotic and prokaryotic sponge-associated communities, since both display similar levels of host species specificity.}, }
@article {pmid41836235, year = {2026}, author = {Chang, J and Xiao, S and Su, Y and Sherman, SK and Howe, JR and De Andrade, JP and Hoshi, H and Chan, CHF}, title = {Impact of biliary fungal contamination on outcomes after pancreaticoduodenectomy for pancreatic cancer.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1776853}, pmid = {41836235}, issn = {2234-943X}, abstract = {INTRODUCTION: Many patients with cancer of the pancreatic head will have biliary stenting to relieve malignant obstruction. Biliary stenting is associated with increased rates of bacterial and fungal biliary contamination. Little is known regarding the impact of fungal biliary contamination on postoperative and oncologic outcomes of pancreatic cancer. This study aims to evaluate the effects of fungal biliary contamination on postoperative and oncologic outcomes in patients receiving pancreatoduodenectomy for pancreatic ductal adenocarcinoma (PDAC).<br><br>METHODS: A retrospective study of a prospectively maintained single tertiary institutional database was performed, identifying patients with a diagnosis of PDAC from 2015 to 2022 who underwent curative-intent resection and had intraoperative biliary fungal cultures. Primary outcome measures assessed included overall survival (OS) and recurrence-free survival (RFS). The secondary outcome measure was postoperative complication rate. The Kaplan method estimated OS and RFS, and survival curves were compared with the log-rank test. Clinicopathologic variables were assessed for association with multivariable Cox hazard ratio.<br><br>RESULTS: Among 82 patients included, 87.8% had preoperative stenting. In stented patients, bacterial and fungal contamination had an incidence of 98.7% and 48.6%, respectively. Patients with positive fungal cultures had higher rates of neoadjuvant chemotherapy utilization than those with negative intraoperative fungal bile cultures (p = 0.05). Positive biliary fungal cultures were not independently associated with risk for postoperative complications nor RFS but were associated with worse OS (HR = 2.11 [1.04-4.26], p = 0.04). In the subgroup of patients who received neoadjuvant chemotherapy, positive fungal bile culture was associated with worse OS (HR = 2.70 [1.11-6.60], p = 0.03), but without more pronounced hematological evidence of systemic immunosuppression before and after chemotherapy.<br><br>CONCLUSION: Biliary fungal contamination was not associated with increased risk of postoperative complications in patients with pancreatic cancer but was associated with worse OS, particularly in patients who received neoadjuvant therapy. Investigations regarding the causal relationship between biliary fungus and treatment response and outcome in patients with PDAC are warranted.}, }
@article {pmid41836334, year = {2025}, author = {Corley, C and Swinton, C and McElory, T and Sridharan, B and Thomas, J and Cronin, B and Sridharan, V and Robeson, MS and Allen, AR}, title = {Implications of Cyclophosphamide, Methotrexate, and 5-Flurouracil Chemotherapy on Hippocampal-Dependent Cognition and Gut-Microbiome.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {}, pmid = {41836334}, issn = {2813-4338}, support = {R25 GM083247/GM/NIGMS NIH HHS/United States ; }, abstract = {Chemotherapy-induced cognitive impairment, also called "chemobrain", has been heavily researched as a major side effect of cancer treatment. Although breast cancer has a 91% survival rate in the U.S., this rate is significantly lower in developing countries. Cancer survivors often experience chemobrain which can decrease their quality-of-life post-chemotherapy. The presented study evaluates potential mechanisms for long-term symptoms in cyclophosphamide, methotrexate, and 5-fluorouracil (CMF)-induced cognitive impairments and implications of CMF on the microbiome. Twelve-week-old C57/B6J female mice were treated with a combination of CMF once a week for 4 weeks. Spatial memory was tested with the Morris water maze. Hippocampal tissues were used to probe for immediate-early genes (IEGs) with western blotting techniques. Fecal matter was collected to assess microbial community composition via 16S rRNA gene sequencing. In this study, we showed that chemotherapy impaired spatial memory during the Morris water maze trials and resulted in a significant decrease in immediate early genes (IEGs) c-Fos, Arc, and Zif286 expression. Comparing Alpha diversity, there were no significant differences identified amongst taxa within the CMF group compared to the saline group for Pielou's evenness. However, Beta diversity qualitative metrics, Jaccard and Unweighted Unifrac were significantly different. These results suggest that continual memory deficits may be associated with alterations in synaptic plasticity and long-term potentiation.}, }
@article {pmid41836369, year = {2026}, author = {Kucharski, R and Kosiński, A and Kalinowski, L and Kaźmierczak-Siedlecka, K}, title = {Ipilimumab, -omics, and head and neck cancers-update in 2025.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1737862}, pmid = {41836369}, issn = {1664-3224}, mesh = {Humans ; *Ipilimumab/therapeutic use/adverse effects ; *Head and Neck Neoplasms/drug therapy/immunology/etiology ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Nivolumab/therapeutic use ; Immunotherapy/methods ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; CTLA-4 Antigen/antagonists &amp; inhibitors/immunology ; *Antineoplastic Agents, Immunological/therapeutic use ; }, abstract = {Immunotherapy employing immune checkpoint inhibitors (ICIs) represents a pivotal approach for the management of recurrent and metastatic head and neck cancers (HNCs). Ipilimumab is a fully human monoclonal IgG1κ antibody against cytotoxic T-lymphocyte antigen-4 (CTLA-4), which can be introduced as a monotherapy or dual immunological regimen with nivolumab (anti-programmed death protein 1, PD-1). The background of the use of these monoclonal antibodies as combination immunotherapy is strongly associated with their different mechanisms of action. CTLA-4 and PD-1 are able to regulate the function of T cells through different mechanisms. Despite the better efficacy of immunotherapy with ipilimumab + nivolumab in HNCs observed in some cases, the overall effect regarding the comparison of ipilimumab versus ipilimumab + nivolumab is still unclear. The microbiome is one of the biomarkers that affect the response to immunotherapy with ICIs, including ipilimumab. Nevertheless, there is a clear lack of data in this context with regard to HNCs. The beneficial signature of the microbiome contributes to the prevention of the immune-related adverse events caused by ipilimumab. Notably, the incidence of gastrointestinal side effects induced by ICIs is significantly increased in the dual regimen with ipilimumab + nivolumab, which affects its recommendation for patients with HNCs.}, }
@article {pmid41836373, year = {2026}, author = {Kim, GC and Do, JS and Kim, SH and Yoon, JH and Kim, J and Jeon, D and Hitayezu, E and Mauliasari, IR and Koo, N and Kim, JJ and Seo, JY and Lee, SB and Nam, KT and Cha, KH and Kwon, HK and Seong, JK}, title = {Akkermansia muciniphila primes lung-resident antiviral immunity via the gut-lung axis during SARS-CoV-2 infection.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1762843}, pmid = {41836373}, issn = {1664-3224}, mesh = {Animals ; *COVID-19/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Mice ; *SARS-CoV-2/immunology ; *Lung/immunology/virology/pathology/microbiology ; Mice, Transgenic ; *Akkermansia/immunology ; Cytokines ; Humans ; Disease Models, Animal ; }, abstract = {INTRODUCTION: The gut microbiota plays a central role in shaping systemic immunity and modulating the gut-lung axis, which is crucial during respiratory infections such as COVID-19. SARS-CoV-2 infection is known to disrupt the gut microbiome, but the downstream functional impacts on microbial metabolism and host immune responses remain insufficiently understood.<br><br>METHODS: Using K18-hACE2 transgenic mice, researchers investigated the effects of SARS-CoV-2 variants (WA and Omicron) on the gut microbiome and host immunity. Microbial composition and functional profiles were assessed post-infection. To test the therapeutic potential of Akkermansia muciniphila (A. muciniphila), live bacteria were administered prophylactically, and various outcomes were evaluated, including weight loss, lung pathology, immune cell phenotypes, and cytokine production.<br><br>RESULTS: In K18-hACE2 transgenic mice infected with SARS-CoV-2, there was a marked reduction in gut microbial diversity, accompanied by a consistent enrichment of A. muciniphila. This microbial shift was associated with functional disruptions in key metabolic pathways, particularly those involved in glycosaminoglycan degradation and lipid metabolism, suggesting a broader impact of infection on microbial functionality. Remarkably, prophylactic administration of live A. muciniphila prior to infection led to significant protective effects. Treated mice exhibited reduced weight loss and improved lung histopathology compared to untreated controls. Local antiviral immune responses in the lung were notably enhanced without triggering excessive systemic inflammation. Mice receiving A. muciniphila also demonstrated elevated production of Th2 and Th17 cytokines, robust expansion of tissue-resident memory T cells, and the formation of inducible bronchus-associated lymphoid tissue (iBALT)-all indicative of potentiated mucosal immunity. These findings highlight a functional role for A. muciniphila not only as a microbial signature of COVID-19-associated dysbiosis but also as an active modulator of host immune responses during respiratory viral infections.<br><br>DISCUSSION: These findings position A. muciniphila as both a biomarker of COVID-19-related gut dysbiosis and a potent live biotherapeutic candidate for respiratory infections. Its ability to enhance mucosal immune responses through gut-lung axis modulation highlights its promise in prophylactic strategies against viral respiratory diseases, including SARS-CoV-2.}, }
@article {pmid41836398, year = {2026}, author = {Li, X and Wang, Q and Yuan, Q and Wang, L}, title = {The intratumoral microbiome in colorectal cancer: origins, microenvironmental interactions, and new horizons in precision medicine.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1795736}, pmid = {41836398}, issn = {1664-3224}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/immunology ; *Tumor Microenvironment/immunology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; Animals ; *Microbiota ; }, abstract = {As a key functional component of the tumor microenvironment (TME), the intratumoral microbiome in colorectal cancer (CRC) has revolutionized the traditional paradigm of the "sterile tumor." Far from being mere "bystanders," these intratumoral microbes act as key drivers deeply implicated in remodeling the TME, influencing tumor progression, and determining therapeutic responses, thus necessitating a comprehensive synthesis of their complex biological characteristics and potential for clinical translation. Therefore, this review systematically summarizes the potential origins, community characteristics, and anatomical heterogeneity of the intratumoral microbiome. It further explores the precise mechanisms driving tumor progression, including the induction of genomic instability, metabolic reprogramming, epigenetic regulation, and immune microenvironment remodeling. We highlight the clinical utility of intratumoral microbes in CRC diagnosis, prognosis, and therapeutic prediction, while also introducing novel intervention strategies based on nanomedicine, engineered probiotics, and phage therapy. Finally, critical challenges such as contamination control in low-biomass samples, sampling heterogeneity, and the delineation of causality are scrutinized, aiming to provide new perspectives for the development of microbiome-guided precision medicine in CRC.}, }
@article {pmid41836406, year = {2026}, author = {Guo, Z and Yang, J and Zang, R and Yang, Y and Wang, Q and Xu, C}, title = {The brain-gut-skin axis in inflammatory and disfiguring skin diseases: mechanistic insights, clinical correlations, and therapeutic strategies.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1737303}, pmid = {41836406}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Skin Diseases/therapy/etiology/metabolism/immunology/microbiology ; *Skin/immunology/metabolism/pathology ; Animals ; *Brain-Gut Axis/immunology ; *Brain/metabolism/immunology ; Inflammation ; Dysbiosis ; }, abstract = {Emerging evidence suggests that the brain-gut-skin axis (BGSA) plays a critical role in the pathogenesis of inflammatory and disfiguring skin diseases. Conditions such as acne, atopic dermatitis, psoriasis, rosacea, vitiligo, and alopecia areata, once regarded as localized disorders driven mainly by cutaneous immune dysfunction, are now recognized as systemic conditions associated with neuroendocrine stress responses, gut microbial dysbiosis, and chronic low-grade inflammation. Mechanistic studies elucidate the intricate interorgan communication mediated by microbial metabolites (e.g., short-chain fatty acids and tryptophan derivatives), cytokine networks, neuropeptides, and hypothalamic-pituitary-adrenal (HPA) axis signaling. Building on these insights, therapeutic strategies are evolving rapidly. Microbiome-directed interventions (probiotics, postbiotics, dietary modification, and fecal microbiota transplantation), together with psychoneuroimmunological approaches, have shown potential to alleviate disease severity. Integrative therapies, including traditional herbal medicine, offer promising effects; however, we emphasize that mechanistic depth and robust clinical validation for these modalities are currently limited. This review integrates mechanistic findings, clinical correlations, and emerging therapeutic approaches, while critically distinguishing between correlation and causation. Future studies should emphasize longitudinal multi-omics analyses and standardized clinical trials to clarify causal pathways and guide precision, patient-centered management for systemic and cutaneous health.}, }
@article {pmid41836424, year = {2026}, author = {Du, Q and Wang, X and Shi, Z and Chen, H and Zhang, Y and Wang, R and Mou, Z and Kong, L and Zhou, H}, title = {Dysbiosis of intestinal microbiota in patients with neuromyelitis optica spectrum disorders.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1747643}, pmid = {41836424}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Neuromyelitis Optica/microbiology/drug therapy/metabolism/immunology ; Female ; Male ; *Dysbiosis/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Immunosuppressive Agents/therapeutic use ; Longitudinal Studies ; *Bacteria/genetics/classification ; Metabolomics/methods ; Metabolome ; }, abstract = {OBJECTIVE: This study aimed to explore the specific microbial signatures and metabolomic profiles of fecal microbiota in patients with neuromyelitis optica spectrum disorders (NMOSD) and assess the effects of immunosuppressants on their gut microbiota using a longitudinal cohort study.<br><br>METHODS: We enrolled 21 treatment-na&#xef;ve NMOSD patients and 21 matched healthy controls (HCs). Fecal microbial composition and metabolomic profiles were compared between groups using 16S rRNA gene sequencing and ultra-high-performance liquid chromatography-mass spectrometry. Subsequently, fecal samples from NMOSD patients were collected and reassessed after immunosuppressant treatment.<br><br>RESULTS: The gut microbial composition and metabolomic profiles of NMOSD patients were distinct from those of HCs. The &#x3b1;-diversity metrics were significantly higher in NMOSD patients than in HCs (P <0.001). Microbiome alterations in NMOSD patients were characterized by increased abundances of Streptococcus and Ruminococcus, and decreased abundances of Faecalibacterium, Ralstonia, and Pseudomonas at the genus level (all with linear discriminant analysis scores > 4 and P < 0.001). Additionally, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis identified 19 differentially abundant metabolites and 44 altered metabolic pathways in NMOSD patients compared to HCs. Immunosuppressive treatment for over six months may reduce these differences, shifting the gut microbiota composition and metabolite profiles of NMOSD patients closer to those of HCs.<br><br>INTERPRETATION: Our study revealed significant gut microbiome dysbiosis and metabolic abnormalities in patients with NMOSD, which were markedly alleviated after six months of immunosuppressive treatment. These preliminary findings suggest the gut microbiota biomarkers could serve as potential therapeutic targets in the future.}, }
@article {pmid41836754, year = {2025}, author = {Gan, G and Chen, R and Zheng, P and Long, K and Cheng, KKY and Sulaiman, JE and Huang, X}, title = {Oral pathogens meet the gut microbiome: new mechanistic insights on systemic disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1673512}, pmid = {41836754}, issn = {2235-2988}, mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; Inflammation/microbiology ; Probiotics ; Animals ; Fusobacterium nucleatum/pathogenicity ; }, abstract = {The oral-gut axis represents a critical bidirectional pathway linking oral microbiota to systemic health. Dysbiosis of the oral microbiome, driven by pathogens like Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus species, and Helicobacter pylori, disrupts gut ecology via direct translocation, metabolite signaling (e.g., TMAO, SCFAs), and immune crosstalk (e.g., Th17). This leads to gut barrier dysfunction, systemic inflammation, and metabolic disturbances, contributing to diverse diseases beyond the oral cavity. Evidence supports causal links with conditions including rheumatoid arthritis, cardiovascular diseases, neurodegenerative disorders, metabolic syndrome, and gastrointestinal cancers. Emerging diagnostic tools exploit these oral pathogens as biomarkers for non-invasive disease detection. Therapeutic strategies, such as probiotics, dietary interventions, and periodontal therapy, target this axis to restore microbial homeostasis and ameliorate systemic inflammation. Future research must focus on longitudinal human studies and multi-omics approaches to elucidate mechanistic details and develop effective clinical interventions for preventing and managing systemic diseases linked to oral-gut microbial dysbiosis.}, }
@article {pmid41836788, year = {2026}, author = {Cha, JH and Jeong, SA and Ye, BS and Lee, I and Jung, BY}, title = {Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2643036}, pmid = {41836788}, issn = {2000-2297}, abstract = {INTRODUCTION: Dementia poses a growing burden in the aging population, prompting the search for noninvasive biomarkers for early detection.<br><br>MATERIALS AND METHODS: We performed shotgun metagenomic sequencing of tongue-coating samples from older adults with dementia (n&#x2009;=&#x2009;30) and cognitively healthy controls (n&#x2009;=&#x2009;28) to identify oral microbiome signatures.<br><br>RESULTS: The analysis revealed distinct microbial compositions associated with dementia, including an enrichment of Veillonella parvula in dementia patients, whereas Lautropia dentalis was more abundant in healthy controls. We also identified functional alterations in the microbiome in the dementia group, including increased abundance of the histidine degradation and biotin biosynthesis pathways, whereas ubiquinol biosynthesis was more abundant in the healthy control group. The abundance of several microbial taxa and metabolic pathways were correlated with scores on the Korean Mini-Mental State Examination 2nd edition (K-MMSE), a clinical assessment of dementia severity. Prevotella pleuritidis, Actinomyces sp., Leptotrichia buccalis, and Leptotrichia sp. were positively correlated, whereas Oribacterium parvum was negatively associated with K-MMSE scores. Among the metabolic pathways, glutamine/glutamate biosynthesis was positively correlated with cognitive performance.<br><br>CONCLUSIONS: These results suggest that specific oral taxa and their metabolic functions are associated with cognitive status and may reflect underlying neurodegenerative processes.}, }
@article {pmid41836789, year = {2026}, author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P}, title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2641915}, pmid = {41836789}, issn = {2000-2297}, abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.<br><br>OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).<br><br>METHODS: Participants (51 dentate and 56 edentulous) aged &#x2265;64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.<br><br>RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.<br><br>CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.}, }
@article {pmid41837390, year = {2026}, author = {Abagnale, V and Palacin-Lizarbe, C and Paul, D and Kerttula, J and Ronkainen, J and Siljanen, HMP}, title = {Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70279}, pmid = {41837390}, issn = {1462-2920}, support = {342362//Academy of Finland/ ; 346516//Academy of Finland/ ; 361980//Academy of Finland/ ; 337550//Academy of Finland/ ; 357905//Academy of Finland/ ; 359343//Academy of Finland/ ; 202400252//Maj ja Tor Nesslingin S&#xe4;&#xe4;tio/ ; 20231200//OLVI-S&#xe4;&#xe4;ti&#xf6;/ ; }, mesh = {*Picea/microbiology ; *Lichens/microbiology ; *Nitrous Oxide/metabolism ; Finland ; Oxidoreductases/genetics/metabolism ; Taiga ; *Bacteria/metabolism/genetics/isolation &amp; purification/classification ; Forests ; Oxidation-Reduction ; Oxygen/metabolism ; }, abstract = {The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N2O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N2O dynamics. We observed net N2O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N2O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N2O, with potential ranging between 0.1 and 0.4 ng N2O-N g DW[-1] h[-1] under aerobic conditions.}, }
@article {pmid41837427, year = {2026}, author = {Xu, J and Zhang, Y and Shi, L and Wang, H and Zeng, M and Lu, Z}, title = {Comparative analysis of the lung microbiota in patients with lung cancer, chronic obstructive pulmonary disease, and community-acquired pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0045025}, doi = {10.1128/spectrum.00450-25}, pmid = {41837427}, issn = {2165-0497}, abstract = {Respiratory diseases pose a significant global public health challenge. Extensive research indicates that respiratory conditions are influenced by lung microbiota; however, the relationships between alterations in pulmonary microbiota and various respiratory diseases remain unclear. This study explores the characteristics and distinctions of lung microbial communities in patients with lung cancer (LC), chronic obstructive pulmonary disease (COPD), and community-acquired pneumonia (CAP). The research involved 114 patients and employed culturomics and 16S rRNA gene sequencing to analyze bronchoalveolar lavage fluid samples. Through culturomics, 168 bacterial species were identified, with variations in bacterial profiles observed across the different diseases. Sequencing results indicated that the dominant phyla among the three groups were Bacillota, Bacteroidota, Pseudomonadota, Actinomycetota, and Fusobacteriota, consistent with the culturomics findings. Notably, the CAP group exhibited higher species richness compared to the LC and COPD groups, with significant differences in beta-diversity among the three groups. Specific bacterial genera, such as Alloprevotella, Abiotrophia, and Mycoplasma, were distinguished as indicative taxa for the LC, COPD, and CAP groups, respectively. Utilizing random forest modeling and receiver operating characteristic curve analysis, several key bacterial genera were identified as capable of differentiating between these diseases. The study highlights distinct differences in lung microbiota among patients with LC, COPD, and CAP, potentially serving as a reference for diagnosis, suggesting that disease-specific microenvironments may influence local microbial communities, thus providing evidence for associations between lung microbiota and various respiratory diseases that warrant further investigation.IMPORTANCEThe human lung microbial community plays a crucial role in various respiratory diseases by regulating the lung's immune system and maintaining lung homeostasis. However, there is a paucity of comparative studies examining the characteristics of the pulmonary microbiome in common respiratory diseases, such as lung cancer (LC), chronic obstructive pulmonary disease (COPD), and community-acquired pneumonia (CAP). This study aims to explore the differences in lung microbiomes among these conditions. By employing culturomics and 16S rRNA sequencing technology, we identified significant variations in their lung microbiota. Notably, Alloprevotella, Abiotrophia, and Mycoplasma were identified as indicative taxa for the LC, COPD, and CAP groups, respectively. This research is essential for enriching the database of cultivable lung bacteria and investigating the interactions between specific strains and diseases at the species level, and identifying potential biomarkers and therapeutic targets.}, }
@article {pmid41837476, year = {2026}, author = {Jung, DH and Cha, JM and Kim, HN and Lee, YR and Nam, GM and Lee, CK and Kim, CH and Lim, HS and Lee, JY and Lim, HS}, title = {Effect of Low-Lactose Processed Milk on Clinical Symptoms and Gut Microbiome Modulation in Lactose-Intolerant Adults.}, journal = {Journal of medicinal food}, volume = {29}, number = {2}, pages = {61-70}, doi = {10.1177/1096620X251412892}, pmid = {41837476}, issn = {1557-7600}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lactose Intolerance/microbiology/diet therapy/metabolism ; Adult ; *Lactose/metabolism/analysis ; Female ; Male ; Middle Aged ; *Milk/metabolism/chemistry ; Breath Tests ; Animals ; Body Composition ; Feces/microbiology ; Young Adult ; Bacteria/classification/isolation &amp; purification/genetics ; }, abstract = {This study aimed to evaluate the effects of low-lactose processed milk consumption on body composition, clinical indicators, hydrogen breath levels, and gut microbiome changes in Korean adults with lactose intolerance. A total of 32 participants diagnosed with lactose intolerance, as determined by a hydrogen breath test, were enrolled in the study. During the 30-day intervention period, participants consumed one serving per day of banana-flavored milk containing 10.2 g of lactose. Stool and breath samples were collected before and after the intervention to assess changes in gut microbiota composition and lactose malabsorption. Following the intervention, significant improvements were observed in body composition, including reductions in body fat percentage (P < .001) and increases in fat-free mass (P < .001), skeletal muscle mass (P < .001), and soft-tissue lean mass (P < .001). Blood pressure also decreased; however, no significant changes were observed in hematological markers. Hydrogen breath test results demonstrated a significant reduction in hydrogen breath levels, and 40.6% of participants were reclassified as negative for lactose intolerance post-intervention. While no significant changes were observed in alpha diversity or overall microbial composition across all participants, a significant increase in the relative abundance of the Weissella confusa group (P = .007) was detected in individuals who tested negative for lactose intolerance after consuming the intervention food. These findings suggest that consuming low-lactose processed milk improves lactose intolerance, body composition, and gut microbiota composition, providing a feasible dietary strategy for managing lactose intolerance in adults.}, }
@article {pmid41837494, year = {2026}, author = {Liu, S and Wang, S and Zhang, J and Tao, C and Xu, X and Wang, Z and Lv, N and Dong, M and Shen, Z and Li, C and Yang, J and Li, R and Shen, Q and Kowalchuk, GA}, title = {Host-mediated rhizosphere microbiome transfer suppresses Fusarium oxysporum in banana.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71071}, pmid = {41837494}, issn = {1469-8137}, support = {ZDYF2024KJTPY003//The key research and development program of Hainan Province, China/ ; ZDYF2025XDNY087//The key research and development program of Hainan Province, China/ ; KJJQ2025018//Fundamental Research Funds for the Central Universities/ ; KJYQ2025053//Fundamental Research Funds for the Central Universities/ ; 2023YFD1901402//National Key Research and Development Program of China/ ; //Priority Academic Program Development of the Jiangsu Higher Education Institutions (PAPD)/ ; HZ610X25070//Achievement Transformation Fund project of Sanya Research Institute of Nanjing Agricultural University/ ; 42477316//National Natural Science Foundation of China/ ; }, abstract = {A plant's phenotype is determined by the traits of both the plant itself and its associated microbiome. However, we still have a poor understanding of the extent to which plant microbial recruitment contributes to disease resistance. We conducted a cross-inoculation experiment in which rhizosphere microbiomes from Fusarium wilt-resistant and susceptible banana varieties were collected and used to colonize the next planting cycle, and microbiome dynamics during recruitment and transfer were tracked. Culture-based approaches were used to construct synthetic microbial communities (SynComs) and test the effects of variety-specific metabolites on isolated strains. Transferring the rhizosphere microbiome from a highly resistant variety to a susceptible variety reduced Fusarium wilt pathogen abundance by 37.65% compared with transferring the susceptible plant's microbiome, while sterilized microbiomes had no detectable effect. Constructed SynComs recapitulated the suppressive effects of their source microbiomes, and metabolites derived from the highly resistant variety, characterized by enrichment of shikimic acid, stearic acid, and D-(-)-ribofuranose, promoted the growth of these beneficial microbes. Our results highlight that plant resistance levels are largely determined by the plant's ability to recruit a disease-suppressive microbiome, suggesting that enhancing microbial recruitment may represent an avenue to improve the disease resistance of susceptible varieties.}, }
@article {pmid41837593, year = {2026}, author = {Mailem, RC and Tsai, PW and Tayo, L and Hsueh, CC and Hsieh, CY and Chen, BY}, title = {Uncovering the Redox and Immunoregulatory Basis of the Chinese Herbal Formula Ping An Fang Yu Yin using Network Pharmacology and In Silico Target Profiling.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113816128418247251211153057}, pmid = {41837593}, issn = {1873-4286}, abstract = {INTRODUCTION: Ping An Fang Yu Yin (PAFYY) is a traditional Chinese herbal tea formula commonly used to treat respiratory infections, including COVID-19. Previous research indicates potential antiinflammatory activities; however, the underlying mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the therapeutic effects of PAFYY, specifically its electron-transport and bioenergetic properties, through network pharmacology, electrochemical analysis, and Microbial Fuel Cell (MFC) assessments.<br><br>METHODS: Active compounds and their respective targets were identified via database searches. Proteinprotein interaction networks were constructed using the STRING database and further analyzed using Cytoscape and MCODE software. Molecular docking was employed to assess the binding affinity between identified key compounds and their targets. Cyclic voltammetry (CV) and MFC assays evaluated the electrontransport characteristics of PAFYY water and ethanol extracts.<br><br>RESULTS: The analysis identified 298 active compounds associated with 1,940 biological targets, highlighting key targets including EP300, CREBBP, ESR1, AKT1, MAPK3, MAPK1, and STAT3. GO and KEGG pathway enrichment analyses revealed that PAFYY significantly influences immune system processes and neuronal signaling pathways. Molecular docking confirmed the anti-inflammatory and antiviral potential of the identified active compounds. Additionally, electrochemical studies demonstrated that PAFYY contains electroactive substances mediating electron-driven redox reactions.<br><br>DISCUSSION: Recent studies have demonstrated that traditional Chinese herbal teas contain electron shuttles capable of mediating electron transfer in electrogenic bacteria. Emerging evidence further indicates that electroactive plant polyphenols can modulate microbial ecology through redox-mediated mechanisms. Our findings suggest that PAFYY may act on the microbiota-immune axis, with its electron-shuttling constituents contributing not only to direct cellular effects and antioxidant activity but also to modulation of the gut microbiome in ways that support antiviral immunity and attenuate inflammation. These results may inform future research into the mechanistic basis of medicinal herbs, while highlighting the potential of MFCs as a functional screening platform for identifying bioactive redox compounds.<br><br>CONCLUSION: The anti-COVID-19 properties of PAFYY may be largely attributed to its electron-transport capabilities, mediated through electroactive compounds. These findings provide novel insights into the mechanistic basis of traditional Chinese medicine prescriptions, potentially enhancing their therapeutic application.}, }
@article {pmid41837716, year = {2026}, author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E}, title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011426}, doi = {10.1128/msystems.00114-26}, pmid = {41837716}, issn = {2379-5077}, abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.<br><br>IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.}, }
@article {pmid41837772, year = {2026}, author = {Yilmaz, A and Ashrafi, N and Guerra, Z and Goniwiecha, D and Saiyed, N and Gordevičius, J and Krinickis, K and Gabrielaite, M and Osentoski, T and Schumacher, N and Khan, S and Pai, A and Ruff, S and Maddens, ME and Imam, K and Monastero, R and Graham, SF}, title = {Salivary metabolomics for early detection of vascular contributions to cognitive impairment and dementia: Exploring microbiome dysbiosis and sex differences.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261423158}, doi = {10.1177/13872877261423158}, pmid = {41837772}, issn = {1875-8908}, abstract = {BackgroundVascular factors contribute to dementia in approximately 20 million individuals, notably in vascular contributions to cognitive impairment and dementia (VCI). However, the lack of specific molecular biomarkers to differentiate VCI from normal aging and Alzheimer's disease (AD) impedes early diagnosis and treatment.ObjectiveTo date the use of saliva for VCI diagnosis has not been previously reported. In this small proof-of-concept study, we aim to explore the feasibility of screening novel salivary diagnostic biomarkers for VCI.MethodsUsing both proton nuclear magnetic resonance ([1]H NMR) spectroscopy and liquid chromatography coupled with mass spectrometry (LC-MS) we biochemically profiled saliva samples collected from individuals with VCI (n = 26) and compared them with cognitively healthy controls (n = 37).ResultsOf the 167 salivary metabolites 56 of them are found to be at significantly different concentrations in the saliva of individuals with VCI as compared to controls. Subsequently, we developed predictive models capable of distinguishing VCI from controls with 0.92 accuracy. Moreover, sex-stratified analysis revealed the perturbation of different metabolic pathways in the saliva of individuals with VCI.ConclusionsThis study underscores the promising role of salivary metabolomics as a non-invasive tool for the early detection of VCI. Our findings suggest that oral microbiome dysbiosis may contribute to VCI pathogenesis, offering novel mechanistic insights. Given the accessibility of saliva, further validation of these robust salivary biomarkers could facilitate scalable, cost-effective screening for VCI, aiding in timely intervention strategies.}, }
@article {pmid41838175, year = {2026}, author = {Erkert, L and Haag, LM and Becker, C}, title = {Paneth cells as orchestrators of epithelial barrier defense and emerging therapeutic targets in inflammatory bowel disease.}, journal = {Seminars in immunopathology}, volume = {48}, number = {1}, pages = {}, pmid = {41838175}, issn = {1863-2300}, abstract = {First described by Joseph Paneth in 1888 in the small intestine, particularly in the crypts of Lieberkühn, Paneth cells have since emerged as a critical subtype of intestinal epithelial cells (IECs), which together constitute the body’s largest interface with the external environment, continuously exposed to pathogens, dietary components, and toxins. Paneth cells represent a unique, long-lived secretory IEC population located at the crypt base, where they play indispensable roles in antimicrobial defense and stem cell niche maintenance. Their differentiation, positioning, and survival are governed by tightly regulated signaling networks, including the Wnt and Notch pathway. Although traditionally viewed as terminally differentiated, emerging evidence suggests Paneth cells possess a certain level of plasticity, enabling functional adaptation or dedifferentiation under stress or injury. These characteristics position Paneth cells as central regulators of intestinal homeostasis and epithelial barrier integrity. Over the last decades, accumulating evidence has established that Paneth cell dysfunction is closely linked to microbial dysbiosis and the development of inflammatory bowel disease (IBD), highlighting their contribution to disease pathogenesis. Recent discoveries on how Paneth cell dysfunction contributes to intestinal inflammation are uncovering new therapeutic approaches aimed at reestablishing Paneth cell homeostasis and alleviating IBD progression. In this review, we comprehensively summarize current knowledge on Paneth cell differentiation, function, and their role in gut host defense and epithelial barrier maintenance. We further discuss mechanisms by which Paneth cell dysfunction disrupts intestinal homeostasis, promoting IBD development, and highlight emerging therapeutic strategies that target Paneth cells to reestablish barrier integrity and restore gut health.}, }
@article {pmid41838229, year = {2026}, author = {Jones, OX and Kelly, KD and Khoo, SK and Kelly, RR and Sidles, SJ and LaRue, AC}, title = {The PTSD-Bone Axis: Evidence, Mechanisms, and Management.}, journal = {Current osteoporosis reports}, volume = {24}, number = {1}, pages = {}, pmid = {41838229}, issn = {1544-2241}, abstract = {PURPOSE OF REVIEW: This review explores the relationship between post-traumatic stress disorder (PTSD) and bone health, focusing on how chronic psychological stress influences skeletal integrity through neuroendocrine, immune, and behavioral pathways.<br><br>RECENT FINDINGS: Clinical and preclinical studies demonstrate PTSD is associated with reduced bone mineral density, impaired healing, and fracture risk. Mechanistic insights implicate hypothalamic-pituitary-adrenal (HPA) axis dysregulation, sympathetic nervous system (SNS) overactivation, and chronic inflammation in disrupting bone remodeling. Additional risk modifiers include sex-specific biology, early-life adversity, and glucocorticoid sensitivity. However, selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), anti-inflammatory agents, and emerging tools like exosomal profiling and microbiome modulation show promise in mitigating stress-related bone loss.<br><br>SUMMARY: PTSD contributes to skeletal fragility through complex, multisystem mechanisms. Trauma-informed care integrating bone health screening and personalized interventions may improve psychological and musculoskeletal outcomes. Future research should prioritize longitudinal, mechanistic studies to guide holistic management of trauma-related disease.}, }
@article {pmid41838256, year = {2026}, author = {Bahar, A and Moazzen, M and Khazaei, M and Yosefi, S and Tahmasebi, H}, title = {Control of HELLP syndrome and pre-eclampsia with microbiota.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41838256}, issn = {1573-4978}, }
@article {pmid41838730, year = {2026}, author = {Bayrón-Ho, DI and Rivera-Rodríguez, AJ and Morales-Cintrón, AJ and Cardona-Sierra, HA and Rodríguez-Morales, RE}, title = {Brain and Gut Dissection in Surface Fish and Cavefish Populations of Astyanax mexicanus.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {228}, pages = {}, doi = {10.3791/70412}, pmid = {41838730}, issn = {1940-087X}, mesh = {Animals ; *Brain/surgery/anatomy &amp; histology ; *Characidae/anatomy &amp; histology ; *Dissection/methods ; Caves ; Gastrointestinal Microbiome ; *Gastrointestinal Tract/surgery/anatomy &amp; histology ; }, abstract = {Teleost fish are used to answer a wide range of research questions spanning from development to genetics and neuroscience, and more recently, to understand the complexities of the gut-brain axis, and even in a wider context, the gut-brain-liver axis. The Mexican tetra, Astyanax mexicanus, has been increasingly used in comparative and developmental evolution frameworks due to the availability of morphologically and physiologically distinct morphotypes, including river-dwelling surface fish and cave-adapted, blind cavefish. Adaptation to cave habitats is associated with changes in morphological traits, behavioral traits, and gut microbiota diversity that are also found in laboratory conditions. This has opened up the possibility to ask questions about the interactions between the microbiome, metabolic activity, neural adaptation, and complex behavioral outputs. These interactions can now be addressed through whole-brain mapping studies with cleared brains and gut microbiota sequencing to detect bacterial diversity associated with surface and cave-adapted phenotypes. However, most of these studies would benefit from intact, carefully dissected, and preserved whole organs and tissues, which allow for post-processing in downstream applications. This protocol describes a step-by-step method for brain and gut dissection, where the whole brain and abdominal organs are removed and isolated for both surface fish and cavefish morphotypes.}, }
@article {pmid41838875, year = {2026}, author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C}, title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, pmid = {41838875}, issn = {1477-4054}, support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Databases, Genetic ; *Software ; Computational Biology/methods ; Algorithms ; }, abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.}, }
@article {pmid41839322, year = {2026}, author = {Danese, T and Asti, V and Ablondi, M and Raspa, F and Cavallini, D and Valle, E}, title = {Clinical nutrition in equine colic: a scoping review from an equine nutritionist's perspective.}, journal = {Journal of equine veterinary science}, volume = {}, number = {}, pages = {105852}, doi = {10.1016/j.jevs.2026.105852}, pmid = {41839322}, issn = {0737-0806}, abstract = {BACKGROUND: Colic represents one of the leading causes of morbidity and mortality in equine medicine, with nutritional management recognized as a key modifiable factor influencing postoperative recovery. However, guiding principles for nutritional enteral support in horses after colic remain limited, and current practices are largely empirical.<br><br>OBJECTIVES: This scoping review aimed to (1) examine enteral nutritional support protocols reported in literature through a scoping review to map the available evidence on equine clinical nutrition in the context of colic, and (2) propose a physiology-based interpretative framework to consider when formulating dietary plans for post-colic horses, from a clinical nutritionist's perspective.<br><br>METHODS: PRISMA 2020-ScR guidelines were applied in Scopus and Web of Science databases using "horse colic" AND "clinical nutrition." Inclusion criteria comprised English-peer-reviewed studies reporting nutritional interventions in horses with colic. Data were extracted into predefined different categories.<br><br>RESULTS: Twenty-three studies met the inclusion criteria, revealing marked heterogeneity. Early reintroduction of enteral nutrition (12-24 h postoperatively) was associated with faster recovery, whereas parenteral nutrition was reserved for severe intestinal dysfunction. Evidence supports the use of forage-based, low-starch diets to promote intestinal motility and microbiome stability, while prolonged fasting or high-NSC feeds increase the risk of dysmotility and recurrence. Post-colic horses benefit from the "feed pyramid" approach-maximizing forages, low-NSC, balanced supplements, avoiding fasting and offering small frequent meals in wet, digestible feed forms.<br><br>CONCLUSIONS: Current evidence underscores the central role of early, forage-based enteral feeding in post-colic management. The integration of nutritional planning within multidisciplinary decision-making is essential to balance clinical, metabolic, and nutritional priorities.}, }
@article {pmid41839398, year = {2026}, author = {Kawuribi, V and Awere-Duodu, A and Adjei, FA and Osman, AH and Bomansaan, H and Madadi, MM and Tampuri, JU and Adu-Amankwaah, J}, title = {The gut-tumor metabolic axis: A comprehensive exploration of bidirectional crosstalk in cancer immunotherapy.}, journal = {Critical reviews in oncology/hematology}, volume = {222}, number = {}, pages = {105280}, doi = {10.1016/j.critrevonc.2026.105280}, pmid = {41839398}, issn = {1879-0461}, abstract = {The gut-tumor metabolic axis represents a bidirectional immunometabolic network in which tumor-derived metabolites reshape microbial ecology, while gut microbiome-derived metabolites recalibrate systemic and intratumoral immunity, ultimately influencing cancer progression and immunotherapy outcomes. Tumor aerobic glycolysis generates excess lactate and acidity that suppress cytotoxic immune function, remodel the tumor immune microenvironment, and indirectly perturb intestinal microbial composition. In turn, microbial metabolites including short-chain fatty acids, bile acid derivatives, tryptophan catabolites, inosine, and trimethylamine N-oxide signal through defined host pathways such as GPR109A, AHR, and adenosine A2A receptors to regulate antigen presentation, T-cell differentiation, macrophage polarization, and immune checkpoint sensitivity. Preclinical and emerging clinical evidence demonstrates that dietary modulation, rational probiotics, and fecal microbiota transplantation can enhance immune checkpoint inhibitor efficacy in selected contexts. However, metabolite effects are highly context dependent, with dose, timing, tumor type, and immune state critically shaping therapeutic benefit or resistance. This review integrates mechanistic insights and clinical evidence, highlights translational challenges including safety, donor heterogeneity, and biomarker validation, and proposes a framework for biomarker-guided microbiome-based strategies to advance precision cancer immunotherapy.}, }
@article {pmid41839407, year = {2026}, author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D}, title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134433}, doi = {10.1016/j.biortech.2026.134433}, pmid = {41839407}, issn = {1873-2976}, abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.}, }
@article {pmid41839432, year = {2026}, author = {Martínez-Guzmán, O and Cáceres-Chacón, M and Rivera-López, M and Hernández-Busot, G and Forty-Díaz, J and Haddock-Martínez, HG and Sierra-Mercado, D}, title = {Mild concussion impairs extinction of avoidance and alters respective brain circuits in male rats.}, journal = {Experimental neurology}, volume = {}, number = {}, pages = {115734}, doi = {10.1016/j.expneurol.2026.115734}, pmid = {41839432}, issn = {1090-2430}, abstract = {Concussive brain injury is a risk factor for anxiety disorders. Pre-clinical models demonstrate that concussion increases passive fear responses, such as conditioned freezing, yet provide limited insight to active responses like avoidance of perceived threats. This is important because persistent avoidance is characteristic of anxiety disorders. Moreover, brain injury can induce an imbalance of the gut microbiome, which can alter emotions. Adult male rats were trained on a platform-mediated avoidance task where they learned to step onto a platform to avoid a foot shock following a conditioned auditory tone. A sucrose reward was provided via a lever press that is opposite to the platform. Next, closed head injury was delivered to produce a mild concussion. After recovery, separate cohorts of rats were tested to dissociate between changes in avoidance expression and extinction-related processes. Cellular activity was assessed using c-Fos immunohistochemistry in brain regions implicated in avoidance: amygdala, medial prefrontal cortex, insular cortex, ventral striatum, and ventral hippocampus. Fecal pellets were collected to extract genetic material to identify potential changes in populations of bacteria in the gut microbiome. Closed head injury induced persistent avoidance by impairing extinction. Injured rats showed decreased activity in the basomedial amygdala and the CA1 subregion of the ventral hippocampus, increased activity in the rostral insular cortex and ventral striatum, and no change in the medial prefrontal cortex. Closed head injury did not induce changes in gut microbiota. Understanding mechanisms of concussion-induced avoidance is crucial for developing rehabilitation strategies for mental health disorders impacted by brain injury.}, }
@article {pmid41839435, year = {2026}, author = {Liu, H and Liang, J and Du, X and Lee, Y and Lee Binti Abdullah, A and Tay, YJ and Han, M}, title = {Toxic Effects of Tire Wear Particle Leachate on Benthic Fish Misgurnus anguillicaudatus: An Integrated Assessment of Immunosuppression, Metabolic Disruption, and Microbiome Dysbiosis Across Concentration Gradients.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {127958}, doi = {10.1016/j.envpol.2026.127958}, pmid = {41839435}, issn = {1873-6424}, abstract = {Tire wear particles (TWPs) are a major source of microplastic pollution, entering aquatic environments via stormwater runoff, and other transport mechanisms. Their leachate contains heavy metals and organic contaminants that exert diverse toxic effects on aquatic organisms. However, the toxic effects of TWP leachate on the benthic fish Misgurnus anguillicaudatus remain poorly understood. In this study, we used an integrative multi-omics approach to investigate the effects of TWP leachate exposure on M. anguillicaudatus. TWP leachate downregulated type I interferon signaling, impairing antiviral defense and immune function. It also significantly increased levels of lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs), which are biomarkers of membrane damage and excessive inflammatory cytokine production. Furthermore, concentration-dependent compensatory mechanisms were triggered, including enhanced biosynthesis of cholesterol and long-chain fatty acids to maintain membrane stability. TWP exposure also altered gut microbiota composition and interaction networks, with reduced abundances of immunomodulatory taxa and increased proliferation of energy metabolism-related families. These findings indicate that TWP leachate disrupts immune competence, cellular structural homeostasis, and energy metabolism in M. anguillicaudatus through interconnected molecular pathways. Our study provides essential evidence to guide mitigation strategies in aquaculture and offers a reference for ecological risk assessment of TWP leachate contamination across concentration gradients.}, }
@article {pmid41839452, year = {2026}, author = {Rautemaa-Richardson, R and Sobel, JD and Stone, N and De Seta, F and Cassone, A and Vieira-Baptista, P and Comar, M and Warris, A and Roselletti, E}, title = {State-of-the-Art Review: Managing Vulvovaginal Candidiasis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {3}, pages = {371-382}, doi = {10.1093/cid/ciaf673}, pmid = {41839452}, issn = {1537-6591}, support = {//MRC Centre for Medical Mycology/ ; MR/N006364/2//University of Exeter/ ; MR/V033417/1//University of Exeter/ ; NIHR203320//NIHR Exeter Biomedical Research Centre/ ; //Department of Health and Social Care/ ; }, mesh = {Humans ; *Candidiasis, Vulvovaginal/drug therapy/diagnosis/microbiology/therapy/physiopathology ; Female ; *Antifungal Agents/therapeutic use ; Risk Factors ; Recurrence ; Microbiota ; Vagina/microbiology ; Candida/drug effects ; }, abstract = {Vulvovaginal candidiasis is one of the most prevalent infections in women worldwide. Together with its recurrent form, it affects millions of women annually, causing significant symptoms and severely impacting quality of life. This review examines the pathophysiology, risk factors, microbiome interactions, clinical manifestations, and challenges in diagnosing and managing vulvovaginal candidiasis, with emphasis on recurrent vulvovaginal candidiasis. While Candida albicans is the primary cause, non-albicans species are increasingly common. Multiple factors contribute to both forms, including hormonal changes, diabetes, antibiotic use, immune dysfunction, and genetics. The vaginal microbiome plays a key role in maintaining homeostasis and preventing Candida overgrowth. Symptoms such as itching, discharge, and soreness overlap with other conditions, complicating the diagnosis. Standard treatment involves topical or systemic antifungals, but recurrence and resistance are frequent. Emerging strategies include novel antifungals, immunomodulators, and vaccines. Future approaches should focus on modulating host and environmental factors to prevent recurrence, reduce resistance, and improve outcomes.}, }
@article {pmid41839646, year = {2026}, author = {Byrd, MC and Wang, M and Li, G and Bhaumik, D and Gibson, K and Su, CL and Salzman, E and Head, JR and Mody, L and Foxman, B}, title = {Clinical Predictors of Nose/throat Bacteriome and Fungal Colonization in Skilled Nursing Facility Residents.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag166}, pmid = {41839646}, issn = {1537-6613}, abstract = {BACKGROUND: Microbiomes resist or facilitate pathogen invasion and modulate host immune responses and infection susceptibility. We describe nose/throat bacteriome composition and predicted functional changes associated with Candida albicans colonization, antibiotic use, and medical devices among adults receiving short-term sub-acute care in a skilled nursing facility (SNF).<br><br>METHODS: We collected combined nose/throat swabs from 301 adults every three days for up to five visits. Bacteriome composition was detected via 16S rRNA amplicon sequencing and C. albicans colonization by qPCR. Functional potential was inferred using PICRUSt2. We used ADAPT software to evaluate bacteriome compositional and functional differences by C. albicans colonization adjusting for age, sex, antibiotic exposure, and medical device presence.<br><br>RESULTS: C. albicans colonization was more common among participants with devices and antibiotic use, but not statistically significantly. Participants had mean age 77 years, 63.8% female, 48.5% received antibiotics, and 20.3% had device at entry. Nose/throat bacteriome was significantly less diverse and rich in the presence of C. albicans, antibiotic exposure, and device use (p<0.05), but composition varied little during follow-up. With C. albicans, predicted bacteriome function favored acid-tolerant, biofilm-forming species (S. wiggsiae, L. fermentum; p<0.01), and depleted glycolate degradation (log10fold change -0.45; adjusted p=0.01).<br><br>CONCLUSION: Nose/throat bacteriome composition and function were significantly associated with C. albicans colonization and C. albicans colonization was strongly associated with antibiotic exposure and medical device use. These findings underline the importance of integrating fungal colonization assessment and clinical factors into microbiome studies aimed at preserving bacteriome resilience and reducing infection risk in vulnerable populations.}, }
@article {pmid41839668, year = {2026}, author = {Nadeem, SA and Ali, I and Hussain, H and Ullah, I and Ali, W and Alzahrani, KJ and Ali, H and Khan, ZI and Abass, KS and Rahman, RU}, title = {Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {24}, number = {1}, pages = {100643}, pmid = {41839668}, issn = {2090-5920}, abstract = {BACKGROUND: The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.<br><br>METHODS: Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.<br><br>RESULTS: We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.}, }
@article {pmid41840154, year = {2026}, author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A}, title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {41840154}, issn = {1678-4405}, support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; CAR-21861//Universidad Aut&#xf3;noma de Yucat&#xe1;n/ ; }, abstract = {UNLABELLED: The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01905-z.}, }
@article {pmid41840216, year = {2026}, author = {Glascock, A and Maguire, C and Phan, HV and Lydon, EC and Schaenman, J and Calfee, CS and Melamed, E and Greenland, J and Corry, DB and Kheradmand, F and Baden, LR and Sekaly, R and McComsey, GA and Haddad, EK and Cairns, CB and Geng, LN and Pulendran, B and Fernandez-Sesma, A and Simon, V and Metcalf, JP and Agudelo Higuita, NI and Messer, WB and Davis, MM and Nadeau, KC and Kraft, M and Bime, C and Erle, DJ and Atkinson, MA and Brakenridge, SC and Ehrlich, LIR and Montgomery, RR and Shaw, AC and Hough, CL and Hafler, DA and Augustine, AD and Becker, PM and Peters, B and Ozonoff, A and Hoch, A and Kim-Schulze, S and Krammer, F and Bosinger, S and Eckalbar, W and Altman, MC and Wilson, M and Guan, L and Maecker, H and Steen, H and ,  and Diray-Arce, J and Rouphael, N and Kleinstein, SH and Jayavelu, ND and Reed, EF and Levy, O and Chu, VT and Langelier, CR}, title = {Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41840216}, issn = {2058-5276}, abstract = {Azithromycin is a widely used antibiotic and was frequently used to treat hospitalized patients during the COVID-19 pandemic. The impact of empiric azithromycin use on the respiratory microbiome in patients with viral respiratory infections is unclear. Here we used longitudinal metatranscriptomics on nasal swabs from a prospective multicentre cohort of 1,164 patients hospitalized for COVID-19. We compared the upper respiratory microbiome, resistome and systemic immune response in patients treated with azithromycin (n = 366) with those who received no antibiotics (n = 474) or other antibiotics (n = 324). We found that azithromycin altered microbiome composition and increased the expression and relative proportion of macrolide/lincosamide/streptogramin (MLS) resistance genes. These changes occurred after 1 day of exposure and persisted for over a week. MLS resistance gene expression was associated with commensals and potential pathogens, while there were no differences in host inflammatory gene expression in blood and airways. This demonstrates that empiric azithromycin treatment impacts the upper respiratory microbiome and resistome without apparent anti-inflammatory benefit.}, }
@article {pmid41840217, year = {2026}, author = {Chapman, JA and Masi, AC and Beck, LC and Watson, H and Young, GR and Browne, HP and Shao, Y and Kiu, R and Nelson, A and Doyle, JA and Palmowski, P and Lengyel, M and Connolly, JPR and Lamb, CA and Porter, A and Lawley, TD and Hall, LJ and Embleton, ND and Perry, JD and Berrington, JE and Stewart, CJ}, title = {Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41840217}, issn = {2058-5276}, support = {221745/Z/20/Z//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; }, abstract = {Infant gut microbiome development is strongly impacted by breastmilk and human milk oligosaccharides (HMOs), which can protect preterm infants against pathologies including necrotizing enterocolitis. HMO metabolism in bifidobacteria is well characterized and linked to health outcomes, but the scope of HMO-utilizing species remains unclear. Here, using a combination of genomics, proteomics and metabolomics, we show that Clostridium species isolated from preterm infants (born at <32 weeks gestation), in particular Clostridium perfringens lacking the toxin perfringolysin O (PfoA), metabolized HMOs. Clostridium species produced beneficial metabolites including short-chain fatty acids and tryptophan catabolites at higher quantities than Bifidobacterium species in vitro. Cell-free supernatant from C. perfringens was non-toxic to colonic cell lines, promoted the growth of commensal bifidobacteria and inhibited growth of pathobionts isolated from the preterm infant gut in vitro. It also suppressed inflammation in preterm-derived intestinal organoids. These findings expand our understanding of HMO-metabolizing microbes and suggest that pfoA[-] C. perfringens strains could contribute to healthy infant gut development.}, }
@article {pmid41840421, year = {2026}, author = {Liu, S and Tan, S and Li, Q and He, D and Xu, L and Zhang, H and Wang, R and Guan, Y and Cheng, Z and Wu, J and Xu, W and Zhang, H and Tang, M and Fan, J and Liu, L and Xie, J}, title = {PagMYB74 orchestrates flavonoid-mediated plant-microbe feedback for drought resilience in poplar.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71086}, pmid = {41840421}, issn = {1469-8137}, support = {2025D01E61//Xinjiang Science Fund for Distinguished Young Scholars/ ; }, abstract = {The interactions between plants and the soil microbiome play critical roles in regulating plant resistance to stresses. However, the process partly results from the complex interaction between root exudates and microbes, a relationship that remains poorly understood. Here, we investigated the interconnected responses of the root microbiome associated with the perennial tree Populus under drought stress. This was achieved via molecular genetics approaches and multi-omics analyses, combined with integrative comparisons of microbiome structure against both the host plant's metabolomic profiles and transcriptomic data, using samples collected over a 13-wk period of progressive drought treatment. We demonstrate that progressive drought triggers a phased transcriptional cascade in roots, culminating in the activation of a flavonoid biosynthesis program. Moreover, we confirm that Pseudomonas is strongly associated with flavonoid biosynthesis and identify that gene PagMYB74 is critical for quercetin and kaempferol secretion. We further found that Pseudomonas putida S110 colonization establishes positive feedback through enhanced phenylpropanoid metabolism and activation of nutrient transport pathways in PagMYB74-overexpressing plants, reinforcing the symbiotic interaction. Our findings establish a complete mechanistic continuum from a single host gene to metabolite-driven recruitment and symbiotic reprogramming, facilitating the improvement of environmental adaptation by regulating their interaction with beneficial soil microorganisms.}, }
@article {pmid41840446, year = {2026}, author = {You, T and Parmar, P and Decke, G and Baikie, K and Ryckewaert, L and Marette, A and Niculita-Hirzel, H}, title = {Water-vapor treatment of shower systems in healthcare facilities: reshaping built-environment microbiomes to improve Legionella control and protect at-risk patients.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02355-3}, pmid = {41840446}, issn = {2049-2618}, support = {61963.1 INNO-EE//Swiss Innovation Agency Innosuisse/ ; 61963.1 INNO-EE//Innosuisse - Schweizerische Agentur f&#xfc;r Innovationsf&#xf6;rderung/ ; }, abstract = {BACKGROUND: Legionnaires' disease (LD) is a severe form of pneumonia caused by inhalation of aerosols containing Legionella spp., most commonly L. pneumophila, which proliferates within protozoa embedded in established biofilms of engineered water systems, such as shower systems. Despite water management plans, durable control of L. pneumophila at terminal outlets remains challenging, partly because the effects of disinfection treatments on microbial community assembly, ecological interactions, and functional organization within biofilms are poorly understood. This study aimed to investigate how an emerging water/vapor disinfection treatment reshapes shower biofilm microbiomes at critical developmental stages - from early adhesion and biomass peak when L. pneumophila first appears, to mature biofilms associated with pathogen persistence - relative to conventional hot water disinfection, and to identify microbial taxa and functions selectively affected by these interventions.<br><br>RESULTS: We applied a sequential water flushing followed by high-pressure vapor (120&#x2103;) protocol either during early biofilm formation or on mature biofilms, all grown on standardized shower systems installed in healthcare, nursing home, and residential buildings subject to L. pneumophila routine control. Compared with conventional thermal disinfection of shower systems (65&#xa0;&#xb0;C, 10&#xa0;min), water-vapor treatment more effectively removed established biofilm communities as supported by scanning electron microscopy, flow cytometry of residual cells, and culture. Amplicon sequencing of the V3-V4 region of 16S rRNA genes revealed treatment-specific shifts in microbial community composition and predicted functional profiles (R[2]&#x2009;=&#x2009;0.285, p&#x2009;=&#x2009;0.001). Beyond Legionella removal, water-vapor treatment disrupted 70 metabolic pathways (FDR&#x2009;<&#x2009;0.05), including pathways related to lipopolysaccharide synthesis, central metabolism, and the Legionella-specific CMP-legionaminate pathway, indicating selective impacts on biofilm integrity and pathogen-supportive functions.<br><br>CONCLUSION: Water-vapor treatment induces substantial ecological restructuring of shower biofilm microbiomes, affecting both taxonomic composition and functional capacity associated with biofilm resilience and pathogen persistence. These findings support that perturbation of key ecological functions within built-environment microbiomes can influence opportunistic pathogen dynamics and encourage the development of microbiome-informed strategies to complement conventional water safety management, particularly in healthcare settings. Video Abstract.}, }
@article {pmid41840696, year = {2026}, author = {Roca, C and Hemphill, CC and Speen, AM and Jaspers, I and Wolfgang, MC and Drummond, MB}, title = {Dysbiosis of the nasal microbiome is associated with prospective acute exacerbation of COPD.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02357-1}, pmid = {41840696}, issn = {2049-2618}, support = {R01 HL150081/HL/NHLBI NIH HHS/United States ; R01HL150081/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is often associated with respiratory viral infection and the need for increased medical intervention. The nasal mucosa plays a critical role in infection susceptibility and severity, with the nasal microbiome shaping mucosal immunity. This study investigated the association between the bacterial nasal microbiome and AECOPD. Participants included 41 individuals with COPD and 15 healthy non-COPD controls. Nasal microbiome composition was assessed from nasal epithelial lining fluid and compared at baseline between healthy participants and individuals with COPD, stratified by AECOPD history. COPD subjects who experienced one or more AECOPD in the year prior to enrollment were categorized as Ever AECOPD. COPD participants without a history of AECOPD in the prior year were categorized as Never AECOPD. Prospective exacerbation data were collected and used in a case-control analysis to identify clinical and microbiological markers predictive of future AECOPD in COPD-diagnosed subjects.<br><br>RESULTS: We found two distinct nasal microbiome architectures with enrichment of protective taxa (healthy signature) or pathobionts (pathogenic signature). Nasal microbiome analysis demonstrated significant differences in nasal bacterial composition between COPD-diagnosed individuals with prior AECOPD (Ever AECOPD) compared to healthy controls. For COPD individuals with no prior AECOPD (Never AECOPD), we identified two underlying community structures; Cluster 1 subjects harbored a nasal microbiome significantly similar to healthy controls (healthy signature) and Cluster 2 subjects were significantly similar to the Ever AECOPD cohort (pathogenic signature). We evaluated the baseline microbiome of COPD-diagnosed participants based on the occurrence of at least one AECOPD 1-year after baseline sample collection (prospective AECOPD) and found that the nasal microbiome was associated with the occurrence of future AECOPD events. Prospective exacerbation was associated with reduced relative abundance of Dolosigranulum pigrum. Further analysis by qPCR showed that decreased D. pigrum abundance was associated with lower lung function and higher risk of future AECOPD.<br><br>CONCLUSIONS: Our data indicates that the nasal microbiome is associated with AECOPD phenotypes. Moreover, participants with decreased nasal Dolosigranulum pigrum abundance had lower lung function and a higher risk of future exacerbations. These findings suggest that D. pigrum may serve as a biomarker for AECOPD risk; however, validation of these findings in a larger multicenter cohort is needed. Video Abstract.}, }
@article {pmid41840712, year = {2026}, author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z}, title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02388-8}, pmid = {41840712}, issn = {2049-2618}, support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; }, abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.<br><br>RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (&#x3b3;-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.<br><br>CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.}, }
@article {pmid41840729, year = {2026}, author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T}, title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02385-x}, pmid = {41840729}, issn = {2049-2618}, support = {JPMJND2206//Japan Science and Technology Agency/ ; }, abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.<br><br>RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were&#x2009;>95% completeness and&#x2009;<1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and&#x2009;~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.<br><br>CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.}, }
@article {pmid41841008, year = {2026}, author = {Peng, T and Zhang, Z and Ding, N and Zhang, J}, title = {Mechanistic Investigation of Exercise Interventions in Rodent Models of Alzheimer's Disease and Prospects for Clinical Translation.}, journal = {Neural plasticity}, volume = {2026}, number = {1}, pages = {e6718671}, doi = {10.1155/np/6718671}, pmid = {41841008}, issn = {1687-5443}, support = {2025023//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Alzheimer Disease/therapy/physiopathology/metabolism ; Animals ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; *Physical Conditioning, Animal/physiology ; *Exercise Therapy/methods ; Humans ; Translational Research, Biomedical ; Mice ; Brain/metabolism ; Mice, Transgenic ; Neuronal Plasticity/physiology ; }, abstract = {Alzheimer's disease (AD) is a progressive and debilitating neurodegenerative disorder for which existing pharmacotherapies are inadequate to arrest pathological progression, highlighting the imperative to identify safe and effective nonpharmacological interventions. Exercise, as a multi-target therapeutic modality, has been shown to reverse multiple facets of AD-related neuropathology through diverse mechanisms. In this systematic review, we synthesize evidence on the effects of voluntary running, structured swimming, and modulation of the gut microbiota in transgenic murine models of AD. Exercise was found to ameliorate AD pathology by modulating amyloid precursor protein (APP) processing and β-amyloid (Aβ) production/clearance, restoring mitochondrial integrity and function, attenuating neuroinflammatory responses, enhancing synaptic plasticity, and upregulating neurotrophic factors. Moreover, exercise reshapes the intestinal microbiome and thereby modulates the gut-brain axis, further promoting neuroimmune homeostasis and cognitive resilience. Through RNA sequencing data analysis, key genes such as Tlr4, Cdc42, and F13a1 were identified, which may play significant roles in neuroimmune regulation and cognitive protection. By integrating multi-omics evidence, we propose a coordinated "exercise-microbiota-brain" mechanistic framework that offers theoretical support for personalized, exercise-based therapeutic strategies and translational applications in AD. We also emphasize the necessity of future studies combining exercise with complementary interventions to accelerate the clinical translation of multimodal therapeutic approaches.}, }
@article {pmid41841157, year = {2026}, author = {Ruiz-Malagón, AJ and Herraiz-Vilela, M and Pinazo-Bandera, J and Toro-Ortiz, JP and López-Gómez, C and Ho-Plagaro, A and Garrido-Sánchez, L and Robles-Díaz, M and Taminiau, B and Daube, G and Sanabria-Cabrera, J and Matilla-Cabello, G and Lucena, MI and Andrade, RJ and García-Fuentes, E and García-Cortes, M and Rodriguez-Diaz, C}, title = {An Exploratory Study on the Pathogenic Role of Faecal Extracellular Vesicles in Metabolic Dysfunction-Associated Steatotic Liver Disease Progression and in Drug-Induced Liver Injury.}, journal = {Journal of extracellular vesicles}, volume = {15}, number = {3}, pages = {e70240}, doi = {10.1002/jev2.70240}, pmid = {41841157}, issn = {2001-3078}, support = {101095679//Horizon 2020 Framework Programme/ ; FORT23/00013//Instituto de Salud Carlos III/ ; PI18/01804//Instituto de Salud Carlos III/ ; PI19/00883//Instituto de Salud Carlos III/ ; PI21/01248//Instituto de Salud Carlos III/ ; PI-0285-2016//Consejer&#xed;a de Salud y Consumo, Junta de Andaluc&#xed;a/ ; PI18-RT-3364//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ ; UMA18-FEDERJA-194//Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a/ ; }, mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Chemical and Drug Induced Liver Injury/metabolism/microbiology/pathology ; Male ; Female ; Hep G2 Cells ; Middle Aged ; *Fatty Liver/metabolism/microbiology/pathology ; Disease Progression ; Aged ; Adult ; }, abstract = {The role of extracellular vesicles secreted by the gut microbiota present in faeces (fEVs) is not well known in metabolic dysfunction-associated steatotic liver disease (MASLD) and idiosyncratic drug-induced liver injury (DILI). We identify the microbiome profiles of fEVs in these liver diseases, and analyse the effects of fEVs from MASLD, without (F≤2) or with (F≥3) significant liver fibrosis, and DILI patients on inflammation, steatosis and mitochondrial function. DILI patients showed a consistent pattern in fEVs, characterised by a decrease in Paraprevotella and an increase in AAP99, Acinetobacter, Actinobacillus, Aerococcus and Anaeroglobus. A higher presence of 16S rDNA was observed in plasma EVs from MASLD and DILI patients. HepG2 cells treated with DILI and MASLD F≥3 fEVs increased TLR4, TLR5, IL6 and CASP3 expression, and accumulation of lipid droplets. DILI fEVs enhanced the hepatotoxic impact of diclofenac on the response to microbial components (TLR4, TLR5), inflammatory response (IL1B, IL6), accumulation of lipid droplets and mitochondrial dysfunction (OPA1, DNM1L). In conclusion, bacterial EVs enter the bloodstream and could modulate the immune response. DILI and MASLD F≥3 fEVs are drivers of the pro-inflammatory response and hepatocyte steatosis. DILI fEVs have a distinct bacterial profile that enhances the hepatotoxic potential of diclofenac.}, }
@article {pmid41841328, year = {2026}, author = {Akachoud, O and Langrand, J and Bouamama, H and Facon, N and Laruelle, F and Qaddoury, A and Lounès-Hadj Sahraoui, A}, title = {Comparative Analysis of Lavandula Dentata Rhizosphere Microbiota Across Different Developmental Stages in a Semi-Arid Area.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70318}, doi = {10.1111/1758-2229.70318}, pmid = {41841328}, issn = {1758-2229}, support = {45884PG//PHC-TOUBKAL/21/115-Campus France/ ; //VPMA4 Moroccan project/ ; //CPER Alibiotech and BiHauts Eco de France projects/ ; //Bio-TEAM project (ANR-25-PRIM-0002)/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Lavandula/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; Morocco ; Mycorrhizae/classification/isolation &amp; purification/genetics ; Biomass ; Fungi/classification/genetics/isolation &amp; purification ; Desert Climate ; Plant Roots/microbiology ; }, abstract = {The positive effects of soil microbiota on plant growth and stress tolerance are well established. However, their role in aromatic and medicinal plants, particularly under arid conditions, remains underexplored. This study examined rhizospheric microbial community dynamics across developmental stages of wild Lavandula dentata L., a semi-arid species threatened with extinction in Morocco. Results showed total microbial biomass peaked at senescence, mainly due to increases in Gram-negative (25.02 μg/g) and Gram-positive (18.11 μg/g) bacterial biomasses. Beta diversity analysis revealed consistent dominance of Actinobacteria, with peaks during senescence and the vegetative phase. Saprotrophic fungi (8.81 μg/g) and arbuscular mycorrhizal fungi (AMF) (4.16 μg/g) biomasses peaked at flowering. The fungal community was dominated by the Ascomycota phylum, with no significant variation across stages. The AMF genus Glomus remained most abundant throughout development. Senescence featured the most complex interkingdom interaction network and high ecological niche heterogeneity, reflected by more negative associations. Overall, the rhizospheric microbial community of L. dentata shifts with plant development, with flowering and senescence as key phases for microbial biomass accumulation and community diversification. Flowering and senescienceez stages seem to represent promising targets for developing biostimulant consortia to improve soil health and crop productivity in arid environments.}, }
@article {pmid41841409, year = {2026}, author = {Chu, J and Xu, X and Xu, Y and Hu, K and Chan, HF and Chen, W and Cheung, KH and Ning, X and Yung, KKL}, title = {Bioengineered Probiotic-Prebiotic Hierarchical Microspheres With pH-Responsive Architecture Reprogram Immunometabolism in Obesity-Related Disorders.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e14910}, doi = {10.1002/smll.202514910}, pmid = {41841409}, issn = {1613-6829}, support = {82361168640//National Natural Science Foundation of China/ ; XJ2024043//Hong Kong Scholars Program/ ; 2021YFF1000700//National Key Research and Development Program of China/ ; N_EdUHK205/23//Joint Research Scheme/ ; JSTJ-2025-292//Jiangsu Youth Science and Technology Talent Support Program/ ; 20220ZB23//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 82361168640//Joint Research Fund for Overseas Chinese Scholars and Scholars in Hong Kong and Macao/ ; }, abstract = {Obesity is increasingly recognized as a chronic immunometabolic disorder driven by dysregulated gut-adipose communication and microbiota imbalance. Here, we present bioengineered pH-responsive probiotic-prebiotic hierarchical microspheres (MicroSym) that coordinate localized microbial restoration with systemic immune reprogramming to treat obesity-related disorders. MicroSym is fabricated via microfluidic-assisted phase separation coupled with electrostatic spraying, embedding probiotic bacteria within a lotus-derived prebiotic matrix to form a protective yet responsive microenvironment that preserves viability during gastric transit. At intestinal pH, the hierarchical architecture selectively disassembles to release probiotics and prebiotic substrates, fostering beneficial colonization and metabolite production. This symbiotic modulation reshapes the gut immune landscape, suppresses proinflammatory macrophage polarization, and restores adipose tissue homeostasis. In diet-induced obese mice, oral treatment with MicroSym remodels the gut microbiota, improves glucose tolerance, reduces lipid accumulation, and normalizes cytokine profiles without overt toxicity. Transcriptomic profiling and microbiome analyses further validate comprehensive systemic immunometabolic benefits. Collectively, this work establishes a biofabricated symbiotic microsphere platform for controlling microbiota-immune-metabolic crosstalk and offers a translatable therapeutic strategy for obesity-associated immunometabolic disease.}, }
@article {pmid41841412, year = {2026}, author = {Sabuz, O and Folz, J and Deepika, D and Blanco, J and Schuhmacher, M and Aichinger, G and Kumar, V}, title = {Microbiota-Driven Metabolic Alterations Induced by BPA, TDCPP and PFOA in an Ex Vivo Human Fecal Fermentation Model.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.5c00516}, pmid = {41841412}, issn = {1520-5010}, abstract = {The gut microbiome is increasingly recognized as a key contributor to chemical toxicity. Endocrine-disrupting chemicals (EDCs) such as bisphenol A (BPA), tris(1,3-dichloro-2-propyl) phosphate (TDCPP), and perfluorooctanoic acid (PFOA) are widespread environmental contaminants with the potential to affect host health. To characterize microbiota-specific response to these compounds, we employed an ex vivo fecal fermentation model using samples from healthy adult donors. Fecal slurries were exposed to BPA, TDCPP and PFOA (75 μM) for up to 24 h under anaerobic conditions. Targeted LC-MS/MS quantified parent compounds over time, while untargeted metabolomics profiled microbial metabolic alterations at 4 and 24 h. TDCPP levels decreased similarly in fecal and abiotic controls, suggesting a nonmicrobial loss (e.g., instability or adsorption), whereas PFOA levels remained stable across donors. Untargeted metabolomics revealed compound- and time-dependent perturbations, with PFOA eliciting the strongest metabolic shifts. A curated set of 124 annotated metabolites indicated disruptions in bile acid transformation short-chain fatty acid production, nucleotide turnover, redox balance, and phytochemical catabolism. Several altered metabolites have been previously linked to immunomodulatory processes, suggesting potential implications for host-microbiota interactions. Overall, this study demonstrates the utility of ex vivo fermentation systems for assessing microbiota-mediated metabolic responses to xenobiotics and highlights the relevance of incorporating microbiome-related end points into chemical risk assessment.}, }
@article {pmid41841444, year = {2026}, author = {Yin, P and Qiu, B and Xu, L and Xie, S and Zhang, S and Zhang, J and Berglund, B and Yao, M and Li, L}, title = {Ligilactobacillus salivarius Li01 enhances gut microbiota-derived indole-3-propionic acid to alleviate 5-fluorouracil-induced diarrhea in mice.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo00050a}, pmid = {41841444}, issn = {2042-650X}, abstract = {As a widely applied chemotherapeutic agent, 5-fluorouracil (5-FU) frequently causes significant gastrointestinal side effects, particularly diarrhea, a process in which the gut microbiome serves as a crucial mediator. In this study, we evaluated the effect of oral administration of Ligilactobacillus salivarius Li01 (Li01) on 5-FU-induced intestinal mucositis in mice. We discovered that intake of Li01 was associated with alleviated diarrheal symptoms by mitigating inflammation, reducing oxidative stress, and restoring intestinal barrier function. Moreover, transcriptome analysis revealed that the Th17 signaling pathway was significantly suppressed. We also confirmed the essential contribution of the gut microbiota in mediating these effects, since the protective benefits of Li01 were not observed when the gut microbiota was depleted by antibiotics. Furthermore, administration of Li01 markedly increased the production of indole-3-propionic acid (IPA) by the gut microbiota. This key molecule was shown to contribute to the protection against 5-FU-associated diarrhea by activating the pregnane X receptor (PXR). Additionally, a close correlation was identified between IPA levels and the abundance of two bacterial species that form a mutualistic relationship with strain Li01: Lactobacillus reuteri and Lactobacillus johnsonii. In conclusion, our study demonstrates that Li01 alleviates 5-FU-induced diarrhea and microbiota dysbiosis by enhancing gut microbiota-derived IPA, supporting its potential as a probiotic.}, }
@article {pmid41841524, year = {2026}, author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y}, title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2645267}, doi = {10.1080/19490976.2026.2645267}, pmid = {41841524}, issn = {1949-0984}, mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; }, abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.}, }
@article {pmid41841608, year = {2026}, author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K}, title = {Gut Microbiome Composition and Function, Diet and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.}, journal = {The American journal of gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ajg.0000000000003997}, pmid = {41841608}, issn = {1572-0241}, abstract = {BACKGROUND: Specific foods are associated with abdominal bloating, which can significantly impact quality of life.<br><br>OBJECTIVE: To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.<br><br>DESIGN: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or &#x3b1;-galacto-oligosaccharides (&#x3b1;-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics) and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized prior to each challenge to identify factors predicting response, and after the challenge to elucidate mechanisms underpinning food-induced bloating.<br><br>RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 &#x3b1;-GOS). Overall, seven (7/39, 17.9%) participants were fructan responders and eight (8/40, 20%) were &#x3b1;-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and non-responders to both challenges, including greater abdominal girth (fructan, p = 0.009; &#x3b1;-GOS, p = 0.030). &#x3b1;-GOS responders had higher breath hydrogen (H2) pre-challenge than &#x3b1;-GOS non-responders (p = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (pre-challenge, adjusted p-value (padj) = 0.024; post-challenge, padj = 0.042), and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in &#x3b1;-GOS responders (padj = 0.041).<br><br>CONCLUSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for &#x3b1;-GOS, higher repeated fasting breath H2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.ClinicalTrials.gov (Identifier: NCT04802798).}, }
@article {pmid41841712, year = {2026}, author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE}, title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.}, journal = {Biomeditsinskaia khimiia}, volume = {72}, number = {1}, pages = {62-74}, doi = {10.18097/PBMCR1644}, pmid = {41841712}, issn = {2310-6972}, mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation &amp; purification ; Prevotella ; }, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.}, }
@article {pmid41841726, year = {2026}, author = {Laakso, H and Hashem Taha, M and Flegal, M and Surette, J and Mysara, M and Klokov, D}, title = {Impact of chronic low-dose external gamma- and internal tritium beta-irradiation on the gut microbiome in the context of intestinal tumorigenesis in Apc[Min/+] mice.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0115625}, doi = {10.1128/msystems.01156-25}, pmid = {41841726}, issn = {2379-5077}, abstract = {UNLABELLED: The gut microbiome (GM) plays an essential role in health, and its dysbiosis can increase the risk of colon cancer. While the detrimental effects of high-dose ionizing radiation on GM have been documented, little is known about the effects of low doses, including from internal exposure to tritium, which is produced by nuclear power generation and emits beta radiation, making it a public concern. We examined the effects of chronic irradiation with internal tritium beta radiation or external [60]Co gamma radiation on GM and intestinal tumorigenesis in the Apc[Min/+] mouse model of colorectal cancer. Mice were exposed to tritiated drinking water (HTO) or gamma radiation at cumulative doses of 0, 10, 100, and 2,000 mGy, followed by intestine, blood plasma, and fecal sample collections at 12, 16, and 20 weeks of age. HTO- and gamma-exposed cohorts had distinct tumor size and multiplicity patterns, with non-monotonous dose-responses. Complex patterns of blood cytokine changes with age, dose, and type of irradiation were recorded. GM analyses using 16S rRNA amplicon sequencing revealed significant changes in alpha and beta diversity in irradiated mice compared to controls, indicating altered microbial dynamics. HTO and gamma radiation induced distinct microbiome changes that did not correlate with tumor and blood cytokine readouts. Our results suggest that chronic exposure to low-dose gamma- or internal HTO beta radiation can affect GM in a radiation type and dose-dependent non-linear manner. Our results provide novel insight into the effects of low-dose gamma- and tritium beta radiation on GM and a possible association with tumorigenesis.<br><br>IMPORTANCE: Low-dose ionizing radiation is one of the few environmental stressors that simultaneously reshapes host physiology and the structure-function landscape of resident microbiomes, yet mechanistic insight at ecologically relevant doses has been scarce. By integrating longitudinal 16S rRNA profiling, multiplex cytokine analyses, and quantitative tumor phenotyping in the Apc[Min/+] mouse model, our study demonstrates that continuous exposure to either external [60]Co &#x3b3;-photons or tritium beta particles perturbs gut microbial community structure in radiation-quality-specific ways and that these shifts track with, and sometimes precede, complex, non-monotonic changes in intestinal tumor burden. The work expands the traditional radiobiology focus from host-centric DNA damage to a systems-level view in which microbe-host-radiation interactions form a dynamic network influencing early colorectal carcinogenesis.}, }
@article {pmid41841743, year = {2026}, author = {Deblais, L and Derippe, G and Horvat, M and Ranjit, S and Moulia, V and Jimenez Madrid, AM and Kauffman, M and Rotondo, F and Ivey, MLL and Miller, SA and Rajashekara, G}, title = {Dairy manure, glyphosate, and antimicrobials (copper, streptomycin, and triazole) modulated the composition of antimicrobial resistance at the gene and microbial levels in a processing tomato field.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0200325}, doi = {10.1128/spectrum.02003-25}, pmid = {41841743}, issn = {2165-0497}, abstract = {Intensive pesticide use drives antimicrobial resistance (AMR) in agriculture, yet the effects of specific practices remain poorly understood. This study evaluated the impact of dairy manure and agrochemicals (glyphosate, copper, streptomycin, and propiconazole) on the composition of culturable AMR bacteria (CARB), AMR genes (ARGs; n = 87), and the microbiome in a processing tomato field (n = 64 experimental plots). Glyphosate-treated plots harbored the lowest levels of CARB, but the highest prevalence of ARGs (especially tetA, tetB, OXA-50, and OXA-58) in the tomato leaves (P < 0.05). Manure-treated plots had the highest levels of CARB and ARGs in the soil and in tomato leaves (especially ACT-1, LAT, MIR, aadA1, and aphA6). The prevalence of multiple ARGs (IMP-12, ACT-1, DHA, MIR, MOX, OXA-58, OXA-60, ermB, oprj, and oprm) was lower in streptomycin- or propiconazole-treated plots compared to non-treated plots. Shifts in the soil and leaf microbiome correlated with changes in ARG composition, particularly aminoglycoside-, fluoroquinolone-, and beta-lactamase-associated genes. These findings show that dairy manure, glyphosate, and propiconazole significantly alter the tomato field microbiome and ARG landscape, indicating that fungicide and herbicide applications may contribute to AMR development and dissemination similar to conventional antibacterial agents in agricultural ecosystems.IMPORTANCEPlant agricultural practices are commonly used by farmers to assure the yield and quality of crops; however, they are also associated with the emergence and dissemination of antimicrobial-resistant (AMR) pathogens. AMR is a critical concern in plant agriculture, as it can affect food safety, security, and sustainability. To combat this issue, it is critical to understand the impact of agricultural practices on AMR. Our study demonstrated that biological amendment (dairy manure) and pesticides (glyphosate, copper, streptomycin, and propiconazole) significantly exacerbated the AMR burden in the applied tomato field, which could increase the food safety risk of the fruit. Findings from this study will raise awareness among farmers, policymakers, and consumers, promote responsible and judicious use of antimicrobial agents in plant agriculture, and prioritize the development of sustainable practices to mitigate current and future AMR challenges.}, }
@article {pmid41841761, year = {2026}, author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L}, title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0231325}, doi = {10.1128/spectrum.02313-25}, pmid = {41841761}, issn = {2165-0497}, abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.}, }
@article {pmid41842611, year = {2026}, author = {Chen, Y and Pan, J and Li, R and Lin, W and Ye, Y and Chen, B and He, H}, title = {Microbiota-Derived Butyrate Preserves Epithelial Integrity Through SIRT1-Mediated Metabolic-Epigenetic Crosstalk in Vulvar Lichen Sclerosus.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71670}, doi = {10.1096/fj.202502946RR}, pmid = {41842611}, issn = {1530-6860}, support = {Y20240609//Wenzhou Science and Technology Bureau/ ; }, mesh = {Female ; Humans ; *Sirtuin 1/metabolism/genetics ; Animals ; *Vulvar Lichen Sclerosus/metabolism/microbiology/genetics/pathology ; Mice ; *Epigenesis, Genetic ; *Butyrates/metabolism/pharmacology ; *Microbiota ; Adult ; Middle Aged ; Gastrointestinal Microbiome ; }, abstract = {Vulvar lichen sclerosus (VLS) is increasingly understood as a disorder shaped by systemic immune-metabolic disturbances and microbiome dysregulation. This study investigated how temporal changes in the gut and reproductive tract microbiota influence gene expression, metabolic status, and therapeutic responses in VLS. Fecal and vaginal samples from 20 VLS patients and 20 healthy women were collected at baseline and four follow-up time points and analyzed using multi-omics profiling. VLS patients exhibited consistently reduced microbial diversity, with increased abundances of Prevotella and Gardnerella and decreased Bifidobacterium and Lactobacillus. These microbial shifts were accompanied by significant upregulation of inflammatory genes (IL-6 and TNF-α) and downregulation of metabolic regulators (FOXO3 and SIRT1), with dynamic changes closely paralleling clinical progression. Metabolomic analysis further revealed marked disruptions in lipid and carbohydrate metabolism, particularly reduced levels of short-chain fatty acids (SCFAs). Functional assays demonstrated that patient-derived microbiota impaired cellular homeostasis by suppressing proliferation, enhancing apoptosis, and amplifying inflammatory signaling in vulvar epithelial and fibroblast models. In vivo, SCFA supplementation most effectively restored SIRT1 expression, reduced inflammatory cytokines, and improved metabolic balance in a DMBA-induced VLS mouse model. Together, these findings highlight a mechanistic link between microbiome dysbiosis, inflammatory activation, and metabolic dysfunction in VLS. They also underscore the therapeutic potential of targeting microbial and metabolic pathways, providing a foundation for microbiome-informed and personalized interventions for VLS.}, }
@article {pmid41842880, year = {2026}, author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G}, title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.}, journal = {Puerto Rico health sciences journal}, volume = {45}, number = {1}, pages = {3-10}, pmid = {41842880}, issn = {2373-6011}, mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; }, abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.<br><br>METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.<br><br>RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.<br><br>CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.}, }
@article {pmid41843072, year = {2026}, author = {Tavassoli Razavi, F and Yazdanpanah, E and Shadab, A and Emami, A and Haghmorad, D}, title = {The crosstalk between iron metabolism and immune tolerance in autoimmunity.}, journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]}, volume = {75}, number = {1}, pages = {}, pmid = {41843072}, issn = {1420-908X}, mesh = {Humans ; Animals ; *Iron/metabolism/immunology ; *Immune Tolerance ; *Autoimmunity ; *Autoimmune Diseases/immunology/metabolism ; }, abstract = {BACKGROUND: Iron metabolism has emerged as a critical regulator of immune homeostasis, influencing both innate and adaptive immune responses. Dysregulation of iron balance is increasingly recognized as a key driver of autoimmunity, contributing to oxidative stress, ferroptosis, immune cell dysfunction, and the breakdown of immune tolerance.<br><br>FINDINGS: This review explores the complex interplay between iron metabolism and autoimmune diseases, including multiple sclerosis (MS), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). We highlight how iron overload and deficiency impact immune cell differentiation, macrophage polarization, Treg/Th17 balance, and B cell activation, thereby promoting chronic inflammation and tissue damage. Moreover, we discuss disease-specific mechanisms such as iron accumulation in the CNS in MS, synovial iron overload in RA, and hepcidin-driven anemia and ferroptosis in SLE.<br><br>CONCLUSIONS: Emerging therapeutic approaches, including iron chelation, hepcidin modulation, ferroptosis inhibition, and microbiome-targeted interventions, are examined as potential strategies to restore immune tolerance and mitigate autoimmune pathology. Finally, we emphasize the need for precise iron-targeted therapies, integration with immunomodulatory treatments, and the development of reliable iron-related biomarkers to optimize clinical management of autoimmunity.}, }
@article {pmid41833046, year = {2026}, author = {Baghel Chauhan, S and Jaitawat, DPS and Jain, C and Singh, I}, title = {Synergistic Neuroimmune Modulation by Cannabidiol and Probiotics for Therapeutic Advancement in CNS Disorders: A Systematic Review.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715273411035251111055748}, pmid = {41833046}, issn = {1996-3181}, abstract = {INTRODUCTION: The gut-brain axis (GBA) is a complex, bidirectional communication network connecting the gastrointestinal tract and central nervous system. Cannabidiol (CBD) and probiotics have shown promising neuroprotective, anti-inflammatory, and immunomodulatory effects. However, the synergistic potential of these agents on the GBA has not been fully explored.<br><br>METHODS: A systematic review of recent preclinical and clinical studies was conducted using databases such as PubMed, Scopus, Web of Science, Science Direct, and Google Scholar. The review focused on the individual and combined effects of CBD and probiotics on gut microbiota composition, neuroinflammation, neurotransmitter modulation, and immune signalling. Mechanistic insights involving the endocannabinoid system and microbiome-derived metabolites were also analyzed.<br><br>RESULTS: Evidence suggests that both CBD and probiotics can enhance gut microbial diversity, regulate pro-inflammatory cytokines, and increase neuroactive metabolites like serotonin and short-chain fatty acids. These effects may improve vagus nerve activity and gut-brain communication, indicating therapeutic potential for managing anxiety, depression, and neurodegenerative conditions. However, human studies remain limited in scale and duration.<br><br>DISCUSSION: The observed benefits of CBD and probiotics suggest a synergistic mechanism through gut-brain axis modulation, addressing both neurological and immunological pathways. While animal studies are promising, translation to clinical practice requires further evidence.<br><br>CONCLUSION: CBD and probiotics represent a novel combinatorial approach for managing central nervous system disorders through GBA modulation. Future clinical trials should establish optimal dosing, long-term safety, and therapeutic efficacy to validate their use in neuroimmune conditions.}, }
@article {pmid41833200, year = {2026}, author = {Roach, T and Stegner, M and Clara, D and Ametrano, CG and Compant, S and Gerna, D}, title = {Seed ageing increases the influence of native microorganisms on germination.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128493}, doi = {10.1016/j.micres.2026.128493}, pmid = {41833200}, issn = {1618-0623}, abstract = {Improper seed storage conditions, such as elevated temperature and moisture, accelerate ageing and compromise seed quality. However, the impacts of ageing on the seed microbiome and the resulting consequences for germination performance remain poorly understood. Here, we characterised how ageing soybean (Glycine max) seeds at 45 °C and 75% RH affects seed fungal communities, metabolism relevant to microbial growth, and sensitivity of germination to fungal challenge. Additionally, we assessed a role for endophytic bacteria in controlling pathogenic fungi. Amplicon sequencing revealed that ageing decreased fungal richness and reshaped community structure and composition of dominant taxa in seeds. Fusarium and Rhizopus isolates inhibited germination of non-aged seeds, whereas Sarocladium, Plectosphaerella, and Cladosporium impaired germination of aged seeds only. During imbibition, ageing increased seed metabolite leakage, including pinitol, glucose, and fructose, which promoted fungal growth in vitro. Among 39 endophytic bacteria previously isolated from soybean seeds, Bacillus toyonensis C55 and B. pumilus AM26 antagonised fungal growth, consistent with genomic regions associated with antifungal activity. Ageing oxidised the seed cellular redox state, and fungi tolerated oxidative growth conditions better than bacteria. In two cultivars, seed inoculation with B. toyonensis C55 increased germination, supporting a role in regulating fungal infections, whereas B. pumilus AM26 impaired germination. Notably, neither Bacillus strain affected germination of high-vigour non-aged seeds. Fluorescence in situ hybridisation microscopy revealed that both strains recolonised the seed endosphere following ageing. We conclude that oxidation during seed ageing contributes to increased sensitivity to fungal pathogens, which can be modulated by certain bacteria.}, }
@article {pmid41833276, year = {2026}, author = {Cao, J and He, K and Chen, X and Wang, J and Yin, Q and Ouyang, W and Wang, H and Lin, J and Fan, C}, title = {Multi-omics profiling complements physicochemical monitoring by revealing functional signatures of dissolved oxygen status in the Xijiang River.}, journal = {Water research}, volume = {297}, number = {}, pages = {125609}, doi = {10.1016/j.watres.2026.125609}, pmid = {41833276}, issn = {1879-2448}, abstract = {This study established a multi-level diagnostic framework for dissolved oxygen (DO) variation and associated degradation risk by integrating conventional water quality analysis, untargeted metabolomics, and microbiome profiling. This framework aims to identify DO-related functional degradation signals that are difficult to resolve using conventional indicators alone. The results show that, although nutrient concentrations were broadly comparable between high-DO waters (6.14 ± 0.9 mg/L) and low-DO waters (3.52 ± 0.6 mg/L), pronounced differences were observed in microbial community structure and metabolic profile composition. Among the 794 metabolites identified, 79 metabolites were significantly associated with DO variation, with nitrogen-containing organic compounds and short-chain fatty acids showing systematic enrichment under low-DO conditions, suggesting reduced efficiency of aerobic organic matter transformation. Further integration of differential analysis and correlation analysis enabled the construction of a DO-associated network consisting of six key microbial functional groups (|log2FC| = 0.58-2.53, |r| = 0.51-0.83) and 32 differential metabolites, which was primarily linked to aerobic transformation processes of steroids and xenobiotic organic compounds. At the pathway level, the arginine-proline metabolic axis exhibited a stable association with DO variation, and the intermediate metabolite N-carbamoylputrescine showed a significant positive correlation with DO concentration (|r| = 0.57), indicating its potential as a process-related indicator of oxygen consumption status. Overall, this study expands the scope of DO-oriented water quality diagnosis from molecular, microbial, and metabolic pathway perspectives, and provides multi-omics diagnostic clues that may inform the development of process-informed approaches for earlier detection and refined assessment of DO-related water-quality risks.}, }
@article {pmid41833509, year = {2026}, author = {Brinker, P and Salles, JF and Beukeboom, LW and Fontaine, MC}, title = {Host-Associated Bacterial Community Changes After Laboratory Introduction Vary With Wolbachia Presence.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70265}, pmid = {41833509}, issn = {1462-2920}, support = {//Adaptive Life scholarship of the University of Groningen, The Netherlands/ ; }, mesh = {*Wolbachia/physiology/genetics ; Animals ; *Wasps/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Female ; *Host Microbial Interactions ; }, abstract = {Translocating organisms from their natural habitats to laboratories can significantly alter their microbial communities, yet this impact is often overlooked. While common in research, the effects on microbiomes and how laboratory findings relate to natural field dynamics require further study. Symbionts may stabilise microbial communities or increase susceptibility to change, influencing results. This study investigates the effects of laboratory translocation on host-microbiome interactions using the parasitic wasp Asobara japonica and its endosymbiont Wolbachia. Three infected (asexual) and three uninfected (sexual) lines, each with seven iso-female lines, were introduced into the laboratory to track microbial community changes over four generations via 16S rRNA gene sequencing. Our results show laboratory translocation reduces bacterial diversity, with stochastic processes driving changes in the microbial community. Changes in bacterial composition differed between sexual and asexual lines. Over four generations, the asexual wasps' bacterial community became more similar, while sexual wasps exhibited greater diversity. Notably, changes in bacterial communities emerged over generations rather than in the first generation. Finally, Wolbachia abundance varied following laboratory introduction, likely impacting bacterial community structure and assembly over time. Overall, our research highlights how laboratory conditions can affect host-associated microbial communities in different ways, potentially impacting their functions and host interactions.}, }
@article {pmid41833536, year = {2026}, author = {Li, H and Cai, LQ and Mou, Q and Sun, YF and Yang, KY and Liang, YS and Li, HS and Pang, H}, title = {A free-living Serratia symbiotica strain enhances aphid development, potentially through alteration of host nutritional composition.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70719}, pmid = {41833536}, issn = {1526-4998}, support = {//Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; //National Natural Science Foundation of China/ ; //National Key Research and Development Program of China/ ; JCYJ20250604175510013//the Shenzhen Science and Technology Program/ ; }, abstract = {BACKGROUND: Aphids harbor diverse microbial communities that influence their development, reproduction, and stress tolerance. In our previous work, we identified a free-living strain of Serratia symbiotica, SsMj, which is highly abundant in the gut of Megoura crassicauda. However, the biological effects of SsMj on its aphid host remain largely unknown.<br><br>RESULTS: In this study, SsMj- M.&#x2009;crassicauda were generated by rearing newly hatched nymphs separately from their parthenogenetic SsMj+ parents. Absolute quantification of the microbiome revealed that, apart from the loss of SsMj, the overall bacterial abundance and diversity did not differ significantly between SsMj- and SsMj+ aphids. Nevertheless, SsMj- individuals exhibited slower development, smaller body size, reduced survival, and produced more offspring compared to their SsMj+ counterparts. Metabolomic analyses further showed that SsMj- aphids accumulated higher levels of several sugars but lower concentrations of multiple amino acids. Consistently, the insulin-like peptide (ILP) gene showed elevated expression across developmental stages in SsMj- aphids, which is likely to reflect a response to nutrient imbalance. RNA interference targeting ILP significantly delayed development, confirming its regulatory role in aphid growth. Comparative genomics showed that the SsMj genome contains a high number of genes involved in amino acid synthesis pathways than both obligate and facultative S.&#x2009;symbiotica strains, a pattern consistent with other free-living strains.<br><br>CONCLUSION: Our findings indicate that S.&#x2009;symbiotica plays an essential role in aphid nutrient metabolism, and is likely to be facilitating the conversion of dietary sugars into amino acids to support host development. The fitness benefits conferred by this free-living S.&#x2009;symbiotica strain suggest a close, mutualistic-like association with its aphid host, highlighting its ecological and physiological significance in insect-microbe interactions. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid41833558, year = {2026}, author = {Karampela, AI and Druce, M}, title = {The Relationship Between Polycystic Ovary Syndrome (PCOS) and Depression.}, journal = {Clinical endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1111/cen.70124}, pmid = {41833558}, issn = {1365-2265}, abstract = {OBJECTIVE: Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, frequently accompanied by psychological comorbidities including depression. The aim of this narrative review is to summarise the latest research regarding potential contributors to and underpinning mechanisms of this relationship.<br><br>DESIGN: A detailed search of the PubMed database was carried out beginning with systematic reviews and using the 'snowballing' method to identify further studies. The results yielded were assessed for quality using the GRADE framework. Depression in all studies was assessed using validated questionnaires.<br><br>RESULTS: The association of PCOS and depression is bidirectional and multifactorial. The role of biological factors such as hyperandrogenism, metabolic dysregulation, chronic low-grade inflammation, gut microbiome, and genetic and epigenetic factors are highlighted. Also, psychosocial contributors includingillness perception (obesity, acne and hirsutism), menstruation, infertility issues, and sexual dysfunction, as well as eating disorders have a prevalent role. The majority of the studies included were systematic reviews and cross-sectional original research studies.<br><br>CONCLUSION: Given the complex pathophysiology underpinning both diseases independently as well as in combination, despite evolving research, there is no single unifying link. However, this highlights the need for mental health risk stratification, addressing possible contributing factors, and offering the support required for patients with PCOS and depression.}, }
@article {pmid41833567, year = {2026}, author = {De la Vega-Camarillo, E and Quattrone, AC and Okumoto, S and Rajan, N and Hernández-Rodríguez, C and Bernal, JS and Antony-Babu, S}, title = {Bridging the Cultivation Gap in Plant Microbiomes: A Comparative Study of Aerial Root Mucilage Microbiome Characterization by Conventional Isolation, Prospector High-Throughput Cultivation, and Molecular Profiling.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70268}, doi = {10.1002/mbo3.70268}, pmid = {41833567}, issn = {2045-8827}, support = {13322389//USDA NIFA-AFRI/ ; 2208267//USDA NIFA-AFRI/ ; 20240945//SIP projects/ ; 20251163//SIP projects/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; *Sorghum/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; DNA, Bacterial/genetics ; *Plant Mucilage ; }, abstract = {The "great plate count anomaly" represents a fundamental challenge in microbiome research, with vast microbial diversity remaining uncultivable. We systematically compared three methodological approaches for characterizing plant-associated bacterial communities: conventional plate cultivation, the high-throughput Prospector platform, and full-length 16S rRNA nanopore sequencing. Using mucilage-associated bacteria from teosinte and sorghum as model systems, we evaluated efficiency, taxonomic coverage, and inherent biases. The Prospector platform dramatically outperformed conventional cultivation, achieving 8x to 13.5x improvements in isolate recovery (342 vs. 43 isolates from sorghum; 379 vs. 28 from teosinte) and 1.5x to 1.8x improvements in genus-level detection. While metabarcoding detected 82 total genera, cultivation methods captured only 35.4% of this diversity, with Prospector recovering 16.9%-25.7% compared to 11.3%-14.3% for conventional methods. Each approach exhibited distinct taxonomic biases: conventional plating favored fast-growing taxa (Pseudomonas, Pantoea, Bacillus), Prospector accessed slower-growing bacteria (Sphingomonas, Curtobacterium), while metabarcoding exclusively detected 59-85 cultivation-resistant genera. We propose an integrated framework leveraging complementary strengths: metabarcoding for comprehensive profiling, Prospector for enhanced cultivation efficiency, and conventional isolation for targeted applications. Together, our findings establish quantitative benchmarks for method comparison and support an integrative framework that combines metabarcoding for comprehensive profiling, the Prospector platform for enhanced cultivation efficiency, and conventional isolation for targeted applications, highlighting how methodological choices fundamentally shape our understanding of microbial diversity.}, }
@article {pmid41833719, year = {2026}, author = {Zheng, L and Huang, J and Ni, H and Kuang, X and Liao, J and Qu, Z and Liu, H and Huang, C and Yu, L and Dai, L and Leung, EL}, title = {Systematic profiling of human gut bacteria with cyclic di-AMP secretion to enhance anti-tumor immunity.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.03.013}, pmid = {41833719}, issn = {2090-1224}, abstract = {INTRODUCTION: Gut microbiota-derived metabolites play pivotal roles in clinical tumor treatment and progression. Cyclic di-AMP serves as both a bacterial signaling molecule and an immune activator of the STING pathway. However, knowledge on cyclic di-AMP production by gut commensals remains limited, hindering the rational application of gut bacteria in cancer therapy.<br><br>OBJECTIVES: This study systematically characterizes the metabolic profiles and genotypes associated with cyclic di-AMP synthesis in human gut commensals. We further validate the immune-activating and anti-tumor effects of high cyclic di-AMP-producing probiotics in both in vitro and in vivo non-small cell lung cancer models.<br><br>METHODS: Cyclic di-AMP levels (intracellular and extracellular) were quantified via LC-MS in 51 representative gut bacterial species derived from 442 strains isolated from 119 human fecal samples. STING pathway activation was assessed by co-culturing THP-1 cells with supernatants from high cyclic di-AMP-producing gut probiotics. Anti-tumor efficacy was evaluated in a non-small cell lung cancer mouse model.<br><br>RESULTS: Screening of 51 gut bacterial species identified 24 high cyclic di-AMP producers, with 18 exhibiting robust secretion capacity. Bioinformatic annotation revealed genes governing cyclic di-AMP synthesis, degradation, and secretion. Two food-grade probiotics, Limosilactobacillus fermentum DA785 and Lacticaseibacillus rhamnosus R7970, demonstrated efficient cyclic di-AMP secretion. Their supernatants significantly upregulated STING pathway-related gene expression and IFN-&#x3b2; secretion in THP-1 cells. Oral administration of these strains suppressed tumor growth in mice by activating immune responses within the tumor microenvironment. And Limosilactobacillus fermentum DA785 suppresses tumor growth via the STING pathway.<br><br>CONCLUSION: This study highlights the therapeutic potential of food-grade probiotics with high cyclic di-AMP production to augment anti-tumor immunity, offering a novel microbiome-based strategy for cancer treatment.}, }
@article {pmid41833797, year = {2026}, author = {Pinos-Tamayo, EA and Domínguez-Borbor, C and Morales, I and Ramírez, M and Sonnenholzner, S and Rodríguez, J}, title = {Breaking paradigms: Reconsidering the role of harmless vibrios in shrimp health.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108597}, doi = {10.1016/j.jip.2026.108597}, pmid = {41833797}, issn = {1096-0805}, abstract = {Vibriosis is a leading cause of economic losses in the shrimp industry worldwide, affecting both larvae and juveniles. Vibrio species (Vibrio spp.) are ubiquitous in marine and aquaculture environments, and their ability to thrive in warm, nutrient-rich conditions makes them omnipresent in shrimp microbiota. While pathogenic species such as Vibrio parahaemolyticus are responsible for acute hepatopancreatic necrosis (AHPND), there is increasing evidence on non-pathogenic Vibrio strains that can naturally limit the proliferation of pathogenic species. This review examines the environmental and ecological factors that help explain the predominance of Vibrio spp. in aquaculture systems and synthesizes the current knowledge on how microbial imbalance caused by pathogenic vibrios, particularly V. parahaemolyticus, affects shrimp health. We highlight the emerging evidence that beneficial Vibrio strains can improve microbiota stability, modulate immune responses, and competitively exclude pathogens. The focus is on Vibrio diabolicus (Ili strain) and its potential role in strengthening shrimp resilience against pathogenic Vibrio spp. Biosecurity considerations and challenges in incorporating beneficial Vibrio spp. into vibriosis management strategies are also addressed. By reframing vibrios as both threats and potential allies, this review proposes a new perspective for developing microbiome-based approaches for the sustainable control of vibriosis in shrimp aquaculture.}, }
@article {pmid41833938, year = {2026}, author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L}, title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00964-2}, pmid = {41833938}, issn = {2055-5008}, support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.}, }
@article {pmid41833944, year = {2026}, author = {d'Haens, EJ and Debast, SB and Rossen, JWA and Visser, DH and Bergman, KA and Termote, JUM and Wolfs, TFW and Loeffen, YGT and Hutten, MC and Lorente Flores, C and Kornelisse, RF and Bekker, V and Nijholt, IM and Hemels, MAC}, title = {Short Antibiotic Treatment for Coagulase-negative Staphylococcal Sepsis in Premature Infants: A Multicenter Noninferiority Study.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000005209}, pmid = {41833944}, issn = {1532-0987}, abstract = {BACKGROUND: Optimizing antibiotic duration in neonatal intensive care units is essential for antimicrobial stewardship and microbiome preservation. However, the safety of short antibiotic courses for uncomplicated late-onset coagulase-negative staphylococcal (CoNS) sepsis remains uncertain.<br><br>AIM: To determine whether short (&#x2264;96 hours) antibiotic treatment of uncomplicated CoNS sepsis in premature infants admitted to a neonatal intensive care unit is noninferior to long treatment (>96 hours) by comparing relapse rates.<br><br>METHODS: This multicenter, observational cohort study reviewed all proven neonatal CoNS sepsis in premature births <32 weeks admitted to 8 neonatal intensive care units in the Netherlands between 2017 and 2020. Uncomplicated CoNS sepsis was defined as clinical recovery within 24-48 hours, no central venous line in place or removed after the onset of sepsis, no signs of necrotizing enterocolitis or infected thrombus, and no Staphylococcus lugdunensis bacteremia. Data on patient characteristics, antibiotic treatment and relapse rates were systematically collected. The incidence of relapse (<72 hours after discontinuation of treatment) was calculated as the proportion (%) of the total. The noninferiority margin was set at 2%. A Pnoninferiority value <0.025 was considered significant.<br><br>RESULTS: A total of 669 proven late-onset CoNS sepsis were identified. Of these, 390 were uncomplicated. Among uncomplicated cases, 172 were treated &#x2264;96 hours and 218 >96 hours. Patient characteristics showed no significant differences. One relapse occurred in the short-treatment group (0.58%), none in the long-treatment group, with a significant Pnoninferiority value of 0.007.<br><br>CONCLUSIONS: The relapse rate in uncomplicated CoNS sepsis was extremely low (<1%), even with short-course treatment. In premature infants with uncomplicated CoNS sepsis, shorter antibiotic treatment is noninferior to longer treatment, confirming its safety and effectiveness.}, }
@article {pmid41834018, year = {2026}, author = {Straub, D and Englert, T and Beller, A and Stadelmaier, J and Stahl, M and Kilian, J and Borzym, J and Rotermund, C and Akbuğa-Schön, T and Krakau, S and Czemmel, S and Weiler, S and Pettenkofer, M and Pettenkofer, J and Maser, U and Dammeier, S and Nieß, AM and Enderle, MD and Nahnsen, S}, title = {Resistance Training Reshapes the Gut Microbiome in a Longitudinal 8-Week Intervention in Sedentary Adults.}, journal = {Sports medicine - open}, volume = {12}, number = {1}, pages = {}, pmid = {41834018}, issn = {2199-1170}, abstract = {BACKGROUND: The gut microbiome plays a critical role in metabolism, immunity, and aging. While endurance training has been shown to beneficially modulate the microbiome, the effects of resistance training remain less clear, with some studies reporting minimal changes. This project aims to investigate whether structured resistance training elicits significant changes in gut microbiome composition and diversity in sedentary, healthy adults. 150 participants (85 female, 63 male), between 24 and 61 years of age, completed an 8-week supervised resistance training program between May 2022 and July 2023 in the cities of Tübingen and Rottenburg, Germany. Session-level training data, including weights and repetitions, were recorded alongside metrics like load and compliance. Fecal samples were collected throughout the study period at designated timepoints for 16S rRNA gene amplicon sequencing to assess microbiome composition and for metabolomics analyses to evaluate microbial metabolic activity.<br><br>RESULTS: No differences in microbial diversity were observed, and there were no significant changes in microbial community composition or fecal metabolomics across all participants post-training. However, within-individual microbial community changes significantly correlated with strength improvement (Pearson correlation coefficient r&#x2009;=&#x2009;0.167, p&#x2009;=&#x2009;0.0004), and significantly stronger shifts in beta diversity were observed in participants with &#x2265;&#x2009;33% average strength gains compared to those with &#x2264;&#x2009;12.2% gains (Kruskal-Wallis rank sum test, p&#x2009;=&#x2009;0.08). In these high responders, differential abundance analysis revealed time-dependent microbial changes, with 27 taxa enriched or depleted by week 8 of training (ANCOM-BC2, &#x2265;&#x2009;2-fold change, p&#x2009;&#x2264;&#x2009;0.05). Notably, Faecalibacterium and Roseburia hominis-both associated with a healthier, anti-inflammatory microbiome-were significantly enriched. Many differentially abundant taxa belonged to the Lachnospiraceae family.<br><br>CONCLUSIONS: Resistance training drives significant, time-dependent gut microbiome changes, particularly in those demonstrating greater improvements in strength. These shifts mirror endurance training effects and may reflect improved overall health.}, }
@article {pmid41834265, year = {2026}, author = {Bradley, R and A Staab, C and E Jamieson, P and O Langley, B and O Metz, T and F Stevens, J}, title = {Safety and Tolerability of Xanthohumol in Adults With Crohn's Disease: Results of a Triple-Masked, Randomized, Placebo-Controlled Phase 2 Trial.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {6}, pages = {e70438}, pmid = {41834265}, issn = {1613-4133}, support = {R01HL146549/HL/NHLBI NIH HHS/United States ; R01AT010271/AT/NCCIH NIH HHS/United States ; K24AT011568/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; *Propiophenones/adverse effects/therapeutic use ; *Crohn Disease/drug therapy ; Adult ; Male ; Female ; *Flavonoids/adverse effects/therapeutic use ; Middle Aged ; Double-Blind Method ; Young Adult ; gamma-Glutamyltransferase/blood ; Body Mass Index ; Humulus/chemistry ; }, abstract = {Xanthohumol (XN), a flavonoid from hops (Humulus lupulus), exhibits mucosal anti-inflammatory, antioxidant, and microbiome-modulating effects, making it a candidate therapeutic for inflammatory bowel disease. We assessed the safety and tolerability of XN in adults with Crohn's disease (CD) over 8 weeks. In this randomized, triple-masked, placebo-controlled phase 2 trial, 20 adults with unremitted CD received either 24 mg/day XN or placebo for 8 weeks. Primary outcomes included clinical laboratory toxicology parameters, vital signs and adverse events (AEs). Disease activity was screened and assessed using the Crohn's Disease Activity Index (CDAI). XN was well tolerated, with adherence exceeding 95%. Neither halting nor stopping criteria were met, and all laboratory elevations were minor and transient in both groups. There were no attributable serious AEs in either group, and all moderate AEs were short-term and self-resolving. Between-group comparisons demonstrated differences for changes in BMI and gamma-glutamyltransferase (GGT), favoring XN: BMI: -0.67 (0.0, 1.3), p = 0.04 and GGT: -4.8 U/L, 95% CI 0.8-8.8, p = 0.02, which may reflect beneficial effects on hepatic and metabolic health in CD. XN at 24 mg/day was safe and well tolerated in adults with active CD, supporting further research in inflammatory bowel disease.}, }
@article {pmid41834313, year = {2026}, author = {Giacomo Fassini, P and Rezzi, S}, title = {Omega-3 fatty acids and human health: why strong claims remain on fragile consensus.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCO.0000000000001224}, pmid = {41834313}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: Omega-3 (ω-3) polyunsaturated fatty acids (PUFAs) consumption remains widespread despite inconsistent reported health benefits. This review discusses multiple issues related to the efficiency of ω-3 PUFAs on human health including factors driving ω-3 PUFAs bioavailability and growing concerns about product quality.<br><br>RECENT FINDINGS: Recent clinical research reports &#x3c9;-3 PUFAs benefits in various areas including cardiometabolic health, inflammation, cognitive protection, pregnancy outcomes, cancer and certain neuropsychiatric conditions. However, effects on healthy individuals and dietary recommendations need stronger clinical evidence. Heterogeneity in supplementation response involves genetic variability, microbiome, oxidative stress, diet and differences in supplementation protocols. Moreover, some of &#x3c9;-3 PUFAs products are prone to significant oxidative degradation which can drastically reduce health benefits while possibly being detrimental. Yet &#x3c9;-3 PUFAs oxidation status of products remains rarely reported and the effects of long-term consumption of oxidized lipids in humans still need to be established.<br><br>SUMMARY: Future clinical practices and research should shift toward biomarker-guided and personalized &#x3c9;-3 PUFAs intervention strategies with mandatory prerequisite knowledge about product quality, e.g. dietary supplements and &#x3c9;-3 PUFAs rich/fortified foods, and baseline blood-based &#x3c9;-3 PUFAs nutritional status. Standardized reporting of formulation, oxidation status, and participant baseline characteristics is essential to clarify dose-response relationships and optimize therapeutic efficacy of &#x3c9;-3 PUFAs.}, }
@article {pmid41834342, year = {2026}, author = {Wade, SJ and Kumar, AA and Nitschke, SO and Joyce, P and Minaei, E and Reuter Lange, SE and Penney, C and Warren, H and Shepherd, R and Dinoro, JN and Wallace, GG and Dosseto, A and Ansar, S and Islam, N and Lochhead, A and Sharbeen, G and Phillips, PA and Aghmesheh, M and Hawthorne, WJ and Vine-Perrow, KL}, title = {Efficacy and Safety Assessment of 5-Fluorouracil, Irinotecan and Oxaliplatin-Loaded Implants in Mouse and Pig Models for Pancreatic Cancer Therapy.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e22617}, doi = {10.1002/adma.202522617}, pmid = {41834342}, issn = {1521-4095}, support = {APP1165978//Pancare Foundation (administered by Cancer Australia)/ ; 2020/CDF1093//Cancer Institute NSW/ ; RSP-292-2024//Tour de Cure/ ; 2021/CBG0003//Sydney Partnership for Health, Education, Research and Enterprise/ ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains highly resistant to treatment, with mortality rates largely unchanged despite advances in cancer therapies. For ∼80% of borderline, non-resectable, or metastatic cases, chemotherapy is predominantly palliative, underscoring the need for improved drug delivery approaches. This study presents the development, characterization and in vivo evaluation of a novel polymeric implant loaded with 5-fluorouracil, irinotecan, and oxaliplatin (FIRINOX). Scanning electron microscopy of FIRINOX implants showed internal microstructure was preserved upon drug loading, while micro-CT and X-ray imaging revealed valuable insights into the morphology and degradation of implants retrieved from in vivo experiments. In murine PDAC models, dose-escalation identified 4 × FIRINOX implants as the maximum tolerated dose, while 2 × implants achieved significant therapeutic efficacy at lower doses than IV administration, without compromising animal safety. In healthy pigs, 20 × FIRINOX implants were well-tolerated, as confirmed by histopathology and blood analysis. Finally, laser ablation-inductively coupled plasma-mass spectrometry imaging and microbiome analysis confirmed localized drug perfusion within tissues, and minimal off-target effects, including preservation of gut microbiota diversity. These findings support the potential of this implantable platform to improve outcomes in borderline or non-resectable PDAC and enhance tolerability of cytotoxic chemotherapy through localized, controlled delivery, addressing a key gap where current treatment options are limited.}, }
@article {pmid41834639, year = {2026}, author = {Soliman, MS and Abbas, AM and Algebaly, HF and El-Kholy, AA and Soliman, NS}, title = {Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.}, journal = {Acute and critical care}, volume = {41}, number = {1}, pages = {136-147}, pmid = {41834639}, issn = {2586-6060}, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of mortality in children. These infections disrupt the equilibrium of lower respiratory tract (LRT) microbiota, allowing respiratory pathogens to dominate. The conventional culture method has limitations in describing complex microbiomes and may fail in the detection of respiratory pathogens. In the present study, we sought to use the advanced technology of 16S metagenomics next-generation sequencing (16SmNGS) to characterize the LRT microbiome among children with LRTIs and to identify the underlying respiratory pathogens that commonly evade detection by traditional culture.<br><br>METHODS: Twenty LRT specimens from hospitalized children with LRTIs were analyzed using 16SmNGS, as well as standard microbiological culture.<br><br>RESULTS: The 16SmNGS taxonomical analysis revealed the highest relative abundances for Streptococcus (27.7%) and Escherichia (13.3%) genera, which belong to the phyla of Firmicutes (45.4%) and Proteobacteria (45.3%), respectively. Streptococcus pneumoniae (45%), Escherichia coli (45%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%), Acinetobacter baumannii (5%), and Haemophilus influenzae (5%) were the primary respiratory pathogens. Conventional culture failed to detect growth in 100%, 77.7%, and 55.5% of 16SmNGS-positive specimens for H. influenza, S. pneumoniae, and E. coli, respectively.<br><br>CONCLUSIONS: The 16SmNGS technique revealed a predominance of Streptococcus and Escherichia genera belonging to the phyla of Firmicutes and Proteobacteria in pediatric LRTIs. In this exploratory study, 16SmNGS was able to enhance the identification of significant respiratory pathogens, particularly those difficult to isolate in culture. However, to rule out contamination by flora, it is advisable not to interpret metagenomics results independently from culture, clinical, and radiological data. In addition, further clinical correlations are desired to reach appropriate clinical decisions.}, }
@article {pmid41834846, year = {2025}, author = {Jiang, Y and Xiao, D and Zhou, J and Zhang, F and Xiong, Z and Shen, Q and Xiong, X}, title = {Role of probiotic supplementation in preventing ventilator-associated pneumonia among critically ill patients-a critical umbrella review of meta-analyses of randomized controlled trials.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1719310}, pmid = {41834846}, issn = {2296-861X}, abstract = {BACKGROUND: In critically ill patients, gut microbiome balance is often disrupted by antibiotics and disease-related stress. Probiotics may strengthen gut barrier function and lower the risk of ventilator-associated pneumonia (VAP), but their effectiveness in mechanically ventilated patients remains unclear. This umbrella review synthesizes evidence from systematic reviews on the association between probiotic therapy and VAP incidence.<br><br>METHODS: A comprehensive search was conducted in PubMed, Embase, Web of Science, the Cochrane Library, Scopus, and China National Knowledge Infrastructure (CNKI) for systematic reviews published from database inception to July 20, 2025. Data were extracted using a standardized form that had been pilot-tested prior to use. Data were synthesized using both narrative and quantitative approaches. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration ID: CRD420251034247).<br><br>RESULTS: This umbrella review included 24 meta-analyses of randomized controlled trials (RCTs) involving 92,711 mechanically ventilated critically ill patients. Using a measurement tool to assess systematic reviews, version 2 (AMSTAR 2) tool, the methodological quality varied-a total of 4 were rated critically low, 12 were rated low, 1 was rated moderate, and 9 were rated high. Probiotic supplementation was associated with a reduced risk of VAP [odds ratio (OR)&#x202f;=&#x202f;0.67, 95% confidence interval (CI): 0.61-0.75; relative risk (RR)&#x202f;=&#x202f;0.74, 95% CI: 0.69-0.80] and nosocomial infections (OR&#x202f;=&#x202f;0.81, 95% CI: 0.73-0.90; RR&#x202f;=&#x202f;0.84, 95% CI: 0.80-0.88). Probiotics showed modest reductions in intensive care unit (ICU) stay [weighted mean difference (WMD)&#x202f;=&#x202f;-1.30&#x202f;days, 95% CI: -1.59 to-1.02], overall hospital stay (WMD&#x202f;=&#x202f;-1.29&#x202f;days, 95% CI: -1.79 to -0.79), duration of mechanical ventilation (WMD&#x202f;=&#x202f;-1.64&#x202f;days, 95% CI: -2.07 to -1.22), and antibiotic use (WMD&#x202f;=&#x202f;-1.26&#x202f;days, 95% CI: -2.25 to -0.28). The risk of diarrhea decreased based on OR estimates (OR&#x202f;=&#x202f;0.77, 95% CI: 0.67-0.88), whereas RR estimates did not show a statistically significant difference (RR&#x202f;=&#x202f;0.98, 95% CI: 0.94-1.01). Probiotic use was associated with a statistically significant reduction in ICU mortality (OR&#x202f;=&#x202f;0.86, 95% CI: 0.79-0.94; RR&#x202f;=&#x202f;0.94, 95% CI: 0.90-0.98), whereas hospital mortality was reduced only in RR analyses (RR&#x202f;=&#x202f;0.92, 95% CI: 0.88-0.97) and not in OR Analyses (OR&#x202f;=&#x202f;0.92, 95% CI: 0.84-1.01).<br><br>CONCLUSION: Probiotics may offer potential benefits for mechanically ventilated, critically ill patients by reducing infections and improving certain clinical outcomes; however, the overall quality of the available evidence remains insufficient to support definitive conclusions.<br><br>https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420251034247, CRD420251034247.}, }
@article {pmid41834861, year = {2026}, author = {Zhang, Z and Hu, X and Ma, Y}, title = {Gut microbiota and ulcerative colitis: a bibliometric analysis of knowledge structure, research hotspots, and future directions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1765748}, pmid = {41834861}, issn = {1664-302X}, abstract = {BACKGROUND: Ulcerative colitis (UC), a globally prevalent immune-mediated colonic disorder, is fundamentally linked to intestinal dysbiosis. Despite the exponential growth in related papers, systematic, data-driven bibliometric analyses including global productivity trends, international collaboration networks, citation impact distributions, and the temporal evolution of research topics remain lacking.<br><br>METHODS: We conducted a comprehensive bibliometric analysis of 5,879 articles and reviews sourced from the Web of Science Core Collection (WOSCC) and Dimensions (2004-2025). Publication outputs, international collaboration networks, institutional productivity, and keyword evolution were visualized using R-bibliometrix, VOSviewer, and CiteSpace. Lotka's law and Bradford's law were applied to assess author and journal productivity distributions, respectively. Burst detection algorithms identified emerging research frontiers.<br><br>RESULTS: Annual publications demonstrated exponential growth, escalating from 36 in 2004 to a projected 819 in 2024. Geographically, China dominated absolute output (n = 2,559), followed by the USA (n = 1,181), with these two nations collectively accounting for 63.6% of global publications, justifying their prominence as the two major hubs in this research field. Harvard Medical School exhibited the highest citation efficiency (296.6 citations per publication), contrasting with volume leaders like Zhejiang University (92 publications). Co-occurrence clustering revealed 18 distinct knowledge domains, converging on five accelerating frontiers: "fecal microbiota transplantation (FMT)," "short-chain fatty acids," "traditional Chinese medicine," "intestinal barrier mechanisms," and "nanoparticle-based microbiota modulation." Burst analysis confirmed these themes-initiated citation surges post-2017, with "nanoparticles" and "intestinal barrier" exhibiting the strongest recent momentum (2023-2025), indicating a paradigm shift from descriptive microbiome profiling to mechanistic, precision-targeted interventions.<br><br>CONCLUSION: The UC-microbiome research agenda has transitioned from correlative association studies to multi-layered therapeutic modulation. Future efforts should prioritize standardizing FMT protocols through randomized controlled trials, establishing multi-ethnic longitudinal cohorts to address population-specific microbiome signatures, elucidating dose-response relationships of microbial metabolites, and converging nanodelivery systems with microbiome engineering to optimize therapeutic precision and sustain remission.}, }
@article {pmid41834868, year = {2026}, author = {Niu, M and Pan, J and Guo, Y and Zhang, F and Guan, H and Yang, X and Li, H and Xiong, H and Zhang, Y and Chen, Y}, title = {Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761712}, pmid = {41834868}, issn = {1664-302X}, abstract = {BACKGROUND: Neonatal jaundice is a common condition, yet inter-individual variation in its onset and severity cannot be fully explained by traditional clinical risk factors. Emerging evidence suggests that the infant gut microbiome may modulate bilirubin metabolism, but its compositional and functional signatures in jaundiced neonates remain incompletely defined. This study aimed to characterize the taxonomic and functional features of the gut microbiome in neonatal pathologic jaundice and to explore potential causal links using Mendelian randomization (MR).<br><br>METHODS: We conducted a case-control study of term infants with pathologic jaundice and matched healthy controls. Stool samples were subjected to shotgun metagenomic sequencing to assess microbial diversity, taxonomic composition, functional gene repertoires, and carbohydrate-active enzyme families, and publicly available genome-wide association study summary statistics were used to perform bidirectional MR between microbiome-related traits and neonatal jaundice.<br><br>RESULTS: Alpha diversity indices did not differ significantly between groups, whereas beta diversity based on Bray-Curtis dissimilarity showed clear separation of jaundiced and control infants, indicating a restructured microbial community rather than a simple loss of richness. Jaundiced neonates exhibited increased relative abundance of Gram-negative taxa, including Escherichia coli, and reduced levels of putatively beneficial genera such as Bifidobacterium and Lactobacillus. Functionally, pathways involved in bile acid synthesis and metabolism, carbohydrate and energy metabolism, and cofactor and vitamin biosynthesis were enriched in the jaundiced group, accompanied by marked shifts in carbohydrate-active enzyme profiles. Forward MR suggested that several microbial metabolic pathways exert genetically predicted effects on jaundice risk, whereas reverse MR provided little evidence that genetic liability to jaundice substantially alters microbiome traits.<br><br>CONCLUSIONS: Neonatal pathologic jaundice is associated with distinctive compositional and functional alterations in the gut microbiome. Genetic evidence from MR supports a potential causal contribution of specific microbial pathways to jaundice risk, highlighting candidate targets for microbiome-based prevention or adjunctive therapy in early life.}, }
@article {pmid41834873, year = {2026}, author = {Duan, Y and Zhang, H and He, C and Gao, G and Tang, Q}, title = {Effects of different rotation crops on soil physicochemical properties and microbial community structure in continuous cotton fields.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1740768}, pmid = {41834873}, issn = {1664-302X}, abstract = {Cotton monoculture is widespread in the oasis cotton-growing region of Xinjiang. Long-term continuous cropping has led to declines in soil fertility and imbalances in microbial communities, constraining sustainable, green production. Crop rotation is an effective agronomic practice to mitigate the deleterious effects of continuous cropping; however, the selection of rotation crops and the regulatory mechanisms by which rotation reshapes the soil micro-ecology require systematic clarification. Using continuous cotton (CK) cropping as the control, we combined high-throughput amplicon sequencing with soil physicochemical analyses to evaluate the effects of four previous-crop schemes-cotton → peanut (CPC), cotton → soybean (CSC), cotton → rapeseed (CRC), and cotton → maize (CMC)-on soil properties and the microbial community structure. Relative to CK, the CPC, CSC, and CRC treatments led to significantly reductions in yield and gross output value ranging from 38.72 to 62.23% and 34.54 to 55.35%, respectively. Although the net profit under CPC treatment decreased by 36.27% relative to CK, the benefit-cost ratio showed no significant difference. CPC significantly increased soil organic matter, available phosphorus, NH4[+]-N, and NO3[-]-N, while decreasing the pH and electrical conductivity, demonstrating the best overall improvement in soil fertility. In the fungal community, under CPC, Basidiomycota and Mortierellomycota significantly increased by 17.15 and 52.37%, respectively, whereas Basidiomycota significantly increased under CSC and CRC (by 17.15 and 20.58%). Functional guild analysis indicated that all four rotation schemes significantly reduced the relative abundance of plant pathogen fungi, with the greatest decrease under CPC (36.80%), with statistically significant differences. In the bacterial community, CPC significantly increased Actinobacteriota, Gemmatimonadota, and Firmicutes by 16.20, 15.75, and 29.73%, respectively, while CRC rose substantially Bacteroidota by 28.58%. Bacterial metabolism constituted the major predicted functional category (79.27-79.68%), no significant differences between treatments. Redundancy analysis identified soil moisture and the N/P ratio as key drivers of the variation in the fungal community, while bacterial communities were regulated by N/P, pH, and organic matter. Overall, rotation alleviated continuous-cropping constraints by optimizing soil properties and the soil microbial structure. The results provide an empirical basis for improving soil microbiomes and designing sustainable planting strategies in oasis cotton systems.}, }
@article {pmid41834875, year = {2026}, author = {Yang, L and Li, T and Liu, R and Zhang, Y and Ainiwaer, M and Wang, S and Liu, Z and Yang, K and Wang, C}, title = {Effects of letrozole supplementation on growth performance, blood indexes, ruminal fermentation parameters, and microbiome composition of hu lambs.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1734219}, pmid = {41834875}, issn = {1664-302X}, abstract = {This study aimed to explore the effects of dietary letrozole (LE) supplementation on growth performance, rumen microbiota, fermentation profiles, and blood metabolites in Hu lambs, providing insights into its potential for enhancing animal production. Twenty-eight male Hu lambs (20.21 kg ± 0.56 kg, 70 days old) were randomly assigned to four groups, with seven replicates per group: a control group (CON), and three test groups (T1, T2, T3). Lambs in the CON group were fed a basal diet, while T1, T2, and T3 groups received 0.05, 0.1, and 0.2 mg/kg BW of LE, respectively, in addition to the basal diet. The experiment lasted for 46 days. The findings were as follows: (1) There were no significant differences among groups in Initial Body Weight (IBW), Final Body Weight (FBW), Average Daily Feed Intake (ADFI), Average Daily Gain (ADG), and feed conversion ratio throughout the entire trial (P > 0.05). (2) Compared with the CON group, plasma testosterone (T) concentrations in Groups T2 and T3 were significantly elevated at 0 h post-supplementation (P < 0.05). Compared with the control group, nitric oxide (NO) levels in Groups T1 and T2 were significantly reduced 4 h after LE supplementation (P < 0.05). (3)Nitric oxide (NO) levels in experimental groups exhibited a secondary change 4 h after supplementation (P < 0.05). There were no significant differences in plasma Total Antioxidant Capacity (T-AOC), Catalase (CAT), Superoxide Dismutase (SOD), Glutathione Peroxidase (GSH-Px), or Malondialdehyde (MDA) levels between 0 h pre-supplementation and 4 h post-supplementation across all experimental groups (P > 0.05). At 0 h before and 4 h after supplementation, Total Protein (TP), Albumin (ALB), and Globulin (GLB) levels in all experimental groups showed no significant differences compared to the CON group (P > 0.05). (4) Ammonia nitrogen (NH3-N) levels were extremely significantly higher in all test groups compared to the CON group (P < 0.05). Propionic acid and isovaleric acid concentrations in Group T3 were significantly higher than in the CON group (P < 0.01), while the ethyl-to-propyl ratio was significantly lower (P < 0.01). (5) At the phylum level, LE-treated groups showed a higher relative abundance of Firmicutes than the CON group (21.04%), with increases proportional to the LE dose: Group T3 (37.88%), Group T2 (32.74%), and Group T1 (30.66%). At the family level, the relative abundance of Prevotellaceae was significantly lower in all test groups compared to the CON group (P < 0.05), while Lachnospiraceae abundance was significantly higher in the test groups (P < 0.01). Under the experimental conditions, supplemental feeding of LE did not significantly affect the overall growth performance of lambs. but it did increase plasma testosterone concentration, elevated the relative abundance of Firmicutes in the rumen, reduced the relative abundance of Bacteroidetes, and altered the rumen fermentation pattern. This shift occurred by decreasing the acetate-to-propionate ratio, increasing isovaleric acid concentration, and promoting a propionic acid fermentation pattern, thereby improving feed utilization. Among all groups, the optimal supplemental feeding rate was determined to be 0.2 mg/kg BW.}, }
@article {pmid41834876, year = {2026}, author = {Iqbal, M}, title = {Microbial biocontrol agents and the rhizosphere microbiome: integrating ecological function and climate resilience in sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771649}, pmid = {41834876}, issn = {1664-302X}, abstract = {The growing challenges of food insecurity, soil degradation, and climate-induced stresses are exposing the limitations of chemically intensive crop protection systems. In this context, the rhizosphere microbiome, comprising complex microbial networks that regulate plant growth, nutrient acquisition, and immune responses, has emerged as a promising focus for more sustainable agricultural practices. Microbial biocontrol agents (BCAs) are increasingly recognized not only for their pathogen-suppressive properties but also for their potential to modulate rhizosphere microbial communities and contribute to plant tolerance to abiotic stressors. This review synthesizes recent advances in understanding the ecological and mechanistic interplay between BCAs and the rhizosphere microbiome, highlighting how microbial inoculants can influence community assembly, functional processes, and microbiome resilience under biotic and abiotic stress conditions. Drawing on molecular and ecological evidence, the synthesis integrates current knowledge of BCA-mediated regulation of plant defense signalling, nutrient cycling, and stress-associated responses. Key knowledge gaps related to inoculant persistence, ecological compatibility, and microbiome-level trade-offs that limit field-scale effectiveness are also identified. To address these challenges, a microbiome-informed conceptual framework is proposed, emphasizing precision-designed synthetic microbial communities (SynComs), trait-based screening, host-microbiome co-optimization, and integration of BCAs into resilient Integrated Pest Management (IPM) strategies. In summary, this review provides a systems-level perspective on how rhizosphere microbiome dynamics can be leveraged to support sustainable climate-smart crop production.}, }
@article {pmid41834955, year = {2026}, author = {Zhou, X}, title = {[The Oral Microecological Theory of Dental Caries].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {1-7}, pmid = {41834955}, issn = {1672-173X}, mesh = {*Dental Caries/microbiology/prevention &amp; control ; Humans ; *Microbiota/physiology ; *Mouth/microbiology ; Homeostasis ; Dysbiosis/microbiology ; Oral Health ; }, abstract = {The microecological theory represents the current understanding of dental caries etiology, emphasizing that the dynamic balance of the structure and function of the oral microbial community plays a central role in the initiation and progression of caries. This theory posits that dental caries is not caused by a single specific pathogen, but rather results from dysbiosis-an imbalance-of the entire oral microecosystem. By redefining caries from an "infectious disease" to an "ecological imbalance disorder," the microecological theory offers a novel perspective for caries prevention, early intervention, and precision treatment. It underscores that maintaining the homeostasis of the oral microecology is more critical than simply eradicating bacteria, and that ecological approaches represent a key strategy for population-level caries prevention. Homeostatic medicine emphasizes that the dynamic equilibrium of the body's internal environment is fundamental to health. As a major microbial habitat and immunological interface, the oral cavity plays a pivotal role in the body's overall homeostatic network. The stability of the oral microbiome is thus a crucial node in systemic homeostasis. Homeostatic medicine provides a systems-oriented framework for understanding dental caries, shifting the paradigm ofcaries management from "fighting pathogens "toward "preserving ecological balance". This integrative approach aims to achieve the broader goal of promoting systemic homeostasis through local oral health promotion.}, }
@article {pmid41834958, year = {2026}, author = {Wan, K and Yang, C and Chen, N and Chen, F}, title = {[The Impact of Oral Microecology on the Development of Inflammatory Bowel Disease].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {30-36}, pmid = {41834958}, issn = {1672-173X}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Mouth/microbiology ; *Dysbiosis/microbiology/complications ; *Microbiota ; Gastrointestinal Microbiome ; Fusobacterium nucleatum ; Porphyromonas gingivalis ; }, abstract = {This article systematically reviews the associations and mechanisms between the oral microbiome and inflammatory bowel disease (IBD). Relevant literature was retrieved from the PubMed database from January 2000 to October 2025, and 77 articles meeting the criteria for inductive analysis were selected. The results confirm a bidirectional causal relationship between oral dysbiosis and IBD: patients with IBD exhibit reduced oral microbial diversity, increased abundance of pathogenic bacteria (such as Fusobacterium nucleatum and Porphyromonas gingivalis), and a more active oral immune environment. Oral pathogens can migrate to the gut via the oral-gut axis, directly disrupting the intestinal barrier and microbial homeostasis or activating systemic and intestinal immune responses through pathways such as miRNAs carried by exosomes and immune cell migration, thereby exacerbating IBD. However, current studies have several limitations, including small sample sizes, high heterogeneity in conclusions, lack of longitudinal data, and insufficient technical compatibility. Future research should expand investigations into the roles of oral fungi and viruses and integrate multiomics technologies to advance the clinical translation of oral microbiota in IBD diagnosis and treatment.}, }
@article {pmid41834964, year = {2026}, author = {Ma, T and Lian, B and Wu, Z and Zhao, J}, title = {[Differences in Oral and Gut Microbiome Composition Among Preschool Children in Urumqi During the Deciduous and Mixed Dentition Periods].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {82-89}, pmid = {41834964}, issn = {1672-173X}, mesh = {Humans ; Child, Preschool ; *Tooth, Deciduous/growth &amp; development/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Dentition, Mixed ; Saliva/microbiology ; Male ; Female ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; China ; }, abstract = {OBJECTIVE: To analyze the oral and gut microbial composition in preschool children during the deciduous and mixed dentition stages, and to investigate the characteristics of microbiota across different dentition stages.<br><br>METHODS: Using 16S rRNA gene-based third-generation sequencing, this study analyzed saliva and fecal samples collected from 10 children with deciduous dentition and 10 with mixed dentition. The composition and differences in oral and gut microbiota between the two groups were compared.<br><br>RESULTS: The differences in microbial richness (Chao1 index) and evenness (Shannon index) between the oral cavity and intestine were statistically significant (P = 0.001). Firmicutes, Proteobacteria, and Bacteroidetes were the three dominant phyla at both sites. At the genus level, Neisseria and Streptococcus were abundant in the oral cavity, while Bacteroides and Faecalibacterium predominated in the gut. o_Lactobacillus (LDA = 5.04, P < 0.001) was identified as a marker genus in the oral cavity during the deciduous dentition period, while g_Neisseria (LDA = 5.15, P < 0.001) served as an oral marker genus in children with mixed dentition. In the gut, marker genera during the deciduous dentition period included o_Bacteroides (LDA = 5.17, P < 0.001) and f_Lachnospiraceae (LDA = 5.16, P < 0.001), whereas f_Ruminococcus (LDA = 5.09, P < 0.001) and g_Faecalibacterium (LDA = 5.03, P < 0.001) were marker genera during the mixed dentition period. Upregulation of pathways including lactose degradation and nitrate reduction was observed in the oral microbiota, in contrast to the gut microbiota, where enhanced activity of the methanogenesis from acetate pathway was noted.<br><br>CONCLUSION: The composition of oral and gut microbiota varies among children at different dentition stages. As dentition changes, the structural diversity and metabolic functions of both oral and gut microbiota also change.}, }
@article {pmid41834973, year = {2026}, author = {Zhang, S and Li, Y and Yang, Z and Huang, H and Pan, Y}, title = {[Recent Research Progress and Prospects on Periodontitis Affecting Systemic Comorbidities via the Oral-Gut Axis].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {15-23}, pmid = {41834973}, issn = {1672-173X}, mesh = {Humans ; *Periodontitis/complications/microbiology ; Animals ; *Gastrointestinal Microbiome ; Comorbidity ; *Mouth/microbiology ; Arthritis, Rheumatoid/epidemiology ; Cardiovascular Diseases/epidemiology/etiology ; Diabetes Mellitus/epidemiology/etiology ; Dysbiosis ; Inflammatory Bowel Diseases/epidemiology/etiology ; Inflammation ; }, abstract = {Periodontitis is a prevalent chronic infectious and inflammatory disease worldwide, which imposes harms extending far beyond the oral cavity. A large body of research has demonstrated that periodontitis is closely associated with various systemic diseases, such as diabetes mellitus, cardiovascular diseases, inflammatory bowel disease, and rheumatoid arthritis. Serving as a crucial pathway connecting the oral cavity to the entire body, the oral-gut axis becomes the core mechanism through which periodontitis affects systemic health, primarily via the ectopic colonization of salivary microbiota, intestinal dysbiosis, intestinal barrier disruption, and systemic inflammation. This review summarizes recent studies focusing on how periodontitis influences systemic comorbidities via the oral-gut axis, encompassing clinical studies, animal experimental and in vitro research. We summarize the research progress regarding how periodontitis perturbs intestinal homeostasis through ectopic colonization of oral pathogenic bacteria, immunoinflammation, host factor regulation, and metabolic disorders, and eventually affects systemic diseases via the oral-gut axis. This review aims to provide a new perspective for the prevention and treatment of periodontitis-related systemic comorbidities.}, }
@article {pmid41834983, year = {2026}, author = {Shang, X and Wang, Z and Ge, S}, title = {[Research Progress on Microbiome-Driven Mechanisms and Intervention Strategies for Oral Malodor].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {1}, pages = {37-43}, pmid = {41834983}, issn = {1672-173X}, mesh = {*Halitosis/microbiology/prevention &amp; control/therapy ; Humans ; *Microbiota/physiology ; *Mouth/microbiology ; Probiotics/therapeutic use ; Porphyromonas gingivalis/metabolism ; Fusobacterium nucleatum/metabolism ; Antimicrobial Peptides/therapeutic use ; Periodontitis/microbiology ; }, abstract = {Oral malodor, a common oral symptom, is primarily caused by the metabolic activities of oral microorganisms. The characteristic odors mainly originate from volatile sulfur compounds produced and released by oral bacteria (such as Fusobacterium nucleatum and Porphyromonas gingivalis) through specific enzymatic systems that break down sulfur-containing amino acids in saliva, gingival crevicular fluid, and food debris. Research indicates that various factors, including periodontitis, fungal infections, smoking, and obesity, can worsen oral malodor by altering the oral microenvironment. For prevention and treatment, novel interventions such as plant extracts, antimicrobial peptides, and probiotics demonstrate superior microbiological safety compared to traditional antimicrobial drugs. These approaches specifically inhibit pathogenic bacteria, disrupt biofilm structures, and regulate oral microbial balance. This review summarizes relevant research advances to provide new theoretical foundations and practical directions for the precise prevention and treatment of oral malodor.}, }
@article {pmid41835006, year = {2026}, author = {Ho, YS and Christidis, M}, title = {Commentary: Global research on the crosstalk between intestinal microbiome and colorectal cancer: a visualization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779577}, pmid = {41835006}, issn = {2235-2988}, }
@article {pmid41835010, year = {2026}, author = {Mei, S and Ye, J and Teng, Y and Chen, Y and Long, Y and Zhao, X and Cen, X and Zhang, X and Zhu, C}, title = {Longitudinal associations between PM2.5 with gestational diabetes mellitus mediated by gut microbiome and potential mechanism: based on a prospective pregnant women cohort in China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1749504}, pmid = {41835010}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Diabetes, Gestational/epidemiology/etiology/microbiology ; *Particulate Matter/adverse effects ; *Gastrointestinal Microbiome/drug effects ; China/epidemiology ; Adult ; Feces/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Air Pollutants/adverse effects ; Dysbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; Longitudinal Studies ; }, abstract = {BACKGROUND: Exposure to particulate matter pollution with aerodynamic diameters < 2.5 μm (PM2.5) has been linked to gestational diabetes mellitus (GDM) and gut microbiota dysbiosis. However, few studies have illustrated the associations among PM2.5 exposure, gut microbiota, blood metabolites, circular RNAs (circRNAs) and GDM risk. This study aimed to explore the moderating effects of the gut microbiota on the association between PM2.5 exposure and GDM, and to analyze the interaction network of PM2.5 exposure, gut microbiota, blood metabolites and circRNAs.<br><br>METHODS: Participants (n = 1,248) were selected from the Pregnancy Metabolic Disease and Adverse Pregnancy Outcome (PMDAPO) cohort in Guangzhou, China. Demographic information, blood and fecal samples were collected from the participants. The fecal microbial composition and relative abundance were characterized using 16S rRNA gene sequencing, while blood differential metabolites and circRNAs of pregnant women with GDM were assessed using non-targeted metabolomics and RT-qPCR, respectively. Exposure levels of air pollutants were assessed using data from the nearest monitoring station. Spearman correlation and regression models were conducted to estimate the associations among PM2.5 exposure, gut microbiota, blood metabolites, circRNAs and GDM.<br><br>RESULTS: Elevated PM2.5 exposure levels were significantly associated with an increased risk of GDM, impaired glucose homeostasis and gut microbiota dysbiosis. Solobacterium and Escherichia_Shigella showed a positive effect modification on the association between PM2.5 exposure and fasting blood glucose, while Fusicatenibacter, Ruminococcaceae_UBA1819, Raoultibacter, Anaerofustis and Phascolarctobacterium showed a negative effect modification on the association between PM2.5 exposure and 2-h OGTT glucose. GDM-associated gut microbiota, including Catabacter, Angelakisella, Romboutsia and Fusicatenibacter, were associated with both GDM-associated metabolites (such as sphinganine-1-phosphate, sphingomyelin) and GDM-associated circRNAs (such as hsa_circ_0006732 and hsa_circ_0001439), which were involved in glycerophospholipid metabolism, sphingolipid metabolism and insulin signaling pathway.<br><br>CONCLUSIONS: The gut microbiota may moderate the associations between PM2.5 exposure and blood glucose levels, and both PM2.5 exposure and gut microbiota may be related to GDM, potentially involving pathways such as glycerophospholipid metabolism, sphingolipid metabolism and the insulin signaling pathway. However, lifestyle factors (diet and physical activity) and residential mobility were not measured, and the fecal microbiota was assessed at a single time point in mid-pregnancy. Thus, these limitations may contribute to residual confounding, exposure misclassification, and limited causal inference.}, }
@article {pmid41835129, year = {2026}, author = {Milke, F and Garcia, SL and Simon, M and Pacheco-Valenciana, A and Lennartz, ST}, title = {Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag037}, pmid = {41835129}, issn = {2730-6151}, abstract = {Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to infer community structure, revealing (not exclusively) potential biotic interactions. Such networks have been inferred for diverse biomes and repeatedly found to be modular, yet the ecological significance of this modularity remains underexplored. We tested whether clusters within co-occurrence networks ("cohorts"), are universal and ecologically meaningful units by assessing their ubiquity, stability, and environmental specificity across diverse ecosystems. Our meta-analysis spans 25 previously published 16S rRNA gene amplicon sequencing datasets (14 160 samples) and covers high environmental variability ranging from aquatic, terrestrial to anthropogenic environments. Microbial co-occurrence networks consistently exhibited high modularity across biomes. Inferred cohorts were ubiquitous and represented up to 90% of the community composition. Our findings demonstrate that modularity is a fundamental and generalizable feature of microbial community organization, indicating the existence of stable subcommunities. Highly similar cohorts were inferred even across different, unconnected environments and datasets, and showed consistent responses to environmental gradients, indicating that their composition is to a large degree deterministic and predictable. The overall cohort structure and environmental preferences were independent of the sample size and the inference algorithm, underlining the robustness and applicability of the results. Recognizing these microbial cohorts as a meaningful level of microbial organization will refine microbial community ecology, cultivation strategies, and predictive modelling of microbial dynamics.}, }
@article {pmid41835221, year = {2026}, author = {Malykhina, AP}, title = {Shaping the future of abdominal and pelvic pain research with novel scientific and technological advances.}, journal = {Frontiers in pain research (Lausanne, Switzerland)}, volume = {7}, number = {}, pages = {1738762}, pmid = {41835221}, issn = {2673-561X}, abstract = {Abdominal and pelvic pain often originates from one or more visceral organs of the gastrointestinal, musculoskeletal (pelvic floor), urinary, or reproductive systems. Over the past decade, research efforts on abdominal and pelvic pain have advanced considerably, driven by the discovery of new molecular targets, signaling pathways, targeted genetic editing, the use of human tissues, and comprehensive multiomic analyses. Increasingly, the field prioritizes combinatorial and integrative studies that bridge human clinical research with relevant animal models to accelerate the development of novel therapies for affected patients. In addition to established areas of pain research-such as the modulatory role of the central nervous system in chronic pelvic pain (CPP), stress-induced visceral hypersensitivity, sex differences, brain-gut interactions, microbiome influences, comorbidities, and neuromodulation-new research directions continue to emerge. These include exploring the effects of inflammaging and immune regulation in transition from acute to CPP, applying microphysiological systems (MPS) in pain research studies, integrating multiomics analyses, and employing combined artificial intelligence (AI) approaches. This article presents current perspectives on cutting-edge scientific trends and technological innovations shaping the field of abdominal and pelvic pain research.}, }
@article {pmid41835234, year = {2026}, author = {Mandolini, E and Szedlacsek, S and Abramczyk, B and Szucs, A and Staykova, A and Seybold, A and Knapp, M and Pawłowska, J and Ladurner, P and Peintner, U}, title = {Cryptocalciella - a new Mortierellaceae genus from Alpine glacier forefields.}, journal = {IMA fungus}, volume = {17}, number = {}, pages = {e177912}, pmid = {41835234}, issn = {2210-6340}, abstract = {Mortierellaceae are cosmopolitan, soil-inhabiting fungi that can be found in nearly all terrestrial habitat types and are therefore considered an essential part of the core soil microbiome. Many species of this family are known to endure harsh environments, including highly exposed and nutrient-depleted terrains such as glacier forefields. In these environments, microbial communities are taxonomically and functionally diverse, greatly contributing to nutrient cycling, soil organic matter formation, and plant establishment. However, there is growing understanding that Mortierellaceae diversity in these habitats remains largely undescribed. In this study, we isolated multiple fungal strains belonging to a previously unknown Mortierellaceae taxon from early stages of soil development in calcareous glacier forefields of the Alps and comprehensively characterized them using different tools: physiological tests, detection of associated bacteria, and microscopic observations (e.g., light, fluorescence, and scanning electron microscopy) to visualize their morphology and surface structure. Additionally, whole-genome sequencing and phylogenomics were used to determine their placement within Mortierellaceae. Our results show that the isolated strains represent a new species within a previously undescribed fungal genus. Due to the strains' origin in hidden, calcareous sediments of the earliest soil developmental stages at glacier forefields, we propose the name Cryptocalciella humilis Mandolini, Szedlacsek &amp; Peintner for this fungus.}, }
@article {pmid41828642, year = {2026}, author = {Sadurski, J and Ostrowska, M and Staniszewski, A and Waśko, A}, title = {Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828642}, issn = {1422-0067}, mesh = {*Cheese/microbiology ; Animals ; Goats ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Metagenome ; Food Microbiology ; Phylogeny ; }, abstract = {This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.}, }
@article {pmid41828645, year = {2026}, author = {Smolińska, K and Tomaszewska, E and Hułas-Stasiak, M and Muszyński, S and Szopa, A and Serefko, A and Dobrowolski, P}, title = {The Regulatory Role of FABP4 in Microbiome-Brain-Gut Communication Under High-Fat-Diet Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828645}, issn = {1422-0067}, mesh = {*Fatty Acid-Binding Proteins/metabolism ; *Gastrointestinal Microbiome ; Humans ; *Diet, High-Fat/adverse effects ; Animals ; *Brain/metabolism ; Dysbiosis/metabolism ; Inflammation/metabolism ; }, abstract = {High-fat diets (HFDs) are major environmental factors influencing metabolic homeostasis, immune regulation, and brain function, largely through their effects on gut microbiota and intestinal barrier integrity. Disruption of the microbiome-brain-gut axis has been increasingly implicated in systemic and neuroinflammatory processes; however, the molecular mediators that integrate dietary lipid signals with microbial and host responses remain incompletely defined. This review synthesizes the current evidence on the role of fatty acid-binding protein 4 (FABP4) as an integrative node linking HFD-induced gut dysbiosis to systemic and central inflammatory signaling. We critically evaluated experimental and translational studies addressing HFD-driven alterations in gut microbiota composition, intestinal barrier function, and inflammatory pathways, with particular emphasis on FABP4-mediated mechanisms across epithelial, immune, and neural compartments. The available data indicate that FABP4 responds to dietary and microbiome-derived cues and contributes to coordinated metabolic and inflammatory responses, affecting both peripheral tissues and the central nervous system. These findings support a model in which FABP4 participates in diet-driven feedback loops that amplify gut barrier dysfunction, immune activation, and neuroinflammation. In conclusion, FABP4 emerges as a central molecular mediator within the microbiome-brain-gut axis under HFD conditions, highlighting its potential relevance in understanding the pathophysiology of metabolic and neuroinflammatory disorders and guiding future integrative research strategies.}, }
@article {pmid41828691, year = {2026}, author = {Oršolić, N and Toljanić, B and Odeh, D and Čuljak, N and Šešelja, K and Baus Lončar, M and Đikić, D and Leboš Pavunc, A and Kos, B}, title = {Anti-Atherogenic Activities of Exopolysaccharides and Their Producing Strain Limosilactobacillus fermentum MC1 in Mice.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828691}, issn = {1422-0067}, support = {IP-2019-04-2237 and IP-2024-05-6548//The Croatian Science Foundation/ ; }, mesh = {Animals ; *Limosilactobacillus fermentum/metabolism/chemistry ; Mice ; *Atherosclerosis/metabolism/prevention &amp; control/drug therapy/pathology ; *Polysaccharides, Bacterial/pharmacology ; Male ; Biomarkers ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; }, abstract = {Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques within the artery wall. Accumulating evidence indicates that intestinal microbiota plays an important regulatory role in atherosclerosis at all stages of the disease. Through numerous metabolites, the intestinal microbiota can regulate immune and inflammatory cells and their mediators, as well as lipid metabolism, thereby contributing to the development and progression of atherosclerosis. With these assumptions in mind, we investigated the possibility of using Limosilactobacillus fermentum MC1 (L. fermentum MC1) and its exopolysaccharides (EPSs) in the reduction of lipid and atherogenic parameters as a preventive strategy in preventing the occurrence of cardiovascular diseases (CVD). We investigated the effect of L. fermentum MC1 and its EPSs on the health status of mice by monitoring the following parameters: body weight, colon length and weight, relative weight of organs, hematological (Hgb, WBC, number of erythrocytes, MCHC, MCV, MCH), and biochemical blood parameters including glucose, serum enzymes (ALT, ALP, amylase), urea, creatinine and lipid profile (total cholesterol, triglycerides, HDL, VLDL, LDL), different atherogenic parameters, blood biomarkers such as lymphocyte-to-monocyte (LMR) and neutrophil-to-lymphocyte (NLR) ratios, molecular inflammatory markers (IL1β, IL6, MCP1, IL1α, TLR4, TNFα, CD68, TGFβ), apoptosis markers (BCL2, AIFM1, IGF-1R), and endoplasmic reticulum stress markers (CHOP and GRP94) as well as oxidative stress (NOX2) markers in the colon. Furthermore, the level of lipid peroxidation, nitric oxide and glutathione concentrations in the liver, kidneys and spleen were measured. L. fermentum MC1 and its EPSs may prevent the development of atherosclerosis and the progression of CVD through antioxidant, anti-inflammatory, immunomodulatory activities, and regulation of the gut microbiome and lipid metabolism. The observed reduction in lipid and atherogenic determinants suggests that L. fermentum MC1 and its EPSs may contribute to atheroprotection and confer multiple health benefits.}, }
@article {pmid41828882, year = {2026}, author = {Kurashov, EA and Krylova, JV and Chernova, AM and Bataeva, YV and Belyakov, EA and Lapirov, AG and Anikina, VV and Grebennikov, VA and Yavid, EY}, title = {Major Low-Molecular-Weight Metabolites from Freshwater Aquatic Macrophytes: Ecological Aspects.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {5}, pages = {}, pmid = {41828882}, issn = {1420-3049}, support = {Scientific topic &#x2116;: 124032100076-2//The topic of the state assignment of the Institute of Biology of Inland Waters of the Russian Academy of Sciences/ ; }, mesh = {*Fresh Water ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; Molecular Weight ; Ecosystem ; Metabolomics/methods ; *Aquatic Organisms/metabolism ; }, abstract = {Freshwater macrophytes shape not only the morphological "architecture" of shallow-water ecosystems but also their chemical milieu via low-molecular-weight organic compounds (LMWOCs) that may regulate phytoplankton, periphyton, and the microbiome within the leaf/shoot diffusive boundary layer and the surrounding water column. In this study, GC-MS (gas chromatography-mass spectrometry) was used to identify major LMWOCs of the low-molecular-weight metabolome (LMWM) in 11 widely distributed macrophyte species (Myriophyllum spicatum L., Sparganium emersum Rehm., Sparganium gramineum Georgi, the hybrid Sparganium × foliosum A. A. Bobrov, Volkova, Mochalova et Chemeris, Persicaria amphibia (L.) Delarbre, Potamogeton perfoliatus L., Nuphar lutea (L.) Sibth. &amp; Sm., Potamogeton pectinatus L., Potamogeton natans L., Lobelia dortmanna L., and Ceratophyllum demersum L.). Compounds contributing more than 1% to the total LMWOCs pool were considered major, increasing the ecological realism of interpretations by focusing on metabolites more likely to reach effective concentrations in the plant microenvironment. For interspecific comparisons, the maximum recorded values of relative abundance and concentrations were used to estimate species "potential". In total, 137 major LMWOCs were detected (four remained unidentified), and their numbers varied markedly among taxa (from 11 in N. lutea to 71 in P. perfoliatus). Similarity analyses (Jaccard, Sørensen-Czekanowski, Morisita-Horn) indicated that similarity based on compound lists and similarity based on dominance structure may diverge, reflecting differences between the "LMWOCs set" and the quantitative architecture of LMWOCs within the LMWM. Fatty acids formed the core of the major fraction in all species: they were among the top three compounds in all 11 macrophytes and ranked first or second in 10 of 11, highlighting the lipid module as a universal "structure-signaling-defense/allelopathy" hub in aquatic plants. Also, an analysis of the ecological-biochemical role of the main major LMWOCs in the studied aquatic macrophytes is presented. Overall, the data offer a comparable, ecologically oriented framework for interpreting chemical regulation of communities in macrophyte-dominated habitats and for selecting target compounds/species for subsequent bioassay and field studies.}, }
@article {pmid41828913, year = {2026}, author = {Tian, K and Zhu, J and Qi, R and Yang, Y and Li, J and Tian, W and Tan, Q and Hu, B and Jian, Y}, title = {Associations Between Fine Particulate Matter-Associated Bacteria and Respiratory Tract Microbiota in Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828913}, issn = {2076-2615}, support = {NCTIP-XD/B07//National Center of Technology Innovation for Pigs/ ; }, abstract = {Environmental health and biosecurity in pig farms and surroundings are increasingly threatened by pathogenic bacteria carried by fine particulate matter with an aerodynamic diameter of 2.5 μm or less (PM2.5) in enclosed piggeries. However, limited attention has been given to these pathogens and their association with the respiratory microbiome of pigs. Using high-throughput sequencing, we investigated the overall and pathogenic bacterial communities attached to PM2.5 in pig houses, as well as those in the upper (URT) and lower respiratory tracts (LRT) of healthy fattening pigs. Concentrations of PM2.5, particulate matter with an aerodynamic diameter of 10 μm or less (PM10), ammonia (NH3), total volatile organic compounds (TVOCs), and hydrogen sulfide (H2S) were significantly higher inside the piggery than in the surrounding environment. The composition of PM2.5-associated bacteria varied with sampling height and showed greater similarity to the microbiota of the URT, particularly the oropharynx, than to that of the LRT. Additionally, 140 core potential bacterial pathogens were identified via Venn analysis in both PM2.5 and respiratory tracts. Co-occurrence network analysis and community assembly patterns revealed that microbial communities in PM2.5 and the respiratory tract exhibit distinct interaction and assembly characteristics. These findings highlight the potential role of PM2.5 as a vector for respiratory pathogens and underscore the importance of air quality management in pig farming to safeguard environmental health.}, }
@article {pmid41828957, year = {2026}, author = {Guan, X and Ma, H and Liu, R and Xu, Y and Gnagna, D and Yin, X and Zhang, Y and Li, Y}, title = {Impact of Exposure of Dairy Cow Feed to Polystyrene Microplastics on 24 h In Vitro Rumen Fermentation Responses, Microbiota Biodegradation Potential and Metabolic Pathways.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828957}, issn = {2076-2615}, support = {2023YFD2000700//National Key Research and Development Program of China/ ; ZL2024C018//the Joint key project of Natural Science Foundation of Heilongjiang Province/ ; }, abstract = {Microplastic pollution is increasingly serious worldwide, threatening human and animal health. The cow rumen is a key organ for nutrient digestion and absorption, and its fermentation is closely related to rumen microorganisms. Here, we investigated how polystyrene microplastics (PS-MPs) with varying particle sizes and concentrations affect rumen fermentation and the biodegradability of PS-MPs by rumen fermentation. The results reveal that exposure to PS-MPs lowered gas production and gas concentrations, as well as volatile fatty acid content, and these decreases were positively correlated with PS-MP concentration. However, higher PS-MP concentration and larger particle size increased the activity of carboxymethyl cellulose, β-glucosidase, and xylanase. Furthermore, PS-MP exposure reduced the abundance of certain rumen microorganisms and altered metabolic pathways and metabolites linked to PS-MP biodegradation. It was also found that PS-MP content decreased significantly after 24 h fermentation. Therefore, PS-MPs can inhibit rumen fermentation by affecting the rumen microbiome, and rumen microorganisms and their secreted enzymes can biodegrade PS-MPs to produce styrene and derivatives; such small molecules may further disrupt rumen homeostasis, thereby affecting lactation performance. In addition, rumen microbial degradation of PS-MPs provides a new idea to resolve future microplastic contamination challenges.}, }
@article {pmid41828960, year = {2026}, author = {Yu, H and Dong, S and Wang, L and Liu, S}, title = {Integrated Gut Microbiome and Metabolome Analysis in Largemouth Bass (Micropterus salmoides) Following Viral Infection.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828960}, issn = {2076-2615}, abstract = {Largemouth bass (Micropterus salmoides) is an important aquaculture species increasingly threatened by viral diseases, particularly largemouth bass virus (LMBV), which can cause significant mortality. However, integrative analyses linking LMBV-induced gut microbiota dysbiosis to metabolomic dysfunction are limited. In this study, we profiled the intestinal microbiome and metabolome alterations in largemouth bass following LMBV infection and conducted an integrated analysis. Infected fish showed reduced alpha diversity and significant shifts in community structure, including increased relative abundances of Bacteroidota and Fusobacteriota and a decrease in Proteobacteria. Opportunistic taxa, such as Pseudomonas and Mycobacterium, were enriched after infection. Metabolomic profiling revealed differential metabolites primarily involved in amino acid and carbohydrate metabolism. Integrative correlation analyses further identified significant associations between opportunistic bacteria and putative harmful metabolites, suggesting that LMBV-induced dysbiosis disrupts host metabolic homeostasis and contributes to immune dysfunction. These findings may clarify the microbiota-metabolite landscape during LMBV infection.}, }
@article {pmid41828967, year = {2026}, author = {Taylor, S and Tewson, C and Edmondson, V}, title = {Resolution of Chronic Diarrhoea Following Treatment of Periodontal Disease in a Cat.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41828967}, issn = {2076-2615}, abstract = {An association between periodontal disease and comorbid disorders, including gastrointestinal signs, has been reported in cats and investigated in humans, where a bidirectional relationship between oral and gastrointestinal microbiomes exists. A 5-year-old neutered female domestic shorthair cat was presented with a 2-year history of small-bowel diarrhoea. The cat's appetite was reduced, and coat quality had deteriorated. On examination, the cat was found to have periodontal disease affecting multiple teeth and a matted coat. Biochemistry revealed mild hyperproteinaemia, haematology was unremarkable, cobalamin was normal, folate was elevated, and retroviral testing was negative. Abdominal ultrasound showed diffuse muscularis thickening without other abnormalities, and dental examination and radiography revealed missing teeth, a root remnant, stage 4 periodontal disease, and tooth resorption. Multiple extractions were performed, and multimodal analgesia was provided, including locoregional dental blocks. The cat's appetite, body condition, energy levels, and coat quality improved after the procedure, and the diarrhoea completely resolved within a month of the procedure without any changes in diet, physical, social environment, or the use of any medications, and did not recur during the following 7 months. This case illustrates the potential role of periodontal disease in the development of gastrointestinal disease and the benefits outside the oral cavity of managing dental disease in cats.}, }
@article {pmid41829039, year = {2026}, author = {Luo, L and Li, J and Li, M}, title = {Intratumoral Staphylococcus pseudintermedius Promotes Proliferation and Migration of CMT-U27 Cells Through the TLR2/PI3K/Akt Signaling Pathway.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41829039}, issn = {2076-2615}, support = {32402964//Young Scientists Fund of the National Natural Science Foundation of China/ ; 840003//Jiangsu Qinglan Project/ ; 804127//Meng Li's Nanjing Agricultural University Research Start-up Fund/ ; }, abstract = {Increasing evidence suggests that intratumoral microorganisms and their metabolites can modulate cancer initiation and progression. However, the composition and functional role of intratumoral bacteria in canine mammary tumors (CMTs) remain unclear. In this study, we investigated the functional significance of tumor-derived Staphylococcus in CMTs, focusing on its effects on the proliferation and migration of CMT-U27 cells. 16S rRNA sequencing revealed reduced alpha diversity in CMT tissues, with Staphylococcus pseudintermedius identified as the most frequently isolated species. Functional assays, including CCK-8, wound healing, RT-qPCR, and Western blot analyses, demonstrated that intratumoral Staphylococcus pseudintermedius significantly enhanced cellular proliferation and migration. Mechanistically, Staphylococcus pseudintermedius significantly upregulated the expression of TLR2, as well as the phosphorylation levels of PI3K, Akt and P70S6K. The inhibition of TLR2 using C29 suppressed the mRNA expression of VEGF, MMP9, MMP2, and EGFR. Collectively, these findings indicate that intratumoral Staphylococcus pseudintermedius promotes the proliferation and migration of CMT-U27 cells through activation of the TLR2/PI3K/Akt pathway, highlighting a functional link between tumor-associated bacteria and cancer progression.}, }
@article {pmid41829048, year = {2026}, author = {Liu, X and Ying, C and Ma, F and Yang, Y and Liu, K}, title = {Gut Microbiome Signatures Across Migratory, Sedentary, and Aquaculture Ecotypes of Coilia nasus.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41829048}, issn = {2076-2615}, support = {2022YFF0608201//National Key R&amp;D Program of China/ ; ZF2022-18-0399//Monitoring of aquatic resources in key waters of Anhui province/ ; NO.2023TD11//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {Coilia nasus, a typical species with migratory-sedentary polymorphism, shows different intestinal microbiota characteristics among its different ecotypes. This is attributed to differences in feeding habits and habitat environments (such as water temperature, salinity, etc.). This study constructed a database of intestinal microbiota for three ecological types of C. nasus, namely migratory type (comprising marine populations and freshwater populations), sedentary type and aquaculture-reared type, through 16S rRNA amplicon sequencing technology. This study investigates the ecological mechanisms underlying microbiota differentiation, focusing on three key drivers: environmental selection, host nutritional metabolism requirements, and host life history strategies. The results showed that the core flora of C. nasus consisted of Firmicutes, Proteobacteria, and Actinobacteria. Both the depletion of microbial taxa and the enrichment of marine-adapted bacterial lineages-including Proteobacteria and Psychrobacter-are associated with elevated salinity in the migratory marine population of C. nasus. In contrast, the elevated relative abundance of Actinobacteria in aquaculture-reared C. nasus is likely attributable to dietary supplementation with protein- and lipid-rich artificial feed. Functional correlation analysis holds promise for partially predicting the microbiota's metabolic functional succession patterns. The dominance of Pseudomonas_E in the migratory freshwater population is consistent with its well-documented physiological versatility and adaptive capacity in dynamically fluctuating aquatic habitats. The elevated abundance of Cyanobacteria in the sedentary population C. nasus coincides with the water bloom in their habitat, suggesting that the structure of the microbiota may serve as a novel biomarker for indicating the ecosystem. In conclusion, this study identifies potential molecular markers for tracing genetic resources and distinguishing ecological types of C. nasus, while establishing a theoretical foundation for elucidating the co-evolutionary dynamics between fish hosts and their associated microbiota-and thereby informing both conservation strategies for wild populations and microbiota-informed aquaculture practices.}, }
@article {pmid41829053, year = {2026}, author = {Nopparatmaitree, M and Loor, JJ and Arjin, C and Hwanhlem, N and Sudchamrong, P and Buapa, B and Intawicha, P and Incharoen, T}, title = {Phytosynbiotic Containing Double-Layer Microencapsulated Pediococcus acidilactici V202 and Tiliacora triandra Leaf Extract Improve Growth Performance and Gut Health in Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41829053}, issn = {2076-2615}, support = {R2567B037//Naresuan University (NU) and the National Science, Research and Innovation Fund (NSRF)/ ; R2569A014//Reinventing University Program 2026, the Ministry of Higher Education, Science, Research and Innovation, Thailand/ ; R2569C002//Frontier Research and Innovation Cluster Fund, Naresuan University/ ; 2278//Fundamental Fund 2026, University of Phayao/ ; }, abstract = {This study investigated the effects of a novel phytosynbiotic feed supplement derived from double-layer microencapsulated Pediococcus acidilactici V202 and Tiliacora triandra leaf extract (DMP) on the growth performance, nutrient utilization, gut fermentation, intestinal morphology, and cecal microbiota of broiler chickens. A total of 250 one-day-old male Ross 308 broilers were randomly assigned to five dietary treatments: basal control diet, antibiotic growth promoter (AGP) with chlortetracycline at 0.07%, and DMP supplementation at 0.25, 0.50, or 1.00% (w/w) for 42 days. Compared with the control diet, feeding the DMP led to linear or quadratic responses (p < 0.05) on average daily gain, feed efficiency, productive index, and economic returns. Apparent digestibility of dry matter, crude protein, and apparent metabolizable energy was enhanced in DMP-fed broilers, indicating improved nutrient utilization efficiency. These performance responses were accompanied by pronounced alterations in cecal fermentation, characterized by increased lactic acid, total volatile fatty acids, and particularly acetic and butyric acid levels (p < 0.01). Microbiome analysis revealed that the DMP selectively enriched fermentative SCFA-producing bacterial orders, including Lachnospirales, Oscillospirales, and Lactobacillales. It also reduced the relative abundance of less desirable taxa. As evidenced by an increased villus height and surface area in the duodenum and jejunum, along with a higher villus height-to-crypt depth ratio in the ileum, feeding the DMP also enhanced small intestinal morphology. These coordinated morphological adaptations are indicative of enhanced epithelial maturation and reduced crypt hyperplasia, likely mediated by elevated microbial SCFA production in the gut. In conclusion, the DMP improved broiler growth performance by coordinating the modulation of the gut microbiota, SCFA levels, and intestinal morphology, resulting in enhanced nutrient digestibility and productivity. This phytosynbiotic strategy represents a sustainable plant-based alternative to antibiotic growth promoters for environmentally responsible poultry production.}, }
@article {pmid41829073, year = {2026}, author = {Yuan, S and Tu, R and Shan, B and Liu, Y and Jiang, X and Zheng, M and Yang, L and Liu, H and Zhao, T and Yang, P and Zhai, Q and Mao, J and Liu, S and Liu, X}, title = {Turning-Modulated Vertical CO2 Gradients Drive Microbial Stratification and Amadori Product Accumulation in Winter Daqu.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829073}, issn = {2304-8158}, support = {22138004//the National Natural Science Foundation of China/ ; 2024YFFK0436//the Key Research and Development Program of Sichuan Province/ ; }, abstract = {High-temperature Daqu (HTD)'s quality determines the characteristics and yield of the Chinese sauce-aroma baijiu. However, winter production frequently encounters challenges such as fermentation instability and metabolic fluctuations, primarily stemming from complex, unmonitored microenvironmental changes within the HTD pile. This study established a closed-loop system linking the microenvironment, HTD quality, microbiome, and metabolome. Through continuous monitoring of the winter fermentation pile's microenvironmental conditions and integrating multi-omics analyses, we revealed that CO2 concentration within fermentation piles is the core factor causing quality variations in HTD. By breaking the respiratory bottleneck formed by carbon dioxide (CO2) accumulation through the turning anaerobic stress can be alleviated, thereby driving metabolic succession. The study found that vertical CO2 concentration heterogeneity severely restricts the enrichment of aerobic core functional microbial communities such as the Bacillus species. This directly blocks key metabolic pathways including amino acid metabolism and energy supply via ABC transporters. Moreover, the specific accumulation of Amadori products further confirms that this low-temperature environment under CO2 stress causes the Maillard reaction to stall at intermediate stages. Consequently, this study proposes a steady-state control strategy centered on oxygen and CO2 gas characteristics. By actively regulating the gaseous microenvironment to eliminate metabolic heterogeneity, it provides theoretical support for standardizing traditional fermentation processes.}, }
@article {pmid41829134, year = {2026}, author = {Ma, M and He, W and Lin, X and Wang, Y and Jiang, S and Yang, L and Li, G and Gu, Y}, title = {Using Integrated Microbiome-Metabolome-Genome Axis Data to Elucidate the Mechanism by Which Polyphenol Content in the Extract from C. osmantha Leaves (PECOL) Regulates Broiler Flavor.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829134}, issn = {2304-8158}, support = {Guilin Scientific Research [2025KX] No.03//Guangxi Forestry Science and Technology Extension Project/ ; U25A20701//the Natural Scientific Foundation of China/ ; CARS-41-G06//the China Agriculture Research System of MOF and MARA/ ; R2024YJ-YB3004 and R2023PY-QY012//the Science and Technology Program of Guangdong Academy of Agricultural Sciences/ ; 2024E04J0562//the Science and Technology Plan Project of Guangzhou/ ; 2023A1515111031//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {The quality and flavor of chicken meat are the key factors that influence consumers' purchase decisions. Recent studies have demonstrated that polyphenol can modulate meat quality. In this study, an integrated multi-omics approach was utilized to systematically identify the regulatory effect of dietary supplementation with polyphenols extracts of C. osmantha leaves (PECOL) on chicken flavor. It was found that dietary PECOL supplementation enhanced breast meat flavor and increased fatty acid ethyl ester compounds in the breast muscle. Moreover, PECOL supplementation reshaped the composition and proportions of gut microbiota across multiple taxonomic levels, with a notable enrichment of taxa within the phylum Firmicutes (e.g., g_Massilistercora). Furthermore, the addition of PECOL altered the contents of cecal metabolites related to lipid and glucose metabolism, such as PC (14:1(9Z)/21:0), PC (P-16:0/15:1(9Z)), LysoPE (20:4(8Z, 11Z, 14Z, 17Z)/0:0), and glycerol 3-phosphate. Notably, we found that g_Massilistercora was significantly correlated with the content of these metabolites related to lipid and glucose metabolism. Further analysis revealed that these metabolites might interact with GPAT4 to jointly regulate chicken flavor. These findings further clarify the regulatory role played by PECOL in shaping the flavor of broiler meat.}, }
@article {pmid41829711, year = {2026}, author = {Liu, M and Liu, Y and Wang, H and Ruan, Y and Wang, X and Du, X and Zhou, M and Fu, Y and Tang, J and Zhang, J and Cao, L}, title = {GsEXPA8 Improves Alkaline Tolerance in Lupinus angustifolius by Modulating Root Architecture, Stress-Responsive Gene Expression, and Rhizosphere Microbiome.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829711}, issn = {2223-7747}, support = {32001505//National Natural Science Foundation of China/ ; LH2023C006//Natural Science Foundation of Heilongjiang Province/ ; }, abstract = {Lupinus angustifolius is an important leguminous ornamental species, but its productivity is often compromised by alkaline soil stress. GsEXPA8, an expansin gene identified in wild soybean (Glycine soja), has been implicated in alkali stress tolerance. In this study, we examined how heterologous expression of GsEXPA8 in lupinus affects its biochemical, molecular, and rhizospheric responses to alkali stress. Under NaHCO3-induced alkaline conditions, transgenic lines overexpressing GsEXPA8 displayed improved leaf vigor, greater root biomass and length, elevated activities of antioxidant enzymes (CAT and POD), increased proline accumulation, and reduced malondialdehyde levels compared to the wild type. Expression analysis revealed time-dependent up-regulation of several alkali-responsive genes (LaSOS1, LaNCED3, LaMYB39, LaNAC56, LaNHX6, and LaP5CS). Moreover, the rhizosphere microbial community was significantly restructured, with a marked increase in beneficial microbial taxa such as Pseudomonas and Lysobacter. We also found that the endogenous lupinus homolog LaEXPA8 is alkali-inducible. Overexpression of LaEXPA8 similarly enhanced alkaline tolerance, whereas CRISPR/Cas9 knockout lines showed no clear phenotypic alteration, suggesting potential functional redundancy within the expansin family. Notably, LaEXPA8 and GsEXPA8 differed in their temporal regulation of downstream genes, indicating both conserved and distinct regulatory roles. Our results demonstrate that GsEXPA8 improves alkali tolerance in lupinus through integrated mechanisms: promoting root growth, enhancing antioxidant and osmotic adjustment capacity, dynamically modulating stress-related gene expression, and enriching beneficial rhizosphere microbiota. This work provides the critical report of modifying alkali tolerance by manipulating an expansin gene alongside the associated rhizosphere microbiome, offering a combined strategy for breeding stress-resistant ornamentals.}, }
@article {pmid41829784, year = {2026}, author = {Zhakypbek, Y and Kossalbayev, BD and Tursbekov, S and Tursbekova, G and Berdaliyeva, Z and Belkozhayev, AM}, title = {Application of Beneficial Bacteria to Enhance Plant Drought Resilience.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829784}, issn = {2223-7747}, support = {BR24993218//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Drought stress is one of the most severe abiotic constraints limiting crop productivity worldwide, a challenge that is intensifying under ongoing climate change. In recent years, beneficial microorganisms have emerged as sustainable, nature-based tools to enhance plant drought tolerance and stabilize agricultural production under water-limited conditions. This review synthesizes current knowledge on the major groups of beneficial bacteria involved in drought stress mitigation, including plant growth-promoting rhizobacteria (PGPR), a functional subgroup of rhizosphere-associated microbes, endophytic bacteria, rhizosphere-associated microbes, and cyanobacteria, highlighting their primary physiological, biochemical, and soil-mediated mechanisms. These microorganisms enhance drought resilience through multiple complementary pathways, such as modulation of abscisic acid (ABA) and auxin (IAA) signaling, ACC deaminase activity, osmotic adjustment, antioxidant defense, improved nutrient acquisition, and enhancement of soil structure and water retention. The review further discusses practical application strategies, including seed inoculation, soil and root application, foliar spraying, the use of single strains versus microbial consortia, and advances in bioformulations and carrier materials that improve microbial survival and field efficacy. Emphasis is placed on recent experimental and field studies demonstrating the effectiveness of microbial inoculants under drought conditions. Collectively, the evidence highlights the potential of beneficial bacteria as key components of climate-resilient agriculture and underscores the need for integrated, formulation-driven approaches to translate laboratory success into consistent field performance.}, }
@article {pmid41829785, year = {2026}, author = {Bao, S and Cai, Z and Li, F and Zhang, H and Fu, S and Lv, L and Liu, Q and Shi, J}, title = {Changes in Soil Nutrients and Bacterial Communities in Perennial Grass Mixtures in Alpine Ecological Zones After 20 Years of Establishment.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829785}, issn = {2223-7747}, abstract = {Monoculture and mixed sowing are common practices for restoring degraded alpine meadow grasslands. To investigate the effects of different sowing patterns on soil bacterial community characteristics in alpine artificial grasslands, this study examined a 20-year-old established artificial grassland, systematically analyzing plant community attributes, soil physicochemical properties, and the diversity and functional structure of soil bacterial communities under various monoculture and mixed-sowing treatments. The results showed that: (1) Mixed-sowing treatments significantly improved soil physicochemical properties and plant community characteristics. The P4 (Elymus nutans + Poa pratensis + Festuca sinensis + Poa crymophila) mixed-sowing treatment notably enhanced vegetation performance and soil conditions. Compared with the monoculture P1 (Elymus nutans) treatment, aboveground biomass (AGB) and soil organic matter (SOM) content increased by 57.23% and 68.25%, respectively, indicating that perennial grass mixtures improve soil water and nutrient retention, thereby promoting plant growth. (2) Microbiome analysis revealed that mixed sowing significantly optimized the structure of rhizosphere bacterial communities. Operational Taxonomic Units (OTUs), which represent sequence-based taxonomic units and their abundance information, were most abundant in the P4 mixed-sowing treatment, reaching a total of 5685 OTUs. In terms of bacterial diversity indices, the OTU richness, Ace index, and Chao1 index in the P4 mixed-sowing treatment were 26.12%, 25.81%, and 24.34% higher, respectively, than those in the monoculture P1 treatment, with all differences being statistically significant (p < 0.05). (3) Mantel test and redundancy analysis (RDA) revealed that soil electrical conductivity (SEC) and pH were negatively correlated with bacterial diversity indices, while soil organic matter (SOM) was identified as the key environmental driver shaping bacterial community assembly. In summary, appropriate grass mixtures effectively enhance "plant-soil-microbe" interactions, leading to improved soil fertility and optimized bacterial communities, representing a viable strategy for long-term ecological restoration and sustainability of alpine artificial grassland ecosystems. The P4 treatment-comprising a four-species mixture of Elymus nutans, Poa pratensis, Poa crymophila, and Festuca sinensis-achieved the best overall performance.}, }
@article {pmid41829788, year = {2026}, author = {Ortiz, J and Herrera, NB and Dias, NB and Vidal, C and Ruiz, A and Peña, OL and de Souza, BM and Palma, MS and de la Luz Mora, M and Arriagada-Escamilla, C and Soto, J}, title = {Beneficial Effects of a Root-Endophytic Bacterium with Quorum-Sensing Traits on Growth and Drought Tolerance in the Vulnerable Conifer Araucaria araucana.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829788}, issn = {2223-7747}, support = {FONDECYT Postdoctoral 323066//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; }, abstract = {Climate change-induced drought threatens the persistence of Araucaria araucana, an endangered and endemic conifer of the Southern Andes. Beneficial plant-microbe interactions may contribute to drought resilience. Here, we evaluated the effects of a root-endophytic bacterium with the capacity to produce N-acyl homoserine lactones (AHLs) on the growth and drought tolerance of A. araucana. For this, a root endophytic bacterium was isolated from A. araucana and identified as Erwinia billingiae. It was characterized for plant growth-promoting traits, and inoculated into A. araucana seedlings under drought conditions). The bacteria produced N-butyryl-L-homoserine lactone (C4-HSL) under control conditions and C4-HSL and N-hexanoyl-L-homoserine lactone (C6-HSL) under drought stress. The strain also produces indoleacetic acid, ammonia, siderophores and solubilizes phosphate. Under drought stress, non-inoculated seedlings showed marked reductions in shoot and root biomass, chlorophyll content, relative water content (RWC), and soluble sugars. In contrast, inoculated seedlings under drought displayed significantly higher shoot and root biomass, reaching levels comparable to those of well-watered controls. Chlorophyll content increased from 5.42 to 9.35 mg L[-1], and RWC increased from 62% to 71% in inoculated plants under drought conditions. Soluble sugar content increased from 25.74 to 36.34 mg g[-1] fresh weight following inoculation. Drought-induced oxidative stress was significantly alleviated in inoculated seedlings, with lower malondialdehyde and proline accumulation compared to non-inoculated drought-stressed plants. Antioxidant responses were modulated, indicating improved redox balance under water limitation. These results demonstrate that a root-endophytic bacterium with AHL production can enhance drought tolerance in A. araucana seedlings. This study provides novel evidence supporting the role of beneficial endophytes in microbiome-based strategies for conserving native forest species under climate change.}, }
@article {pmid41829816, year = {2026}, author = {Al-Sawa'eer, AS and Al-Samydai, A and Odeh, L and Haj Ahmad, F and Obekh, R and Elqader, YMA and Khaleel, A and Al-Athamneh, AM and Gabriele, M and Di Simone, SC and Ferrante, C and Menghini, L and Ali Agha, ASA}, title = {Early Plant Development as a Systems-Level Trait: Integrating Omics, Artificial Intelligence, and Emerging Biotechnologies.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829816}, issn = {2223-7747}, abstract = {Seed germination and early seedling development are critical determinants of crop establishment, stress tolerance, and yield stability, yet these stages remain insufficiently integrated into contemporary crop improvement strategies. Recent advances across genome editing, microbiome-assisted seed treatments, nanotechnology-enabled priming, and artificial intelligence-guided phenotyping have generated substantial but fragmented insights into early developmental regulation. This review synthesizes recent advances across early plant development research. It demonstrates that seemingly diverse technologies converge on a limited set of regulatory control nodes, including abscisic acid-gibberellin balance, redox homeostasis, and root system architectural plasticity. By integrating evidence from molecular, microbial, physicochemical, and computational studies, early plant ontogeny is presented as a tunable regulatory state governed by quantitative thresholds rather than as a strictly predetermined genetic process. Advances in deep learning, reinforcement learning, and high-throughput phenotyping further enable the modeling and optimization of early developmental trajectories across genotype by environment contexts. Together, these insights establish early development as a programmable target for crop improvement and provide a mechanistic foundation for designing integrated interventions that enhance developmental uniformity, stress resilience, and yield stability across diverse agroecological systems.}, }
@article {pmid41829833, year = {2026}, author = {Kumar, D and Sattiraju, KS and Reddy, MS}, title = {A Systems Approach to Endophyte-Mediated Plant Holobiont and Microbiome Dynamics.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829833}, issn = {2223-7747}, abstract = {The plant holobiont comprises the host plant and its associated microbial communities functioning together as a single ecological and evolutionary unit that influences plant health, productivity, and environmental adaptability. Endophytes, formerly classified primarily as plant growth-promoting agents, are currently gaining traction as integral components of plant-associated microbiomes such as the rhizobiome and phytobiome. They can alter host-mediated root exudation patterns, microbial community structure, and nutrient dynamics within the rhizosphere. Endophytes play an important role in modulating host signaling pathways, thus influencing plant growth. Various mechanisms by which endophytes contribute to improved plant performance include soil microbiome dynamics, carbon sequestration, and strengthening the host's ability to tolerate abiotic stressors. Multi-omics, single-cell, and systems-level approaches integrated with CRISPR, metabolic engineering, and AI, together with systems biology, guided by in vitro and field studies, support predictive modeling and provide evidence for the evolution of system-driven strategies for developing effective bioinoculants. This review highlights the potential of endophytes to serve as a scalable and sustainable component of climate-resilient and regenerative agricultural systems, while acknowledging ecological variability and field-level constraints.}, }
@article {pmid41829863, year = {2026}, author = {Thomaidis, G and Boutzikas, G and Alexopoulos, A and Zamioudis, C}, title = {Local and Systemic Transcriptional Responses of Tomato to a Growth-Promoting Streptomyces Consortium.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, pmid = {41829863}, issn = {2223-7747}, support = {3082//Hellenic Foundation for Research and Innovation (H.F.R.I.) under the "2nd Call for H.F.R.I. Research Projects to support Faculty Members &amp; Researchers/ ; }, abstract = {Members of the genus Streptomyces are prominent inhabitants of the plant rhizosphere and endosphere and are increasingly recognized for their roles in plant growth promotion and disease suppression. In this study, we isolated genetically distinct Streptomyces from the tomato (Solanum lycopersicum L.) rhizosphere, designated as TOM isolates, and assembled them into a defined 12-member TOM consortium. Application of the TOM consortium significantly promoted root and shoot growth in tomato. RNA-seq analysis revealed coordinated local and systemic transcriptional responses characterized by a predominance of down-regulated genes in both roots and leaves. In roots, differential gene expression reflected selective attenuation of defense- and cell wall-related processes, alongside increased expression of genes associated with phytoalexin biosynthesis, phosphate starvation responses, and hormonal regulation. In leaves, transcriptional reprogramming was dominated by reduced stress-related responses together with activation of metabolic and growth-associated functions. The TOM consortium also reduced disease severity caused by Fusarium oxysporum f. sp. radicis-lycopersici by approximately 60% compared to infected controls. To further characterize functional traits of individual consortium members, isolates were evaluated in vitro for antifungal activity and five strains displaying inhibition were selected for hybrid whole-genome sequencing. Genome analyses revealed diverse taxonomic affiliations and a rich repertoire of biosynthetic gene clusters, including clusters associated with known antimicrobial metabolites as well as numerous low-similarity clusters indicative of substantial unexplored biosynthetic potential. Collectively, this study provides new insights into plant interactions with beneficial Streptomyces, while revealing molecular signatures involved in Streptomyces-mediated plant growth promotion and pathogen suppression.}, }
@article {pmid41829888, year = {2026}, author = {Kouraki, A and Franks, S and Vijay, A and Kurien, T and Taylor, MA and Smith, SL and Smith, B and Kelly, A and Valdes, AM}, title = {Effect of Prebiotic Supplementation With and Without Physiotherapy on Pain and Pain Sensitivity in People with Knee Osteoarthritis.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829888}, issn = {2072-6643}, support = {MR/W026813/1//Advanced Pain Discovery Platform (APDP) and the Medical Research Council (MRC)/ ; 23139/VAC_/Versus Arthritis/United Kingdom ; }, mesh = {Humans ; Female ; Male ; *Prebiotics/administration &amp; dosage ; Aged ; *Osteoarthritis, Knee/therapy/physiopathology ; *Inulin/administration &amp; dosage ; Middle Aged ; *Dietary Supplements ; *Physical Therapy Modalities ; Gastrointestinal Microbiome ; Pain Measurement ; Treatment Outcome ; *Pain Management/methods ; Pain Threshold ; Glucagon-Like Peptide 1/blood ; Fatty Acids, Volatile/blood ; Hand Strength ; }, abstract = {Background: Emerging evidence links the gut microbiome to chronic pain processing. Inulin, a prebiotic fibre, modulates the gut microbiome, while physiotherapy-supported exercise (PSE) improves pain and function. We evaluated the effects of inulin supplementation with and without PSE on knee osteoarthritis (OA) pain. Methods: In a 2 × 2 factorial RCT, 117 community-dwelling adults with knee OA received 6 weeks of: (A) 20 g/day inulin, (B) digital PSE (Joint Academy™), (C) inulin +PSE, or (D) 10 g/day maltodextrin. Primary outcome: pain (Numerical Rating Scale). Secondary: 30 s sit-to-stand (30-CST), timed up and go (TUG), grip strength, and quantitative sensory testing. Serum short-chain fatty acids (SCFAs) and glucagon-like peptide-1 (GLP-1) were measured. The study was not powered to detect synergistic interaction. Results: A total of 117 participants (58.1% female; mean ± SD age = 67.5 ± 9.4 years; BMI = 29.5 ± 5.3 kg/m[2]; NRS = 3.96 ± 2.67) completed the trial. Pain improved with inulin (baseline-adjusted between-group mean difference (Δ) = -1.11 [95%CI -2.18, -0.04], p = 0.045) and PSE (Δ = -1.55 [95%CI -2.52, -0.58], p = 0.002) compared to placebo, with no synergistic effect. PSE improved TUG (p = 0.02) and 30-CST (p = 0.0004), while inulin improved grip strength (p = 0.002), pressure pain thresholds (p = 0.009) and temporal summation (p = 0.025) compared to placebo and had significantly lower dropout rates (3.6%) compared with PSE (21% p < 0.01). Only inulin increased SCFA butyrate (p = 0.0248) and GLP-1 (p = 0.0109), and higher GLP-1 was associated with improved grip strength, suggesting a gut-muscle link. Conclusions: Inulin and PSE each produced meaningful pain reductions. Only inulin improved pain sensitivity and grip strength, the latter paralleled by increased GLP-1, and had much higher rates of retention compared to PSE.}, }
@article {pmid41829891, year = {2026}, author = {Kozák, M and Sitku, T and Hodossy-Takács, R and Sápi, F and Várkonyi, I and Barta, Z}, title = {Migraine and the Gut-Brain Axis-The Role of Microbiome-Targeted Biotics.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829891}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Migraine Disorders/microbiology/physiopathology/therapy ; *Probiotics/therapeutic use/administration &amp; dosage ; Prebiotics/administration &amp; dosage ; Dysbiosis/complications ; *Brain/physiopathology ; *Brain-Gut Axis/physiology ; Synbiotics/administration &amp; dosage ; }, abstract = {Background: Migraine is a highly prevalent and disabling primary headache disorder frequently accompanied by gastrointestinal symptoms and comorbid gastrointestinal diseases. Increasing evidence suggests that alterations in the gut microbiota and dysregulation of the microbiome-gut-brain axis may contribute to migraine pathophysiology through immune activation, oxidative stress, impaired intestinal barrier function, and neuroinflammatory signaling. Objectives: This narrative review aims to summarize current mechanistic and clinical evidence linking the gut-brain axis to migraine, with a particular focus on the potential roles of probiotics, prebiotics, and postbiotics as adjunctive strategies in migraine management. Methods: A narrative synthesis of experimental, translational, and clinical studies was performed, focusing on microbiome composition, gut barrier integrity, immune and oxidative pathways, and interventional trials evaluating probiotics, prebiotics, synbiotics, and microbiota-derived metabolites in adult and pediatric migraine populations. Results: Migraine has been associated with intestinal dysbiosis, increased gut permeability, and low-grade systemic inflammation. Probiotics, most commonly strains of Lactobacillus and Bifidobacterium, may modulate inflammatory cytokine profiles, enhance tight junction integrity, reduce oxidative stress, and influence neurotransmitter-related pathways along the gut-brain axis. Clinical trials evaluating probiotic supplementation report heterogeneous but promising signals, including reductions in migraine frequency, severity, disability scores, and analgesic use, particularly in chronic migraine and pediatric populations. Emerging evidence also supports a potential role for prebiotics (e.g., inulin-type fructans) and microbiota-derived metabolites such as short-chain fatty acids, although direct clinical data remain limited. Conclusions: Modulation of the microbiome-gut-brain axis represents a biologically plausible adjunct approach in migraine management. While probiotics, prebiotics, and postbiotics show potential benefits with favorable safety profiles, current evidence of their strain-, formulation-, and population-specific characteristics is lacking. Well-powered, placebo-controlled trials with standardized migraine endpoints and integrated microbiome and metabolomic analyses are needed to define responders, optimal interventions, and clinical relevance.}, }
@article {pmid41829907, year = {2026}, author = {Fritz, R and Tóbiás, Z and Bere, Z and Fritz, P}, title = {Malnutrition, Skeletal Muscle Loss and Mucosal Toxicity in Head and Neck Cancer: Nutritional Targets Beyond Energy Replacement.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829907}, issn = {2072-6643}, support = {8353//University of Szeged/ ; }, mesh = {Humans ; *Head and Neck Neoplasms/therapy/complications ; *Malnutrition/etiology/therapy ; *Muscle, Skeletal/physiopathology ; *Mucositis/etiology ; *Sarcopenia/etiology/therapy ; Nutritional Status ; Inflammation ; Body Composition ; }, abstract = {Head and neck cancer represents one of the most nutritionally vulnerable oncologic populations, driven by tumor-related functional impairment, treatment toxicities, and complex metabolic alterations. Malnutrition and skeletal muscle loss are highly prevalent at diagnosis and frequently worsen during therapy, impairing treatment tolerance, functional status, and clinical outcomes. This narrative review synthesizes clinical and mechanistic evidence on the interrelated roles of malnutrition, low skeletal muscle mass, mucosal toxicity, and systemic inflammation across the perioperative, definitive treatment, and post-acute recovery phases. Particular emphasis is placed on the limitations of body mass index-based assessment and the importance of integrating validated screening tools with context-appropriate phenotypic evaluation of muscle depletion. Beyond conventional energy replacement, we examine the evidence supporting perioperative immunonutrition, discuss the contextual limitations of immune-modulating strategies during chemoradiotherapy, and consider emerging adjunctive metabolic approaches. Mucositis is conceptualized not only as a local toxicity but also as a contributor to reduced intake and inflammation-driven catabolism. The post-treatment phase is highlighted as a critical period for continued monitoring of body composition and functional recovery. Collectively, the available evidence supports a shift from weight-centered nutritional paradigms toward an integrated, body composition-oriented and inflammation-aware framework for supportive care in head and neck oncology.}, }
@article {pmid41829913, year = {2026}, author = {Marano, G and d'Abate, C and Ianes, I and Sorrenti, G and Traversi, G and Esposito, R and Pavese, F and D'Angelo, T and Fuso, P and Franceschini, G and Paris, I and Mazza, M}, title = {The Gut Microbiota in Perimenopausal Anxiety: A Novel Therapeutic Pathway Through Diet.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829913}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Perimenopause/psychology ; Female ; *Anxiety/microbiology/diet therapy ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; *Diet ; }, abstract = {Background: Perimenopause is characterized by pronounced fluctuations in ovarian steroids, which are associated with an increase vulnerability to anxiety symptoms. Growing evidence indicates that declining estrogen levels influence gut microbiota composition and microbial metabolic activity, thereby modulating neuroimmune and neuroendocrine pathways involved in emotional regulation. This review explores gut microbiota alterations occurring during the menopausal transition and critically evaluates dietary strategies targeting microbiota-gut-brain mechanisms potentially relevant to perimenopausal anxiety. Methods: A structured literature search was conducted in PubMed, Scopus, and Web of Science to identify clinical, translational, and preclinical studies addressing: (i) gut microbiota changes across perimenopause and menopause; (ii) microbiota-gut-brain pathways implicated in anxiety; and (iii) dietary patterns, nutrients, probiotics, and prebiotics with documented microbiota-modulating effects. The available evidence was synthesized narratively, with particular attention to biological plausibility and clinical relevance. Results: The perimenopause transition is associated with reduced microbial diversity, depletion of Lactobacillus, Bifidobacterium, and short-chain fatty acid (SCFA)-producing taxa, and enrichment of pro-inflammatory microbial signatures. These alterations are linked to increased intestinal permeability, altered tryptophan-kynurenine metabolism, immune activation, and dysregulated hypothalamic-pituitary-adrenal axis activity. Dietary interventions, including Mediterranean-style diets, fiber- and polyphenol-rich foods, fermented products, and selected probiotic and prebiotic formulations, have been shown to modulate gut microbial composition, enhance SCFA production, and attenuate inflammatory and neuroendocrine stress pathways. Preliminary evidence suggests potential anxiolytic benefits; however, randomized controlled trials specifically targeting perimenopausal populations remain limited. Conclusions: Gut microbiota dysbiosis may contribute to anxiety vulnerability in perimenopausal women through interconnected immune, metabolic, and neuroendocrine mechanisms. Dietary modulation of the intestinal microbiota represents a biologically plausible and low-risk complementary approach to support emotional well-being during this transitional period. Well-designed, perimenopause-specific clinical trials are needed to confirm efficacy and inform microbiome-based nutritional strategies.}, }
@article {pmid41829917, year = {2026}, author = {Deng, W and Li, X and Hu, M and Gao, D and Huang, J}, title = {Exploring the Underlying Mechanisms of Aerobic Exercise-Improving Cardiovascular Function by Integrating Microbiome, Metabolome, and Proteome Analysis in a High-Fat Diet-Induced Obesity Rat Model.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829917}, issn = {2072-6643}, support = {2023ZDZX2033//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution/ ; 2025WCXTD012//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution/ ; 2025KQNCX035//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/physiology ; *Obesity/physiopathology/metabolism/therapy/etiology/microbiology ; *Physical Conditioning, Animal/physiology ; Male ; Rats ; *Proteome ; *Metabolome ; Disease Models, Animal ; Proteomics ; Metabolomics ; Rats, Sprague-Dawley ; }, abstract = {Objective: This study aimed to investigate the potential mechanisms by which moderate-intensity aerobic exercise improves cardiovascular dysfunction in high-fat diet-induced obese rats through integrated multi-omics analysis. Methods: Animals were assigned to three groups: normal diet, HFD, and HFD with exercise. Cardiovascular function was assessed by echocardiography and vascular tension measurement. Gut microbiota, serum metabolites, and protein expression were analyzed using 16S rRNA sequencing, untargeted metabolomics, and proteomics, respectively. Integrated multi-omics analysis was performed using Mantel tests and mediation effect analysis. Results: Eight weeks of aerobic exercise significantly improved cardiovascular function in obese rats, including enhanced acetylcholine-induced vasodilation and increased left ventricular ejection fraction. Furthermore, exercise also reshaped the gut microbiota composition, notably altering the relative abundances of Lactobacillus and Ruminiclostridium_9. Metabolomics revealed that exercise shifted the metabolic phenotype from high-fat diet-induced basal metabolic disorder toward beneficial pathways, including fatty acid biosynthesis and ubiquinone biosynthesis. Proteomics identified key differentially expressed proteins such as APOE, FN1, and Lap3. Integrated multi-omics analysis for the first time revealed a core regulatory axis: exercise may influence Lap3 expression, modulate the abundance of Lactobacillus, and thereby systematically regulate the level of palmitoyl lysophosphatidylcholine, ultimately improving cardiovascular function. Conclusions: Aerobic exercise counteracts HFD-induced cardiovascular dysfunction through systemic remodeling of the gut microbiota-host metabolism-protein network. The discovery of the Lap3-Lactobacillus-palmitoyl lysophosphatidylcholine axis provides new molecular insights into the exercise-mediated protective mechanisms of the gut-cardiovascular system axis.}, }
@article {pmid41829938, year = {2026}, author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW}, title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829938}, issn = {2072-6643}, support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Dietary Supplements ; Male ; Whey Proteins/administration &amp; dosage ; Young Adult ; Adult ; Pea Proteins/administration &amp; dosage ; *Plant Proteins/administration &amp; dosage ; Oryza ; Resistance Training ; *Soccer ; RNA, Ribosomal, 16S/genetics ; Athletes ; *Animal Proteins, Dietary/administration &amp; dosage ; Animals ; }, abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.<br><br>METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.<br><br>RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.<br><br>CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.}, }
@article {pmid41829951, year = {2026}, author = {Toderescu, CD and Parveen, M and Trifunschi, S and Oancea, A and Jurj, GCC and Cresneac, IG and Munteanu, MF and Ciopanoiu, I and Boru, C and Pogurschi, EN and Ionite, C and Stefanache, A and Lungu, II}, title = {Dietary Polyphenols as Modulators of Bifidobacterium in the Human Gut Microbiota.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829951}, issn = {2072-6643}, mesh = {Humans ; *Polyphenols/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium/drug effects ; *Diet ; Hydroxybenzoates/pharmacology ; Flavonoids/pharmacology ; }, abstract = {BACKGROUND: Polyphenols-bioactive compounds abundant in plant-based foods-are increasingly recognised for their capacity to modulate the gut microbiota. As the gut microbiome plays a central role in metabolic regulation, immune function, and disease prevention, understanding how specific polyphenol subclasses influence microbial diversity and functionality remains essential. Despite growing evidence of their benefits, the precise effects of flavonoids, phenolic acids, and anthocyanins on gut microbial composition are not yet fully clarified.<br><br>OBJECTIVE: This study aimed to evaluate the impact of dietary polyphenols on gut microbiota composition and function, with a particular focus on the abundance of Bifidobacterium, a key beneficial genus associated with metabolic and immune health. It was hypothesised that polyphenol-rich interventions were associated with increases in Bifidobacterium abundance and enhance overall microbial diversity.<br><br>DESIGN: A systematic review and meta-analysis were conducted following PRISMA guidelines. Human intervention studies published between January 2015 and February 2025 were retrieved from PubMed, Scopus, and Web of Science. A predefined PICO framework guided study selection. Twenty-two studies were synthesised using thematic analysis, and four of these were eligible for quantitative meta-analysis. The meta-analysis was performed in R (version 4.4.1) using the metafor and meta packages, calculating standardised mean differences (SMD) under a random-effects model to account for heterogeneity. Extracted data included study design, population characteristics, polyphenol subclass, intervention type, microbiome assessment method, and key outcomes.<br><br>RESULTS: Across the 22 reviewed studies, polyphenols-particularly flavonoids and phenolic acids from foods such as berries, grape pomace, and green tea-consistently increased beneficial microbial taxa including Bifidobacterium, Faecalibacterium, and Lactobacillus. These microbial shifts were associated with improved metabolic markers, reduced inflammation, and enhancements in gut barrier integrity. Polyphenol-rich dietary patterns also showed benefits in conditions such as NAFLD, prediabetes, and depression. However, findings were influenced by interindividual variability, short intervention durations, and inconsistent methodologies. The meta-analysis revealed a significant positive effect of polyphenol intake on Bifidobacterium abundance (SMD = 0.81; 95% CI: 0.18-1.44; p = 0.0114), corresponding to a moderate-to-large effect size. Substantial heterogeneity (I[2] = 77.4%) suggested considerable variation in intervention types, dosage, study design, and microbiome analysis methods.<br><br>CONCLUSIONS: Polyphenol-rich diets were associated with increased Bifidobacterium abundance and favourable modulation of gut microbiota composition, supporting their potential as a nutritional strategy to enhance gut and metabolic health. However, interstudy variability highlights the need for more standardised, long-term, and mechanistically focused human trials. Future research should incorporate multi-omics approaches, personalised nutrition frameworks, and consistent microbiome analysis methods to better understand the pathways linking polyphenol intake and host health outcomes.}, }
@article {pmid41829987, year = {2026}, author = {Menni, AE and Theodorou, H and Tzikos, G and Stavrou, G and Theodorou, IM and Semertzidou, E and Venieri, J and Ioannidis, A and Shrewsbury, AD and Kotzampassi, K}, title = {Neurocosmetics or Hype? Psychobiotic Potential of Strain-Specific Cosmeceuticals.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41829987}, issn = {2072-6643}, mesh = {Humans ; *Probiotics/pharmacology/administration &amp; dosage ; *Cosmeceuticals/pharmacology ; *Skin/microbiology/drug effects ; Skin Aging/drug effects ; Microbiota/drug effects ; }, abstract = {Background: There is increasing interest in cosmeceuticals-cosmetic regimes incorporating a specific probiotic or postbiotic strain, fully characterized genetically and phenotypically-which, when topically applied, have the ability to modulate the skin microbiome, exhibit anti-inflammatory properties and improve the overall skin appearance by reducing signs of aging. In addition, claims have been made that emotional and psychological well-being can be improved by neuroactive substances released by the probiotics in cosmeceuticals, acting via the skin-brain axis. However, claims are somewhat generalized and imprecise, and we deemed it important to look more precisely at published research relating to cosmeceuticals. There have been very few research publications on these products, identified as neurocosmetics, and they immediately provoked strong reactions from dermatologists and psychiatrists, mainly with regard to the ethical and safety aspects of their use. Objectives/Method: The present strain-centered literature evaluation aimed to select from peer-reviewed publications referring to cosmeceuticals only those dealing with fully characterized, specific probiotic strains with documented beneficial skin properties. Eligible strains found were subsequently subjected to a secondary search to ascertain whether they also demonstrated clinical, or even experimental, evidence of strain-specific psychobiotic properties. Results: From 33 strain-specific cosmeceuticals identified, only three strains-Lactococcus lactis subsp. cremoris H61, Limosilactobacillus reuteri DSM 17938, and Weizmannia coagulans MTCC 5856-demonstrated reproducible evidence of psychobiotic potential. Conclusions: Current evidence does not support the notion that cosmeceuticals are likely to directly modulate emotional states through topical application, since the coexistence of cosmeceutical and psychobiotic properties within the same probiotic strain seems to be both uncommon and highly strain-specific and therefore of little practical, generalized use.}, }
@article {pmid41830018, year = {2026}, author = {Benslimane, FM and Alser, M and Elgamal, AM and Mohammed, LI and Zakaria, ZZ and Sokary, S and Sohail, MU and Hammad, AS and Abbasi, SA and Al-Asmakh, M}, title = {Structured Exercise Modulates Gut Microbiota Composition and Protects Against Diet-Induced Dysbiosis in a Rat Model.}, journal = {Nutrients}, volume = {18}, number = {5}, pages = {}, pmid = {41830018}, issn = {2072-6643}, support = {QUCP-CHS-2019-2//Qatar University/ ; QUST-1-CHS-2024-1813//Qatar University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/prevention &amp; control/microbiology/etiology ; *Physical Conditioning, Animal/physiology ; Rats, Wistar ; *Diet, High-Fat/adverse effects ; Male ; Rats ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Disease Models, Animal ; Bacteria/classification ; }, abstract = {Background/Objectives: Dietary composition and physical activity are major determinants of gut microbiome structure, and dysbiosis is strongly associated with metabolic disorders. While both diet and exercise independently influence the gut microbiome, their interactive effects-particularly across different exercise modalities-remain incompletely understood. This study investigated the combined effects of diet type (normal chow [NC] vs. high-fat diet [HFD]) and exercise modality (control [C], voluntary [V], and forced [F]) on gut microbiota composition in rats. Methods: Sixty-three Wistar rats were randomized into six groups according to diet and exercise status. Fecal samples were collected and analyzed using full-length 16S rRNA gene sequencing (Oxford Nanopore Technologies). Alpha and beta diversity metrics were calculated, and taxonomic composition was assessed at phylum and genus levels. Results: HFD groups exhibited significantly higher alpha diversity than NC groups (Shannon index: 3.47-3.63 vs. 2.76-2.94, p < 0.001), with forced exercise associated with a greater diversity than voluntary exercise. Beta-diversity analysis confirmed diet as the dominant factor influencing microbial structure (PERMANOVA p = 0.001), with exercise providing an additional modulatory effect. Firmicutes, Bacteroidota, Deferribacterota, and Proteobacteria predominated, with Firmicutes decreasing under HFD. Forced exercise significantly enriched beneficial genera, including Akkermansia (detected exclusively in exercised HFD groups; p = 0.03), Blautia, Coprococcus, and Roseburia. Akkermansia abundance correlated positively with exercise distance (p < 0.001) and negatively with body weight (p < 0.01). Conclusions: Structured exercise, particularly forced treadmill training, attenuates HFD-associated dysbiosis and promotes the beneficial gut bacteria that is associated with metabolic health. These findings highlight exercise modality as a critical factor in dietary strategies targeting gut microbiome modulations.}, }
@article {pmid41830102, year = {2026}, author = {Guan, Y and You, C and Sun, T and Nong, C and Wu, Z and Xu, Y and Shen, Q and Wei, Z}, title = {Stillage-based reductive soil disinfestation with organic materials reshapes the microbiome of continuous tomato soil and suppresses Fusarium wilt.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70727}, pmid = {41830102}, issn = {1526-4998}, support = {//This work was supported by the Anhui Provincial Postdoctoral Research Project (2024A778), the Jiangsu Province Excellent Postdoctoral Program (2024ZB584), the National Natural Science Foundation of China (32500093), the China Postdoctoral Science Foundation (2025M772497), and the National Key Research and Development Program of China (2024YFC3406003 and 2022YFC3501501)./ ; }, abstract = {BACKGROUND: Reductive soil disinfestation (RSD) can suppress soil-borne diseases in continuous cropping systems, yet the effectiveness of stillage and distillers' grains and the soil mechanisms associated with their use in tomato remain unclear. Here, we tested stillage-based RSD with or without solid amendments (distillers' grains, corn straw or sheep manure) and assessed plant performance, soil properties, enzymes activities and microbial community responses.<br><br>RESULTS: All RSD treatments increased tomato biomass and reduced the disease index. RSD increased soil pH, ammonium nitrogen (NH4 [+]-N), available phosphorus (AP) and labile organic carbon, while decreasing nitrate nitrogen. Bacterial communities were strongly reshaped, with enrichment of Firmicutes, Bacteroidota, and anaerobic fermenters (e.g. Proteiniphilum, Azospira) and depletion of Nitrospira and Fusarium. NH4 [+]-N, AP and pH were associated with microbial community composition and plant performance. Canonical correspondence analysis (CCA) and Mantel tests indicated that these variables were among the soil properties most closely linked to microbial community patterns and tomato growth under RSD.<br><br>CONCLUSION: Our findings demonstrate that stillage-based RSD, when co-applied with distillers' grains, sheep manure, or corn straw, effectively mitigates tomato continuous-cropping obstacle and promotes the valorization of liquor by-products by reconstructing a beneficial soil microbe-plant-nitrogen network. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid41830215, year = {2026}, author = {Halpin, AL and McDonald, LC}, title = {Uncovering the Hidden Impacts of Modern Medicine's Expanding Pharmacopeia on Clostridioides difficile Infection Risk.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag011}, pmid = {41830215}, issn = {1537-6613}, }
@article {pmid41830216, year = {2026}, author = {Brown, KA and Coburn, B and Hernandez, A and Langford, BJ and Leung, V and MacFadden, D and Rooney, AM and Schwartz, KL and Daneman, N}, title = {Antibiotic and Nonantibiotic Drugs Associated With Clostridioides difficile Infection Risk: a Pharmacopoeia-Wide Case-Cohort Study.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag001}, pmid = {41830216}, issn = {1537-6613}, abstract = {BACKGROUND: Clostridioides difficile infection (CDI) is principally precipitated by antibiotics, due to their disruption of gut commensal bacteria. The comparative role of nonantibiotic drugs is poorly characterized.<br><br>METHODS: We examined the contribution of antibiotic and nonantibiotic drugs to CDI risk among residents age >65 years old and not hospitalized in the prior 30 days, between 2018 and 2023. The study used a case-cohort study design, with logistic regression analysis. The case definition consisted of first incident CDI, identified using comprehensive C. difficile testing, hospitalization, and treatment data. Outpatient oral drug exposures were measured in a 1-90-day window prior to case and control days. Adjusted regression models included covariates for age, sex, year and quarter, region, comorbid conditions, healthcare exposures, and drug exposures.<br><br>RESULTS: Among 16 196 CDI case patients and 549 831 controls, 335 drugs were included. After adjustment, the antibiotics amoxicillin-clavulanate (odds ratio [OR], 6.05 [95% confidence interval (CI), 5.69-6.43]), clindamycin (16.83 [15.53-18.24]), ciprofloxacin (3.83 [3.59-4.09]), and cephalexin (3.05 [2.86-3.25]), were the largest contributors to CDI risk. Nonantibiotic drugs pantoprazole (OR, 1.33 [95% CI, 1.27-1.39]) and ferrous fumarate (1.71 [1.61-1.82]) were the next largest. Metformin had a protective association (OR, 0.67 [95% CI, .63-.72]). In a meta-regression on a subset of 182 drugs, in vitro anticommensal activity was positively associated with CDI risk (P < .001).<br><br>CONCLUSIONS: This study provides insights into CDI etiology and avenues for stewardship and drug repurposing to combat CDI and antimicrobial resistance.}, }
@article {pmid41830530, year = {2026}, author = {Bahia, W and Soltani, I and Ferchichi, S and Almawi, WY}, title = {Mechanisms and Therapeutic Implications of Microbiome-Mediated Immune Dysregulation in Recurrent Pregnancy Loss and Implantation Failure.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {3}, pages = {e70219}, pmid = {41830530}, issn = {1600-0897}, mesh = {Humans ; Female ; *Abortion, Habitual/immunology/microbiology ; Pregnancy ; *Dysbiosis/immunology ; *Gastrointestinal Microbiome/immunology ; Embryo Implantation/immunology ; Animals ; Immune Tolerance ; *Microbiota/immunology ; }, abstract = {PROBLEM: Recurrent pregnancy loss (RPL), defined as two or more consecutive pregnancy losses before 20 weeks of gestation, affects 1%-5% of couples of reproductive age worldwide. Growing evidence indicates a role for the microbiome in reproductive health, particularly in unexplained RPL.<br><br>METHOD OF STUDY: Based on a review of literature from PubMed, EMBASE, and Web of Science databases from January 2020 to September 2025, this comprehensive overview explores the current understanding of the link between microbiome dysbiosis and RPL.<br><br>RESULTS: Microbiome dysbiosis, especially a reduction in Lactobacillus dominance and increased diversity, is strongly linked to RPL across multiple reproductive sites. RPL is associated with the loss of protective Lactobacillus crispatus and a higher presence of potentially harmful bacteria, including Gardnerella vaginalis and Atopobium vaginae. An altered gut microbiome, particularly with lipopolysaccharide-producing gram-negative bacteria, contributes to systemic inflammation and immune dysfunction by disrupting maternal-fetal immune tolerance. The microbiome-immune axis is essential for establishing maternal-fetal tolerance, with dysbiosis promoting pro-inflammatory Th1/Th17 responses while suppressing regulatory T cells. Multiple mechanisms connect microbiome dysbiosis to RPL, including local inflammation, systemic immune issues, disruption of maternal-fetal immune tolerance, molecular mimicry, and autoimmunity.<br><br>CONCLUSIONS: The microbiome is a promising new target for RPL treatment, with personalized microbial profiling and targeted therapies showing potential to improve pregnancy outcomes. Clinical implementation requires standardized protocols, larger randomized controlled trials, and validation of microbiome-targeted interventions.}, }
@article {pmid41830551, year = {2026}, author = {Wang, Y and Huang, B and Wei, X and Guan, Y and Li, L and Zheng, Y and Sun, W}, title = {Gut microbiota metabolic reprogramming drives the development of metabolic diseases in the host.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2644681}, doi = {10.1080/19490976.2026.2644681}, pmid = {41830551}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Metabolic Diseases/microbiology/metabolism ; Animals ; *Dysbiosis/microbiology/metabolism ; Bacteria/metabolism/genetics/classification ; Metabolic Networks and Pathways ; Lipid Metabolism ; Metabolic Reprogramming ; }, abstract = {Metabolic diseases pose a major global health challenge, the pathogenesis of which centers on "metabolic reprogramming"; that is, the adaptive or pathological rewiring of metabolic pathways. Emerging evidence indicates that gut microbiota dysbiosis triggers its metabolic reprogramming prior to host disease onset and plays a pivotal role in the development of metabolic disorders. However, unlike host metabolic reprogramming, which has been well characterized, the pathogenic mechanisms resulting from gut microbiota metabolic reprogramming remain poorly understood, creating a critical knowledge gap regarding its role in systemic metabolic diseases. To address this gap, this review introduces the concept of gut microbiota metabolic reprogramming and establishes its foundational role in systemic metabolic disease. We propose that gut microbiota metabolic reprogramming constitutes an early pathogenic event, preceding and potentially driving subsequent metabolic alterations in the host. Within this framework, we systematically reveal that an imbalance in the gut microbiota leads to its significant metabolic reprogramming, including lipid, glucose, amino acid, and uric acid metabolism, which in turn regulates host-wide metabolic and immune homeostasis and contributes to the development of metabolic diseases. By integrating these mechanisms into a coherent model, our work provides a novel paradigm for understanding metabolic regulation. This model refines the fundamental pathophysiology of metabolic disorders and highlights new possibilities for targeting the microbiome for the prevention and treatment of metabolic disorders.}, }
@article {pmid41830747, year = {2026}, author = {Li, Z and Yue, Z and Gu, J and Wang, S and Zhang, L and Yu, Z and Deng, R and Wang, J}, title = {Hidden acidification beneath soil-covered mine waste dumps: links to oxygen-limited sulfur oxidation.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129292}, doi = {10.1016/j.jenvman.2026.129292}, pmid = {41830747}, issn = {1095-8630}, abstract = {Soil covering is widely applied in mine-site restoration to suppress sulfide oxidation by limiting oxygen diffusion and promoting the enrichment of sulfate-reducing bacteria. However, increasing evidence indicates that acidification can recur beneath soil covers, raising concerns about the long-term stability of restored mine sites. In this study, we combined geochemical profiling with microbial community and ecological assembly analyses to investigate the processes associated with subsurface acidification in soil-covered waste dumps. Our results show that, despite initial lime neutralization, strong acidity re-emerged in amended layers within two years (pH < 4), accompanied by elevated metal (loid) bioavailability and upward acid migration. These geochemical changes were associated with a restructuring of the microbial community toward acidophilic taxa, including Sulfobacillus and Acidithiobacillus, and an increased representation of sulfur-related metabolic potentials inferred from functional prediction. Null model and network analyses further revealed a shift toward more deterministic community assembly and tightly connected microbial networks under low-pH conditions. Together, these findings suggest that subsurface acidification beneath soil covers is sustained by coupled geochemical processes and a specialized acidophilic microbiome. This study provides insight into the mechanistic underlying soil-cover restoration failure and highlights the need for restoration strategies that integrate long-term geochemical control with microbial process management.}, }
@article {pmid41830789, year = {2026}, author = {Zhang, Y and Wang, X and Feng, G and Zheng, J and Sang, A and Jiang, J and Wu, J}, title = {Longitudinal Characterization of Gingival Microbiota Following Periodontally Accelerated Osteogenic Orthodontics Surgery in Skeletal Class III Orthognathic Patients.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109475}, doi = {10.1016/j.identj.2026.109475}, pmid = {41830789}, issn = {1875-595X}, abstract = {OBJECTIVE: Periodontally accelerated osteogenic orthodontics (PAOO) combines selective alveolar decortication with orthodontic force to accelerate tooth movement, but its influence on the gingival crevicular fluid (GCF) microbiome and early periodontal condition remains unclear.<br><br>METHODS: In this repeated-measures, within-subject longitudinal study, 18 GCF samples were collected from 6 skeletal class III orthognathic patients at baseline (A0), 2 weeks after PAOO (A2), and 4 weeks post-PAOO coinciding with 2 weeks of active orthodontic force application (A4). Microbiota were profiled by 2bRAD-M sequencing, and periodontal indices (plaque index, bleeding index, probing depth, keratinized gingiva width) were recorded.<br><br>RESULTS: Periodontal indices remained stable with no significant increase in plaque, bleeding, or probing depth; notably, keratinized gingiva width increased significantly at A2 and A4. &#x3b1;-diversity showed stable richness but reduced evenness at A4. &#x3b2;-diversity demonstrated progressive shifts, with A2 as a transitional stage. Multi-level taxonomic analysis was performed to characterize temporal changes in microbial community structure during treatment progression. At the phylum level, Proteobacteria remained dominant throughout the study, followed by Firmicutes, Actinobacteriota, and Bacteroidota. Genus-level analysis revealed core genera including Neisseria, Streptococcus, and Prevotella, while species-level comparison showed that Haemophilus parainfluenzae and Actinomyces oris were present across timepoints with varying abundance. LEfSe analysis identified stage-specific microbial markers across A0/A2/A4. Functional prediction suggested potential involvement in lysine biosynthesis, necroptosis, &#x3b2;-lactam resistance, and immune signalling pathways.<br><br>CONCLUSIONS: In this pilot repeated-measures cohort, PAOO combined with early orthodontic force was associated with distinct temporal changes in the GCF microbiome while maintaining overall periodontal stability and increasing keratinized gingiva width. Predicted functional shifts may be relevant to host responses during early healing; however, mechanistic inferences require confirmation in larger longitudinal studies.}, }
@article {pmid41830828, year = {2026}, author = {Chen, Y and Qi, Z and Yin, L and Chang, F and Ju, H and Jing, H and Diao, X}, title = {Multi-level holobiont dysregulation increases the ecological risk of combined ocean acidification and benzo[a]pyrene pollution to the reef-building coral Porites lutea.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141743}, doi = {10.1016/j.jhazmat.2026.141743}, pmid = {41830828}, issn = {1873-3336}, abstract = {Reef-building corals are increasingly threatened by the combined effects of global climate change and localized organic pollutants. However, the holistic impacts of co-exposure to ocean acidification (OA) and benzo[a]pyrene (BaP) on coral holobionts remain poorly understood. Here, we investigated the multi-level responses of the reef-building coral Porites lutea to short-term (7-day) exposure to OA (pH 7.80), BaP (10 µg/L), and their combination, by integrating physiological measurements with microbiome profiling (ITS2 and 16S rRNA). We found that combined stress was associated with a dysregulated response in Symbiodiniaceae, characterized by a significant increase in cell density without a parallel rise in chlorophyll content, suggesting a possible compensatory but inefficient proliferation response. Despite this, the dominant symbiont Cladocopium C15 remained stable. The bacterial diversity increased (e.g., enrichment of Ruegeria and Acanthopleuribacter, decline of Endozoicomonas), which may suggest enhanced functional redundancy, while the archaeal community was significantly restructured, most notably a marked decline of the putative obligate Nanoarchaeota-Halobacterota symbiosis. At the host level, combined stress was associated with suppressed antioxidant enzyme activities (SOD/POD) but upregulated genes related to protein folding (Hsp90) and calcium homeostasis (NCX1, VAMP4). These findings suggest a complex holobiont reconfiguration under combined stress, involving a stabilized core symbiont, altered microbiomes, and a shifted host defense strategy. Our study suggests that the ecological risk of combined OA and organic pollution may not be extrapolated from single-stressor responses, indicating the need to incorporate multi-stressor frameworks into coral reef risk assessments.}, }
@article {pmid41830897, year = {2026}, author = {Huang, J and Zhou, D and Sun, H and Hong, X and Huang, Y and Chen, W and Zhu, H and Wang, X and Yang, Y and Liu, C}, title = {Seasonal dynamics of host-associated microbiome and potential human pathogen in Crassostrea ariakensis and Perna viridis.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119540}, doi = {10.1016/j.marpolbul.2026.119540}, pmid = {41830897}, issn = {1879-3363}, abstract = {The microbial communities and foodborne pathogenic bacteria in bivalves have long been topics of interest due to their fundamental economic and ecological roles. This study investigated the seasonal dynamics of microbial composition and foodborne pathogen loads in the gills and visceral mass of Crassostrea ariakensis and Perna viridis, cohabiting the same aquatic environment. Both bivalve species exhibited higher bacterial richness and diversity than the surrounding water. They shared 5682 ASVs, accounting for over 50% of total ASVs. Core microbiota in both species was dominated by Firmicutes and Proteobacteria, though P. viridis gills showed higher Spirochaetota abundance. At the family level, Lactobacillaceae and Acetobacteraceae were predominant in June but decreased markedly in other months. Spirochaetaceae relative abundance was consistently higher in P. viridis than in C. ariakensis. C. ariakensis exhibited a greater relative abundance of potential pathogens (up to 10.75%), primarily Escherichia-Shigella and Bacteroides, whereas P. viridis was dominated by Lactiplantibacillus and Escherichia-Shigella. Plate counting identified V. parahaemolyticus and V. vulnificus as the dominant culturable foodborne bacteria, with higher abundances in March and December. The visceral mass often harbored higher bacterial levels than gills. Potential pathogen profiles from 16S rRNA data were influenced by temperature, pH, chlorophyll-a, ammonia nitrogen, and phosphate, whereas total culturable bacteria were affected by all measured factors except chlorophyll-a. Temperature and nitrate significantly influenced V. vulnificus abundance in both bivalves. This study highlights how host species, tissue type, season, and environmental factors interact to shape bivalve-associated microbiomes and pathogen prevalence, providing insights for seafood safety management.}, }
@article {pmid41830975, year = {2026}, author = {Hesarooeyeh, ZG and Khalili, E and Michel, TM and Vafaee, MS}, title = {The pathogenic role of gut microbiota dysbiosis in Alzheimer's disease: a narrative review of neuroimaging evidence.}, journal = {Journal of neural transmission (Vienna, Austria : 1996)}, volume = {}, number = {}, pages = {}, pmid = {41830975}, issn = {1435-1463}, }
@article {pmid41831181, year = {2026}, author = {Jankowski, WM and Fichna, J and Tarasiuk-Zawadzka, A}, title = {Can Nutrition Modulate the Progression of Alzheimer's Disease? A Narrative Review.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {41831181}, issn = {2161-3311}, support = {#503/1-156-04/503-11-001//Uniwersytet Medyczny w Lodzi/ ; }, }
@article {pmid41831243, year = {2026}, author = {Wang, J and Zhao, W and Zhu, S and Huang, K and Zhang, Y and Cheng, H and Ma, Q and Song, D and Liu, J and Zhang, XH and Wang, X}, title = {Vertical distribution pattern, preferred life strategies and environmental response of prokaryotic microbiome in the eastern tropical indian ocean.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107979}, doi = {10.1016/j.marenvres.2026.107979}, pmid = {41831243}, issn = {1879-0291}, abstract = {The eastern tropical Indian Ocean (ETIO) features strong water stratification that forms typical oligotrophic conditions, making it an ideal region to study the environmental response of microbes. However, there is still a lack of understanding the vertical distribution patterns of prokaryotic microbiome with different lifestyles. In this study, we investigated the abundance, diversity, and distribution characteristics of free-living (FL) and particle-associated (PA) microorganisms along depth in the ETIO. Microbial abundance and alpha diversity indices decreased significantly with depth, dropping from 7.45 ± 1.20 to 6.35 ± 0.42 lg copies/L (FL) and from 5.72 ± 0.43 to 5.17 ± 0.43 lg copies/L (PA), respectively. The community composition and network complexity showed significantly vertical differentiation. Several bacteria become depth-specific microbial indicators, i.e., Cyanobacteria and Rhodospirillaceae in the mixed layer (<100m; SL), SAR324 clade and Salinisphaeraceae enriched in the mesopelagic zone (100-1,000m; mesopelagic zone, ML), whereas Acidobacteriota, Gemmatimonadota and Alteromonadaceae in the deep layer (>1,000m; bathypelagic layer, BL). The clustered patterns of microbes were mainly affected by temperature, salinity and dissolved oxygen (DO) in SL, and shifted toward dominance by stochastic processes with increasing depth. Our findings reveal strategies of microbes with different lifestyles to adapt to stratified marine environments through community restructuring, providing a theoretical basis for assessing their ecological roles in biogeochemical cycles.}, }
@article {pmid41831436, year = {2026}, author = {Liang, S and Sun, Y and Miao, Z and Li, BY and Xing, Z and Xie, Y and Cai, E and Li, S and Liu, P and Yang, M and Shuai, M and Gou, W and Jiang, W and Wang, Y and Gao, H and Zhang, K and Yu, J and Cai, X and Wang, X and Zhu, Y and Chen, YM and Zheng, JS and Guo, T}, title = {Large-scale metaproteomics of human gut microbiota reveals microbial functions in metabolic diseases and aging.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2026.02.012}, pmid = {41831436}, issn = {1932-7420}, abstract = {The protein-level functionalities of the human gut microbiota in large populations, and their associations with host factors, remain unexplored. This study reports a metaproteomic study of 1,967 fecal samples from 1,399 middle-aged and elderly Chinese individuals, identifying microbial functions linked to 44 phenotypes. We uncover aging-associated functional shifts in carbon metabolism and energy production driven by species within the Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota. Across metabolic diseases, we observe the consistent depletion of Bacillota species and their proteins involved in carbohydrate, energy, amino acid metabolism, and short-chain fatty acid production. We also identify medication-associated features across diabetes, hypertension, and dyslipidemia. Validated in an independent cohort, Megasphaera elsdenii emerged as a hub species in type 2 diabetes. Experimental validation indicates that M. elsdenii is promoted by antidiabetic drugs and may regulate glucose homeostasis through butyrate production. This study provides protein-level evidence of microbial functions in health and disease, highlighting potential therapeutic targets.}, }
@article {pmid41831475, year = {2026}, author = {Figueroa, AG and Joshi, CN and Patel, MN}, title = {From clinical practice to mechanistic insights in ketogenic diets for epilepsy.}, journal = {The Lancet. Neurology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1474-4422(26)00008-6}, pmid = {41831475}, issn = {1474-4465}, abstract = {Ketogenic diet therapies, including the classic ketogenic diet, modified Atkins diet, and low glycaemic index treatment, have shown effectiveness in controlling seizures, in part by shifting metabolism from glucose to ketone bodies. They improve mitochondrial function, reduce neuroinflammation, and modulate neurotransmitters. Ketogenic diet therapies also affect the gut microbiome, potentially impacting neurotransmitter balance in ways that contribute to seizure control. A classic ketogenic diet is effective yet restrictive, whereas the modified Atkins diet and low glycaemic index treatment offer greater flexibility, tolerability, and ease of implementation, particularly in resource-limited settings. Cochrane reviews and meta-analyses rank the certainty of randomised controlled trial evidence for ketogenic diet therapies as limited. Early initiation of ketogenic diet therapies, particularly in children or patients with metabolic epilepsies, improves seizure outcomes, potentially preventing further mitochondrial and neuronal damage and reducing the risk of developing resistance to antiseizure medications. Research using rigorous, large-scale comparative effectiveness study designs that accounts for differences in age, epilepsy type, dietary therapy modality, sociodemographic background, care delivery contexts, and that minimises performance and observation bias is needed to resolve remaining uncertainties regarding the efficacy and real-world challenges of ketogenic diet therapies in epilepsy.}, }
@article {pmid41831535, year = {2026}, author = {Chen, J and Xiao, C and Cao, M and Hu, Y and Yan, Y and Tong, J and Cheng, C and Huang, J}, title = {Association between gut virome and prenatal stress-induced changes in behavior and immune responses in male offspring.}, journal = {Brain, behavior, and immunity}, volume = {135}, number = {}, pages = {106532}, doi = {10.1016/j.bbi.2026.106532}, pmid = {41831535}, issn = {1090-2139}, abstract = {Maternal stress during gestation is associated with an increased risk of neurodevelopmental disorders in offspring. The gut-brain axis is considered a potential mediating pathway. As a key component of the gut microbiome, the bacteriophages can remodel bacterial community structure and function. However, whether gut viruses contribute to prenatal stress-induced behavioral alterations in offspring remains unclear. Here, we reported that prenatal stress induces anxiety-like behaviors and alters the gut virome and bacteriome specifically in male offspring. By comparing the gut virome and bacteriome between dams and their offspring, we found that the gut microbial profile of male offspring is more similar to that of their mothers than that of female offspring. To investigate whether changes in the gut virome are causally linked to stress-related behavioral or physiological outcomes, we transplanted gut viromes from control offspring into the offspring exposed to maternal prenatal stress. The results showed that transplantation of the gut virome from control offspring alleviated anxiety-like behaviors, restored the gut microbiome, and modulated immune responses in prenatally stressed offspring. Our findings highlight the critical role of gut bacteriophages in mediating prenatal stress-induced behavioral changes and demonstrate that fecal virome transplantation (FVT) can mitigate such alterations. Thus, we establish a causal link between prenatal stress, the gut virome, immune function, and behavior, pointing to FVT as a potential therapeutic strategy for certain neurodevelopment-related behavioral abnormalities.}, }
@article {pmid41831647, year = {2026}, author = {Tashiguano, VM and Sierra, K and Black, T and Sirmon, M and Leeds, P and Jones, J and Doster, J and Smith, C and Jia, Z and Garner, L and Cho, S and Hanna, J and Trout, K and Almasri, M and Li, H and Morey, A}, title = {A Multidisciplinary Approach for Predicting the Microbiological Spoilage of Chicken Breast Fillets due to Cold-chain Disruption.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100754}, doi = {10.1016/j.jfp.2026.100754}, pmid = {41831647}, issn = {1944-9097}, abstract = {Cold-chain disruptions during storage and distribution of raw poultry can significantly reduce product shelf-life and safety. This study evaluated the effects of short-term cyclic temperature abuse (TA) on the retail shelf-life of fresh chicken breast, using a multidisciplinary approach that combined food microbiology, machine learning (ML), metagenomics, and volatile compound (VC) analysis. Boneless, skinless chicken breast trays (n = 450) were obtained from a commercial poultry processor and transported under refrigeration (4°C) to Auburn University. In three independent trials, trays were randomly assigned to one of three treatments: (1) Control at 4°C for 24 h; (2) TA Cycle 1: alternating 30 min at 4°C and 1 h at 30°C; and (3) TA Cycle 2: alternating 30 min at 4°C and 1 h at 37°C. TA cycles lasted 7.5 h, after which all trays were stored at 4°C. Samples were analyzed on days 0, 2, 4, 6, and 8 for aerobic, facultative anaerobic, and lactic acid bacteria (LAB) counts, and for VCs using an electronic nose. Rinsates from Trial 3 were stored at -80°C for metagenomic analysis. TA Cycle 2 resulted in the highest spoilage rates, followed by TA Cycle 1. A neural network model moderately predicted bacterial growth (R[2] = 0.65-0.75 for aerobic and facultative anaerobic microorganisms; lower for LAB). Metagenomics demonstrated a shift toward Pseudomonas spp. dominance under TA conditions, while control samples retained microbial diversity. These findings underscore that even short-term TA significantly alters the microbiome and accelerates spoilage in raw poultry, emphasizing the importance of cold-chain integrity. Practical Relevance. This study shows that short, high-temperature abuse events from refrigeration failure, handling delays, or other supply chain disruptions can accelerate spoilage in raw chicken. By combining rapid spoilage-detection tools with predictive models, poultry producers and retailers may better monitor these events, helping to maintain cold-chain integrity and reduce losses.}, }
@article {pmid41831719, year = {2026}, author = {Shen, CL and Elmassry, MM and Kahathuduwa, C and Lee, J and Day, MR and Edwards, DS and Parmar, H and Wager, TD and Liu, X and Baccus, M and Hamood, A and Neugebauer, V}, title = {Influence of Ginger Root Extract Supplementation on the Microbiota-Gut-Brain Axis in Individuals with Sciatica: Study Protocol for a Double-Blind, Placebo-Controlled Randomized Trial.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {103117}, doi = {10.1016/j.clnesp.2026.103117}, pmid = {41831719}, issn = {2405-4577}, abstract = {Neuropathic pain (NP) is caused by damage to the peripheral or central nervous system and is associated with adverse complex sensory and affective symptoms. There are few current treatment options for NP, and opioid analgesics have severe side effects which can lead to opioid abuse. Therefore, the development of innovative, effective, and safe alternatives is urgently needed. This study will assess the effects of ginger root extract's anti-inflammatory and anti-oxidant properties on individuals with sciatica via the microbiome-gut-brain axis. Eighty participants (18-85 years) with chronic sciatica, classified as lean (n=40, BMI <25 kg/m[2]) or obese (n=40, BMI ≥30 kg/m[2]), will be stratified by age, sex, and BMI to receive 2,000 mg/day of ginger extract or placebo for eight weeks. Primary outcomes are pain-associated outcomes and brain neuroplasticity by assessing functional (resting state-fMRI) and structural (Diffusion Tensor Imaging) connectivity. Secondary outcomes include gut function (gut microbiota composition using 16S rRNA sequencing analysis, intestinal permeability assessing concentrations of plasma lipopolysaccharide binding protein and fecal zonulin, and fecal metabolites using LC-MS/MS analysis) and neuroinflammation: nCounter® Neuroinflammation Panel analysis. We will evaluate outcomes at baseline and end of study. We will employ intention-to-treat principle and per-protocol for data analysis. Hierarchical linear modeling is utilized to estimate ginger supplementation's effects while properly accounting for data dependency and identified covariates. This study was approved by the Bioethics Committee of the Texas Tech University Health Sciences Center, Lubbock, TX. Participants will sign an informed consent form before enrolling in the study. Our team will actively disseminate the results from this trial through academic conference presentations and peer-reviewed journals. We are now actively recruiting subjects for this study. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT06817018.}, }
@article {pmid41831799, year = {2026}, author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P}, title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {449}, number = {}, pages = {134410}, doi = {10.1016/j.biortech.2026.134410}, pmid = {41831799}, issn = {1873-2976}, abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.}, }
@article {pmid41831878, year = {2026}, author = {Yang, S and Li, Y and Zong, C and Pan, X and Wang, H and Fang, Q and Shi, L and Dong, F and Cao, H}, title = {LDH-based avermectin nanopesticide modulates bioaccumulation, antioxidant responses, and microbiota stability in earthworms' gut.}, journal = {Pesticide biochemistry and physiology}, volume = {219}, number = {}, pages = {107010}, doi = {10.1016/j.pestbp.2026.107010}, pmid = {41831878}, issn = {1095-9939}, mesh = {Animals ; *Ivermectin/analogs &amp; derivatives/toxicity/pharmacology/chemistry ; *Oligochaeta/drug effects/microbiology/metabolism ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; Oxidative Stress/drug effects ; *Nanoparticles/chemistry ; *Pesticides/toxicity/chemistry/pharmacology ; *Insecticides/toxicity ; }, abstract = {Nanopesticides offer a promising route to improve the safety and environmental performance of conventional agrochemicals by leveraging their small size and structured surfaces to modify behavior within the earthworm gut. Here, a Mg/Al-LDH nanocarrier loaded with avermectin (LDHs-AVM) was synthesized and characterized by plate-like, hexagonal morphology with nanoscale dimensions (<100 nm). Earthworm bioaccumulation assays showed that LDHs-AVM, despite slightly lower peak tissue levels than AVM (0.13-0.17 and 0.15-0.20 mg/kg), persisted longer, indicating formulation-dependent enhancement of stability. Consistent with these kinetic profiles, histopathology revealed that AVM induced severe epidermal and intestinal lesions, whereas LDHs-AVM caused only mild structural disturbances, demonstrating substantial attenuation of tissue toxicity. Gut biomarker assays further showed reduced oxidative damage and enhanced antioxidant/detoxification responses under LDHs-AVM exposure, confirming mitigation of AVM-induced oxidative stress. Fluorescence imaging demonstrated strong intestinal enrichment of LDHs-AVM with limited systemic diffusion, supporting gut-targeted biodistribution (0.094 and 0.041 mg/kg). At the microbiome and transcriptome levels, NGS profiling showed that LDHs-AVM enhanced microbial diversity while AVM caused marked dysbiosis, and RNA-seq indicated far fewer DEGs with suppression of AVM-activated PI3K-AKT/MAPK stress pathways, together evidencing mitigation of AVM-induced molecular disruption. Collectively, these results demonstrated that LDHs-AVM reduces toxicity, preserves gut microbial homeostasis, and enhances intestinal protection in Eisenia fetida, establishing an integrated framework for nanopesticide safety assessment and highlighting LDH-based systems as promising platforms for sustainable and environmentally responsible agrochemical design.}, }
@article {pmid41832088, year = {2026}, author = {Schwalbe, M and Bosch, T and El Aidy, S}, title = {Gut motility as a driver of microbial community architecture and host-microbe evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.12.016}, pmid = {41832088}, issn = {1878-4380}, abstract = {Digestive systems are dynamic, contractile ecosystems that continually shape the physical and chemical niches inhabited by gut microbes. Patterns of mixing and propulsion generate flow, shear, and nutrient gradients that select for microbial traits such as adhesion, biofilm formation, and metabolic timing. Microbial metabolites, in turn, influence smooth muscle excitability and enteric neural circuits, creating bidirectional feedback that structures microbial communities and affects host physiology. We argue that gastrointestinal motility, an ancient and nearly universal feature of metazoan digestive systems, functions as an evolutionary scaffold, linking microbial spatial organization with host neuromuscular diversification. Comparative evidence from cnidarians to mammals highlights how these interactions have shaped both microbial ecology and host adaptation, with relevance for understanding modern dysmotility-microbiome disorders.}, }
@article {pmid41832138, year = {2026}, author = {Li, G and Liu, T and Chuai, H and Ma, H and Yang, Z and Xu, Y and Li, H and Shen, Q and Hu, F and Geisen, S and Jousset, A and Wei, Z and Hogle, S}, title = {Predator-driven microbial feedback loops promote plant health.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70413-3}, pmid = {41832138}, issn = {2041-1723}, support = {42577332//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Top-down trophic interactions are major drivers of microbiome dynamics, yet their outcomes are difficult to predict and their consequences for pathogen control remain unclear. We combine synthetic bacterial communities of varying complexity with field studies and microcosm assays to test whether microbivorous nematodes reorganize microbiomes to suppress soilborne disease. Field studies show stronger nematode-microbe associations around healthy plants, and microcosm assays confirm that nematode presence produces stable suppression, whereas microbe-only communities collapse under pathogen invasion. Nematode predation depletes non-preferred bacterial taxa and enriches metabolically versatile taxa within Proteobacteria, increasing community-level antagonistic potential and promoting complementary resource-use interactions linked to pathogen inhibition, yielding suppression beyond individual or pairwise effects. A minimal four-component feedback loop linking a nematode predator, plant pathogens, and two plant-associated bacteria with complementary functions accounts for the emergent outcome. Together, these results reveal an animal-mediated pathway of microbiome assembly that enhances resistance to pathogen invasion and provide a trophically informed framework for designing stable, disease-suppressive microbiomes in agriculture.}, }
@article {pmid41832256, year = {2026}, author = {Mendes, K and Gomes, ATPC and Resende, CMM and Ribeiro, IS and Oliveira, RMC and Rosa, N and Muniz, MTC and Correia, MJ}, title = {Standardizing oral microbiome sampling for qPCR: methodological and exploratory insights into nutritional status.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-43909-7}, pmid = {41832256}, issn = {2045-2322}, support = {CEECINST/00070/2021-CIIS-J&#xfa;nior//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04279/2025 and DOI identifier https://doi.org/10.54499/UID/04279/2025 - Centro de Investiga&#xe7;&#xe3;o Interdisciplinar em Sa&#xfa;de//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04279/2025 and DOI identifier https://doi.org/10.54499/UID/04279/2025 - Centro de Investiga&#xe7;&#xe3;o Interdisciplinar em Sa&#xfa;de//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/04279/2025 and DOI identifier https://doi.org/10.54499/UID/04279/2025 - Centro de Investiga&#xe7;&#xe3;o Interdisciplinar em Sa&#xfa;de//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CAPES - Finance code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Standardization of oral sample collection methods is essential for accurate and reproducible microbiota quantification. This methodological study aimed to evaluate different oral collection methods to identify the most consistent approach for bacterial quantification by qPCR using samples from adolescent individuals. In addition, to assess the biological applicability of the best method, an exploratory analysis compared bacterial profiles between eutrophic and overweight/obese adolescents and explored associations between bacterial abundance and body composition parameters. Samples of unstimulated saliva, cheek swabs, and biofilm were collected from the same individuals, and qPCR was used to quantify total bacteria (16 S rRNA gene), Bacillota, and Bacteroidota phyla. Unstimulated saliva produced the lowest variability in bacterial quantification compared with other methods (p < 0.05). Moderate correlations were observed between saliva and biofilm, whereas saliva and cheek swab showed weak associations. Although bacterial copy numbers tended to be higher in overweight/obese individuals, these differences were not statistically significant. Correlation matrices suggested group-specific associations between bacterial taxa and body composition parameters, demonstrating the potential of saliva for microbiome assessment in studies of nutritional and metabolic health. This study validated unstimulated saliva as a reproducible, non-invasive, and cost-effective biofluid for oral microbiota quantification by qPCR. The method provides consistent results suitable for large-scale, translational, or point-of-care applications.}, }
@article {pmid41832285, year = {2026}, author = {Islam, SMN and Iqbal, MM and Haider, MN and Chowdhury, MZH and Mim, MF and Sultana, R and Rahman, GM and Jahangir, MMR}, title = {Temporal variation of bacterial community structure and dynamics in urea-fertilized irrigated rice rhizosphere.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41832285}, issn = {1614-7499}, abstract = {Due to a lack of understanding of plant-microbe-soil interaction, nitrogen (N) biogeochemistry in rice ecosystems remains a mystery. Specifically, data on temporal shifts in rhizospheric microbial communities under urea fertilization in irrigated rice systems are limited. This study investigated the temporal dynamics of bacterial community structure in the rhizosphere of urea-fertilized irrigated rice. The bacterial community exhibited higher species richness and evenness following the first and second dose of urea application but declined after the third dose. The results also revealed that soil N content had the most impact on the structures of the bacterial communities. The application of urea reduced bacterial families such as Sphingomonadaceae, Nocardioidaceae, and Kineosporiaceae, related to N fixation, organic matter decomposition, nutrient solubilization and methanogenesis, indicating their sensitivity to increased N levels. Conversely, Methylocystaceae, a methene oxidizing group, was increased after urea application suggesting their ability to proliferate under these conditions. Functional annotation using the KEGG pathway revealed elevated isoquinoline alkaloid biosynthesis after N applications. The findings of this study provide a basis for uncovering the bacterial community structure in the rice rhizosphere that is influenced by N fertilizer application.}, }
@article {pmid41832672, year = {2026}, author = {Haddadi, A and Heidari, A and Rezaei, N}, title = {Alzheimer's Disease, Circadian Rhythms, and the Immune System: Potential Interconnections.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113816128433445251211165723}, pmid = {41832672}, issn = {1873-4286}, abstract = {Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder, marked by the accumulation of amyloid-β plaques and neurofibrillary tangles. Its incidence is rising as the global population ages. This narrative review explores the emerging interconnections among AD, circadian rhythms, and the immune system. The circadian system, governed by endogenous clocks, regulates key physiological processes and exhibits disruptions in the early stages of AD. Chronodisruption, disturbance of circadian rhythms, has been implicated in AD pathogenesis through its effects on metabolism, sleep, and neuroinflammation. The immune system also plays a central role in AD, with microglia and astrocytes contributing to disease progression. Immune function displays circadian variation, and disruptions in sleep and circadian timing may impair immune responses, promote inflammation, and compromise amyloid-β clearance. Therapeutic strategies targeting circadian regulation, including melatonin agonists and orexin receptor antagonists, may help mitigate cognitive decline. Additionally, the gut microbiome, modulated by circadian and sleep patterns, has emerged as a potential contributor to AD pathophysiology. This review also highlights interventions that support immune health, such as the Mediterranean diet, antiviral therapies, and physical activity, which may collectively attenuate AD risk. Finally, the bidirectional relationship between immune signaling and circadian rhythms, evidenced by immune modulation of clock genes, underscores a complex, integrated regulatory network. Understanding these interrelated systems may uncover novel approaches for prevention and treatment. By elucidating these interconnections, this review aims to shed light on novel therapeutic strategies and interventions that address multiple facets of the disease, offering potential avenues to improve outcomes for individuals with AD.}, }
@article {pmid41832741, year = {2026}, author = {Fields, BC and Traweek, RS and Jiang, K and Witt, RG and Damania, A and Chiang, YJ and Ajami, N and Nassif-Haddad, E and Keung, EZ and Chelvanambi, M and Zhang, X and Peterson, CB and Wargo, JA and Daniel, CR and Roland, CL and Holder, AM}, title = {High dietary fiber is associated with improved outcomes in patients with melanoma and sarcoma treated with immunotherapy regardless of gut microbiome dysbiosis and social vulnerability.}, journal = {Cancer}, volume = {132}, number = {6}, pages = {e70335}, pmid = {41832741}, issn = {1097-0142}, support = {//Bristol-Myers Squibb/ ; T32 CA 009599/NH/NIH HHS/United States ; 1R01 CA219896-01A1/NH/NIH HHS/United States ; 1R01CA291965-01/NH/NIH HHS/United States ; P30-CA016672/NH/NIH HHS/United States ; //Andrew Sabin Family Foundation/ ; //University of Texas MD Anderson Cancer Center/ ; /MRA/Melanoma Research Alliance/United States ; //American Association for Cancer Research/ ; //Sarcoma Foundation of America/ ; //Society of Surgical Oncology/ ; //American College of Surgeons/ ; //Congressionally Directed Medical Research Programs/ ; }, mesh = {Humans ; *Dietary Fiber/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Melanoma/drug therapy/mortality/microbiology/therapy/immunology/pathology ; Female ; Male ; Middle Aged ; *Dysbiosis/microbiology ; *Sarcoma/drug therapy/mortality/microbiology/therapy/immunology ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Prospective Studies ; Treatment Outcome ; Adult ; }, abstract = {BACKGROUND: Social vulnerability, dietary fiber, and the gut microbiome have been individually implicated in clinical outcomes for melanoma and sarcoma patients. This study hypothesized that increasing social vulnerability is associated with insufficient dietary fiber intake and negatively associated with microbiome composition and clinical outcomes.<br><br>METHODS: Clinicopathologic data, baseline fiber intake, and gut microbiome profiles were assessed in 153 patients with melanoma or sarcoma treated with immune checkpoint blockade (ICB) and prospectively followed. Patients' social vulnerability index (SVI) and fiber intake were evaluated for associations with microbiome composition, treatment response, and overall survival (OS).<br><br>RESULTS: SVI percentile was 0.4 (interquartile ratio [IQR], 0.2-0.7), and median dietary fiber intake was 17 (IQR, 15-20) g/day. SVI was inversely correlated with dietary fiber intake (r, -0.18, p&#xa0;=&#xa0;.0398). Gut microbiome analyses revealed community and compositional differences by SVI, including inverse associations with &#x3b1;-diversity and the relative abundance of favorable bacteria such as Bifidobacterium longum (p&#xa0;<&#xa0;.001), contrasting the positive associations observed between fiber and these microbial markers. Increased dietary fiber intake was associated with measurable response to ICB. A difference in OS was not observed in more socially vulnerable patients (SVI, not reached vs. 81.7 months), however, a survival advantage was evident with higher dietary fiber intake (not reached, 58.9 months).<br><br>CONCLUSIONS: Increased social vulnerability was associated with a less favorable gut microbiome composition but not worse OS among melanoma and sarcoma patients treated with ICB. Consistent with prior findings, high dietary fiber intake emerged as a potentially modifiable pathway to improve outcomes in patients initiating ICB, particularly those with increased SVI.}, }
@article {pmid41832868, year = {2026}, author = {Urku, R and Yilmaz, SS and Çakan, H}, title = {Profiling microbiome signatures on mobile phones for forensic insights.}, journal = {Forensic science international}, volume = {384}, number = {}, pages = {112915}, doi = {10.1016/j.forsciint.2026.112915}, pmid = {41832868}, issn = {1872-6283}, abstract = {The use of mobile phones is increasingly widespread in daily life. Microorganisms present on phone surfaces can act as trace bacterial evidence at crime scenes, with potential applications in forensic sciences. In this study, we aimed to assess the presence, diversity, and forensic relevance of bacterial microbiomes on mobile phones. Swab samples were collected from the personal mobile phones of 50 individuals, with both the front and back surfaces sampled. All these samples (n = 100) were then cultured using conventional microbiological methods, followed by standard phenotypic tests and MALDI-TOF MS for microbial identification. A total of 161 colonies corresponding to 18 microbial species were identified on mobile phone surfaces, including both common skin flora and less common organisms. The presence of fungal species and gram-negative bacteria, although in lower abundance, highlights the complexity of microbial communities on these devices. Variations in bacterial diversity were influenced by handwashing frequency, phone cleaning habits, use of protective accessories, and gender, demonstrating that microbial signatures are shaped by a combination of behavioral and environmental factors. These findings provide sufficient depth to characterize microbiota on mobile phones and illustrate their potential as distinctive microbial patterns for forensic analysis. Moreover, significant differences were observed in relation to socio-demographic characteristics, handwashing habits, and use of protective accessories (p < 0.05). These results indicate that bacterial communities on mobile phones vary between individuals and that distinctive microbial patterns may serve as supportive forensic indicators.}, }
@article {pmid41833034, year = {2026}, author = {Goel, A and Das, S and Mazumder, A and Sinha, A}, title = {Microbiota-Gut-Brain Axis: A Novel Paradigm in the Neurobiology of Anxiety.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715273411443251201153434}, pmid = {41833034}, issn = {1996-3181}, abstract = {INTRODUCTION: The gut microbiome and the central nervous system are intricately connected through a bidirectional communication system that plays a vital role in maintaining gut homeostasis and overall health. Disruptions in this interaction are linked to gastrointestinal and neuropsychiatric disorders, including anxiety. This review aims to provide a comprehensive analysis of the gut microbiota's role in anxiety and evaluate the therapeutic potential of prebiotics.<br><br>METHODS: This review synthesizes recent literature from databases including PubMed, Scopus, Web of Science, and Google Scholar, focusing on the gut microbiota's role in anxiety and the therapeutic potential of prebiotics.<br><br>RESULTS: The microbiota-gut-brain axis communicates through multiple pathways, including the vagus nerve, immune signaling, microbial metabolites, and the hypothalamic-pituitary-adrenal (HPA) axis. Prebiotics modulate these pathways by enhancing beneficial microbial populations and influencing the production of neuroactive compounds. Key molecular targets implicated in this communication include brain-derived neurotrophic factor (BDNF), glucocorticoid receptors, and shortchain fatty acids, which modulate neurotransmitters such as GABA and serotonin, and influence neuroinflammatory pathways implicated in anxiety pathophysiology.<br><br>DISCUSSION: The findings highlight the immunological, neurochemical, and endocrine mechanisms through which the gut microbiota interacts with neurophysiological systems. These mechanisms underscore the pharmacological potential of prebiotics in the management of psychiatric illnesses.<br><br>CONCLUSION: The interplay between the gastrointestinal microbiota and neurophysiological systems provides key pharmacological insights into the potential of prebiotics as a therapeutic approach for managing psychiatric illnesses, detailing their mechanistic pathways and translational applications in clinical practice.}, }
@article {pmid41820450, year = {2026}, author = {Kim, TM and Jeong, S and Choi, B and Kim, Y and Kim, E}, title = {Seed endophytic bacteria from invasive Lactuca serriola increase soil available phosphorus under phosphorus deficiency.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41820450}, issn = {2045-2322}, support = {RS-2024-00456189, RS-2025-00558787//the National Research Foundation of Korea (NRF)/ ; }, abstract = {UNLABELLED: Invasion by alien plant species can alter soil biogeochemical processes, including phosphorus (P) cycling. Plant litter and root exudates have been proposed to influence soil chemistry either directly through the release of diverse metabolites or indirectly by modifying the rhizosphere microbiome. Notably, some seed endophytic bacteria co-dispersed with seeds possess phosphate-solubilizing activity (PSA), suggesting their potential contribution to soil P dynamics. However, this possibility has rarely been tested. In this study, we conducted in vitro PSA assays on bacterial strains isolated from seeds of the invasive Lactuca serriola. To comprehensively assess their capacity, both individual isolates and their synthetic consortia were examined. Individual isolates exhibited variable PSA, and two isolates showed synergistic PSA when combined with other isolates. Based on these results, we constructed dual-strain consortia containing either of the synergistic strains with another isolate and inoculated them onto L. serriola seeds. Plants were then grown under P-deficient conditions, and both plant and soil traits were measured. Seed inoculation with specific dual-strain consortia significantly increased soil P, and these effects exceeded those of individual strains, indicating synergistic interactions between bacterial partners. The plant root-to-shoot ratio was negatively associated with soil P. Our results imply that plants harboring specific seed endophytic bacteria can enhance soil P under P-limiting conditions. In addition, they suggest the importance of bacterial interactions when evaluating the effects of bacteria on plant and soil traits.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40933-5.}, }
@article {pmid41826382, year = {2026}, author = {Slevin, MC and Houtz, JL and Vitousek, MN and Anderson, RC}, title = {Challenges associate with microbiome diversity, glucocorticoids, and condition in a wild songbird.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41826382}, issn = {2045-2322}, abstract = {UNLABELLED: Wild animals experience daily fitness challenges, and the resulting stress responses can disrupt an animal’s gut microbiome. Given the links between health and microbiome composition, it is essential to understand how challenges affect microbial communities. We showed that a fitness challenge significantly alters the cloacal microbiome of free-living Northern cardinals (Cardinalis cardinalis), and these shifts covary with changes to the glucocorticoid stress response, condition, and beak ornamentation. Treatment significantly related to beta diversity, while it only influenced alpha diversity indirectly through interactions with health-related traits. Birds held for an extended time before release showed greater cloacal microbiome community changes 11 days later vs. birds administered a simulated territorial intrusion challenge, or control birds administered no challenge. We also detected relationships between beta diversity and change in body condition and beak ornamentation. Birds showing the greatest alpha diversity decrease and largest beta diversity between timepoints experienced the greatest corticosterone response to handling. Finally, several Amplicon Sequence Variants were differentially abundant in challenged birds compared to control birds. To our knowledge, this study is the first to demonstrate proximate effects of fitness challenges on the microbiome of an adult, free-living songbird, while simultaneously tracking changes in glucocorticoid levels, body condition, and ornamentation—providing a uniquely integrative perspective on how stress shapes host-microbe interactions in the wild.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42507-x.}, }
@article {pmid41826507, year = {2026}, author = {Drewnowska, JM and Lewandowska, W and Zieliński, P and Jadwiszczak, P and Jaroszewicz, B and Keczyński, A and Hummel, O and Majewski, P and Święcicka, I}, title = {Bacteria-soil-plant linkages underlie the mosaic structure of the soil bacterial communities in near-natural stands of Białowieża Primeval Forest.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40694-1}, pmid = {41826507}, issn = {2045-2322}, abstract = {Primary temperate forests serve as a natural framework for studying linkages between vegetation, soil properties and microbial communities under minimal human disturbance. Here, we characterize how soil bacterial communities and functional potential vary across five dominant forest types of the Białowieża National Park, representing a natural mosaic of vegetation and edaphic conditions. Using full-length 16S rRNA Oxford Nanopore sequencing, functional profiling via BIOLOG EcoPlates, and applying multivariate analyses, we detected clear differences in bacterial composition and carbon-substrate utilization profile among forest types. Distance-based redundancy analysis (dbRDA) identified soil pH as the primary abiotic gradient shaping bacterial communities, while RLQ, fourth-corner and multiblock sPLS analyses consistently supported bacteria-soil-vegetation linkages. Three consistent ecological clusters emerged across the forest mosaic. Coniferous forests with acidophilic bacterial assemblages linked to strongly acidic soils and ericaceous understoreys, broadleaf forests with bacterial genera associated with moderately acidic, nutrient-depleted soils and shade-tolerant vegetation, and alder forests characterized by richer, more metabolically active microbial communities occurring in less acidic soils with tall-herb understoreys. Mixed forests displayed broad internal variability, reflecting their wide range of vegetation and soil conditions. Overall, environmental filtering structures distinct bacterial communities of this primary temperate forest, providing a valuable baseline for future plant-soil-microbiome studies.}, }
@article {pmid41826906, year = {2026}, author = {Mosavat, SH and Sahraian, A and Kalani, M and Namjoyan, F and Ghasemi, Y}, title = {Effect of probiotic supplement on improvement of depressive symptoms in patients with substance-induced depressive disorder: a randomized, double-blind, placebo-controlled clinical trial.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-07903-7}, pmid = {41826906}, issn = {1471-244X}, abstract = {BACKGROUND: Substance-Induced Depressive Disorder (SIDD) accounts for a high health burden and requires new therapies. Bidirectional communications between the gut and the brain mediated by the microbiota point to a possible influence of probiotics as a tool for preserving mental health.<br><br>MATERIALS AND METHODS: Double-blind, placebo-controlled, randomized clinical trial on a sample of 40 patients with SIDD. Patients were then randomly assigned into probiotic and placebo arms and underwent interventions for four continuous weeks. The clinical assessment was done using BDI and HAM-A. Immunologic outcomes were measured through analysis of inflammatory markers, cytokines, and other immunological parameters. The trial was registered with ClinicalTrials.gov, under the identifier NCT06790823 (18/1/2025).<br><br>RESULTS: The change in the intensity of depression and anxiety in both probiotic and placebo groups was statistically significant after intervention. No differences were also noted between the two groups. Immunologic results showed a suggestive changes in IL6 and INFG levels in the probiotic group as compared with placebo, which may indicate possible immune-modulating effects.<br><br>CONCLUSION: In this randomized, double&#x2011;blind, placebo&#x2011;controlled pilot trial, both probiotic and placebo groups showed significant improvements in depressive and anxiety symptoms over time, with no significant between&#x2011;group differences. Probiotic supplementation was associated with non&#x2011;significant trends in selected inflammatory markers, suggesting possible immunological effects that warrant further investigation. Larger, multicenter trials with comprehensive microbiome and immunologic assessments are needed to clarify the potential role of probiotics as an adjunctive strategy in substance&#x2011;induced depressive disorder.}, }
@article {pmid41826961, year = {2026}, author = {Becker, HEF and Mohren, R and Le, NG and Derijks, LJJ and Jonkers, DMAE and Penders, J}, title = {6-mercaptopurine and tofacitinib alter microbial protein expression but not composition in fecal microbiota incubations from Crohn's disease patients.}, journal = {BMC biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12915-026-02569-9}, pmid = {41826961}, issn = {1741-7007}, abstract = {BACKGROUND: Crohn's disease (CD) is a chronic, relapsing-remitting gastrointestinal inflammatory condition with a multifactorial etiology. At present, drug therapy is the most important treatment option. However, a substantial number of CD patients experience side effects and/or nonresponse to medical drugs. In part, this might be attributed to the interaction of the intestinal microbiome with xenobiotics, such as medical drugs. The aim of this study was to explore the effect of the common CD drugs budesonide, 6-mercaptopurine (6-MP), as well as tofacitinib on the CD patient's microbiome in vitro.<br><br>RESULTS: We performed 16S rRNA gene-based bacterial community profiling and metaproteomic analyses on anaerobic ex vivo incubations of CD patient-derived fecal microbiota (FM) that were exposed to CD drugs or control conditions. Both bacterial community profiling and metaproteomics revealed larger differences in 24-h FM incubations between the five donor-derived FM samples than between the various drug incubations. Incubation of the FM of one of the donors with 6-MP or tofacitinib resulted in a significant alteration in the metaproteome when compared to the control condition, whereas no effect could be observed upon incubation with budesonide. Considering only bacterial proteins detected in at least 80% of either the drug or control FM incubations, 33 proteins were consistently more abundant and 93 less abundant in all five donor-derived samples with 6-MP incubation, distinguishing 6-MP from control conditions. In contrast to metaproteomic analyses, bacterial community profiling only detected a significantly lower relative abundance of Colidextribacter in 15&#xa0;&#xb5;g/ml tofacitinib FM incubations. No alterations were detected in overall bacterial richness, diversity, or community structure in response to incubation with any of the drugs.<br><br>CONCLUSIONS: Tofacitinib and especially 6-MP significantly affect microbial function, but barely microbial composition in vitro. These drug-induced functional changes may subsequently influence host physiology and potentially inflammation in CD. Our findings emphasize the relevance to include functional microbial studies when investigating drug-microbiota interactions. Further research is needed to elucidate the impact of 6-MP-induced microbial alterations on intestinal physiology and inflammation in CD.}, }
@article {pmid41827072, year = {2026}, author = {Takkar, B and Maddheshiya, A and Adhikary, P and Reddy, VA and Majumder, PP and Mukherjee, S and Das, T and , }, title = {Gut microbiome changes in people with diabetic retinopathy in India. DRMS-India report # 1: operational protocol and trends from first 100 participants.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00821-9}, pmid = {41827072}, issn = {1757-4749}, abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM), and the leading cause of vision impairment and blindness. India is among the top three countries in DM prevalence, and both DM and DR are projected to rise sharply in the future. There is no accepted strategy for the prevention of DR other than DM control. Recent studies suggest that DM is associated with alterations in a core group of gut microbiota, and progression to DR may be influenced by changes within this core group, highlighting a potential link between DR and gut microbiome. We studied these changes in a protocol-driven large case-control study, the Diabetic Retinopathy Microbiome Study-India (DRMS-India: CTRI/2024/02/062511), analysed the results of the first 100 individuals, and evaluated variations in gut microbiome in DR.<br><br>METHODS: The DRMS is designed to recruit 462 people aged&#x2009;&#x2265;&#x2009;30 years into three cohorts: healthy controls (HCs), DM, and DR, at 17 independent sites in India. Shotgun metagenomic sequencing of first-pass morning fecal samples is performed at a centralized laboratory and correlated with disease status, lifestyle, dietary, and systemic factors.<br><br>RESULTS: The first 100 participants included 26 HC, 33 DM, and 41 DR. The trends showed the DR group had 1, 6, and 10 unique core phyla, genera, and species, respectively. Alpha diversity was highest in the DR group; Beta diversity plots showed separate clusters of HCs and DR, with DM overlapping both. Firmicutes (highest in DR), Proteobacteria (highest in DM), Bacteroidetes, and Actinobacteria (highest in HC) were common phyla. Segatella was the most common genus, and Segatella copri was the most common species across all groups to date. Most microbial gene families were annotated to Molecular Functions (MF), and the pathways attributed to carbohydrate, amino acid, lipid, and nucleotide metabolism, indicating distinct functional adaptations in their gut microbiome.<br><br>CONCLUSION: Trends from the first 100 individuals indicate that the gut microbiome of Indians with DR exhibits discriminatory features in microbial diversity and abundance, as well as in gene families and pathways that impact host gut metabolism. Data trends from DRMS-India indicate a region-specific non-invasive biomarker that may guide preventive therapy for DR.}, }
@article {pmid41827077, year = {2026}, author = {Linz, C and Tsenova, K and Dettmer, K and Ellmann, L and Oefner, PJ and Gronwald, W and Farowski, F and Rüb, AM and Freedberg, DE and Koehler, P and Borrega, JG and Naendrup, JH and Vehreschild, MJGT and Böll, B}, title = {Integrating intestinal microbiome and urinary metabolome data to predict secondary infection in critically ill patients.}, journal = {Critical care (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13054-025-05818-5}, pmid = {41827077}, issn = {1466-609X}, }
@article {pmid41827204, year = {2026}, author = {Elbehiry, A and Marzouk, E and Alhumaydhi, FA and Abalkhail, A}, title = {Diabetes Mellitus as an Integrated Microbiome, Immune, and Metabolic Disorder with Clinical Implications for Multisystem Complications and Public Health.}, journal = {Journal of clinical medicine}, volume = {15}, number = {5}, pages = {}, pmid = {41827204}, issn = {2077-0383}, abstract = {Diabetes mellitus is one of the most common health problems worldwide; however, increased blood glucose alone cannot adequately explain its pathophysiology. Although high blood glucose is a defining feature, evidence increasingly proves that diabetes arises from systemic disturbances involving the gut microbiome, immune system, and metabolic control. From this perspective, diabetes can be viewed as a systemic condition shaped by the dynamic interactions between the gut microbiome, the immune system, and metabolic pathways. Alterations in gut microbiome composition and function can influence nutrient metabolism, microbial metabolite production, bile acid signaling, and intestinal barrier integrity. Any damage of the gut barrier allows movement of microbiome-derived molecules that activate innate immune pathways and provoke chronic low-grade inflammation. This inflammatory state interferes with insulin signaling, contributes to immune maladaptation, and exacerbates metabolic dysfunction. Over time, these processes contribute to the advance of multisystem complications, including cardiovascular disease, diabetic nephropathy, neuropathy with cognitive impairment, delayed wound healing, and increased susceptibility to infection. The review also integrates environmental and public health factors, demonstrating how diet, antibiotic exposure, circadian disruption, and social conditions shape the microbiome, immune function, metabolic regulation, and disease risk across the life course. By bringing together clinical, experimental, and population-based evidence, this review illustrates the limitations of care models that concentrate only on glucose. It also points out how integrated approaches targeting the microbiome, immune system, and metabolic pathways can improve diabetes prevention, management, and guide future research.}, }
@article {pmid41827267, year = {2026}, author = {Oksuz, S and Kinikoglu, O and Ozkerim, U and Isik, D and Surmeli, H and Ay, S and Odabas, H and Turan, N}, title = {Impact of Peri-Immunotherapy Antibiotic Exposure on Survival Outcomes in Metastatic Renal Cell Carcinoma: A Real-World IMDC Risk-Stratified Analysis.}, journal = {Journal of clinical medicine}, volume = {15}, number = {5}, pages = {}, pmid = {41827267}, issn = {2077-0383}, abstract = {Background: Antibiotic exposure has been shown to negatively affect immune checkpoint inhibitor (ICI) efficacy in several cancers, possibly by disrupting gut microbiota. It represents a potentially modifiable clinical factor that may influence immunotherapy efficacy in RCC. However, data on renal cell carcinoma (RCC) remain limited, especially regarding prognostic risk groups. Methods: We conducted a retrospective cohort study of 120 RCC patients treated with ICIs between 2018 and 2024 at Kartal Dr. Lütfi Kırdar City Hospital. Patients were classified based on systemic antibiotic exposure within ±30 days of ICI start. Survival outcomes were compared using Kaplan-Meier and Cox regression analyses. Subgroup analyses were performed according to the International Metastatic RCC Database Consortium (IMDC) risk classification. Results: Of the 120 patients, 38 (31.7%) received antibiotics during the peri-ICI period. Median progression-free survival (PFS) was significantly shorter in the antibiotic-exposed group (5.1 vs. 9.4 months; p = 0.004), as was overall survival (OS) (14.8 vs. 22.5 months; p = 0.03). Antibiotic use remained an independent predictor of both PFS (HR = 1.87; 95% CI: 1.21-2.89) and OS (HR = 1.64; 95% CI: 1.04-2.59). In subgroup analyses, intermediate-risk patients had worse OS with antibiotics (13.5 vs. 20.6 months; p = 0.035), as did poor-risk patients (8.1 vs. 13.9 months; p = 0.049). Conclusions: Antibiotic exposure during the peri-immunotherapy period is linked to significantly poorer outcomes in RCC patients, especially those with intermediate and poor IMDC risk scores. These findings emphasize the importance of antimicrobial stewardship and suggest a potential role for microbiome-informed patient management in RCC.}, }
@article {pmid41827462, year = {2026}, author = {Jakubowska, Z and Wantoch-Rekowski, F and Małyszko, JS and Małyszko, J}, title = {IgA Nephropathy: Epidemiology, Outcomes, and Insights for Primary Glomerulonephritides.}, journal = {Journal of clinical medicine}, volume = {15}, number = {5}, pages = {}, pmid = {41827462}, issn = {2077-0383}, abstract = {According to the Global Burden of Disease 2019 analysis, there were 606,300 new cases of chronic kidney disease due to glomerulonephritis worldwide, with 17.3 million prevalent cases and 183,700 deaths More interestingly, between 1990 and 2019, the global burden of glomerulonephritis increased by 77% in incidence and 81% in prevalence, mainly due to demographic aging and population growth. Among primary glomerulopathies, IgA Nephropathy (IgAN), also known as Berger's disease, is the most common primary glomerulopathy worldwide, with significant geographic and ethnic variation in incidence, with the highest prevalence in Europe and Asia and the lowest in Africa. Its pathogenesis reflects a complex interaction between polygenic susceptibility and environmental modifiers, mucosal immune activation, infections of the upper respiratory and gastrointestinal tracts, dietary factors, and alterations in the gut microbiome. In addition, IgAN increasingly coexists with other chronic diseases, such as hypertension and diabetes, which complicates both diagnosis and treatment in aging societies. All these observations suggest that in the coming years, the epidemiology of IgAN will gradually transform from a description of "case counts" to a predictive tool that integrates genetic, environmental, and molecular biomarker data. In this sense, epidemiology is increasingly becoming the foundation of precision nephrology-allowing not only for disease risk prediction but also for the design of effective therapeutic strategies. The conceptual shift in IgAN-from a disease defined by biopsy prevalence to one understood through integrative epidemiology-illustrates the broader transition of GN research toward biomarker-based risk stratification and precision medicine. This review focuses on IgA nephropathy as the most prevalent primary glomerulonephritis and uses it as a reference disease to illustrate broader epidemiological patterns, outcome trajectories, and methodological limitations relevant to primary glomerulonephritides.}, }
@article {pmid41827759, year = {2026}, author = {Haque, I and Kambhampati, S and Banerjee, SK}, title = {Converging Pathways in Cancer Biology: How Do the Microbiome, Angiogenesis, Senescence, Fibroblast Plasticity, and Immunotherapy Intertwine?.}, journal = {Cancers}, volume = {18}, number = {5}, pages = {}, pmid = {41827759}, issn = {2072-6694}, abstract = {Cancer continues to be a major cause of death, with an anticipated 2,114,850 new cases and almost 626,140 deaths from the disease in 2026 [...].}, }
@article {pmid41827785, year = {2026}, author = {Cataldi, C and Karaoğlan, BB and Liotta, E and De Dosso, S}, title = {Decoding Immunotherapy Response in Colorectal Cancer: Translational Insights Beyond MSI.}, journal = {Cancers}, volume = {18}, number = {5}, pages = {}, pmid = {41827785}, issn = {2072-6694}, abstract = {Background/Objectives: Immune checkpoint inhibitors (ICIs) are among the transformative and manageable systemic therapies for several cancer types, including colorectal cancer (CRC). Nevertheless, their clinical benefit is limited to mismatch-deficient or microsatellite instability-high diseases, which represent only a small percentage of cases. Despite this initial major and stringent selection, primary and acquired resistance remain clinically relevant. Therefore, the identification of additional biomarkers is essential to refine patient selection and guide rational combinational strategies. This review aims to summarize the current evidence regarding established and emerging biomarkers of response and resistance to ICIs in CRC. Methods: This narrative review identified and synthesized relevant clinical trials, translational studies, and reviews through a literature search of emerging biomarkers of immunotherapy response in colorectal cancer. Results: Deficient mismatch repair/high microsatellite instability remains the most reliable predictive biomarker of ICI response, emphasized by high tumor mutational burden, POLE/POLD mutations, and specific tumor microenvironment features. Emerging indicators, including molecular alterations, antigen presentation machinery integrity, PD-L1-mediated signaling, microbiome connections, and circulating tumor DNA kinetics, have demonstrated significant potential as sources for therapeutic response prediction and have informed the development of innovative combination strategies in both MSI-H and MSS CRCs. Conclusions: Immunotherapy response in CRC is determined by a complex interplay between tumor-intrinsic, immune, microenvironmental, and systemic factors. Integrating multiple biomarkers may provide superior stratification and guide therapeutic strategies. Prospective validation and standardized biomarker assessment will be imperative to translate these insights into clinical practice.}, }
@article {pmid41827802, year = {2026}, author = {Ciappina, G and Toscano, E and Di Mauro, G and Franchina, T and Basile, F and Vanni, G and Facchini, G and Nasti, G and Quagliariello, V and Maurea, N and Marafioti, M and Bottari, A and Buonomo, OC and Ottaiano, A and Berretta, M}, title = {A Silent Saboteur of Immunotherapy: Antibiotic Use and Its Impact on Immune Checkpoint Inhibitors Efficacy, a Systematic Review and Meta-Analysis of Recent Studies.}, journal = {Cancers}, volume = {18}, number = {5}, pages = {}, pmid = {41827802}, issn = {2072-6694}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have transformed the management of solid tumors, yet only a subset of patients achieve durable benefit. The gut microbiota is a key modulator of antitumor immunity, and systemic antibiotic therapy (ABT), frequently prescribed-and sometimes overused-in oncology, can profoundly disrupt microbial homeostasis. Observational studies suggest that ABT may impair ICI efficacy, but results remain heterogeneous, warranting an updated synthesis.<br><br>METHODS: We conducted a systematic review and meta-analysis in accordance with the PRISMA 2020 guidelines. PubMed, Scopus, and EMBASE were searched for studies published between 2018 and 2025 evaluating the association between ABT exposure and time-to-event outcomes in patients with solid tumors treated with ICIs. Studies were required to report explicit definition of the ABT exposure window. Random-effects models were considered primary. A sensitivity analysis was performed in non-small cell lung cancer (NSCLC).<br><br>RESULTS: Fifteen studies encompassing 52,489 patients were included. ABT exposure was associated with significantly worse OS (random-effects HR 1.16, 95% CI 1.03-1.29) and PFS (random-effects HR 1.11, 95% CI 0.95-1.27), indicating an increased risk of death and disease progression compared with no ABT exposure. In the NSCLC sensitivity analysis, ABT was consistently associated with inferior PFS and, when accounting for heterogeneity, with significantly reduced OS, supporting the robustness of the association.<br><br>CONCLUSIONS: ABT administered in temporal proximity to ICIs is associated with clinically meaningful worsening of survival outcomes across solid tumors, consistent with microbiome-mediated impairment of immunotherapy efficacy. These findings support cautious ABT stewardship in patients receiving ICIs and highlight the need for prospective studies integrating microbiome profiling and standardized ABT exposure assessment.}, }
@article {pmid41827840, year = {2026}, author = {Antoniadou, M and Varzakas, T}, title = {Oral Cellular Homeostasis and Occupational Wellbeing in Healthcare Professionals Under the Lens of Salivary, Immune, and Microbiome Mechanisms.}, journal = {Cells}, volume = {15}, number = {5}, pages = {}, pmid = {41827840}, issn = {2073-4409}, mesh = {Humans ; *Saliva/metabolism/immunology/microbiology ; *Microbiota ; *Homeostasis ; *Health Personnel/psychology ; Biomarkers/metabolism ; *Occupational Stress ; *Occupational Health ; Burnout, Professional ; }, abstract = {BACKGROUND: Healthcare professionals experience continuous biological and psychosocial stressors that may disturb oral and systemic homeostasis. Alterations in salivary secretion, mucosal immunity, and microbiome composition reflect adaptive cellular responses to chronic occupational stress. Understanding these mechanisms may provide a biological framework for resilience and wellbeing in everyday clinical practice.<br><br>OBJECTIVE: To narratively review the evidence linking oral cellular and molecular mechanisms-salivary biomarkers, epithelial and immune cell activity, and microbiome dynamics-with stress, fatigue, burnout, and wellbeing outcomes among healthcare professionals.<br><br>METHODS: This narrative review employed a PRISMA-guided literature search of PubMed, Scopus, Web of Science, and Cochrane Oral Health to enhance transparency and coverage across databases. Given the heterogeneity of study designs and outcomes, data were synthesized thematically without quantitative pooling or formal meta-analysis. Methodological strength was evaluated qualitatively, focusing on biomarker validity, sampling conditions, and conceptual relevance. Eligible designs included observational, experimental, and interventional studies.<br><br>RESULTS: Evidence from 99 studies suggests that chronic occupational stress elevates salivary cortisol, oxidative stress markers, and pro-inflammatory cytokines (IL-6, TNF-&#x3b1;), while reducing protective salivary immunoglobulin A and microbiome diversity. Balanced oral immune and microbial profiles were associated with better psychological adaptation and lower fatigue indices.<br><br>CONCLUSIONS: Oral cellular homeostasis offers a promising window into the biological underpinnings of occupational stress and resilience in healthcare professionals. Systematic integration of salivary and mucosal biomarkers into workplace wellbeing programs could enhance early detection of dysregulated stress physiology. Future interdisciplinary research should bridge oral biology, occupational medicine, and mental health to strengthen sustainable wellbeing strategies across the health workforce.}, }
@article {pmid41827859, year = {2026}, author = {Muraleedharan, A and Rangavajhula, K and Ray, SK}, title = {Exosome Engineering for Blocking Gut Dysbiosis and Inducing Cell Death Mechanisms in Glioblastoma Multiforme.}, journal = {Cells}, volume = {15}, number = {5}, pages = {}, pmid = {41827859}, issn = {2073-4409}, mesh = {Humans ; *Exosomes/metabolism ; *Glioblastoma/pathology/therapy/microbiology ; *Dysbiosis ; *Gastrointestinal Microbiome ; Animals ; *Brain Neoplasms/pathology ; Cell Death ; Apoptosis ; }, abstract = {Glioblastoma multiforme (GBM) is the most lethal primary brain tumor in adults. Emerging evidence endorses that gut dysbiosis contributes to GBM progression through the gut-brain axis (GBA), promoting inflammation and therapeutic resistance via abnormal short-chain fatty acid production and cytokine dysregulation. Exosomes, naturally occurring nanovesicles (30-150 nm), offer promising therapeutic potential due to their blood-brain barrier permeability, biocompatibility, and versatile cargo capacity. This review examines exosome engineering strategies for dual targeting: inhibiting alterations in gut microbiome and inducing regulated cell death mechanisms such as apoptosis and ferroptosis in GBM. We describe exosome engineering with detailed focus on cargo loading approaches (e.g., genetic modification, electroporation, and sonication), exosome surface functionalization with specific ligands (e.g., antibodies), and exosome biogenesis pathway manipulation. Engineered exosomes can deliver anti-inflammatory agents and gut microbiome modulators to restore GBA homeostasis while simultaneously transporting tumor-suppressive non-coding RNAs (e.g., miRNAs, siRNAs) and therapeutic agents to induce apoptosis by overcoming temozolomide resistance, and trigger ferroptosis-inducing components in GBM stem cells. Preclinical studies make obvious that this dual-targeting approach ought to enhance therapeutic efficacy by creating systemic immunity and eliminating tumor cells. However, clinical translation brings forth challenges, such as manufacturing, targeting specificity, and standardized quality control, and warrants further study.}, }
@article {pmid41827905, year = {2026}, author = {Braile, A and Bani, A and Hosseininasab, SF and Regno, ND and Orabona, N and Bove, A and Braile, M}, title = {Profiling Osteoporosis via Integrated Multi-Omics Technologies.}, journal = {Cells}, volume = {15}, number = {5}, pages = {}, pmid = {41827905}, issn = {2073-4409}, mesh = {Humans ; *Osteoporosis/genetics/metabolism ; *Metabolomics/methods ; Proteomics/methods ; *Genomics/methods ; Biomarkers/metabolism ; Epigenomics ; Multiomics ; }, abstract = {BACKGROUND: Osteoporosis is a complex disorder involving bone loss and muscle degeneration. Multi-omics technologies provide novel insights into its molecular mechanisms and may support biomarker discovery, patient stratification, and therapeutic development.<br><br>OBJECTIVE: This scoping review aimed to synthesize current evidence on the application of multi-omics approaches in osteoporosis, focusing on molecular insights, methodological diversity, and translational potential.<br><br>METHODS: A literature search of PubMed, Embase, and Scopus retrieved 433 records using the keywords "osteoporosis," "osteosarcopenia," and "omics." After removing duplicates and screening titles, abstracts, and full texts, 30 studies met the inclusion criteria. Data on study populations, biological samples, multi-omics techniques, and integration methods were extracted.<br><br>RESULTS: Studies employed transcriptomics, proteomics, metabolomics, lipidomics, epigenomics, and metagenomics, often combined in multi-omics analyses with computational modeling. Key pathways included osteoclast differentiation, immune regulation, ferroptosis, and microbiome-metabolite interactions. Multi-omics integration enabled the identification of molecular subtypes, candidate biomarkers, and potential therapeutic targets. Limitations included small or single-center cohorts, heterogeneous designs, and limited validation, restricting generalizability and clinical translation.<br><br>CONCLUSIONS: Multi-omics approaches offer a powerful framework to uncover the molecular mechanisms underlying bone and muscle degeneration and to guide precision diagnostics and interventions. Future studies should prioritize large, multicenter, longitudinal designs integrating multi-omics data with clinical and functional validation to facilitate clinical application.}, }
@article {pmid41827963, year = {2026}, author = {Alakilli, SYM and Ibrahim, MN and Alanazi, A and El Azab, EF and Alzhrani, K and Shahin, OR and Mazhari, BBZ and Ahmed, MAAS}, title = {AI-Driven Microbial Diagnostics: Predicting Disease Signatures Through Microbial Pattern Recognition.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, pmid = {41827963}, issn = {2075-4418}, abstract = {Background/Objectives: Predicting diseases based on the gut microbiome pattern is still difficult because of compositional shortcomings, batch heterogeneity, and scanty modeling of inter-taxon interactions. This study introduces a Dysbiosis-Aware Multiset Transformer Framework called DysbioFormer, which predicts state diseases by recognizing patterns of microbes. Methods: The current methods are mainly based on flat abundance representations or fixed-order models which limit the capability of describing intricate interactions of communities and evolutionary structure. Results: DysbioFormer is a solution to these shortcomings, in which each sample of the microbiome is modeled as a permutation-invariant multiset of taxonomic tokens with compositional, phylogenetic, and harmonized cohort data. Stacked Set Attention Blocks are used to learn relational dependencies between taxa, whereas Pooling-by-Multihead-Attention is used to aggregate global disease-level embeddings and this is not based on sequence assumptions. The model has been tested on MicrobiomeHD, which consists of a wide variety of human gut microbiome samples at a variety of disease conditions and healthy controls. Experimental results demonstrate strong diagnostic performance, achieving an accuracy of 97%, an AUC of 0.97, and an F1-score of 96%, consistently outperforming classical machine learning models under identical evaluation protocols. Attention-derived signatures also can give interpretable connections among predictive results and disease-linked microbial taxa, enhancing biological plausibility. Conclusions: The suggested architecture enables scalable, cohort-agnostic microbial diagnostics, and provides a principled route to transforming the complex information of the microbiome into reliable clinical information. DysbioFormer creates a universal basis of future microbiome-based disease screening and precision health uses. Its design allows extending towards multi-omics integration, longitudinal studies, and decision-support infrastructure, supporting microbiome-informed translational medicine in a variety of clinical research settings.}, }
@article {pmid41827997, year = {2026}, author = {Kaltsas, A and Pantazis, N and Tzikoulis, V and Roidos, C and Palapela, N and Tsiampali, C and Symeonidis, EN and Zachariou, A and Sofikitis, N and Dimitriadis, F}, title = {Prostatitis-Related Male Infertility: From Inflammation and Dysbiosis to Sperm DNA Damage.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, pmid = {41827997}, issn = {2075-4418}, abstract = {Prostatitis includes infectious and noninfectious inflammatory phenotypes that can impair male reproductive potential and may influence couple-level reproduction via seminal inflammatory and microbial exposure. This review summarizes mechanisms linking prostatic inflammation and dysbiosis to semen dysfunction and sperm DNA damage and proposes an infertility-oriented diagnostic and management framework. This is a narrative review of clinical and translational evidence addressing semen inflammation, oxidative stress, sperm DNA fragmentation (SDF), microbiome signatures, and reproductive outcomes in prostatitis (National Institutes of Health (NIH) categories I-IV). Across prostatitis phenotypes, leukocytospermia and elevated seminal cytokines (especially interleukin-8) are associated with impaired motility, altered viscosity and liquefaction, oxidative stress, and higher SDF. Persistent infection or dysbiosis may sustain immune activation and redox injury, while ductal remodeling and pain-related sexual dysfunction can further reduce natural conception. Seminal cytokines and microbes may affect female reproductive tract biology, although clinical outcome data remain limited. Prostatitis-related infertility requires evaluation beyond routine semen analysis. A biomarker-guided workup integrating inflammatory markers, oxidative stress testing, targeted microbiology (culture plus nucleic acid amplification tests when indicated), SDF testing in selected men, and imaging when obstruction is suspected can identify treatable drivers and guide timing and selection of assisted reproduction strategies. Future studies should standardize fertility endpoints and validate biomarker-guided and microbiome-directed interventions.}, }
@article {pmid41828029, year = {2026}, author = {Hamod, A and Mihaela, O and Grigore, M and Vasilache, IA and Ursu, RG and Popovici, R and Grigore, AM and Lozneanu, L and Andronic, DC and Ciorpac, M and Ciocoiu, M}, title = {Cervicovaginal Microbiome Signatures Across Cervical Disease States: A Prospective Cross-Sectional Analysis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, pmid = {41828029}, issn = {2075-4418}, abstract = {Background/Objectives: The cervicovaginal microbiome has emerged as a critical determinant of cervical health. In this study, we aimed to characterize the cervicovaginal microbiome across a spectrum of cervical health states and to identify community-level features that distinguish invasive disease from precursor states. Methods: We analyzed cervicovaginal samples of 86 patients with normal epithelium, low-grade (LSIL) and high-grade (HSIL) intraepithelial lesions, and cervical carcinoma (CCU) and available HPV genotyping. Vaginal samples were subjected to full-length 16S rRNA gene sequencing and genus-level taxonomic profiles were generated using ONT-supported workflows. Microbiome diversity and composition were assessed using Aitchison-based beta-diversity, non-parametric testing, and PERMANOVA. Differential abundance was evaluated using ANCOM-BC2 with false discovery rate correction. Disease-associated community shifts were quantified using log-ratio indices and co-occurrence network analysis. Results: Microbial diversity increased with disease severity, with cervical cancer showing the highest alpha diversity and distinct community composition. Normal samples were uniformly dominated by Lactobacillus, whereas LSIL and HSIL exhibited transitional communities with partial loss of lactobacillar dominance and increasing representation of anaerobic taxa. Cervical cancer was associated with depletion of Lactobacillus and expansion of anaerobic consortia. A Lactobacillus-to-anaerobe log-ratio declined monotonically with disease severity and robustly discriminated invasive cancer from precursor states. Microbial co-occurrence networks became progressively more structured with disease severity, transitioning to dense anaerobic networks in cervical cancer. Conclusions: Cervicovaginal microbiome signatures reflect cervical disease stage and may complement existing screening and risk stratification strategies.}, }
@article {pmid41828373, year = {2026}, author = {Imbrizi, M and Magro, DO and Santos, A and Assalin, HB and Guadagnini, D and Saad, MJA and Coy, CSR}, title = {A Developmental Perspective on the Intestinal Microbiota in Crohn's Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828373}, issn = {1422-0067}, mesh = {Humans ; *Crohn Disease/microbiology/pathology/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Animals ; }, abstract = {Crohn's disease (CD) is a chronic inflammatory disorder arising from the convergence of genetic susceptibility, immune dysregulation, environmental exposures, and perturbations of the gut microbiome. This review advances a developmental and compartment-aware framework for interpreting dysbiosis in CD, integrating spatial heterogeneity, transmural pathology, and mesenteric interactions. By synthesizing evidence on microbial composition, functional metabolism, and host-immune crosstalk, we describe a dysbiotic profile shaped by disease location, inflammatory activity, and therapeutic exposure, while also considering the emerging roles of non-bacterial members. We propose that microbiome alterations in CD reflect inflammation-driven ecosystem instability rather than a static taxonomic imbalance. Moving beyond descriptive compositional profiling toward a dynamic ecological model that incorporates disease trajectory and anatomical compartmentalization is essential to refine disease stratification and guide future microbiome-informed precision therapies.}, }
@article {pmid41828431, year = {2026}, author = {Peterson, AR and Eggenhuizen, PJ and Gan, PY and Keung, C and Ooi, J and Moore, GT and Goldberg, R}, title = {Are All Cells Created Equal? Novel Cell-Based Regenerative Therapies in Inflammatory Bowel Disease.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828431}, issn = {1422-0067}, mesh = {Humans ; *Inflammatory Bowel Diseases/therapy ; *Regenerative Medicine/methods ; Mesenchymal Stem Cells/cytology/metabolism ; Extracellular Vesicles/metabolism/transplantation ; *Cell- and Tissue-Based Therapy/methods ; Amnion/cytology ; Animals ; T-Lymphocytes, Regulatory ; Epithelial Cells/cytology ; Mesenchymal Stem Cell Transplantation ; }, abstract = {Regenerative medicine, and in particular cell-based therapies, are under investigation as therapeutics in the management of inflammatory bowel disease, where despite significant advancements in management, prolonged remission is achieved in less than half of patients experiencing these disorders. In contrast to conventional immunomodulatory medications, these therapies are hypothesised to act through multiple pathways including via regenerative mechanisms, which may enable them to break through the current therapeutic ceiling. Potential therapy candidates include mesenchymal stem cells, human amnion epithelial cells, and regulatory T-cells, as well as their derivatives including extracellular vesicles. Extensive preclinical studies have demonstrated the multi-modal nature of these therapies as well as shared and unique properties. Controversy remains regarding contradictory study outcomes and the efficacy of regenerative therapies in human trials. In this narrative review, we first examine the mechanisms of these candidate cell therapies, including signalling via cytokines and extracellular vesicles, and interactions with immune cells, stromal cells, and the microbiome to determine differences and similarities between them. The second part delves into the current state of regenerative and cell-based therapy, focusing on mesenchymal stem cell, human amnion epithelial cell, T regulatory cells, and their respective extracellular vesicles in IBD treatment. Finally, we close by identifying the major literature gaps and barriers to bringing regenerative medicines to clinical use, resulting in recommendations for future research.}, }
@article {pmid41828438, year = {2026}, author = {Magini, A and Datti, A}, title = {Curcumin Between Pleiotropic Potential and Translational Constraints.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828438}, issn = {1422-0067}, mesh = {*Curcumin/pharmacology/therapeutic use/pharmacokinetics ; Humans ; Animals ; }, abstract = {Curcumin is widely recognized for its anti-inflammatory and antioxidant properties; however, this conventional framing obscures a broader, complex, and mechanistically diverse pharmacology. Here, we advance a refined perspective that situates curcumin within a hierarchical and multilayered architecture shaped by the dynamic interplay of intrinsic chemical reactivity, metabolic transformation and exposure, and microbial modulation. From this standpoint, curcumin functions as a network-level modulator, producing context-dependent outcomes rather than uniform or linear responses. Consequently, its biological influence extends well beyond traditional paradigms, engaging pathways involved in xenobiotic metabolism, membrane transport, immune and metabolic signaling, and host-microbiome interactions, with downstream implications for drug disposition and biomarker interpretation. This complexity is further compounded by rapid clearance and limited systemic availability, although partially offset by the functional relevance of bioactive metabolites. Consistent with this pleiotropic model, clinical signals of curcumin activity tend to emerge in conditions characterized by multifactorial dysregulation, including metabolic, neurocognitive, and musculoskeletal disorders, as well as microbiome-associated alterations. Notably, human studies and meta-analyses frequently report divergent outcomes, with some trials demonstrating benefit and others showing substantial between-study heterogeneity. To reconcile these discrepancies, we advocate a High Input, Rational Integration paradigm that unifies experimental, preclinical, and clinical evidence obtained through logically rigorous and strictly consistent procedures applied across comprehensive, convergent, and reproducible datasets. Within the hierarchical organization of curcumin's pharmacology, this approach enables the synthesis of mechanistic diversity within pharmacokinetic and physiological constraints and, more broadly, provides a coherent framework for interpreting pleiotropic bioactives in human studies.}, }
@article {pmid41828445, year = {2026}, author = {Maftei, NM and Ambrose, L and Dogaru, E and Răileanu, R and Mierlan, OL and Amariței, O and Ramos-Villarroel, A and Răuță Verga, GI and Gurău, TV and Gurău, G}, title = {From Probiotics to Postbiotics-An Update on Their Biotherapeutic Potential and the Emerging Strategies in Human Health.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828445}, issn = {1422-0067}, mesh = {Humans ; *Probiotics/therapeutic use/pharmacology ; *Gastrointestinal Microbiome ; Animals ; }, abstract = {Probiotics and postbiotics have gained increasing attention in microbiome research due to their potential roles in maintaining gut homeostasis and supporting human health. While probiotics are defined as live microorganisms that confer health benefits when administered in adequate amounts, postbiotics represent preparations of inanimate microorganisms and/or their components that also exert biological effects on the host. This narrative review provides an updated overview of the current knowledge on probiotics and postbiotics, with a particular focus on their mechanisms of action, production strategies, and emerging applications in human health. The review discusses key mechanisms through which probiotics and postbiotics interact with the host, including modulation of the gut microbiota, enhancement of epithelial barrier integrity, immune system regulation, metabolic modulation, and systemic signaling pathways. Advances in production technologies, ranging from conventional fermentation to innovative inactivation and stabilization approaches, are also examined, alongside challenges related to yield optimization, stability, safety, and standardization. Although a growing body of evidence suggests potential benefits of probiotics and postbiotics in metabolic, inflammatory, gastrointestinal, and immune-related conditions, much of the available data is derived from preclinical studies or small-scale clinical trials. Consequently, their clinical efficacy, optimal dosing, and long-term safety require further validation. By integrating current findings and highlighting existing gaps in the literature, this review aims to clarify the therapeutic potential of probiotics and postbiotics and to support the development of more robust, evidence-based strategies for their application in functional foods, supplements, and future biotherapeutic interventions.}, }
@article {pmid41828495, year = {2026}, author = {Salazar-Ulbrich, N and Haro-Solis, D and Aguayo, F and Quezada-Monrás, C and Cárcamo, L and Collado, L and Carrillo-Beltrán, D}, title = {Genotoxic Bacteria and Oncogenic Viruses in Colorectal Cancer: Evidence, Gaps, and a Proposed Interaction Model.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828495}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/virology/pathology/genetics ; DNA Damage ; *Oncogenic Viruses/pathogenicity ; Animals ; *Bacteria/pathogenicity/genetics ; Carcinogenesis ; Signal Transduction ; }, abstract = {Colorectal cancer (CRC) remains a significant global health burden, with growing evidence highlighting microbial contributions to its pathogenesis. Certain genotoxigenic bacteria, such as Escherichia coli, Campylobacter jejuni, and Helicobacter pylori, produce virulence factors that induce DNA damage, genomic instability, and chronic inflammation-key features of carcinogenesis. At the same time, viruses such as JC polyomavirus (JCPyV), considered potentially oncogenic, and established oncogenic viruses like Epstein-Barr virus (EBV) and human papillomavirus (HPV) have been detected in colorectal tissues and are linked to cell cycle regulation, apoptosis, and DNA repair through their viral proteins. Intriguingly, recent findings suggest that bacterial genotoxins may promote the reactivation or transcriptional activity of persistent viruses such as JCPyV and EBV, possibly through DNA damage-induced stress and activation of NF-κB- or ATM-dependent signaling pathways. Despite these advances, interactions between oncogenic viruses and bacteria within the colon microbiome remain underexplored. This review integrates current evidence and provides future perspectives for addressing potential genotoxic collaboration between bacteria and viruses that could contribute to colorectal tumorigenesis. Elucidating these interactions could reveal novel biomarkers and therapeutic targets for the prevention and treatment of CRC.}, }
@article {pmid41828500, year = {2026}, author = {Karadachi, HH and González-Gallardo, E and Rauschenbach, L and Dinger, T and Zwanziger, D and Schmidt, B and Michel, A and Engel, A and Schock, L and Zhu, Y and Gembruch, O and Darkwah Oppong, M and Jabbarli, R and Ahmadipour, Y and Sure, U and Dammann, P}, title = {Molecular Pathways and Circulating Biomarkers in Cerebral Cavernous Malformations-A Systematic Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828500}, issn = {1422-0067}, mesh = {Humans ; *Hemangioma, Cavernous, Central Nervous System/blood/metabolism/diagnosis/genetics ; *Biomarkers/blood ; Signal Transduction ; }, abstract = {Cerebral Cavernous Malformations (CCMs) are low-flow vascular lesions located within the central nervous system, with a reported prevalence in the general population of 0.16-0.5%. Patients with CCMs may remain asymptomatic or present new onset symptoms such as seizures or focal neurological deficits often related to the occurrence of intracerebral hemorrhage. CCM may appear sporadic or as part of familial forms linked to mutations in the CCM-gene cluster, affecting endothelial cell integrity and triggering molecular cascades, including the MEKK3/KLF2/4 signaling pathway. Recent studies have highlighted the roles of inflammatory, angiogenic, and coagulation pathways alongside the emerging evidence of a gut-brain axis influencing microbiome-driven TLR4 signaling. This systematic review aims to describe molecular biomarkers associated with CCM pathophysiology, emphasizing their potential use as diagnostic and prognostic tools. Circulating plasma biomarkers such as CRP, vitamin D, and interleukins may reflect ongoing inflammatory and endothelial processes, while some imaging biomarkers like Quantitative Susceptibility Mapping (QSM) have shown a correlation with iron deposition and vascular leakage. Leveraging both circulating and imaging biomarkers may improve the therapeutic decision-making process. Further studies are encouraged to validate these findings and to facilitate the development of personalized, evidence-based strategies for the management of CCM.}, }
@article {pmid41828516, year = {2026}, author = {Liu, M and Su, N and Ma, Z and Chen, W and Zhang, Y and Yan, X and Liu, W}, title = {Meat Quality Differences Correlated with Rumen Microbiota and Lipid Metabolism in Beef Cattle vs. Castrated Cattle.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828516}, issn = {1422-0067}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lipid Metabolism ; Male ; *Red Meat/analysis ; *Gastrointestinal Microbiome ; *Meat/analysis ; Muscle, Skeletal/metabolism ; Orchiectomy ; }, abstract = {Intramuscular fat (IMF) significantly influences meat quality, particularly flavor. The gastrointestinal microbiota can regulate lipid metabolism. The relationship between intramuscular fat metabolism, rumen microbiota, and beef quality remains unclear. This study enrolled 22 30-month-old Xinjiang Brown Beef cattle, which were randomly allocated to two groups: an intact bull group (n = 15) and a castrated bull group (n = 7). All experimental animals were housed and maintained under consistent feeding and management conditions throughout the entire experimental period. By combining in vivo ultrasonography, slaughter trials, rumen microbiome diversity analysis, and metabolomics techniques, and after adjusting for covariates including intramuscular fat (IMF) content, body weight, and backfat thickness, the present study demonstrated that castration regulates muscle lipid metabolism by reshaping the composition of the rumen microbial community, thereby exerting a cascading effect on key beef quality traits. (1) Production and meat quality: Live weight, carcass weight, eye muscle area, backfat thickness, and intramuscular fat (IMF) content were significantly higher in the YN group than in the GN group (p < 0.01). Conversely, dressing percentage, shear force value, and muscle protein content were significantly lower in the YN group than in the GN group (p < 0.01 or p < 0.05). (2) Rumen microbiota-metabolite correlation: Significant differences existed in microbial composition and community structure between groups (with significant differences in both α and β diversity). Core microbes regulated by castration exhibited distinct co-variation patterns with metabolites: genera such as Anaeroplasma showed significant positive correlations with hydroxy fatty acids, while Sharpea and others showed significant negative correlations with saturated fatty acids. (3) Microbial-metabolite axis and host phenotype correlation: Axes composed of Eubacterium uniforme and others showed significant positive correlations with IMF, while Docosapentaenoic acid (22n-3) exhibited significant negative correlations with IMF. Anaeroplasma and others showed significant positive correlations with oleic acid and others, as well as BFT, while saturated fatty acids showed significant negative correlations with BFT. (4) Covariate validation: After adjusting for covariates including body weight, backfat thickness, and IMF, castration was confirmed to significantly regulate the abundance/content of core genera such as Anaeroplasma, Eubacterium uniforme, as well as key metabolites such as hydroxy fatty acids and docosapentaenoic acid (22n-3) (p < 0.05 after adjustment), making it a core driver regulating rumen microbial composition and muscle lipid metabolism. After adjustment, the regulatory effects of IMF, body weight, and backfat thickness on the aforementioned microorganisms and metabolites were no longer significant (adjusted p > 0.05). Intramuscular fat (IMF), body weight, and backfat thickness are not independent drivers but rather indirect effects resulting from castration-induced physiological state remodeling. This study did not include feeding rate measurements, which represents a limitation. Future research should incorporate this data to further validate the conclusions. This study elucidates the interactive mechanisms between rumen microbiota and their metabolites, identifies the key pathways governing intramuscular fat (IMF) deposition, pinpoints potential regulatory targets for beef quality optimization, and clarifies the intermediate regulatory mechanisms underlying the modulation of meat quality traits by castration.}, }
@article {pmid41828538, year = {2026}, author = {Chen, J and Xu, Y and Liu, Z}, title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828538}, issn = {1422-0067}, mesh = {*Gastrointestinal Microbiome ; Animals ; Biotransformation ; Mice ; *Stress, Physiological ; Fermentation ; *Metabolic Networks and Pathways ; Lactiplantibacillus plantarum/metabolism ; Metabolomics/methods ; Male ; }, abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.}, }
@article {pmid41828545, year = {2026}, author = {Čuljak, N and Oršolić, N and Odeh, D and Leboš Pavunc, A and Butorac, K and Banić, M and Novak, J and Šešelja, K and Baus Lončar, M and Ramić, S and Jurkin, T and Šušković, J and Kos, B}, title = {In Vivo Evaluation of the Effect of Limosilactobacillus fermentum MC1 and Its EPSs on the Microbiota and Inflammatory Processes in the Mouse Intestine.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828545}, issn = {1422-0067}, support = {IP-2024-05-6548//Croatian Science Foundation/ ; IP-2024-05-6548; IP-2019-04-2237//Croatian Science Foundation/ ; }, mesh = {Animals ; Mice ; *Limosilactobacillus fermentum/chemistry/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced/microbiology/pathology/drug therapy ; *Probiotics/pharmacology ; Dextran Sulfate ; *Polysaccharides, Bacterial/pharmacology ; Inflammation/microbiology ; Disease Models, Animal ; Male ; Macrophages/metabolism ; Intestines/microbiology ; Mice, Inbred C57BL ; }, abstract = {Limosilactobacillus fermentum MC1 is an exopolysaccharide (EPS)-producing strain with previously determined probiotic potential in vitro. This study aimed to investigate the in vivo capacity of the MC1 strain or its EPSs to modulate intestinal microbiota and assess its anti-inflammatory effects in both healthy and dysbiotic conditions. Therefore, Lb. fermentum MC1 and its EPSs were administered to a mouse model of dextran sulfate sodium (DSS)-induced colitis (DIC) and to a healthy group, and the effects were observed. Microbiome analysis was used to detect taxonomic differences between treatments. According to the results, administration of the MC1 strain and MC1-EPSs significantly altered gut microbiome composition at different taxonomic levels. The most notable effect was an increased relative abundance of Firmicutes and decreased levels of Candidatus saccharibacteria. Llb. fermentum MC1, and its EPS administration positively affected several disease parameters: reduced disease activity index (DAI), reduced mouse colitis histology index (MCHI), reduced expression of inflammation-related genes and levels of bleeding, and induced polarization of M1 macrophages to the M2-like macrophage phenotype in the DIC mice. These results, along with those related to the induction of antioxidant enzymes and changes in NF-κB-related gene expression, suggest that strain MC1 and MC1-EPSs could be further investigated for their capacity to alleviate DSS-induced histopathological changes and modulate pro-inflammatory cytokine gene expression in colon tissue, which positively correlates with the secretion of inflammatory cytokines, the delay of intestinal inflammation and the maintenance of intestinal barrier function. The obtained data provide a basis for further research into the potential application of intact or microencapsulated Llb. fermentum MC1 cells and its EPSs in colitis therapy.}, }
@article {pmid41828553, year = {2026}, author = {Alba, C and Palomino, L and Vergara, B and Rodríguez-Belvis, MV and Aragón, A and Zaghlul, MADC and Jurado, R and Martín-Fernández, C and Vázquez-Gómez, JA and González-Vicent, M and Molina-Angulo, B and Sánchez-Llorente, P and García-Hernández, P and Rodríguez, JM and Muñoz-Codoceo, RA and Herranz, C}, title = {Metataxonomic Analysis and Fatty Acid Profiling of Feces from Children Undergoing Hematopoietic Stem Cell Transplantation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828553}, issn = {1422-0067}, support = {XVIII//Mutua Madrile&#xf1;a/ ; PR17/24-31883//Comunidad de Madrid/ ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Feces/microbiology/chemistry ; Child ; *Graft vs Host Disease/etiology/microbiology ; Male ; Female ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/analysis ; Child, Preschool ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Infant ; Bacteria/genetics/classification ; *Fatty Acids ; }, abstract = {Allogeneic hematopoietic stem cell transplantation (HSCT) is a medical procedure to treat hematologic malignancies and restore bone marrow function. However, this approach may lead to graft-versus-host disease (GvHD), a major cause of mortality and morbidity after allogeneic HSCT. Some studies have suggested the involvement of gut microbiota in the development and prognosis of GvHD. In this context, the main objective of this study was to compare the fecal microbiome composition and short-chain profile of pediatric patients who underwent successful HSCT, developed GvHD or died. The bacterial composition was analyzed using 16S rRNA gene sequencing, while short-chain fatty acids (SCFAs) were quantified by gas chromatography. Fecal samples at engraftment were mainly characterized by a loss of bacterial diversity, a depletion of sequences belonging to the genus Blautia and significantly lower concentrations of fecal butyrate and acetate compared with those obtained before HSCT and 100 days after HSCT. Our findings confirm that children experiencing GvHD after HSCT have distinct gut microbiota and SCFA profiles, which might contribute to developing new microbiota-targeted strategies for GvHD prevention during HSCT procedures.}, }
@article {pmid41828603, year = {2026}, author = {Reytor-González, C and Román-Galeano, NM and Aules-Curicama, LS and Cevallos-Villacis, CD and González, E and Jima Gavilanes, D and Horowitz, R and Simancas-Racines, D}, title = {The Oral-Gut-Immune-Nutrition Axis in Rheumatoid Arthritis: Molecular Mechanisms and Therapeutic Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828603}, issn = {1422-0067}, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; Diet ; Animals ; *Mouth/microbiology/immunology ; }, abstract = {Rheumatoid arthritis is a chronic systemic autoimmune disease that arises from complex interactions among genetic susceptibility, environmental factors, and immune dysregulation. Growing evidence indicates that microorganisms residing in the oral cavity and gastrointestinal tract, together with dietary factors, play a central role in shaping inflammatory and autoimmune responses in rheumatoid arthritis, forming an interconnected microbiome-immune-nutrition axis. Alterations in the composition and function of oral and intestinal microbial communities are associated with disruption of mucosal barrier integrity, activation of innate and adaptive immune pathways, increased differentiation of proinflammatory T lymphocyte subsets, and loss of immune tolerance that promotes autoantibody production. In addition, microbially derived metabolites, particularly short-chain fatty acids, provide a mechanistic link between microbial ecology, immune regulation, and bone metabolism. Diet represents a key upstream modulator of this axis. Dietary patterns rich in anti-inflammatory nutrients support microbial diversity and immunoregulatory metabolite production, whereas diets high in processed foods and saturated fats favor proinflammatory microbial profiles. Accumulating clinical evidence suggests that nutritional strategies and microbiome-targeted dietary interventions may reduce systemic inflammation and disease-related comorbidities when used alongside standard pharmacological treatments. Taken together, the microbiome-immune-nutrition axis represents a modifiable and clinically meaningful target in rheumatoid arthritis, emphasizing the need for interdisciplinary research and well-designed clinical trials to translate these insights into personalized approaches for disease management. The aim of this review is to integrate current mechanistic and clinical evidence on the interactions between the microbiome, immune system, and nutrition in rheumatoid arthritis, with a focus on their pathogenic relevance, therapeutic potential, and implications for personalized, diet-based interventions.}, }
@article {pmid41828607, year = {2026}, author = {Hsu, CN and Tain, YL}, title = {Melatonin as a Redox Modulator in Developmental Programming: Implications for Cardiovascular-Kidney-Metabolic Risk.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828607}, issn = {1422-0067}, support = {114-2314-B-182A-048 and 114-2314-B-182A-036-MY3.//National Science and Technology Council/ ; }, mesh = {*Melatonin/pharmacology/metabolism ; Humans ; Pregnancy ; Animals ; *Fetal Development/drug effects ; *Cardiovascular Diseases/metabolism/etiology/prevention &amp; control ; Female ; Oxidation-Reduction/drug effects ; Oxidative Stress/drug effects ; Kidney/metabolism/drug effects ; *Kidney Diseases/metabolism/prevention &amp; control ; Antioxidants/pharmacology ; *Metabolic Diseases/metabolism/prevention &amp; control/etiology ; Prenatal Exposure Delayed Effects ; }, abstract = {Melatonin, a multifunctional hormone with antioxidant, anti-inflammatory, and chronobiotic effects, is essential for a healthy pregnancy and fetal development. In the context of the Developmental Origins of Health and Disease (DOHaD), excessive oxidative stress acts as a key driver of maladaptive fetal programming, increasing lifelong susceptibility to cardiovascular, kidney, and metabolic (CKM) disorders. Importantly, most evidence derives from rodent models, and the protective effects of maternal melatonin supplementation appear partial and model-dependent rather than universal. Experimental studies indicate that maternal melatonin supplementation can prevent programmed hypertension, renal dysfunction, and metabolic derangements by restoring redox homeostasis, influencing epigenetic and nutrient-sensing pathways, and modulating the gut microbiome. Early clinical investigations in pregnancies complicated by preeclampsia or intrauterine growth restriction suggest that melatonin is well tolerated, improves placental function, and benefits neonatal outcomes. However, optimal dosing and long-term safety for offspring remain to be established. This review synthesizes mechanistic and translational evidence, framing melatonin as an integrative biological mediator with potential to guide preventive strategies and mitigate the intergenerational risk of CKM syndrome.}, }
@article {pmid41828628, year = {2026}, author = {Parise-Vasco, JM and Angamarca-Iguago, J and Cagua-Ordoñez, J and Cabrera, B and Jima Gavilanes, D and Horowitz, R and Reytor-González, C and Simancas-Racines, D}, title = {Traditional Foods, Oral Microbiome, and Systemic Health: Molecular Pathways Linking Nutrition and Oral Disease Prevention.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828628}, issn = {1422-0067}, mesh = {Humans ; *Microbiota ; *Periodontal Diseases/prevention &amp; control/microbiology ; *Mouth/microbiology ; Oral Health ; Diet ; }, abstract = {Periodontal disease affects 10-50% of the global population and is associated with various systemic conditions, including diabetes, cardiovascular disease and adverse pregnancy outcomes. Emerging evidence highlights diet as a critical, modifiable factor that influences the composition of the oral microbiome and periodontal health. This narrative review explores the molecular mechanisms through which traditional foods modulate the oral microbiome and contribute to oral and systemic health. A comprehensive literature search was conducted in PubMed/MEDLINE, the Cochrane Library, LILACS and Epistemonikos, prioritizing systematic reviews, meta-analyses and randomized controlled trials. The oral microbiome harbors over 700 bacterial species, and dysbiosis, characterized by pathogen enrichment, drives periodontal inflammation. Anti-inflammatory dietary patterns, including the Mediterranean diet, demonstrate protective effects. Omega-3 fatty acids, vitamins C and D, polyphenols and dietary fiber support periodontal health, whereas refined carbohydrates, saturated fats and pro-inflammatory nutrients can exacerbate disease. Probiotics show promise as an adjunctive therapy. However, the translation to clinical guidelines is impeded by methodological challenges, including the limited number of randomized controlled trials with oral endpoints, confounding by hygiene practices, and the lack of standardized multi-omics approaches. Nutritional counselling should be integrated into periodontal care as a modifiable risk factor. Future research priorities include precision nutrition approaches, the validation of salivary biomarkers, and interprofessional collaboration between dental and nutrition professionals.}, }
@article {pmid41828632, year = {2026}, author = {Kastuganova, K and Askerov, A and Szabó, A and Barteneva, NS}, title = {Systematic Review: Long-Read Sequencing in Algal Studies.}, journal = {International journal of molecular sciences}, volume = {27}, number = {5}, pages = {}, pmid = {41828632}, issn = {1422-0067}, support = {AP26104995//Ministry of High Education and Sciences, Kazakhstan/ ; FDCRGP grant #SSH2024005//Nazarbayev University/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; Symbiosis/genetics ; Microbiota/genetics ; }, abstract = {Long-read sequencing (LRS) has transformed life science research by introducing third-generation sequencing (TGS) platforms applicable across various research fields, including environmental sciences. In the past decade, LRS platforms have been utilized to extensively study algal systems by improving genomic approaches such as metabarcoding, chromosome-level genome and pangenome assemblies, as well as providing new insights into algae-associated microbiomes and host-symbiont interactions. This review aims to discuss recent advancements in LRS in algal research. To achieve this aim, a systematic review was conducted according to the PRISMA 2020 guidelines and across three electronic databases (Web of Science, Scopus, and Google Scholar), with additional citation searching for relevant studies in four key algal research areas: metabarcoding, genomics, pangenomics, and host-symbionts interactions. Following the inclusion and exclusion criteria, only 51 studies were selected for this review. Throughout the review, we summarize the challenges of short-read sequencing (SRS) and discuss how LRS platforms address these challenges in algal studies. Furthermore, we discuss the future of LRS and explore how artificial intelligence (AI) can advance research on algal biology and ecology.}, }
@article {pmid41826313, year = {2026}, author = {Gudnadottir, U and Prast-Nielsen, S and Wagner, N and Hugerth, LW and Alderheim, VK and Antony, AT and Du, J and Guerreiro, JR and Boulund, F and Wiberg-Itzel, E and Engstrand, L and Schuppe-Koistinen, I and Brusselaers, N and Fransson, E}, title = {Machine learning and the role of the vaginal and fecal microbiome in miscarriage: a matched case-control study.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00956-2}, pmid = {41826313}, issn = {2055-5008}, support = {Region Stockholm, Dnr 2020-0471//ALF/ ; Region Stockholm, Dnr 2020-0471//ALF/ ; Region Stockholm, Dnr 2020-0471//ALF/ ; Dnr M21-0153//&#xc5;ke Wiberg Stiftelse/ ; Dnr M21-0153//&#xc5;ke Wiberg Stiftelse/ ; Dnr M21-0153//&#xc5;ke Wiberg Stiftelse/ ; Dnr 2023-02868//Vetenskapsr&#xe5;det/ ; Dnr 2023-02868//Vetenskapsr&#xe5;det/ ; Dnr 2023-02868//Vetenskapsr&#xe5;det/ ; KAW 2020.0239//SciLifeLab &amp; Wallenberg Data Driven Life Science Program/ ; KAW 2020.0239//SciLifeLab &amp; Wallenberg Data Driven Life Science Program/ ; }, abstract = {Miscarriage occurs in approximately 15% of all pregnancies, and recent studies have suggested a potential role of the microbiome. A nested case-control study from the Swedish Maternal Microbiome cohort was conducted, including 34 participants who sent at least one vaginal or fecal microbiome sample and questionnaire data before miscarrying (n = 34), and matched controls (n = 105 for regression models, n = 27 for machine learning models). Non-vaccine type HPV (aOR 3.95, 95%CI 1.04-15.06) and vaginal microbiome with community state type (CST) II (aOR 6.52, 95%CI 1.58-26.98) or CST-IVB (aOR 4.18, 95%CI 1.08-16.18) in early pregnancy were associated with an increased risk of miscarriage. Furthermore, we explored six machine learning algorithms using 70% of the cohort for training and 30% for testing, for the prediction of miscarriage using vaginal (AUROC 85%), fecal (AUROC 81%) and questionnaire (AUROC 82%) data separately and combined (AUROC 82%). Our results highlight the urgency of HPV screening and vaccine development for women's reproductive health. Despite limitations, including a small number of miscarriage cases, our results indicate the potential for both vaginal and fecal microbiomes in the prediction of miscarriage.}, }
@article {pmid41826284, year = {2026}, author = {Zhang, R and Feng, R and Wang, J and Chen, Y and Liu, H and Zhu, Q and Tian, H and Qin, C and Teng, J and Tang, B and Wu, M and Zeng, J and Wu, E and Ding, X and Wang, X}, title = {Gut microbiota modulation via repeated donor fecal transplantation improves motor and gastrointestinal symptoms in drug-naïve Parkinson's disease: a randomized phase 2 trial.}, journal = {Signal transduction and targeted therapy}, volume = {11}, number = {1}, pages = {}, pmid = {41826284}, issn = {2059-3635}, support = {82201407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82122022,82471272, 82171248, 82471350, 82201407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82130035, 82371308//National Natural Science Foundation of China (National Science Foundation of China)/ ; R04017//Sun Yat-sen University (SYSU)/ ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Parkinson Disease/therapy/microbiology/pathology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; }, abstract = {The gut-brain axis is increasingly recognized as a critical contributor to Parkinson's disease (PD) pathogenesis, yet the therapeutic impact of microbiota modulation remains unclear due to lack of clinical trials in drug-naïve patients. We conducted a randomized, double-blind, placebo-controlled phase 2 trial to evaluate the safety, tolerability, and efficacy of repeated donor fecal microbiota transplantation (dFMT) in de novo PD. FMT was administered for seven days (200 mL on days 1-3; 50 mL on days 4-7) per 4-week cycle. Seventy-two patients were randomized 1:1 to receive dFMT or autologous FMT (aFMT), and 66 completed the trial. At 35 weeks, the dFMT group showed significant improvement in motor symptoms (mean change in Unified Parkinson's Disease Rating Scale [UPDRS] III: -3.8 vs. +0.1; p = 0.0001) and a substantially greater reduction in constipation severity (dFMT vs. aFMT: -6.5 vs. -0.7; p < 0.0001), accompanied by improved quality-of-life scores. Microbiome profiling revealed greater similarity to donor composition and a marked reduction in Escherichia-Shigella, correlating with decreased colonic α-synuclein aggregation (r = 0.3775, p = 0.0277), supporting a gut-brain mechanistic link. Biochemical analyses showed elevated fecal dopamine and 3,4-dihydroxyphenylacetic acid levels, while histological assessments demonstrated strengthened epithelial barrier integrity with increased E-cadherin expression. All adverse events were mild and self-limited; no serious treatment-related events were observed. These findings demonstrate that repeated dFMT is safe, well tolerated, and yields clinically meaningful motor and gastrointestinal improvements in drug-naïve PD, providing integrated mechanistic and clinical evidence that microbiota-targeted modulation represents a promising nonpharmacologic therapeutic strategy for neurodegenerative disease. Trial registration: Chinese Clinical Trial Registry, ChiCTR2200064151.}, }
@article {pmid41825736, year = {2026}, author = {Ferro, LE and Bittinger, K and Trudo, SP and Kim, JK and Hunt, CM and Brewer, B and Polson, SW and Trabulsi, JC}, title = {Influence of Singular First Foods on the Infant Gut Microbiome: A Randomized Controlled Trial.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101470}, doi = {10.1016/j.tjnut.2026.101470}, pmid = {41825736}, issn = {1541-6100}, abstract = {BACKGROUND: The gastrointestinal microbiome, integral to immune function, inflammation, and metabolism, becomes less malleable with age, making early dietary exposures, particularly first complementary foods (CFs), important in its development.<br><br>OBJECTIVE: To evaluate the effect of different first CFs on the infant gut microbiome in a pilot, randomized, controlled trial.<br><br>METHODS: Vaginally delivered, exclusively human milk (HM) fed infants (n=43) with no prior CF exposure were randomized to one of four groups (oatmeal cereal, beef, carrot, prune) (NCT05492253). Infants were fed the randomized food (with HM) for one week (phase 1), followed by oatmeal cereal for another week (phase 2). Daily stool samples were collected and sequenced (full-length V1-V9 16S rRNA gene amplicons).<br><br>RESULTS: In phase 1, oatmeal cereal increased observed ASVs compared to beef (p=0.024). Prune increased Bacteroides ovatus (p=0.001) and Klebsiella pneumoniae (p=0.011), while oatmeal cereal increased Enterococcus spp. (p=0.030) relative to beef. In phase 2, oatmeal cereal following beef resulted in increased Shannon diversity (p=0.0497) and following prune increased Faith's phylogenetic diversity (p=0.015). Unweighted UniFrac distances differed when oatmeal cereal followed prune compared to continuing oatmeal cereal (p=0.042). Veillonella infantium increased with continued oatmeal cereal consumption compared to beef (p=0.002) or carrot (p=0.002) followed by oatmeal cereal. After prune, oatmeal cereal increased Lactobacillus rhamnosus and Enterococcus faecalis, and decreased Klebsiella pneumoniae and Clostridium neonatale (all p<0.05).<br><br>CONCLUSIONS: Beef as a CF is nutritionally desirable as it contains important minerals lacking in HM, yet resulted in a less diverse microbial profile. Since fruit and vegetables yielded comparable diversity to cereal, future research should investigate whether introducing meat alongside fruits and vegetables offers a balanced alternative to early reliance on cereals and further evaluate how first foods influence taxa abundance at the genus and species level and the resulting immune-related and metabolic pathways.}, }
@article {pmid41825693, year = {2026}, author = {Zhao, H and Yin, J and Dong, Y and Feng, Q and Liu, H and Han, S and Xie, Z and Xu, L}, title = {Metatranscriptomics uncovers host immune and microbiome signatures specific to and shared between Human Metapneumovirus and Respiratory Syncytial Virus infections in children.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.03.002}, pmid = {41825693}, issn = {1995-820X}, abstract = {Human metapneumovirus (hMPV) is a prevalent respiratory virus in children with acute lower respiratory tract infections that is highly homologous with respiratory syncytial virus (RSV), the primary etiological agent of pediatric upper and lower respiratory tract infections. Although hMPV and RSV are the only human pathogens within the Pneumoviridae family and share similar clinical manifestations, the mechanisms underlying their divergent pathogenicity remain poorly understood. In this study, we performed transcriptomic analysis on clinical respiratory samples collected between 2017 and 2019 from 61 children: including hMPV-infected, RSV-infected and healthy controls. This analysis revealed a shared upregulation of antiviral response pathways, including neutrophil activation and signaling mediated by interferons and interleukins. Conversely, cilium organization and assembly pathways were commonly downregulated in both infections. hMPV infection uniquely upregulated pathways associated with extracellular component activity, ion channel complexes, and neuroactive ligand‒receptor interactions. In contrast, pathways related to membrane rafts and membrane microdomains were uniquely downregulated in hMPV-infected patients. Analysis of differentially expressed immune-related and interferon-stimulated genes revealed significant hMPV-specific increases in EGF and FCGR1A, alongside decreased EPAS1 expression. The genes that were uniquely upregulated during hMPV infection were enriched in cytokine production regulation, cytokine‒cytokine receptor interactions, and PI3K/AKT signaling, whereas those that were uniquely downregulated involved the viral entry and endocytic vesicle pathways. Both hMPV infection and RSV infection significantly increased the proportions of M1 macrophages and neutrophils but decreased the proportions of M0 and M2 macrophages. Notably, hMPV infection resulted in a significant increase in monocytes and activated NK cells coupled with a decrease in resting memory CD4[+] T cells, compared with RSV infection. The results also revealed a significantly greater relative abundance of Prevotella salivae in the hMPV infection group, whereas Streptococcus salivarius and Streptococcus mitis were enriched in the RSV group. These distinct immune and microbial signatures provide novel insights into the pathogenesis of pediatric hMPV and RSV infections.}, }
@article {pmid41825563, year = {2026}, author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G}, title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134417}, doi = {10.1016/j.biortech.2026.134417}, pmid = {41825563}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.}, }
@article {pmid41825556, year = {2026}, author = {Zeng, T and Niu, C and Cheng, J and Pan, Y and Lu, J and Wu, M and Li, W and Liu, Y and Zhao, D}, title = {Effect of chronic intermittent hypoxia on apoptosis based on microbiome-based co-metabolomics.}, journal = {Experimental neurology}, volume = {}, number = {}, pages = {115726}, doi = {10.1016/j.expneurol.2026.115726}, pmid = {41825556}, issn = {1090-2430}, abstract = {BACKGROUND: Obstructive sleep apnea (OSA) is linked to metabolic dysfunction, but the role of chronic intermittent hypoxia (CIH)-induced mitochondrial apoptosis remains unclear. This study investigated whether CIH-induced lung apoptosis involves gut microbiota and metabolite changes.<br><br>METHODS: Mice exposed to CIH were analyzed using 16S rRNA sequencing and GC-MS metabolomics. Apoptosis markers (Drp1, BAX, Bcl-2, Caspase-3) were assessed via Western blot, immunohistochemistry, TUNEL, and electron microscopy.<br><br>RESULTS: (1) CIH disrupted fatty acid metabolism (e.g., decreased arachidonic acid, increased nervonic acid), reversible with Mdivi-1 (mitochondrial fission inhibitor). (2) CIH altered gut microbiota, partially restored by Mdivi-1. (3) KEGG analysis revealed apoptosis, autophagy, and P53 pathway changes. (4) CIH reduced mouse weight and cognitive performance; Mdivi-1 improved these. (5) CIH increased BAX/Caspase-3 and decreased Bcl-2, worsening mitochondrial damage-exacerbated by CCCP (apoptosis inducer) but mitigated by Mdivi-1.<br><br>CONCLUSIONS: Mdivi-1 alleviated CIH-induced gut dysbiosis, apoptosis, and mitochondrial damage, while CCCP worsened these effects. Gut microbiota and metabolic changes may mediate CIH-induced lung apoptosis.}, }
@article {pmid41825506, year = {2026}, author = {Tang, Y and Guan, L and Li, Z and Li, R and Liu, S and Chen, B and Jin, Y and Tao, F}, title = {Synbiotics inhibits gut microbiome perturbation-induced prolongation of migraine-like pain by restoring short-chain fatty acid signaling.}, journal = {Neuropharmacology}, volume = {}, number = {}, pages = {110914}, doi = {10.1016/j.neuropharm.2026.110914}, pmid = {41825506}, issn = {1873-7064}, abstract = {Migraine is the most common disabling primary headache disorder. However, currently available therapies for migraine pain are still limited. In the present study, we investigated the effects of gut microbiome perturbation and synbiotics supplementation on migraine-like pain in male mice and explored the underlying mechanism. We observed that the supplementation with synbiotics inhibited Broad-spectrum antibiotics (ABX)-prolonged migraine-like pain. Using 16S rRNA sequencing, we analyzed bacterial composition and abundance in the mouse gut, and we found that the supplementation with synbiotics recovered ABX-reduced Bacteroidota, which produces acetate and propionate in the gut, and such supplementation increased the levels of short-chain fatty acids (SCFAs) in the gut. SCFAs, specifically acetate and propionate, reversed the ABX-caused prolongation of migraine-like pain. We further found that ABX treatment decreased the expression of SCFA receptors in the gut and the supplementation with synbiotics restored the expression of SCFA receptor FFAR2, but not FFAR3, in the gut. Moreover, genetic deletion of FFAR2 in the Ffar2 knockout mice blocked the effect of synbiotics on migraine-like pain. Our results suggest that gut microbiome perturbation contributes to the prolongation of migraine-like pain and synbiotics can inhibit such pain prolongation by recovering disturbed gut microbiome and restoring SCFAs-FFAR2 signaling.}, }
@article {pmid41825408, year = {2026}, author = {Zhou, X and Li, P and Cao, Y and Tang, L and Ma, J and Wang, J and Ling, W}, title = {Glomalin related soil protein enhances the capacity of PAH natural attenuation in soils through modulation of soil organic matter and microbiota.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129309}, doi = {10.1016/j.jenvman.2026.129309}, pmid = {41825408}, issn = {1095-8630}, abstract = {Soil contamination by polycyclic aromatic hydrocarbons (PAHs) remains a widespread concern. Glomalin-related soil protein (GRSP), a notable soil organic component secreted by arbuscular mycorrhizal fungi, contributes positively to soil carbon sequestration. While its influence on the fate of inorganic pollutants has been recognized, the specific mechanisms by which GRSP regulates PAHs in soil are still poorly understood. Therefore, this study investigated how GRSP strengthens PAH natural attenuation in contaminated soil through a microcosm experiment, combined with sequential SOM fractionation and high-throughput sequencing. Our results demonstrated that GRSP significantly promoted PAH attenuation, with the removal of phenanthrene and pyrene increasing by 0.09%-1.03% and 1.66%-73.40%, respectively. GRSP addition directly and indirectly increased the content of key SOM components, including humic acid, fulvic acid and dissolved organic matter, thereby altering PAH distribution in soil. Meanwhile, high-throughput sequencing and functional gene predictions analyses further revealed that GRSP enriched indigenous PAH-degrading bacteria (e.g., Massilia, Gemmatimonas, and Mycobacterium) and increased functional genes (e.g., nidA, phe) copy number, ultimately facilitating PAH removal via the protocatechuic acid pathway. These findings clarify the auxiliary role of GRSP in PAH remediation and propose a novel strategy for enhancing soil self-remediation through the management of GRSP level or AMF activity.}, }
@article {pmid41825198, year = {2026}, author = {Li, Y and Fan, D and Bing, X and Kang, N and Wang, Y and Wei, Y and Zuo, YY}, title = {The oral-systemic interface of micro- and nanoplastics.}, journal = {Advances in colloid and interface science}, volume = {353}, number = {}, pages = {103863}, doi = {10.1016/j.cis.2026.103863}, pmid = {41825198}, issn = {1873-3727}, abstract = {Microplastics (MPs, <5 mm) and nanoplastics (NPs, <1 μm) are pervasive pollutants increasingly recognized as emerging threats to human health. While their systemic impacts on the gastrointestinal, respiratory, reproductive, and immune systems are well documented, their relevance to oral health has received limited attention. The oral cavity represents both a primary site of exposure, via ingestion, inhalation, and contact with dental and personal care products, and a sensitive biological interface where local toxicity may arise. This review synthesizes evidence on oral sources of MPs/NPs, including toothbrushes, toothpastes, orthodontic appliances, restorative composites, prostheses, implants, and impression materials. We highlight potential links to oral diseases such as gingivitis, periodontitis, peri-implantitis, denture stomatitis, oral cancer, and xerostomia. Mechanistic studies demonstrate that MPs/NPs trigger oxidative stress, inflammatory signaling, immune dysregulation, microbiome disturbances, and endocrine disruption, with implications for both local pathology and systemic dissemination. Once crossing oral and gastrointestinal barriers, these particles can accumulate in distant organs, exacerbating chronic inflammatory and metabolic disorders. We conclude by outlining key research gaps, emphasizing the need for advanced detection methods, sustainable dental materials, and translational studies to clarify clinical relevance. Collectively, this review underscores the oral cavity as a critical but underexplored interface for plastic particle exposure.}, }
@article {pmid41824752, year = {2026}, author = {Angelakopoulou, EA and Angelakopoulou, IM and Tsolaki, F}, title = {Comment on "intratumorally specific microbial-derived lipopolysaccharide contributes to non-small cell lung cancer progression".}, journal = {Virulence}, volume = {}, number = {}, pages = {2646024}, doi = {10.1080/21505594.2026.2646024}, pmid = {41824752}, issn = {2150-5608}, abstract = {This Letter to the Editor highlights how the finding that LPS drives NSCLC progression may help explain recurring observations in the lung cancer - microbiome literature and proposes next steps, including exploration of specific microbial factors potentially regulated by the mechanisms described in Sha et al.'s article.}, }
@article {pmid41824750, year = {2026}, author = {Kobelyatskaya, AA and Tkacheva, ON and Melnitskaia, AA and Ilyushchenko, AK and Machekhina, LV and Strazhesko, ID and Moskalev, A}, title = {Blood biochemical and gut microbiotic neural network models forecasting human biological age.}, journal = {Aging}, volume = {18}, number = {1}, pages = {102-116}, doi = {10.18632/aging.206360}, pmid = {41824750}, issn = {1945-4589}, abstract = {Biological age reflects the current state of the body, considering the aspects of lifestyle, environment, and hereditary component. Currently there is no universal formula for determining it, but there are markers that can be used to calculate it. This study aims to develop and compare two models for calculating biological age based on laboratory blood tests and composition of gut microbiota. The biochemical model of biological age uses 7 indicators and is gender-specific (general - cystatin-C, IGF-1, DHEAS, only for females - homocysteine, urea, glucose, zonulin, only for males - HbA1c, NT-proBNP, free testosterone, hs-CRP). The microbial model requires the input of percentages of 45 bacterial species as indicators of the gut microbiota. Both methods demonstrate high predictive accuracy (MAE ~ 6 years, R2 > 0.8) and the degree of agreement of assessments both with each other and with PhenoAge (correlation > 0.89). For enhanced interpretability of the models, we applied the SHAP explanation algorithm, which made which allowed us to evaluate the contribution of each predictor to the final assessment of the biological age.}, }
@article {pmid41824481, year = {2026}, author = {Feng, Z and Wang, K and Wang, X and Zhao, B and Huang, Z and Ding, S and Zhang, J and Sun, M and Ma, M and Zhao, Y and Cui, Y and Song, Z and Tao, Y}, title = {Targeting the Gut-Retina Axis in Age-Related Retinopathies: Microbiome-Immunometabolic Pathways and Gerotherapeutic Perspectives.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2025.1248}, pmid = {41824481}, issn = {2152-5250}, abstract = {Age-related retinopathies refer to a spectrum of retinal disorders primarily associated with aging, characterized by chronic oxidative stress, sustained inflammatory responses, and progressive visual impairment. Aging significantly influences the gut-retina axis by altering the gut microbiota and increasing intestinal permeability, thereby contributing to retinal pathology. The gut microbiota undergoes continuous coevolution with the host, and its composition and function are altered with advancing age. A persistent imbalance within the gut microbial community, known as dysbiosis, can increase intestinal permeability. This thereby allows microbes and their metabolites to more easily cross the epithelial barrier. These microbiota and metabolites can migrate to the retina via the gut-retina axis, potentially eliciting inflammatory responses and immune dysregulation. Such mechanisms have been involved in the occurrence and progression of diverse age-related retinopathies. This review delves into these bidirectional interactions within the gut-retina axis and their intricate implications for the pathogenesis of age-related retinopathies. A central focus is the pivotal role of gut microbiota and their metabolites in inducing retinal inflammation and immunological dysregulation. We endeavor to elucidate the synergistic mechanisms through which the neural, immune, and endocrine systems influence the pathology of age-related retinopathies. Furthermore, recent therapeutic trials targeting gut microbiota for the management of retinopathy are also discussed. These findings would provide novel insights and robust theoretical foundation for future advancement of innovative therapeutic strategies.}, }
@article {pmid41824463, year = {2026}, author = {Cerckel, G and Dereinne, D and Ledesma-García, L and Meuric, V and Desguin, B and Mignolet, J and Soumillion, P and Hols, P}, title = {Non-peptide dysbiosis metabolites reprogram a peptide quorum-sensing receptor to induce sustained predation in beneficial streptococci.}, journal = {PLoS biology}, volume = {24}, number = {3}, pages = {e3003718}, doi = {10.1371/journal.pbio.3003718}, pmid = {41824463}, issn = {1545-7885}, abstract = {Cytoplasmic receptors of the RRNPPA superfamily mediate peptide-based quorum sensing in Gram-positive bacteria and are thought to be activated exclusively by short, unmodified pheromones. Here, we show that the RRNPPA regulator ComR in the human commensal Streptococcus salivarius can also be activated by a distinct class of non-peptide metabolites. A screen of ~200 organic compounds identified hydroxyphenylacetic acid (HPAA)-a microbial dysbiosis-associated catabolite-as a potent activator of ComR. Using biochemical and genetic approaches, we demonstrate that HPAA and related aromatic carboxylic acids bind the canonical pheromone pocket and induce sustained expression of predatory bacteriocins, while bypassing the competence program triggered by the native peptide signal (XIP). We further show that the oral pathogen Porphyromonas gingivalis produces physiologically relevant amounts of (H)PAA, enabling metabolite-driven activation of predation in S. salivarius. These findings reveal an unexpected capacity of RRNPPA receptors to sense both peptide and metabolite cues, uncovering a chemical mode of interspecies communication that links dysbiosis to predatory behavior in the oral microbiome.}, }
@article {pmid41824007, year = {2026}, author = {Zhu, S and Zou, M and Wu, Q and Zou, Y and Tan, T and Huang, Z and Gong, Z and Luo, H and Dong, X}, title = {The Gut-Liver Axis in Metabolic Dysfunction-Associated Steatotic Liver Disease: From Mechanistic Insights to Precision Therapeutics.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71687}, doi = {10.1096/fj.202503607RR}, pmid = {41824007}, issn = {1530-6860}, support = {2024GXNSFAA010247//Guangxi Natural Science Fundation/ ; 2024GXNSFBA010227//Guangxi Youth Science Fun Project/ ; QYY-GCRC-202301//Research Foudation for Advanced Talents of The people's and Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Science/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Liver/metabolism/pathology ; *Fatty Liver/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation/methods ; *Precision Medicine/methods ; Dysbiosis/microbiology ; Animals ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) has become the most prevalent chronic liver condition globally, shifting the diagnostic paradigm toward an affirmative, metabolism-focused framework. The gut-liver axis is a central pathophysiological pathway. This review aims to synthesize revolutionary advances from 2023 to 2025 in understanding and treating MASLD by focusing on the gut microbiome's role. This comprehensive review analyzes cutting-edge research published between 2023 and 2025. We examined evidence from landmark clinical trials, developments in next-generation probiotics, the integration of artificial intelligence (AI) with multiomics for diagnostics, and studies clarifying the interplay between host genetics and the microbiome in MASLD pathogenesis. Causal links between gut dysbiosis and MASLD pathology are now firmly established. Fecal microbiota transplantation (FMT) effectively prevents hepatic encephalopathy recurrence, and next-generation probiotics like Akkermansia muciniphila have entered MASLD-specific trials. AI-driven diagnostic tools have achieved regulatory qualification from the European Medicines Agency. Furthermore, host genetics, particularly PNPLA3 variants, are shown to not only predispose to MASLD but also shape specific microbial communities that functionally contribute to disease progression. The field is rapidly advancing from correlative observations to causal evidence, enabling the development of microbiome-based biomarkers and personalized therapies. The future of MASLD management lies in precision strategies, such as bacteriophage therapy and functionally defined probiotics, which integrate metabolic, microbial, and genetic factors into individualized care, heralding a new therapeutic era.}, }
@article {pmid41823868, year = {2026}, author = {Xing, Y and Zhao, X and Li, X and Zheng, J and Huang, W}, title = {Age-Dependent Alterations in Intestinal Barrier Function: Involvement of Microbiota and TLR4 Signaling.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823868}, issn = {2079-7737}, support = {BE2021705//Jiangsu Provincial Key Research and Development Program/ ; }, abstract = {The intestinal barrier undergoes profound changes with age, impacting local immunity and systemic health, yet the mechanisms coordinating immune and microbial dynamics across the lifespan remain incompletely understood. Toll-like receptor 4 (TLR4) serves as a key mediator of host-microbiota interactions. This study investigated age-related changes in barrier function and the role of TLR4 using C57BL/6J and TLR4 knockout (TLR4[-/-]) mice across key developmental stages: pups (postnatal day 9), adults (2-4 months), middle-aged (7-9 months), and old (16-19 months). Through a multi-layered approach integrating histology, microbiome profiling, short-chain fatty acid (SCFA) analysis, cytokine quantification, ex vivo functional assays, and transcriptomics, we identified a multi-phase process of intestinal remodeling. Pup-P9 mice exhibited immature colonic structure, a simple microbiota dominated by Firmicutes and Proteobacteria, and undetectable acetic acid level. Adults reached peak diversity and SCFA concentrations, marked by a rise in Bacteroidota and the emergence of Akkermansia. In middle and old age, pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) increased, Bacteroidota declined while Firmicutes, Actinobacteria, and Turicibacter expanded, and aged colons showed blunted ex vivo responses to IL-1β. This age-associated functional decline phenotype was absent in TLR4[-/-] mice, supporting the involvement of TLR4 signaling. Transcriptomics further revealed biphasic PI3K/Akt activation in both pups-P9 and old mice. Together, these findings suggest a systemic rewiring of host metabolic and immune signaling pathways in response to an aging microbiota, highlighting this dynamic, lifespan-wide microbiota-host signaling axis as a potential intervention target.}, }
@article {pmid41823861, year = {2026}, author = {Zou, Y and Zhang, CY and Cao, XT and Niu, RG and Lan, JF}, title = {Transcriptomic and Microbiome Analyses of Procambarus clarkii Exposed to Different Doses of 20E.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823861}, issn = {2079-7737}, support = {SDAIT 13-03, 13-04//Shandong Modern Agricultural Industry Technology System/ ; }, abstract = {Molting determines survival and growth in cultured crustaceans, yet its specific regulatory mechanisms remain complex. This study integrated transcriptomics and microbiome analyses to elucidate molting regulation in crayfish (Procambarus clarkii). Crayfish were injected with 20-hydroxyecdysone (20E) at 20 and 250 ng/g to simulate early premolt and middle premolt, respectively. The comprehensive upregulation of nuclear receptor family genes confirmed the reliability of the in vivo 20E injection simulation. The results showed that 20 ng/g 20E stimulation induced 13,253 unique DEGs in the epidermis, mainly enriched in protein catabolism (promoting proteolysis to degrade the old exoskeleton), and induced 137 unique DEGs in hemocytes, mainly linked to ribosomal biosynthesis, while the 250 ng/g group showed 2395 unique DEGs in the epidermis, enriched in metabolic processes and biosynthetic processes (supporting the biosynthesis of the new stratum corneum), and 99 unique DEGs in hemocytes enriched in mitochondrial pathways, concomitantly enhancing energy metabolism and antioxidant defense capabilities. Notably, 20E upregulation potentially leads to the dysbiosis of pathogens, specifically Escherichia-Shigella and Vibrio. This study elucidates key biological events in the early and middle premolt of crayfish, clarifies tissue-specific regulatory mechanisms during premolt, and provides molecular-level insights into the growth regulatory network of crustaceans.}, }
@article {pmid41823859, year = {2026}, author = {Zhang, Y and Wei, T and Zhao, C and Zhang, L}, title = {The Role of the Vaginal Microbiome in Gynecological Diseases: Mechanistic Insights and Emerging Interventions.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823859}, issn = {2079-7737}, support = {ZR2024MH220//Shandong Provincial Natural Science Foundation/ ; 82172320//National Natural Science Foundation of China/ ; 82370785//National Natural Science Foundation of China/ ; }, abstract = {The vaginal microbiome (VM), a complex and dynamic microbial ecosystem, is now recognized as a central determinant of female reproductive and gynecologic health. Under homeostatic conditions, a Lactobacillus-dominant ecosystem maintains vaginal acidity, provides colonization resistance, and modulates mucosal immunity. Conversely, vaginal dysbiosis-characterized by Lactobacillus depletion and anaerobic or aerobic overgrowth-is associated with infectious vaginitis, increased susceptibility to sexually transmitted infections, and non-infectious conditions such as genitourinary syndrome of menopause. This review provides an integrated overview of the composition, functional characteristics, and host interactions of the VM across health and disease. We highlight major mechanisms by which microbial dysbiosis contributes to disease pathogenesis, including biofilm formation, altered microbial metabolism, and immune dysregulation. In addition, we discuss the translational potential of the VM as a source of diagnostic and prognostic biomarkers and as a target for emerging microbiome-dependent therapeutic strategies. Collectively, current evidence supports the view that vaginal dysbiosis is a heterogeneous and context-dependent state driven by distinct pathogen- and host-related mechanisms, underscoring the importance of prioritizing microbiome restoration rather than pathogen eradication alone.}, }
@article {pmid41823856, year = {2026}, author = {Ueda, S and Iwasawa, T and Ohki, K and Takeda, S and Tsuchiya, R and Sakuraba, S and Kato, K and Ito, T}, title = {Postbiotic Metabolites from a 31-Strain Lactobacillus/Bifidobacterium Co-Culture Attenuate DSS Colitis with Barrier- and Circadian-Linked Transcriptomic Signatures.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823856}, issn = {2079-7737}, support = {none//Grant-in-Aid for Special Research in Subsidies for ordinary expenses of private schools from The Promotion and Mutual Aid Corporation for Private Schools of Japan./ ; none//Research funding from SOPHIA Co., Ltd./ ; }, abstract = {Postbiotics produced by beneficial bacteria are emerging as safe dietary approaches to intestinal inflammation. We evaluated intestinal bacterial metabolites (IBM), a cell-free fermented soybean extract generated by co-culturing 31 Lactobacillus/Bifidobacterium-related strains, for prophylactic protection in 3% dextran sulfate sodium (DSS)-induced colitis. Male C57BL/6NJ mice received oral IBM (0.4 or 2 mL/kg/day) or vehicle for 7 days before and during 7 days of DSS. Disease activity index (DAI), colon length, and histopathology were assessed, and endpoint serum cytokines were quantified by a multiplex bead assay. DSS-independent responses were examined in healthy mice after 7 days of IBM by rectal RNA sequencing and cecal 16S rDNA profiling, and direct epithelial effects were tested in HCT-116 and DLD-1 cells treated with 2% IBM. IBM attenuated colitis, improving DAI, preventing colon shortening, and ameliorating histopathology, with decreased IL-23 and IL-17A and increased IFN-β and GM-CSF. Rectal transcriptomics showed modulation of circadian programs, upregulation of mucosal/barrier genes, and reduced extracellular-matrix remodeling signatures. IBM increased junctional proteins and barrier-related transcripts in vitro and shifted the microbiota, increasing Lactobacillus and Roseburia while decreasing Streptococcus and Staphylococcus. These coordinated clinical, immunological, transcriptomic, epithelial, and microbiome changes support prophylactic protection by IBM against DSS colitis.}, }
@article {pmid41823831, year = {2026}, author = {Yang, Y and Xu, C and Lin, D and Zheng, C and Dai, X and Zheng, Z and Wang, N and Hu, B and Xia, L and Qian, X and Zhang, L}, title = {Acetoin and 2,3-Butanediol Differentially Restructure Fungal and Bacterial Communities and Their Links to Host Transcription in the Rhizosphere of a Medicinal Plant.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823831}, issn = {2079-7737}, support = {82373990//National Natural Science Foundation of China/ ; 2023J011753//Natural Science Foundation of Fujian Province/ ; KFB23077A//the technological innovation project of Fujian Agriculture and Forestry University/ ; }, abstract = {Microbial volatile organic compounds (VOCs) mediate rhizosphere plant-microbe interactions, yet their integrated effects on plant microbiome assembly and host transcriptional regulation remain unresolved. Here we address this gap by investigating how two common VOCs, acetoin (AC) and 2,3-butanediol (BD), influence growth, rhizosphere communities, and root gene expression in the medicinal plant Pseudostellaria heterophylla using a split-pot system. Bacterial and fungal communities were monitored across three developmental stages via amplicon sequencing, alongside root transcriptome profiling during tuber enlargement. Contrasting with widely reported growth-promoting effects of microbial VOCs, both compounds significantly reduced tuber number and biomass. Bacterial communities remained taxonomically stable, shaped primarily by species replacement, with modest VOC responses but clear shifts across developmental stages. Fungal communities exhibited marked compositional restructuring and greater treatment sensitivity, particularly under BD. Neutral community modeling indicated predominantly stochastic bacterial assembly, while fungal assembly-especially under BD-showed stronger influence of deterministic processes. BD associated with broader transcriptional reprogramming than AC, including downregulation of photosynthesis, specialized metabolism, and defense pathways. Cross-omics network analysis revealed discriminant genera (e.g., Granulicella, Harposporium) that correlated strongly with host genes involved in stress response, development, and epigenetic regulation, with fungal taxa showing tighter associations with host expression than bacteria. Together, these findings establish a mechanistic framework for how microbial VOCs shape rhizosphere communities and host responses, with implications for microbiome-based strategies in medicinal plant cultivation.}, }
@article {pmid41823830, year = {2026}, author = {Chen, Y and Zeng, Y and Jing, B and Zeng, D and Ni, X}, title = {Bifidobacterium animalis subsp. animalis GY007 Mitigates High Fluoride Exposure-Induced Ileal Injury and Restores the Ileal Microbiota-Metabolome Imbalances.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823830}, issn = {2079-7737}, support = {2025YFHZ0278//Sichuan Science &amp; Technology Project/ ; }, abstract = {Exposure to fluoride is strongly associated with impaired intestinal function. Probiotics are widely regarded as an effective strategy to maintain microbial homeostasis and to mitigate the progression of fluoride-induced intestinal injury. This study aimed to evaluate the measurable protective effects of the probiotic strain Bifidobacterium animalis subsp. animalis (B. animalis subsp. animalis) GY007 in reversing high fluoride-induced ileal injury. The results showed that GY007 (1 × 10[9] CFU/mL, once/daily) attenuated intestinal barrier disruption and alleviated ileal mucosal abnormalities in mice receiving fluoride (24 mg/kg) by gavage for eight consecutive weeks. GY007 attenuated elevated oxidative stress and modulated the inflammatory response associated with the TLR9/NF-κb/IRF7 signaling pathway. Microbiome and metabolomic analyses showed that GY007 reversed the dysregulation of the ileal microbial community structure and metabolite profiles. Spearman's rank correlation analysis further supported a regulatory role for Bifidobacterium in this protective process and identified three key functional metabolites meriting further investigation: isocytosine (ISO), 7α,24S-dihydroxy-3-oxocholest-4-en-26-oic acid (OIC-7α), and sinapinic acid (SIA). Our findings demonstrate that GY007 protects against fluoride-induced ileal injury and elucidate the associated changes in the intestinal microbial community and metabolite profiles. This study provides new evidence clarifying the restorative effect of the probiotic GY007 on the ileum under environmental fluoride exposure, offering an integrative perspective on the interaction between microorganisms and their host.}, }
@article {pmid41823815, year = {2026}, author = {Meng, Q and Jiang, W and Ye, T and Cao, Z and Lin, Q and You, F and Zhao, Z and Tian, W and Tian, Y and Dong, K}, title = {Microbiome-Metabolome Analyses Reveal Compound Risks from Multiple-Generation Cocoon Accumulation in Honeybee Combs.}, journal = {Biology}, volume = {15}, number = {5}, pages = {}, pmid = {41823815}, issn = {2079-7737}, support = {32060241//National Natural Science Foundation of China/ ; 31572339//National Natural Science Foundation of China/ ; CARS-44-KXJ13//China Agriculture Research System of MOF and MARA/ ; 2018HB041//Reserve Talents Training Program for Young and Middle-aged Aca-demic and Technical Leaders in Yunnan/ ; }, abstract = {The accumulation of cocoons within brood cells of old combs is a key factor causing a series of negative impacts on bee colonies. Previous studies did not sufficiently address this dynamic nature as the core microenvironment for preimaginal bee development. During this accumulation, the enrichment of potentially harmful microorganisms and chemical substances may pose a latent threat to colony health. This study combined microbiome and metabolomics analyses to systematically investigate the potential colony health risks posed by multi-generational accumulation of cocoons in Apis mellifera combs. The results demonstrated that with the growing number of brood rearing generations, the microbial diversity within the cocoons underwent significant shifts. For the bacterial community within multiple-generation cocoons, the Simpson index exhibited a significant increase, whereas indices including Sobs, Ace, and Chao showed significant decreases (p < 0.05). In the fungal community, the Shannon and Pielou_e indices significantly increased, while the Simpson and Faith_pd indices significantly declined (p < 0.05). Potential pathogens such as Melissococcus and the mycotoxin-producing fungus Wallemia became significantly enriched, reaching alarming relative abundances of 42.70% and 13.52%, respectively, in the multiple-generation cocoons. Metabolomic analysis further revealed the enrichment of 685 differential metabolites, including persistent exogenous pesticides such as cyanazine and pymetrozine, etc. Correlation analysis uncovered a significant positive relationship (r > 0.8) between these pesticide residues and pathogen abundance, indicating interactions between pollutants and pathogens that may exacerbate risks. This study reveals the aggravation of microecological imbalance and chemical pollution load within the cocoons of old combs and therefore provides strong scientific support for risk assessment of comb age in colony health management and offers practical guidance for the sustainable development of beekeeping.}, }
@article {pmid41823710, year = {2026}, author = {Qin, S and Kang, Z and Wu, Q and Hou, C and Qi, S and Cheng, J and Dong, X}, title = {Targeting Myeloid-Derived Suppressor Cells in Sepsis: Pathophysiology, Duality, and Therapeutic Frontiers.}, journal = {Shock (Augusta, Ga.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/SHK.0000000000002817}, pmid = {41823710}, issn = {1540-0514}, abstract = {Sepsis-induced immunosuppression, one of the factors contributing to mortality, is closely mediated by Myeloid-Derived Suppressor Cells (MDSCs). This review first outlines MDSC biology, describing their origin from pathological emergency myelopoiesis and classification into polymorphonuclear (PMN-MDSCs) and monocytic (M-MDSCs) subsets. We then discuss their dual role: an early, protective modulation of cytokine storm that later evolves into harmful immunosuppression associated with secondary infections and death. The underlying mechanisms involve L-arginine depletion (via ARG1/iNOS), oxidative stress (ROS), and induction of regulatory T cells (Tregs). Therapeutic strategies are summarized, including interventions targeting MDSC differentiation (e.g., ATRA), metabolism (e.g., FAO inhibitors), precision depletion (e.g., anti-LOX-1), and microbiome modulation. Finally, we address challenges to clinical translation-phenotypic heterogeneity, metabolic ambiguity, and the "double-edged sword" of MDSC targeting. Deeper insights into MDSC biology may help develop strategies to improve outcomes in this severe syndrome.}, }
@article {pmid41823643, year = {2026}, author = {Gupta, AK and Teasell, EM and Liddy, A and Economopoulos, V}, title = {Scalp Microbiome Alterations in Androgenetic Alopecia: Patterns and Emerging Mechanistic Insights.}, journal = {International journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ijd.70365}, pmid = {41823643}, issn = {1365-4632}, abstract = {Androgenetic alopecia (AGA), the most common cause of hair loss in men and women, involves progressive follicular miniaturization and reduced hair density. Emerging evidence implicates the scalp microbiome as a potential modifier of this process. Preliminary evidence suggests alterations in microbial communities in patients with AGA compared to the general population, with the most robust finding being an enrichment of Cutibacterium acnes, particularly in males. Increases in Malassezia and reductions in Lawsonella and Corynebacterium have also been described, though results are less consistent across studies, while Staphylococcus displays variable patterns. These microbial shifts parallel alterations in scalp sebum composition, such as elevated triglycerides and palmitic acid, that may favor growth of lipophilic microbes. Mechanistic insights from in vitro studies and related inflammatory skin conditions indicate that C. acnes and Malassezia spp. are capable of generating free fatty acids and activating innate immune pathways, such as TLR2- and NLRP3-associated signaling, leading to pro-inflammatory cytokine production, potentially contributing to follicular stem cell apoptosis and hair follicle miniaturization. Although findings remain heterogenous, emerging evidence suggests microbial-lipid-immune interactions may contribute to AGA pathogenesis, providing a rationale for exploring treatments like ketoconazole or other lipid-modulating interventions.}, }
@article {pmid41823474, year = {2026}, author = {Yang, X and Cheng, J and Zhang, X and Tian, H and Weng, X and Zhang, Y and Zhang, D and Xu, D and Huang, K and Li, X and Zhao, Y and Zhao, L and Xu, Q and Ma, Z and Li, F and Wang, W}, title = {Exploring the Role of Rumen Microbiota and KLF15 Gene in the Performance of Growing Hu Sheep.}, journal = {Animal genetics}, volume = {57}, number = {2}, pages = {e70080}, doi = {10.1002/age.70080}, pmid = {41823474}, issn = {1365-2052}, support = {32260818//National Natural Science Foundation of China/ ; 32372850//National Natural Science Foundation of China/ ; 22ZD6NC069//Major science and technology projects of Gansu Province/ ; GAU-XKTD-2022-20//Discipline Team Project of Gansu Agricultural University/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Sheep, Domestic/genetics/growth &amp; development/microbiology ; *Gastrointestinal Microbiome/genetics ; Body Weight ; Diet/veterinary ; Kruppel-Like Transcription Factors/genetics ; Male ; }, abstract = {Exon mutations and the rumen microbiome play crucial roles in influencing growth performance in meat animals, making them key factors for enhancing meat production efficiency. This study aimed to further investigate the effects of host genetics (KLF15 c.6256511 A>G) and rumen microorganisms on the growth performance of Hu sheep. This study selected 50 growing Hu sheep with extreme body weight and uniformly fed them a diet with a concentrateto-roughage ratio of approximately 1.5:1. Rumen content samples were collected for 16S rDNA sequencing. Growth traits and feed efficiency were measured at 80, 100, 120, 140, 160, and 180 days of age. The high body weight (H-BW) group exhibited better production performance, with significant differences found in growth traits, slaughter traits, and fat deposition traits between the H-BW and low weight (L-BW) group (P < 0.05). Among the 23 different bacterial genera identified, Rikenellaceae_RC9_gut_group was significantly correlated with 180-day body weight and muscle fat content of Hu sheep. The relative abundance of Rikenellaceae_RC9_gut_group was lowest in Hu sheep with the AA genotype (P < 0.05). No significant difference in rumen microbial diversity was observed between the H-BW and L-BW groups. Rikenellaceae_RC9_gut_group may activate the mTOR signaling pathway through the metabolic pathway of valeric acid, promote the growth of muscle cells, and thus regulate the body weight of Hu sheep. Utilizing the KLF15 c.6256511 A>G mutation site and the Rikenellaceae_RC9_gut_group provides a valuable approach to enhance the growth traits and overall production performance of Hu sheep.}, }
@article {pmid41823383, year = {2026}, author = {Warthen, R and Cabales, A and Wockenfuss, A and Kaur, C and Kunjapur, AM and Bais, H}, title = {Glutamate facilitates root colonization by plant growth-promoting rhizobacteria Bacillus subtilis in tomato seedlings.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0318125}, doi = {10.1128/spectrum.03181-25}, pmid = {41823383}, issn = {2165-0497}, abstract = {The influence of microbially and plant-synthesized compounds on colonization of plant growth-promoting rhizobacteria (PGPR) on various regions of the plant root is underexplored. Here, we examine the influence of surfactin and glutamate on the level and specificity of colonization of Bacillus subtilis along different regions of tomato root by adding exogenous compounds and testing mutated bacterial strains. First, B. subtilis PY79 was modified to express a full-length phosphopantetheinyl transferase (sfp) native to other surfactin-producing B. subtilis strains, and surfactin biosynthesis was observed under static incubation at 25°C in plant culturing media. Microscopy was performed using PY79 sfp[-] (surfactin null), PY79 sfp[+] (surfactin overproducing), and the wild isolate B. subtilis UD1022 to map the colonization of each strain along the entire root of young tomato plants incubated at 25°C. In addition, experiments involving supplementation of surfactin or glutamate were also performed to evaluate the root colonization of sfp[+] and sfp[-] strains. Root mapping of a tomato seedling shows that B. subtilis prefers to colonize near the mature region of the root and that colonization patterns vary based on exogenous metabolite concentration. Inclusion of glutamate in the media or through transient priming of the plant prior to bacterial inoculation strongly promoted root colonization by B. subtilis strains (both sfp[+] and sfp[-]). In addition, the data shows that the lab strains were less efficient in colonization compared to the wild-type B. subtilis strain. Interestingly, in the presence of glutamate, microbes lost their preference for colonization at the mature region, instead colonizing along the entire root. Overall, our work reveals a preference for colonization of these B. subtilis strains to the mature region of tomato in the absence of glutamate supplementation and demonstrates a smaller than anticipated role of biosynthesized or supplemented surfactin on root colonization, at least in a hydroponic culturing format.IMPORTANCEPlants are associated with large communities of microbes across the rhizosphere. However, comparatively little is known about the drivers underpinning the diversity of microbes, especially regarding how they are recruited by plants. Growing evidence indicates that the rhizospheric microbiome supports plant growth in response to biotic and abiotic stresses. Of late, the usage of a synthetic community of plant growth-promoting rhizobacteria (PGPR), especially Bacillus subtilis, has been recognized for its role as a potential biofertilizer and bio-fungicide agent. The role of PGPR-derived metabolites has been debated as a driver for enhanced root colonization. However, the knowledge pertaining to where and how PGPR colonize on the root surface is currently unknown. Therefore, it is prudent to elucidate the role of bacterially derived compounds and other carbon sources in the rhizosphere that drive root colonization.}, }
@article {pmid41823382, year = {2026}, author = {Li, J and Dong, B}, title = {Distinct clinical and microbial profiles in left-sided and right-sided colorectal cancer: a comprehensive analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0033625}, doi = {10.1128/spectrum.00336-25}, pmid = {41823382}, issn = {2165-0497}, abstract = {This study investigates the clinical and microbial differences between left-sided colorectal cancer (LCC) and right-sided colorectal cancer (RCC), as well as the microbial profiles in tumor tissues (T) and peritumoral tissues (P) of colorectal cancer (CRC) patients. A total of 240 tissue samples were collected from CRC patients and classified based on the tumor location (LCC vs RCC) and tissue type (tumor vs peritumoral). Clinical data were recorded, and microbial analysis was performed using 16S rRNA sequencing. Bioinformatics analysis assessed microbial diversity and community composition, with statistical tests identifying significant differences between groups. LCC patients were older, heavier, and taller, with higher levels of tumor markers (CEA and CA199). Microbial analysis showed no significant differences in species evenness or richness between LCC and RCC; overall beta-diversity patterns did not differ significantly, although several taxa and predicted functions exhibited differential abundance between the two groups. Functional analysis revealed significant differences in KEGG Orthologs (KOs) and Clusters of Orthologous Groups (COGs) between LCC and RCC. Tumor tissue exhibited lower microbial diversity compared to peritumoral tissue, with significant differences in the microbial community structure. Our findings highlight the importance of considering sidedness and microbial composition in CRC management. The distinct microbial profiles in tumor and peritumoral tissues provide potential biomarkers for early detection and treatment response prediction. Future research should further explore these differences and their clinical implications.IMPORTANCEColorectal cancer (CRC) exhibits marked biological and prognostic differences between left-sided (LCC) and right-sided (RCC) tumors, yet the role of the tumor-associated microbiome stratified by sidedness remains poorly defined. In this study of 240 Chinese patients, we report the first integrated analysis combining clinical features with tissue microbial profiles (tumor vs peritumoral) according to the primary tumor location. We report differential abundance of specific taxa and predicted metabolic functions between LCC and RCC, plus significantly reduced diversity and altered structure in tumor tissue (T) compared with the adjacent normal tissue. These findings underscore the necessity of considering tumor sidedness and intratumoral microbiota in CRC classification, risk assessment, and precision therapy and highlight candidate microbial signatures as potential noninvasive biomarkers for early detection, sidedness prediction, and personalized treatment strategies.}, }
@article {pmid41823362, year = {2026}, author = {Li, L and Feng, L and Li, Q and Zhou, Y and Liu, S and Song, H and Kang, S and Chen, H and Cong, H and Liu, S}, title = {Precision Microbial Therapeutics for Infertility: Next-Generation Probiotics, Engineered Biologics and Translational Pathways.}, journal = {Microbial biotechnology}, volume = {19}, number = {3}, pages = {e70330}, doi = {10.1111/1751-7915.70330}, pmid = {41823362}, issn = {1751-7915}, support = {LBH-Z24283//Heilongjiang Province Postdoctoral Fund/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; Female ; *Biological Products/therapeutic use ; Dysbiosis/therapy/microbiology ; Lactobacillus ; *Infertility/therapy/microbiology ; *Precision Medicine/methods ; Microbiota ; }, abstract = {Infertility affects ~1 in 6 people of reproductive age and remains difficult to treat because causes are heterogeneous and diagnostics are incomplete. Recent evidence reframes the female reproductive tract as a low-biomass but biologically active microbial ecosystem. Dysbiosis, typically loss of protective Lactobacillus species (notably L. crispatus) with overgrowth of anaerobic pathobionts, is associated with implantation failure and recurrent pregnancy loss. Framing conditions such as chronic endometritis and reproducible low-Lactobacillus endometrial profiles as dysbiosis-related disorders clarifies opportunities for prevention, companion diagnostics and microbiome-directed therapies. This narrative review contrasts receptive (Lactobacillus-dominant) versus dysbiotic states and summarises mechanisms linking microbiota to fertility: microbial metabolites (lactic acid, short-chain fatty acids) support epithelial barrier function and immune tolerance, whereas dysbiosis provokes inflammation that impairs implantation. Although observational data consistently associate Lactobacillus dominance with better outcomes, evidence quality is low-to-moderate due to retrospective designs, methodological heterogeneity, and a lack of adequately powered, diagnostic-stratified randomised trials. The review highlights precision microbial therapeutics under development, single-strain next-generation probiotics, synthetic consortia, engineered live biotherapeutics, postbiotics, targeted phage/endolysins and vaginal microbiota transplantation, and proposes a diagnostic-driven roadmap that matches microbiome endotypes and clinical contexts (e.g., preconception vs. immediate embryo transfer) to specific interventions. Regulatory and safety issues for reproductive biologics are also considered. The reproductive microbiome is a promising translational frontier but currently offers a consistent signal rather than definitive proof of benefit. To translate promise into practice requires standardised low-biomass sampling/reporting, mechanistic validation in human-relevant models and diagnostic-stratified randomised trials with staged endpoints, alongside strategies to address engraftment, formulation and regulatory pathways.}, }
@article {pmid41823317, year = {2026}, author = {Zhong, S and Zhao, X and Cheng, Q and Cheng, L and Yang, M and Zhang, M and Wan, Q and Wang, J and Xu, Z and Shuai, Y and Yang, M}, title = {Oral Administration of Bombyx mori Silk Fibroin Nanoparticles Modulates the Gut Microbiota in Healthy Mice.}, journal = {Macromolecular bioscience}, volume = {26}, number = {3}, pages = {e00517}, doi = {10.1002/mabi.202500517}, pmid = {41823317}, issn = {1616-5195}, support = {2023YFF1103900//National Key R&amp;D Program of China/ ; 2021C02072-3//Zhejiang Provincial Science and Technology Plan/ ; 2021C02072-6//Zhejiang Provincial Science and Technology Plan/ ; CARS-18-ZJ0501//State of Sericulture Industry Technology System/ ; }, mesh = {Animals ; *Fibroins/chemistry/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Administration, Oral ; *Nanoparticles/chemistry/administration &amp; dosage ; Mice ; *Bombyx/chemistry ; Male ; }, abstract = {Silk fibroin nanoparticles (SFNPs) have shown great promise as oral drug delivery carriers due to their favorable biocompatibility and tunable release properties. However, their effects on the gut microbiota under physiological conditions remain poorly understood. Herein, we systematically investigated the impact of orally administered SFNPs on the composition and temporal dynamics of the gut microbiome in healthy mice. SFNPs were thoroughly characterized, showing stability in intestinal fluid and structural transition to β-sheet conformation. Our results revealed that SFNP administration induced significant, dose-dependent shifts in microbial communities, notably increasing the Firmicutes/Bacteroidota ratio and enriching potentially beneficial genera such as Faecalibaculum and Dubosiella, while reducing taxa associated with inflammation and metabolic disorders. Medium doses (2.4 and 12 mg/kg) promoted sustained potentially beneficial effects, whereas a high dose (60 mg/kg) led to transient dysbiosis and enrichment of the inflammation-related genus Enterorhabdus. These findings underscore the dose-responsive modulatory effects of SFNPs on gut microbiota and highlight the importance of microecological safety in the design of nanocarrier systems for oral administration. This study provides critical insights into the gut-nanoparticle interface and supports the potential of SFNPs in microbiome-based therapeutics.}, }
@article {pmid41823308, year = {2026}, author = {Gramaje, D and Eichmeier, A}, title = {Beyond Koch's postulates: The pathobiome paradigm in grapevine esca disease.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag028}, pmid = {41823308}, issn = {1574-6941}, abstract = {Esca is one of the most damaging fungal diseases of grapevine and continues to defy Koch's postulates. Although Phaeomoniella chlamydospora, Phaeoacremonium minimum and Fomitiporia mediterranea are consistently associated with wood necrosis in esca-symptomatic vines, they also occur in asymptomatic vines and even in apparently healthy wood tissues without visible necrosis, and single-species but also mixed-species inoculations rarely reproduce the characteristic foliar symptoms. We hypothesize that esca is best understood as a stress-mediated pathobiome disorder of the grapevine holobiont rather than a predictable outcome of specific fungal combinations, shifting focus from pathogen identity to holobiont functional state and environmental context. In this Review, we integrate evidence from community ecology, vascular biology and multi-omics studies to link microbial community structure and activity with host hydraulics, defence and environmental drivers. Metabarcoding and metatranscriptomics indicate that symptom expression correlates with functional reprogramming of trunk-inhabiting fungi more than their mere presence, while metabolomics and epigenomics reveal localized physiological disruption combined with systemic regulatory responses. Climatic and edaphic stresses, particularly drought, are strongly associated with holobiont destabilization and dysbiosis, altering symptom expression without necessarily modifying pathogen occurrence. We propose a temporal, multi-phase model integrating colonization history, microbiome restructuring and host stress physiology through long-term feedbacks. This framework emerges through convergent multi-omics evidence and generates testable predictions for early detection, microbiome-informed biocontrol and resilience-oriented vineyard management strategies.}, }
@article {pmid41823302, year = {2026}, author = {Al, KF and Jia, S and Silverman, M and Reid, G and Burton, JP and Parvathy, S}, title = {Prebiotic Modulation of FMT Donor Microbiota Enhances MASLD-Relevant Taxa and Functions in an In Vitro Gut Model.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag074}, pmid = {41823302}, issn = {1365-2672}, abstract = {AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.<br><br>METHODS AND RESULTS: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 hours with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.<br><br>CONCLUSIONS: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.}, }
@article {pmid41822979, year = {2026}, author = {Donnermeyer, D and Schäfer, E and Hagenfeld, D and Ehmke, B and Prior, K and Harmsen, D and Ibing, M and Bürklein, S and Wolf, TG and Matern, J}, title = {A Comparison of Endodontic Microbiomes Associated With Symptomatic and Asymptomatic Apical Periodontitis by Next-Generation Sequencing.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70140}, pmid = {41822979}, issn = {1365-2591}, abstract = {AIM: This cross-sectional study aimed to compare the endodontic microbiome assessed from root canals of teeth associated with either symptomatic or asymptomatic apical periodontitis and analysed by 16S rDNA gene sequencing.<br><br>METHODOLOGY: 60 teeth presenting clinical and radiographic signs of symptomatic or asymptomatic apical periodontitis (n&#x2009;=&#x2009;30) were included in this cross-sectional study after participants had given their written informed consent. After isolation with rubber dam, disinfection and access cavity preparation, glide paths were prepared using C-Pilot Files and K-Files under electronic root canal length control. Microbial samples were collected from a total of 120 root canals (symptomatic apical periodontitis, SAP: n&#x2009;=&#x2009;62, asymptomatic apical periodontitis, AAP: n&#x2009;=&#x2009;58) each with a sterile file (size 20/0.06) in a single length technique. Only one specimen per tooth was included in the analysis; in multi-rooted teeth, the specimen with highest sequencing depth. After DNA extraction, the hypervariable region V4 of the bacterial 16&#x2009;S rRNA gene was amplified and sequenced (Illumina MiSeq). Taxonomy was assigned based on the expanded Human Oral Microbiome Database (eHOMD). Statistical analysis of diversity parameters comprised Mann-Whitney U tests and PERMANOVA. Compositional differences were evaluated by differential abundance analyses using DESeq2, LinDA, and ANCOM-BC2 methods.<br><br>RESULTS: No differences were observed in richness and diversity (Shannon diversity index) on the genus or ASV level (p&#x2009;>&#x2009;0.05). According to PERMANOVA, SAP and AAP microbiomes did not differ significantly both on genus and ASV levels (p&#x2009;>&#x2009;0.05). Among highly abundant genera, Fusobacterium was indicated to be more abundant in SAP samples whereas Actinomyces was more abundant in AAP samples.<br><br>CONCLUSIONS: The expression of clinical symptoms in apical periodontitis does not appear to be determined by specific microorganisms but may instead reflect shifts of the relative abundance of the microbial community.}, }
@article {pmid41822578, year = {2026}, author = {Rakhmatullin, S and Kurilkina, M and Kosyan, D and Deryabin, D and Duskaev, G}, title = {Dose-dependent effects of dietary quercetin on cecal microbiota, hematological responses, and production efficiency in Arbor Acres broiler chickens.}, journal = {Veterinary world}, volume = {19}, number = {1}, pages = {264-281}, pmid = {41822578}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gastrointestinal microbiome plays a key role in nutrient absorption, immune regulation, and growth performance in broiler chickens. As restrictions on antibiotic growth promoters increase, phytogenic compounds like quercetin (QC) have gained attention as potential alternatives. Although QC is recognized for its antioxidant and immunomodulatory effects, its dose-dependent influence on gut microbiota composition and systemic immune parameters remains not fully understood. This study aimed to assess the effects of graded dietary QC supplementation on cecal microbiome structure, hematological profiles, and production performance in Arbor Acres (AA) broiler chickens to identify an optimal and safe inclusion level.<br><br>MATERIALS AND METHODS: A total of 180 seven-day-old AA broiler chickens were randomly divided into four groups (n = 45 per group; three replicates). Birds received either a basal diet (BD, control) and the BD supplemented with QC at 5 mg/kg (QC1), 10 mg/kg (QC2), or 15 mg/kg (QC3) of feed daily for 35 days. Growth performance indicators, including body weight gain, feed conversion ratio, livability, and the European Production Efficiency Factor (EPEF), were recorded. Hematological parameters were analyzed using an automated veterinary hematology analyzer. Cecal microbiota composition was examined through high-throughput 16S Ribosomal ribonucleic acid (rRNA) gene sequencing, followed by alpha- and beta-diversity analyses and differential abundance testing.<br><br>RESULTS: Dietary QC significantly affected broiler performance, immune status, and gut microbiota composition in a dose-dependent way. The QC1 group achieved the highest final body weight, average daily gain, and EPEF, with an 11.6% increase in production efficiency compared to the control. Hematological analysis showed increased total leukocyte and lymphocyte counts, along with decreased neutrophil, monocyte, eosinophil, and basophil levels, reflecting immunomodulatory and anti-inflammatory effects. Microbiome analysis indicated that Bacillota and Bacteroidota were dominant across all groups. QC at 5 mg/kg boosted beneficial, butyrate-producing genera, especially Faecalibacterium, while preserving microbial balance. Conversely, higher doses (10-15 mg/kg) led to a notable rise in Campylobacterota, suggesting a possible shift toward dysbiosis. Alpha-diversity measures were not significantly affected, but beta-diversity analysis confirmed distinct changes in microbial communities among the treatment groups.<br><br>CONCLUSION: Dietary QC has a clear dose-dependent effect on the gut microbiota-immune-performance axis in broiler chickens. Supplementation at 5 mg/kg of feed is the optimal level, improving growth performance, feed efficiency, immune balance, and beneficial microbial populations without increasing pathogenic taxa. Higher supplementation levels may disturb microbial balance and raise the levels of potentially harmful bacteria. These findings support QC as a promising phytogenic alternative to antibiotic growth promoters and provide a scientific basis for its rational use in sustainable, antibiotic-free poultry production systems.}, }
@article {pmid41822499, year = {2026}, author = {Jing, Y and Bai, F and Li, Z and Wang, Q and Li, Y and Liu, W and Zhang, S and Gao, C and Yu, Y}, title = {An integrated analysis of spinal cord transcriptome and gut microbiome unravel age-associated host-microbiome interactions following spinal cord injury.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1602745}, pmid = {41822499}, issn = {1664-3224}, mesh = {Animals ; *Spinal Cord Injuries/microbiology/genetics/metabolism/immunology ; *Gastrointestinal Microbiome ; Mice ; *Transcriptome ; *Spinal Cord/metabolism ; *Aging/genetics ; Disease Models, Animal ; *Host Microbial Interactions ; Gene Expression Profiling ; RNA, Ribosomal, 16S/genetics ; Age Factors ; Male ; Cytokines/metabolism/genetics ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Spinal cord injury (SCI) leads to irreversible neurological deficits, with emerging evidence highlighting the pivotal regulatory role of gut microbiota in neural repair through the bidirectional gut-brain axis. This study investigates age-related differences in SCI progression by longitudinally profiling multi-omics signatures in young versus aged mice, integrating spinal cord transcriptomics with gut microbiome analysis.<br><br>METHODS: A traumatic SCI model was established at the thoracic level 10 in mice. The gut microbiota was analyzed through 16S rRNA sequencing. Spinal cord gene expression was profiled using transcriptome sequencing. Correlation analysis was performed to evaluate associated between gut microbiota shifts and differential cytokines expression.<br><br>RESULTS: Aging significantly altered spinal cord gene expression profiles after SCI, KEGG pathway analysis revealed that differentially expressed genes (DEGs) in young and aged SCI mice were highly similar, predominantly involving immune and inflammatory response pathways. The age-dependent upregulation of inflammatory cytokines were observed under both sham and post-SCI conditions. Additionally, aging was associated with distinct shifts in gut microbiota composition across different phases of SCI. The abundance of certain bacterial genera, such as Lactobacillus and Dubosiella, which was significantly reduced in the acute phase, continued to decline in an age-dependent manner during the chronic phase. Correlation analysis indicated that alterations in the abundance of the gut microbiota were closely associated with variations in spinal cord inflammatory cytokine levels.<br><br>CONCLUSION: This study delineates host-microbiome interactions in SCI and sheds light on potential mechanisms underlying age-related impairment of neural repair capacity.}, }
@article {pmid41822305, year = {2026}, author = {Reale, M}, title = {Editorial: Insights in genetics, genomics and epigenomics of aging: 2025.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1786864}, pmid = {41822305}, issn = {2673-6217}, }
@article {pmid41822263, year = {2025}, author = {Alpuim Costa, D and Barata Coelho, P and Calhau, C and Faria, A}, title = {Editorial: Gut microbiota in health and disease.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {4}, number = {}, pages = {1568509}, pmid = {41822263}, issn = {2813-1169}, }
@article {pmid41822217, year = {2026}, author = {Tsai, YL and Liu, YW and Wang, PN and Lin, CY and Lan, TH}, title = {Correction: Gender differences in gut microbiome composition between schizophrenia patients with normal body weight and central obesity.}, journal = {Frontiers in psychiatry}, volume = {17}, number = {}, pages = {1805447}, doi = {10.3389/fpsyt.2026.1805447}, pmid = {41822217}, issn = {1664-0640}, abstract = {[This corrects the article DOI: 10.3389/fpsyt.2022.836896.].}, }
@article {pmid41822195, year = {2026}, author = {Yang, Z and Wu, S and Yang, X and Sui, B}, title = {Gut microbiota-metabolism axis in digestive tumors: Emerging targets for novel therapies (Review).}, journal = {Experimental and therapeutic medicine}, volume = {31}, number = {4}, pages = {113}, pmid = {41822195}, issn = {1792-1015}, abstract = {Digestive tumors, including malignancies associated with the gastrointestinal tract, represent a notable global health burden. Advances in microbiome research have highlighted that the gut microbiota-metabolism axis and its associated metabolic derivatives are key modulators of tumorigenesis, immune evasion and treatment responses. The present review aimed to comprehensively discuss how key microbial metabolites, such as polyamines, short-chain fatty acids, bile acids and other compounds reshape the tumor microenvironment, modulate cellular signaling and affect immune responses. By integrating insights from microbiology, immunology, oncology and metabolic changes in digestive tumors, evidence suggests that the microbiota contributes to cancer progression through mechanisms involving epigenetic regulation, metabolic reprogramming, genotoxicity and production of inflammatory mediators. Beneficial bacteria, such as Akkermansia muciniphila and Faecalibacterium prausnitzii, exhibit antitumor activity, whereas pathogenic species, such as Helicobacter pylori and Fusobacterium nucleatum, are associated with oncogenic properties. Based on a literature search, microbiota-targeted therapy seems to be promising for the management of pathological conditions, especially digestive diseases. Further investigations into the pharmaceutical application of microbiota through prebiotics, probiotics and metabolite-targeted interventions, along with multi-omics integration and microbiome-host interactome validation, would be promising for improving personalized medicine and precision oncology.}, }
@article {pmid41822128, year = {2026}, author = {Ağagündüz, D and Giono-Cerezo, S and Grant, G}, title = {Editorial: The gut microbiome's role in gastric cancer: mechanisms and therapies.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1804029}, pmid = {41822128}, issn = {1664-302X}, }
@article {pmid41822125, year = {2026}, author = {Berg, G and Antonietti, M and Egamberdieva, D and Korsten, L and Wicaksono, WA}, title = {Microbiome-inspired solutions to save human and planetary health.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1744452}, pmid = {41822125}, issn = {1664-302X}, abstract = {Microbial communities are dynamic networks that regulate nutrient cycling, energy flow, and ecosystem stability, making microbial diversity essential to the health and resilience of all living organisms and ecosystems. However, Anthropocene-driven human activities have led to substantial losses of microbial diversity in environmental and host-associated microbiomes. Despite their critical role, microbiome is underrepresented in conservation and public health strategies, creating a knowledge and intervention gap. Emerging strategies based on microbiome approach offer promising avenues for restoring microbial diversity and enhancing Planetary Health. Achieving these goals requires coordinated global policies, interdisciplinary collaboration, and recognition of microbes as essential partners in sustaining life on Earth.}, }
@article {pmid41821986, year = {2026}, author = {Li, N and Cooper, J and Fleming, T and Lockett, S and Sherman, W and Chami, AA and Hasoon, J and Robinson, CL and Imani, F and Kaye, AD}, title = {Current Concepts and Treatment Options in the Management of Fibromyalgia.}, journal = {Psychopharmacology bulletin}, volume = {56}, number = {2}, pages = {149-162}, pmid = {41821986}, issn = {2472-2448}, mesh = {Humans ; *Fibromyalgia/therapy/diagnosis/physiopathology/epidemiology ; Chronic Pain/therapy/physiopathology ; }, abstract = {Fibromyalgia syndrome is a complex chronic pain syndrome associated with a broad constellation of symptoms, associated disorders, and possible risk factors. Although the pathophysiology of fibromyalgia remains unclear, there is promising research investigating neuroimaging, genetic and epigenetic markers, psychological alterations, and gut microbiome associations. Diagnostic criteria have evolved with time to better identify patients with fibromyalgia and differentiate the syndrome from other conditions. In this regard, diagnosis and treatment of the syndrome continue to present considerable challenges to clinicians related to the complexity, non-specific symptomology, and necessity of a multidisciplinary approach. The present investigation reviews the epidemiology, pathophysiology, presentation, and treatment options of fibromyalgia syndrome.}, }
@article {pmid41821965, year = {2026}, author = {Bak, F and Meier, JK and Markussen, B and Molina-Zamudio, KY and Tang, C and Nicolaisen, MH}, title = {Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag028}, pmid = {41821965}, issn = {2730-6151}, abstract = {The root microbiome is important for plant development. The impact of the root microbiome is the result of multiple complex interactions among microorganisms, the plant and the environment. This complexity can be reduced by designing synthetic bacterial communities (SynComs) consisting of bacteria isolated from the roots, making it possible to study these interactions. However, the translational power from SynCom experiments to explain field observations is still very low, which demonstrates the need for development of SynComs that colonize plants comparable to what is observed in the field. Hence, we developed a SynCom consisting of 13 different strains from 13 genera with varying phenotypes originating from the roots of winter wheat (Triticum aestivum cv. Sheriff). The SynCom was inoculated into gamma-irradiated soil prior to sowing and community assembly was determined over 4 weeks using 16S rRNA amplicon sequencing. Winter wheat plants inoculated with the developed SynCom grew comparably to plants inoculated with a natural community (NatCom) obtained from a soil solution over the 4-week period. Furthermore, the temporal dynamics of the majority of the SynCom strains mimicked the development in relative abundance of their respective genera in field grown winter wheat of the same cultivar. However, this could not be translated to a different cultivar (Heerup). Our results demonstrate how SynComs inoculated into gamma-irradiated soil can provide a promising framework to study root microbiome assembly and relate the findings to field observations. At the same time, it highlights the plant-genotype specific impact on community assembly.}, }
@article {pmid41821964, year = {2026}, author = {Tejada, CJ and Escobar Parra, S and Caro-Quintero, A}, title = {Geographic and species-specific determinants of rhizosphere microbiome assembly in Theobroma cacao wild populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag030}, pmid = {41821964}, issn = {2730-6151}, abstract = {Root-associated microbiome is a fundamental component of plant evolutionary success. Domestication has led to a loss of microbial diversity associated with plant roots. Studying this plant-microbiome relationship in natural ecosystems enhances our understanding of its original dynamics. We characterized bacterial and fungal communities in the rhizosphere and bulk soil of wild Theobroma and Herrania populations across two contrasting Colombian regions: the Amazon (Caquetá and Putumayo) and the Pacific (Chocó). Using 16S rRNA and ITS2 amplicon sequencing, we found that host species structured bacterial communities, while geography shaped fungal assemblages. Theobroma cacao rhizospheres clustered together across >500 km of separation, demonstrating stronger host filtering than wild congeners from identical locations. These communities were distinctively enriched with nitrogen-cycling taxa (Nitrosomonadaceae, Nitrosotalea, and Reyranella) identified as keystone species. Functional predictions showed pronounced enrichment of denitrification and nitrogen fixation genes in T. cacao rhizospheres. We propose T. cacao roots create spatial compartmentalization of nitrogen processes through oxygen consumption and radial oxygen loss, generating anoxic microsites within millimeters of root surfaces where nitrogen-fixers coexist with nitrifiers and denitrifiers. These patterns distinguish T. cacao from wild relatives and suggest evolutionary refinement of microbial recruitment strategies.}, }
@article {pmid41821962, year = {2026}, author = {Crump, BC and Liu, S and Raymond, PA and Bambakidis, T}, title = {Microbiome Damköhler number predicts lotic microbial community succession in river networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag029}, pmid = {41821962}, issn = {2730-6151}, abstract = {River microbiomes are dynamic contributors to ecosystem function and sensitive indicators of hydrologic processes, yet predictive frameworks for their assembly across drainage networks remain limited. We introduce the microbiome Damköhler number (Da m), a simple, mechanistic metric that captures the balance between microbial transport and growth. Adapted from chemical engineering, Da m is defined as the ratio of microbial travel time to microbial community doubling time. Travel time was estimated from mean water residence time and doubling time from temperature-dependent growth rates. We tested this framework using microbiome datasets from four similarly sized US rivers with contrasting hydrology and temperature regimes. Microbial diversity correlated more strongly with Da m than with basin identity, season, or water chemistry. Nearest Taxon Index (NTI) was consistently positive, indicating that environmental filtering controlled community assembly. Moreover, NTI increased with Da m, suggesting stronger selection with longer travel times and shorter doubling times. Faith's phylogenetic diversity declined with Da m, likely reflecting the progressive loss of phylogenetically diverse, non-growing taxa dispersed from surrounding landscapes. To evaluate predictive power, we fit generalized dissimilarity models and found that Da m explained the largest share of phylogenetic turnover and substantially improved out-of-watershed predictions compared to models without Da m. These results suggest that river microbiome succession is governed by the interplay between hydrologic transport and growth timescales. Because Da m can be calculated from residence time and temperature, it provides a scalable, mechanistic predictor of microbiome structure in river networks and offers a unifying framework for forecasting microbial community assembly in flowing waters.}, }
@article {pmid41821943, year = {2026}, author = {Zhou, Q and Wang, Y and Zhou, T and Yusupu, K and Gao, D and Zhao, H and Ma, L}, title = {A minimal cross-kingdom SynCom promotes plant growth and suppresses wheat crown rot via coordinated rhizosphere microbiome remodeling.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1758273}, pmid = {41821943}, issn = {1664-462X}, abstract = {INTRODUCTION: Wheat crown rot (WCR) caused by Fusarium pseudograminearum threatens wheat productivity, and sustainable control strategies are urgently needed.<br><br>METHODS: We constructed a minimal cross-kingdom synthetic community (SynCom) consisting of Trichoderma harzianum T19 and Bacillus rugosus PM16, and evaluated its effects on wheat growth and WCR suppression. Rhizosphere microbiome assembly (full-length 16S rRNA/ITS sequencing) and metabolomic shifts were assessed to elucidate mechanisms.<br><br>RESULTS: The SynCom significantly suppressed WCR and promoted wheat growth under pathogen pressure, improving biomass, chlorophyll content, and yield-related traits. SynCom inoculation remodeled the rhizosphere microbiome by enriching beneficial taxa (e.g., Mortierella) and reducing pathogen-associated fungi, and it enhanced rhizosphere enzyme activities and nutrient availability. Metabolomics revealed accumulation of growth-promoting and defense-related metabolites, supporting coordinated microbiome-metabolome regulation.<br><br>DISCUSSION: A minimal cross-kingdom SynCom can establish a disease-suppressive and growth-promoting rhizosphere through coordinated restructuring of microbial communities and metabolites, highlighting its potential as an eco-friendly strategy for WCR management.}, }
@article {pmid41821875, year = {2025}, author = {Kholwadwala, AS and Quigley, EMM}, title = {Small Intestinal Bacterial Overgrowth and Intestinal Methanogen Overgrowth: Are They Overdiagnosed?.}, journal = {Acta gastroenterologica Latinoamericana}, volume = {55}, number = {4}, pages = {276-291}, pmid = {41821875}, issn = {0300-9033}, abstract = {Small intestinal bacterial overgrowth was originally described as a cause of maldigestion and malabsorption, and its diagnosis was based on the culture of aspirates from the upper small intestine. The application of hydrogen breath tests to assess suspected small intestinal bacterial overgrowth increased the frequency of this diagnosis dramatically, and expanded its clinical context from maldigestion to include a number of non-specific gastrointestinal complaints and even some systemic ills. However, a critical review of recent literature suggests that reliance on breath tests, particularly those using lactulose as the substrate, has led to overdiagnosis of small intestinal bacterial overgrowth. Many aspects of the current concept of its diagnosis are contentious and unresolved. These include diagnostic thresholds, response to antibiotic therapy, as well as the roles of methane, hydrogen sulfide, and other gases emanating from bacterial fermentation in the gastrointestinal tract. We discuss these issues, paying particular attention to the concept of intestinal methanogen overgrowth and exploring the role of methanogens and methane in gastrointestinal homeostasis. We advocate a critical and cautious approach to the diagnosis of small intestinal bacterial overgrowth and intestinal methanogen overgrowth, and that antibiotics are prescribed are with great care. We also look forward to the application of modern molecular microbiology to the study of the small intestinal microbiome and metabolome, including a more complete understanding of methane biology.}, }
@article {pmid41821854, year = {2026}, author = {Mafe, AN and Büsselberg, D}, title = {Microbiome-mycotoxin interactions and probiotic strategies: implications for gut health and cancer.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1783295}, pmid = {41821854}, issn = {2296-861X}, abstract = {This structured, hypothesis-driven narrative review examines how mycotoxins, pervasive food contaminants, disrupt intestinal microbial balance, epithelial barrier integrity, xenobiotic metabolism, and carcinogenic signaling. Emerging evidence indicates that bidirectional interactions between the gut microbiome and mycotoxins modulate these effects, with microbial detoxification enzymes influencing toxin metabolism, immune responses, and epithelial resilience. However, the mechanistic understanding of microbiome-mycotoxin interplay remains incomplete, particularly regarding enzymatic pathways, microbial metabolites, and cancer-associated signaling. This review synthesizes recent (2016-2025) mechanistic studies on gut microbiota-mediated mycotoxin biotransformation, enzymatic detoxification, and probiotic interventions as strategies to mitigate mycotoxin-induced gut and cancer-related damage, focusing on key dietary toxins such as aflatoxin B1, deoxynivalenol, zearalenone, ochratoxin A, fumonisins, and patulin. Evidence indicates that microbial enzymes, including de-epoxidases, lactonases, and reductases, contribute to mycotoxin biotransformation, while probiotics can enhance epithelial barrier function, restore microbial ecosystem balance, and modulate immune responses through toxin binding, competitive exclusion, and anti-inflammatory actions. The review further highlights the strain-specific nature of detoxification, the impact of mycotoxin-induced dysbiosis on short-chain fatty acid production and inflammation, and the modulation of cancer-related pathways including NF-κB, STAT3, and IL-6. Finally, it provides an integrated framework linking microbial mechanisms, bioactive microorganisms, and regulatory considerations, identifies critical knowledge gaps, and outlines mechanistically informed probiotic strategies for mitigating mycotoxin exposure and its associated health risks.}, }
@article {pmid41821853, year = {2026}, author = {Dable-Tupas, G and Maraon, ABA and Bernolo, LJL and Toñacao, NGF and Taylaran, ADM and Plata, MAC and Alcano, JC and Björvang, RD and Zain, SM and Kobayashi, V and Arefayine, MB and Toni, AT and Nacis, JS and Gonzales, GB}, title = {Systems biology insights into the molecular drivers of childhood stunting and implications for intervention.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1761376}, pmid = {41821853}, issn = {2296-861X}, abstract = {Childhood stunting is a condition resulting from chronic malnutrition affecting millions globally, with lasting consequences for growth, cognition, and productivity. This review explores the molecular mechanisms underlying stunting, focusing on evidence obtained from systems biology to uncover biochemical pathways and potential biomarkers for early detection and targeted interventions. Key findings highlight the role of disrupted pathways such as the mechanistic target of rapamycin (mTOR) signaling, the tryptophan-kynurenine pathway, one-carbon metabolism, and chronic inflammation associated with environmental enteric dysfunction and dysbiosis of the gut microbiome. These insights emphasize the multifactorial nature of stunting, influenced by nutrition, infections, socioeconomic and maternal factors. Integrating systems biology to support public health strategies may provide avenues for precision nutrition-driven interventions that address specific deficiencies and systemic biochemical disturbances.}, }
@article {pmid41821330, year = {2026}, author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M}, title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {2}, pages = {202-214}, doi = {10.3967/bes2025.162}, pmid = {41821330}, issn = {2214-0190}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Bile Acids and Salts/metabolism ; Mendelian Randomization Analysis ; Species Specificity ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Bacteria/classification/genetics ; }, abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.<br><br>METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.<br><br>RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).<br><br>CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.}, }
@article {pmid41821139, year = {2026}, author = {Parikh, A and O'Rorke, R and Carroll, EL and Vermeulen, E and Harcourt, R and Constantine, R and Plön, S and Rayment, WJ and Chariton, A}, title = {Characterising the gut microbiomes of two baleen whales with different feeding and migratory strategies.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00538-9}, pmid = {41821139}, issn = {2524-4671}, abstract = {BACKGROUND: Mammalian gut microbiomes are essential for supporting digestion, nutrient absorption and overall host health. While diet and phylogeny are the two main influences on gut microbial composition, other factors, including life history and environment also contribute. Here, we characterised and compared the gut (faecal) bacterial microbiomes of two baleen whale species with contrasting life histories: the Bryde's whale (Balaenoptera edeni brydei), a non-migratory, year-round generalist forager; and the southern right whale (Eubalaena australis; SRW), a seasonal migrating species with a specialised diet of krill and copepods.<br><br>RESULTS: We found that each species harboured distinct gut microbiomes with potential links to their different feeding and migratory strategies. The Bryde's whale gut microbiome bore a strong resemblance to that of toothed whales, with relatively lower bacterial richness and diversity and a high proportion of Proteobacteria after Firmicutes. The core microbiome of these whales included taxa supporting a protein-rich diet and year-round foraging lifestyle, e.g. Carnobacterium and Faecalitalea. In contrast, the SRW had a gut microbiome similar to other baleen whale species, with a higher richness and diversity, and dominated by Firmicutes and Bacteroidetes. The SRW core microbiome featured taxa associated with lipid metabolism, e.g. Erysipelotrichaceae and Coriobacteriia, reflecting a lipid-rich diet and reliance on blubber reserves during migration. We also found that SRWs sampled at different stages in the migratory cycle had significantly different gut microbial compositions. Functional analyses further supported these results, with Bryde's whales being broadly enriched in enzymatic functions including protein digestion and SRWs showing more selective enrichment.<br><br>CONCLUSIONS: Along with species-specific microbiomes, our findings also suggest that migratory behaviour and foraging patterns - key aspects of cetacean life history - may substantially influence gut microbiome composition. The characterisation of the gut microbiomes of the two whales provides a valuable baseline for the future monitoring of cetaceans and their environments.}, }
@article {pmid41821060, year = {2026}, author = {Wu, Q and Wang, X and Mu, Q and Tian, J and Wang, H and Yang, J and Peng, Z and Gao, L and Gao, P and Zhao, F}, title = {Host genome regulation of the porcine gut microbiota and its impact on feed conversion efficiency.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41821060}, issn = {2524-4671}, abstract = {UNLABELLED: This study aims to elucidate the regulatory mechanisms of host genetics on the porcine gut microbiota and their subsequent impact on the feed conversion ratio (FCR). While initial genome-wide association studies (GWAS) did not identify significant SNPs directly associated with FCR, we investigated the gut microbiota as a potential intermediate phenotype influencing feed efficiency. Nonmetric multidimensional scaling (NMDS) based on Bray–Curtis distances demonstrated a distinct separation in microbial community structure between the high-feed conversion ratio (HFCR) and low-feed conversion ratio (LFCR) groups (stress = 0.19), suggesting a link between FCR and gut microbial composition. Furthermore, a significant, albeit weak, negative correlation was observed between the genomic relatedness matrices and microbial Bray‒Curtis dissimilarity (r = −0.0143, p = 0.0031), indicating host genetic control over the microbiome. Microbiome genome-wide association study (mGWAS) identified 117 significant SNPs associated with 28 microbial taxa. Functional annotation highlighted eight candidate genes (DCY8, PATJ, PTPN2, FTO, SLC13A1, ADAM28, MGST1, and PTGS2) involved in the regulation of taxa, including Campylobacter, Faecalibacterium, Streptococcus, Succinivibrio, Treponema, Turicibacter, uncultured Erysipelotrichales, and uncultured Peptococcaceae 2. Collectively, these findings establish that the gut microbiota is a heritable trait influenced by the host genome, providing novel targets for breeding strategies designed to optimize microbial composition for improved feed efficiency.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00527-y.}, }
@article {pmid41820371, year = {2026}, author = {Pillay, N and Short, CS and Mzobe, GF and Mtshali, A and Ngcapu, S}, title = {The vaginal microbiome in pregnancy and preterm birth: mechanisms, disparities, and therapeutic opportunities.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00945-5}, pmid = {41820371}, issn = {2055-5008}, abstract = {Preterm birth is the leading cause of neonatal morbidity and mortality, particularly in low- and middle-income countries. The vaginal microbiome influences pregnancy outcomes by effecting immunity, epithelial integrity and inflammation. Lactobacillus-dominance supports immune tolerance, whereas dysbiosis consisting of anaerobes such as Gardnerella and Prevotella promote inflammation and premature cervical remodelling. This review synthesises evidence linking microbiome composition, ancestry-associated disparities and host responses, and discusses emerging microbiome-based interventions for preterm birth.}, }
@article {pmid41820290, year = {2026}, author = {Eccher, S and Sposito, M and Scaglione, IM and Pasqualin, L and Rota, M and Bonato, A and Longo, L and Avancini, A and Trestini, I and Tregnago, D and Insolda, J and Milella, M and Pilotto, S and Belluomini, L}, title = {Microbiome and EGFR-mutant non-small cell lung cancer: a complex interplay.}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2026.2645844}, pmid = {41820290}, issn = {1744-8409}, abstract = {INTRODUCTION: Epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) exhibits unique biological and therapeutic characteristics. Although EGFR tyrosine kinase inhibitors (EGFR-TKIs) offer substantial clinical benefits, resistance development and treatment-related toxicities remain major challenges. Emerging evidence indicates that the host microbiome may significantly influence the efficacy and tolerability of EGFR-targeted therapies.<br><br>AREAS COVERED: This review summarizes the main microbiome characteristics of EGFR-mutant NSCLC and discusses the interplay between gut, respiratory and intratumoral microbiome and EGFR-TKI therapy in NSCLC, highlighting differential microbiome shifts associated with different TKIs and comparing the role of microbiome in modulating responses to EGFR-TKIs. The review also explores preclinical and early clinical strategies aimed at enhancing TKI efficacy and at, potentially, improving sensitivity of EGFR-mutant NSCLC to immunotherapy.<br><br>EXPERT OPINION: Despite its emerging role, microbiome research in EGFR-mutant NSCLC holds substantial potential to refine therapeutic outcomes. Microbiota-targeted interventions may improve TKIs efficacy, mitigate toxicity, and potentially expand immunotherapeutic options in this molecularly and immunologically 'cold' subgroup. Future integrative studies combining microbiome, metabolome and immune profiling are essential to translate these insights into personalized clinical strategies.}, }
@article {pmid41820089, year = {2026}, author = {Mirji, G and Bhat, SA and Shinde, RS}, title = {Trimethylamine-N-oxide: the microbial cue in immune-mediated disorders.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tem.2026.02.008}, pmid = {41820089}, issn = {1879-3061}, abstract = {Trimethylamine-N-oxide (TMAO), a gut microbial metabolite derived from dietary choline and carnitine, has emerged as a pivotal link between diet, microbial metabolism, and host immunity. Beyond its historical role as a marine osmolyte, TMAO engages core immune pathways-driving oxidative stress, inflammasome activation, and type I interferon signaling-to shape macrophage polarization, T cell responses, and systemic immune tone. These actions place TMAO at the intersection of chronic diseases, exacerbating cardiovascular, metabolic, renal, and neurodegenerative pathology while paradoxically enhancing antitumor immunity in pancreatic and breast cancers. Such duality underscores its significance as both a biomarker and a therapeutic target. We discuss current advances in TMAO biology, immune mechanisms, and strategies to modulate its activity through diet, microbiome interventions, and enzymatic inhibition.}, }
@article {pmid41820045, year = {2026}, author = {Wu, DY and Pan, YT and Zhang, PP and Xu, JF}, title = {[Annual progress in the clinical management and research of bronchiectasis 2025].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {3}, pages = {356-362}, doi = {10.3760/cma.j.cn112147-20251110-00698}, pmid = {41820045}, issn = {1001-0939}, support = {2024ZD0522400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82330070, W2511099//National Natural Science Foundation of China and the Major International Joint Research Program/ ; }, mesh = {Humans ; *Bronchiectasis/therapy/diagnosis/immunology ; Precision Medicine ; Microbiota ; Disease Management ; }, abstract = {This review provides a concise overview of research advances in bronchiectasis between October 1, 2024 and September 30, 2025. The management of bronchiectasis is increasingly moving toward precision medicine. Recent studies have further elucidated the interplay between the airway microbiome and host immunity, highlighting the central roles of microbial diversity and inflammatory networks driven by immune cells. Characterized by neutrophilic inflammation, type 2 helper T-cell responses, or specific microbial communities, distinct endotypes and phenotypes have been identified, paving the way for individualized therapeutic strategies. Innovations in diagnostic technologies have significantly enhanced the objectivity and accuracy of disease evaluation, risk stratification, and etiological diagnosis. Breakthroughs have also been made in therapeutic strategies: dipeptidyl peptidase-1 inhibitors targeting neutrophilic inflammation have demonstrated potential to delay disease progression in clinical trials. Management strategies that address prognostically relevant risk factors and comorbidities have also become more clearly defined. Future efforts to integrate multidimensional biological data for identifying treatable traits will be critical for achieving precision management and improving long-term outcomes in bronchiectasis.}, }
@article {pmid41819935, year = {2026}, author = {Fu, J and He, Y and Qiao, L and Wu, Z and Wei, Y and Hau, EH and Xiao, Y and Ren, D}, title = {Lactiplantibacillus plantarum ZJUIDS51 improves androgenic alopecia via gut-skin axis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {231}, number = {Pt 2}, pages = {118793}, doi = {10.1016/j.foodres.2026.118793}, pmid = {41819935}, issn = {1873-7145}, mesh = {Animals ; *Alopecia/therapy/chemically induced/microbiology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Mice ; Male ; Hair Follicle ; *Skin/metabolism ; Disease Models, Animal ; *Lactiplantibacillus plantarum ; Dihydrotestosterone ; }, abstract = {Androgen dysregulation is the primary driver of androgenetic alopecia (AGA), the most prevalent form of hair loss. This study aimed to evaluate the efficacy of Lactiplantibacillus plantarum ZJUIDS51 (Z51) in alleviating AGA using a C57BL/6 mouse model and to explore the underlying mechanisms associated with the gut-skin axis. The model was induced via intraperitoneal injection of dihydrotestosterone (DHT). Z51 was administered orally via gavage, while topical minoxidil and PBS gavage were used in the control groups. Results showed that Z51 intervention significantly promoted hair regeneration. By day 23, compared to the MC group, Z51 treatment resulted in an approximately 87% increase in hair coverage area and an approximately 68% increase in hair shaft length (both p < 0.0001). These improvements were preceded by enhanced hair follicle cell proliferation observed on day 10. Mechanistically, microbiome and metabolomic analyses suggest that Z51 remodeled the gut microenvironment. It modulated the abundance of androgen- and inflammation-related bacterial strains, thereby enhancing steroid metabolism and replenishing specific plant-derived antioxidant metabolites. In summary, Z51 ameliorated AGA through the gut-skin axis and provided insights into future treatments of AGA and the development of functional probiotics.}, }
@article {pmid41819706, year = {2026}, author = {Barmettler, E and Hartman, K and Valzano-Held, AY and Egli-Künzler, L and Dubuis, PH and Mackie-Haas, KA and Bucheli, TD and Lutz, S and van der Heijden, MGA}, title = {Copper and synthetic pesticides are major drivers of soil bacterial and fungal communities.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141682}, doi = {10.1016/j.jhazmat.2026.141682}, pmid = {41819706}, issn = {1873-3336}, abstract = {Soil microbial communities play a key role in terrestrial ecosystems and provide important agricultural functions. While earlier studies have shown that soil properties, such as pH and soil organic matter, are major drivers of microbial community structure, the roles of copper and synthetic pesticides are poorly understood. Here we focused on intensively managed agricultural systems studying 61 conventional and organic vineyards from three distinct winegrowing regions in Switzerland. We identified the factors shaping bacterial and fungal communities, specifically assessing the importance of copper and synthetic pesticides. Both copper and pesticides were identified as major factors shaping microbial community structure. Copper led to a pronounced reduction in bacterial diversity. Moreover, it affected bacterial and fungal community composition, to a degree comparable to pH. The relative abundances of many large taxonomic groups and functional guilds were positively or negatively impacted by copper, indicating a strong variability in copper sensitivity. Synthetic pesticide concentrations were negatively associated with fungal diversity and community composition, indicating that they are an additional stressor for soil fungi. Finally, we identified several genera negatively related to synthetic pesticides, including the biocontrol fungus Trichoderma, that could be tested for inclusion in improved risk assessments. This is the first study comparing a wide range of field sites which documents consistent negative effects of copper and synthetic pesticides on soil microbial diversity and community composition. Our work points to the need for improved risk assessments, specifically including yet overlooked effects on soil microbes.}, }
@article {pmid41656244, year = {2026}, author = {Çelik, E and Kocyigit, E and Bingöl, FG and Karaçolak, C and Cemali, &#xd6; and Simonelli, M and Ağagündüz, D and Capasso, R}, title = {Multiomics: the intersection of personalized nutrition in cardiometabolic diseases.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41656244}, issn = {1479-5876}, abstract = {BACKGROUND: Cardiometabolic diseases are among the leading causes of increasing morbidity and mortality worldwide. However, current population-based dietary recommendations do not sufficiently account for biological differences between individuals and therefore do not have the same effect on everyone. The multiomic approach, which incorporates genomic, epigenomic, transcriptomic, proteomic, metabolomic, and microbiome data, facilitates more accurate classification of disease risk and selection of appropriate nutritional interventions by mapping food-disease relationships across different biological layers.<br><br>METHODS: Through a narrative synthesis of the current literature, we focused on evidence from multiomic studies to assess their ability to guide personalized nutrition strategies based on individual genetic, metabolic, and microbiome characteristics in cardiometabolic diseases.<br><br>RESULTS: Recent evidence indicates that metabolomic markers have been reported to provide predictive value in addition to classic risk indicators and to increase the predictive power of models when combined with genetic data. Microbiome research shows that glycemic and lipemic responses can be predicted using algorithms based on gut microbiota. Recent clinical studies show that personalized nutrition plans, which evaluate the microbiome and clinical characteristics together, improve continuous glucose monitoring-based glycemic control, glycated hemoglobin levels, and triglycerides more than the classic Mediterranean diet.<br><br>CONCLUSION: This review summarizes the current multiomic evidence, discusses the methodological and practical challenges in this field, and highlights future priorities. The integration of digital biomarkers obtained from wearable technologies with multiomic systems and artificial intelligence-supported models, when developed in accordance with ethical and equitable access principles, has the potential to support the transition from the discovery phase to patient-centered clinical applications.<br><br>GRAPHICAL ABSTRACT: [Image: see text]}, }
@article {pmid41822725, year = {2024}, author = {Mpountouridis, A and Tsigalou, C and Bezirtzoglou, I and Bezirtzoglou, E and Stavropoulou, E}, title = {Gut microbiome in non-alcoholic fatty liver disease.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {3}, number = {}, pages = {1534431}, pmid = {41822725}, issn = {2813-1169}, abstract = {Non-alcoholic fatty liver disease (NAFLD) has a rapidly growing incidence worldwide, affecting approximately one-third of world population. The disturbance of gut commensal bacteria impacting host's homeostasis is referred to as gut dysbiosis. The gut microbiome contributes to the pathogenesis of NAFLD through various pathways. Gut microbiota is at constant interactions with the intestinal epithelial barrier and affects its integrity. Through gut-liver axis, gut microbiota may influence liver immune function. The release of lipopolysaccharides (LPS) from intestines to portal vein which are transported to the liver, may trigger hepatic inflammation, steatosis and even fibrosis. Moreover, the gut microbiome induces the conversion of primary bile acids (BAs) to secondary BAs, which activates intestinal receptors, such as FXR and TGR5. FXR activation decreases fat absorption and thus reduces hepatic lipid accumulation, while TGR5 activation promotes the release of glucagon-like peptide-1 (GLP-1) in blood. Furthermore, gut ethanol-producing bacteria has been implicated in NAFLD development. Additionally, in NAFLD there is a reduction in intestinal levels of short-chain fatty acids, such as butyrate, propionate and acetate. Many bacterial alterations have been observed in NAFLD, including the increased Bacteroidetes and decreased Firmicutes. Many probiotics have been tried in NAFLD prevention and management, including a plethora of strains from Lactobacilli, Bifidobacteria and Streptococcus and some of them have promising perspectives. There is also some promising data from the administration of prebiotics (such as inulin and fructo-oligosaccharides) and symbiotics (probiotics plus prebiotics). Faecal microbiota transplantation (FMT) is yet to be evaluated for its efficacy against NAFLD.}, }
@article {pmid41821950, year = {2025}, author = {De León, ME and Fox, EGP and Dunaj, S and Jenner, RA and Keiser, CN and Macrander, J and Nixon, SA and Nobile, CJ and Petras, D and Rodriguez-Roman, E and Saviola, AJ and Trim, SA and Varona, NS and Yeager, J and Ul-Hasan, S and Herzig, V and Colston, TJ}, title = {A review of the venom microbiome and its utility in ecology and evolution including future directions for emerging research.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {95}, number = {1}, pages = {3-27}, pmid = {41821950}, issn = {0334-5114}, abstract = {Microbes play vital roles in ecological systems, yet their presence and functions within venom environments of venomous organisms remain understudied. Despite the prevalent belief in the sterility of venoms, recent findings reveal diverse microbial communities within venom systems. This review aims to explore the relationships between venoms and microbes, highlighting their potential roles in evolutionary processes, ecological interactions, and therapeutic advancements. Venoms, composed of toxins utilized in hunting or defense, represent a rich source of natural products with applications in drug discovery and therapy, exemplified by FDA-approved venom toxin-derived drugs. Understanding microbial resistance mechanisms against antimicrobial peptides can illuminate coevolutionary processes and guide therapeutic development. Integrating hologenomic evolution and microbial ecology frameworks will facilitate comprehensive research on venom-microbiome interactions, and reveal the evolutionary drivers of venom diversification. Investigating and investing in these relationships promises advancements in understanding evolution, ecology, and biotechnology, with implications for human health and ecological conservation. This review synthesizes existing knowledge, identifies many gaps in literature, and investigates critical unanswered questions in the field of venom microbiology, encouraging ongoing and future collaborative research.}, }
@article {pmid41822715, year = {2024}, author = {Mousa, RS and Invernizzi, P and Mousa, HS}, title = {Innate immune cells in the pathogenesis of inflammatory bowel disease - from microbial metabolites to immune modulation.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {3}, number = {}, pages = {1452430}, pmid = {41822715}, issn = {2813-1169}, abstract = {Inflammatory Bowel Disease (IBD) is a term used to describe a group of disorders characterized by chronic inflammation of the gastrointestinal tract, with Crohn's Disease (CD) and Ulcerative Colitis (UC) being the most common. While still not fully understood, pathogenesis is believed to be multifactorial - the result of an interplay between genetic susceptibility, immune dysregulation and environmental factors that all lead to chronic inflammation and tissue remodeling. Innate immune cells, which orchestrate the initial defense mechanisms and modulate the subsequent immune response, play a central role in disease initiation and progression. This review examines the complex involvement of innate immune cells in IBD, emphasizing their interactions with environmental factors and the gut microbiome. We highlight the importance of microbial dysbiosis and impaired intestinal barrier function in disease pathogenesis, and the role that innate immune cells play not only as first responders, but also as key players in maintaining intestinal barrier integrity and gut microbiome. This review provides a comprehensive summary of the role that innate immune cells play in IBD pathogenesis with emphasis on the increasingly recognized role of the gut microbiome. A better understanding of innate immune cell mechanisms and of microbiome-immune interactions is key for the development of novel targeted therapies.}, }
@article {pmid41822728, year = {2024}, author = {Yao, A and Huang, C and Wang, X and Zhou, R and Hao, W and Lin, Q}, title = {The Reg protein family: potential new targets for the treatment of inflammatory bowel disease and colorectal cancer.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {3}, number = {}, pages = {1386069}, pmid = {41822728}, issn = {2813-1169}, abstract = {Inflammatory bowel disease (IBD) comprises Crohn's disease (CD) and ulcerative colitis (UC), both characterized by chronic intestinal inflammation and an elevated risk of colorectal cancer due to persistent inflammation. The Regenerating gene (Reg) family proteins exhibit properties that promote cell proliferation, inhibit apoptosis, reduce inflammation, combat microbial infections, and potentially modulate the immune system. There is increasing evidence of the potential function of the Reg family of proteins in the development of IBD and colorectal cancer, but the exact mechanism of action of the Reg family of proteins has not yet been fully clarified. In this paper, we reviewed the Reg protein family's involvement in the development of IBD by regulating intestinal microbes and immunity to maintain intestinal homeostasis. We also explored its possible regulatory mechanisms and signaling pathways in the progression and treatment of colorectal cancer, which is expected to serve as a target and a new biomarker for the treatment of IBD and colorectal cancer in the future.}, }
@article {pmid41822714, year = {2024}, author = {Tweedie-Cullen, RY and Wilson, BC and Derraik, JGB and Albert, BB and Opai, K and Edwards, T and O'Sullivan, JM and Cutfield, WS}, title = {Awareness and acceptability of gut microbiome transfer.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {3}, number = {}, pages = {1411898}, pmid = {41822714}, issn = {2813-1169}, abstract = {INTRODUCTION: Gut microbiome transfer (GMT or faecal microbiome transfer) is gaining increasing attention as a potential treatment for a range of medical conditions. However, public awareness and acceptance are not well understood.<br><br>METHODS: To better understand the public perception of microbiome transfer in New Zealand, we undertook a nationwide online survey. The anonymous survey was designed and distributed between 2022-2023. Inclusion criteria included being aged 16 years or older and a resident of New Zealand. Distribution channels included social media advertising, posters in public areas, e-mail newsletters, and a survey facilitation company.<br><br>RESULTS: A total of 2441 completed surveys were analyzed. Most respondents (71%) had tertiary education, 59% were female, with 62% identifying as NZ European, 12% as M&#x101;ori, and 3% as Pacific peoples. The findings identified a high level of awareness and acceptability, with 76% of respondents having heard of GMT, and 96% indicating they would consider it if proven efficacious for a health condition they had. High levels of acceptance were observed across all ethnicities. Encapsulated oral FMT treatment was the preferred transfer method.<br><br>DISCUSSION: Primary concerns related to GMT included the diet, health, and screening of stool donors, as well as the demonstration of safety and efficacy. These findings will help inform health professionals and researchers about the public's needs and preferences regarding GMT.}, }
@article {pmid41821822, year = {2023}, author = {Silva, R and Dinis, L and Peris, A and Novais, L and Calhau, C and Pestana, D and Marques, C}, title = {Fecal microbiota transplantation-could stool donors' and receptors' diet be the key to future success?.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {2}, number = {}, pages = {1270899}, pmid = {41821822}, issn = {2813-1169}, abstract = {Fecal microbiota transplantation (FMT) is indicated in many countries for patients with multiple recurrences of Clostridioides difficile infection (CDI) for whom appropriate antibiotic treatments have failed. Donor selection is a demanding and rigorous process in view of the implementation of FMT programs worldwide. One of the most noteworthy factors that has been shown to affect FMT outcomes is the microbial diversity of the stool donor. A detailed assessment of the donor's microbiota is crucial, as the microbiota is complex, dynamic, and resilient, and a healthy microbiota has several dimensions in addition to the absence of pathogens. Diet is one of the most important factors that modulates the composition and function of the gut microbiome (GM) and has a critical role in orchestrating the host-microbiota crosstalk throughout life. The diversity of the human GM seems to be related to variations in dietary patterns. Currently, the dietary patterns of stool donors and receptors are not taken into consideration in any way for FMT. In this study, we reflect on the importance of including this type of assessment in the stool donor screening process and knowing the impact of diet on the GM, as well as the importance of monitoring receptors' diet to ensure the engraftment of the transplanted microbiota.}, }
@article {pmid41821816, year = {2023}, author = {Steube, A and Stallhofer, J and Stallmach, A}, title = {Fecal microbiota transfer to treat ulcerative colitis: Medical and legal challenges.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {2}, number = {}, pages = {1161610}, pmid = {41821816}, issn = {2813-1169}, abstract = {Ulcerative colitis (UC) is one of the main forms of chronic inflammatory bowel disease; however, despite intensive efforts, its etiology remains unclear. It is generally accepted that disturbances in the gastrointestinal microbiota ("dysbiosis") contribute to the manifestation and perpetuation of UC. To date, treatment has focused on anti-inflammatory strategies; however, their widespread application is limited by side effects and primary/secondary loss of response. Following the resounding success of fecal microbiota transfer (FMT) to treat Clostridioides difficile infection (CDI), numerous studies have shown that FMT is also effective and safe in UC patients. In this review, we discuss the various modifications (e.g., antibiotic preconditioning, multi-donor concept, extension/intensification of application, long-term therapy, and dietary donor conditioning) that increase the efficacy of FMT. We then describe how the continuous need for healthy donors and the associated medicolegal requirements, limit the large-scale application of FMT. We conclude that FMT will likely be viewed as a transitional technology, which will be superceded by recombinantly produced bioproducts once the therapeutically active substances have been identified.}, }
@article {pmid41822096, year = {2022}, author = {Nobre, JG and Alpuim Costa, D}, title = {"Sociobiome": How do socioeconomic factors influence gut microbiota and enhance pathology susceptibility? - A mini-review.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {1}, number = {}, pages = {1020190}, pmid = {41822096}, issn = {2813-1169}, abstract = {The gut microbiota is becoming well recognized as a key determinant of health and disease. As a result, several studies have focused on causality and the predictive/prognostic value of the microbiota in a wide range of diseases. However, it is of greater importance to understand what sparks changes in the microbiota and how these alterations contribute to an increased susceptibility to disease. A few studies have already demonstrated that the gut microbiota could be modified by lifestyle, consequently leading to pathology. What if socioeconomic factors can also impact the gut microbiota composition and, thus, increase the susceptibility to disease? Perhaps, this is one of the factors that may have contributed to the increased inequalities between people with higher and lower socioeconomic status in terms of health. In this review, we aimed to understand more about this topic and the real impact of the "sociobiome." Furthermore, we proposed measures to mitigate the impact of these factors on the gut microbiota composition.}, }
@article {pmid41822065, year = {2022}, author = {Walker, C and Boland, A and Carroll, A and O'Connor, A}, title = {Concurrent functional gastrointestinal disorders in patients with inflammatory bowel disease.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {1}, number = {}, pages = {959082}, pmid = {41822065}, issn = {2813-1169}, abstract = {Approximately 25% of people with quiescent inflammatory bowel disease (IBD) have symptoms caused by a functional gastrointestinal disorder (FGID). The pathophysiology of FGIDs in IBD is multifactorial. The gut-brain axis plays an important role as a bidirectional pathway with reciprocal gastrointestinal and psychological symptoms. Other factors include altered gastrointestinal motility, microbiome dysbiosis, medication use, prior surgery, impaired intestinal permeability, immune-system activation, and visceral hypersensitivity. As both IBD and certain FGIDs can have similar symptoms, it can be difficult to determine which disorder is the precipitant of symptoms. However, a prompt diagnosis of an overlapping FGID helps avoid unnecessary corticosteroid use and escalations of IBD treatment. Despite their prevalence, there have been very few randomized controlled trials conducted on therapeutic interventions for overlapping FGIDs in IBD. Therefore, management usually follows those interventions recommended for FGIDs, with certain adaptations made to allow for an altered gastrointestinal anatomy and functioning, caused by IBD.}, }
@article {pmid41822078, year = {2022}, author = {Stange, EF}, title = {Current and future aspects of IBD research and treatment: The 2022 perspective.}, journal = {Frontiers in gastroenterology (Lausanne, Switzerland)}, volume = {1}, number = {}, pages = {914371}, pmid = {41822078}, issn = {2813-1169}, abstract = {Inflammatory bowel diseases (IBD) have seen major progress in current concepts and treatment regimes. Based on the theory of an inadequate "overshoot" of the mucosal immune response to the intestinal microbiome, therapies have been developed to interfere with the key mediators of inflammation from cytokines, including TNF and IL12/23, to integrins such as α4ß7 and intracellular cytokine signal transducers such as janus kinases. Recently, sphingosine-1-receptor agonists were marketed to suppress mucosal inflammation by sequestering lymphocytes in peripheral lymph nodes. However, the aim of these regimes targeting immunity to induce a long-term deep remission, including mucosal healing, is missed in most patients. Contrasting these anti-inflammatory mechanisms of action, the pathogenic focus has finally shifted to the mucosal antibacterial barrier in both Crohn´s disease and ulcerative colitis. Translating this novel concept requires a completely different approach but, in the end, may come closer to a cure of these devastating diseases, in which an incomplete immune modulation fails to achieve the key endpoints: halting disease activity and progression. This review aims to give an overview of past, current, and future concepts in IBD, focusing on both pathogenesis and consequent therapy. A cure is in sight only if both reflect the actual key mechanisms of slow bacterial entry into the mucosa and are harmonized and in line.}, }
@article {pmid41819687, year = {2026}, author = {Ribeiro, FV and Santos, HF and Fagundes, TSF and Moreira, DL and de Paula, GE and Almeida, P and Saliba, BM and Carmo, FL and Ferreira, CEL and Pereira, RC}, title = {Microbial pollution disables the chemical defenses of sea fans.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119534}, doi = {10.1016/j.marpolbul.2026.119534}, pmid = {41819687}, issn = {1879-3363}, abstract = {In coastal ecosystems, chemically rich species like gorgonians rely on specialized metabolites and symbiotic microbes for health and defense. In the Southwestern Atlantic, the elephant ear coral Phyllogorgia dilatata builds structurally complex forests and provides habitat for several species. Recent declines in cover have been linked to widespread disease, fouling, and necrosis. The loss of chemical defense due to anthropic perturbation has never been reported in the marine environment. We investigated whether pollution-driven stress could lead to a dysfunctional holobiont and impairment of its chemical defense. Using chromatography coupled to high-resolution mass spectrometry and molecular networking, we profiled secondary metabolites and used 16S rRNA gene amplicon sequencing to characterize microbial communities, relating these data to visual surveys of P. dilatata gorgonian forests. Defense compounds were found only in colonies far from pollution sources and correlated with bacteria associated with healthier environments. In contrast, pathogenic and sewage-associated bacteria dominated near the polluted site, where defenseless colonies of P. dilatata showed more disease and impaired health. Our results indicate that microbial pollution affects the capacity to modulate the microbiome through the use of infochemicals and leads to disruption of symbiosis and loss of chemical defense.}, }
@article {pmid41819537, year = {2026}, author = {Baker, JR and Beaulieu, D and Avci, E and Huang, E and Eickelberg, O and Meiners, S and Savai, R and Lehmann, M and Königshoff, M}, title = {Hallmarks of the ageing lung - 10 years later.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.01272-2025}, pmid = {41819537}, issn = {1399-3003}, abstract = {Aging is a crucial factor in the development of chronic lung diseases, including chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and lung cancer. Marking the 10th anniversary of the original "Hallmarks of the aging lung" published in this Journal, we present an updated review highlighting key cellular and molecular features of aging that drive the onset and progression of these conditions. Aging stands as the most significant risk factor for chronic lung diseases, which are characterised by structural and functional changes such as reduced elasticity, persistent inflammation, and impaired repair capacity. Recent evidence confirms that nearly all recognised hallmarks of aging play a role in the pathogenesis of these diseases. Notably, extracellular matrix (ECM) dysregulation - first proposed as a lung aging hallmark in 2015 - has become an integral aspect of aging in lung disease. Environmental exposures, such as cigarette or wildfire smoke, accelerate age-related changes by increasing oxidative stress, promoting cellular senescence, and disrupting tissue homeostasis. In lung cancer, aging contributes to genomic alterations, epigenetic dysregulation, immune evasion, and therapeutic resistance. Additionally, the roles of extracellular vesicles and microbiome changes in shaping these aging phenotypes are emerging areas of research. Early clinical studies are now targeting specific aging hallmarks, such as cellular senescence, with the goal of reducing age-related pathology and improving outcomes. Overall, integrating aging biology into lung disease research paves the way for innovative diagnostic and therapeutic strategies that address common molecular mechanisms across multiple chronic lung conditions.}, }
@article {pmid41819376, year = {2026}, author = {Gamage, ND and Mossion, A and Khan, M and Karim, R and Rabesaotra, V and Wielgosz-Collin, G and Lebeau, T and Méléder, V}, title = {Co-culturing Bacteria with Monospecific Microalgal Biofilms for Improved Biomass and Lipid production.}, journal = {Journal of biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiotec.2026.03.007}, pmid = {41819376}, issn = {1873-4863}, abstract = {Integrating microbiome engineering into microalgal biofilms could offer an environmentally sustainable and economically viable strategy to enhance biomass and lipid yields while leveraging the inherent advantages of biofilm-based systems. Building on this hypothesis, our objective was to improve biomass and lipid production in the naturally biofilm-forming marine benthic diatom, Amphora sp. (NCC169) by co-culturing it with two of its native biofilm associated bacteria, Nitratireductor sp. and Sulfitobacter sp., in a vertical porous substrate biofilm photobioreactor (PSBR) operated in batch mode. Axenic, non-axenic, and co-cultures were maintained in triplicate for 15 days in F/2 enriched artificial seawater at 18±1 °C under continuous light (100 μmol photons.m[-2].s[-1]). Biomass and lipid content were quantified gravimetrically, followed by fatty acid profiling via gas chromatography-mass spectrometry (GC-MS) at three harvesting days (3, 6, and 15). Results showed that the Amphora-Nitratireductor co-culture achieved the highest surface biomass (2.54±0.39g.m[-2]) and productivity (0.99±0.26g.m[-2].day[-1]) on day 3, further peaking on day 6 (7.27±1.31g.m[-2]; 1.24±0.16g.m[-2].day[-1]) and were significantly different from the non-axenic control. The Amphora-Sulfitobacter co-culture recorded a significantly higher lipid yield on day 3 (1.51±0.31g.m[-2]), surpassing axenic cultures by 3-fold, non-axenic by 6-fold, and Amphora-Nitratireductor by 5-fold, with a lipid content of 67.03±17.80% of Amphora dry biomass weight. The fatty acid profile of Amphora sp. remained largely consistent across culture conditions and harvest days, dominated by palmitic acid (16:0) and palmitoleic acid (16:1), with low polyunsaturated fatty acid levels, highlighting its potential for pharmaceutical, nutraceutical, cosmetic, and bioenergy applications.}, }
@article {pmid41819322, year = {2026}, author = {Yu, H and Tonog, G and Kakooza, D and Jeong, J and Lee, S and Park, SY and Moon, SK and Kim, H}, title = {β-Glucan-rich Hericium erinaceus hot-water extract ameliorates acute colitis by suppressing inflammation, preserving the epithelial barrier, and modulating gut microbiota ecosystem.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {151368}, doi = {10.1016/j.ijbiomac.2026.151368}, pmid = {41819322}, issn = {1879-0003}, abstract = {Inflammatory bowel disease (IBD) is a chronic disorder marked by mucosal barrier disruption, immune imbalance, and gut dysbiosis. Polysaccharide-enriched extracts of Hericium erinaceus (HE) have shown anti-colitic effects, but the role of its β-glucan-rich water extract (HE-HW) remains unclear. By investigating a commercially relevant β-glucan-rich extract rather than isolated polysaccharides, this work addresses a key translational gap in HE research. HE-HW, rich in 1,3:1,6-β-glucan (286.4 mg/g), was evaluated using cells and mouse colitis models. In RAW 264.7 macrophages, HE-HW (1-10 μg/mL) suppressed lipopolysaccharide-induced nitric oxide and pro-inflammatory cytokines (IL-6, MCP-1) without cytotoxicity. In DSS-stimulated Caco-2 cells, HE-HW downregulated inflammatory mediators and restored tight junction genes (occludin, ZO-1, MUC2). In DSS-induced colitis mice, oral HE-HW (1 or 5 mg/kg/day) improved disease activity and colon length while normalizing serum and tissue cytokines and immunoglobulins. Histology confirmed reduced mucosal damage, muscle thickening, and collagen accumulation. Microbiome profiling showed HE-HW attenuated DSS-associated enrichment of Erysipelatoclostridium, Faecalibaculum, and Olsenella, suggesting selective remodeling of inflammation-related microbial populations. These findings demonstrate that β-glucan-rich HE-HW protects against colitis by modulating inflammation, reinforcing epithelial integrity, and rebalancing gut microbiota.}, }
@article {pmid41819291, year = {2026}, author = {Kalimuthu, S and Muthusamy, A}, title = {MobiRes: An integrative pipeline for resistome risk prediction through mobilome profiling.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107448}, doi = {10.1016/j.mimet.2026.107448}, pmid = {41819291}, issn = {1872-8359}, abstract = {Antimicrobial resistance (AMR) poses a significant global health challenge, with the environment serving as a crucial reservoir and conduit for resistance determinants. Although antibiotic resistance genes (ARGs) have been extensively studied in environmental contexts, systematic approaches for assessing and prioritizing the risks associated with mobile genetic elements (MGEs), such as plasmids, phages, transposons, and integrative elements (IEs), remain unclear. To address this gap, we present MobiRes, an open-source computational framework designed to predict resistome risk by integrating information from the mobilome and microbiome. The pipeline was evaluated using a wide range of publicly available metagenomic datasets spanning diverse environments, including wastewater, poultry, soil, sediments, and human fecal samples. To validate the framework, statistical analyses and machine learning models were applied to evaluate the role of MGEs in driving ARG dissemination. The pipeline identified transposons as the dominant MGE class while capturing environment-specific variation in plasmid, phage, and IE -associated ARGs. Transposon-associated ARGs showed the most consistent environmental differentiation (ANOVA p = 0.0017; Kruskal-Wallis p = 0.018), whereas plasmid and phage-associated ARGs varied moderately (p = 0.015-0.040) and IE-associated ARGs remained comparatively stable across environments (p > 0.05). The Random Forest (RF) model achieved an AUC of 0.82, and subsequent feature importance and SHapley Additive exPlanations (SHAP) analyses revealed that transposon abundance is the primary factor driving ARG dissemination across diverse environments. By integrating host, mobility, and ecological factors, MobiRes provides a scalable and One Health-oriented framework for comprehensive AMR risk assessment. This pipeline is publicly available at https://github.com/santhiyakc17/MobiRes_Pipeline.}, }
@article {pmid41819216, year = {2026}, author = {Wang, IM and Tsai, IL}, title = {Comparative Pathogenesis and Management of Orbital/Conjunctival and Gastric MALT Lymphoma: Microbial Drivers, Molecular Mechanisms, and Therapeutic Implications.}, journal = {Survey of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.survophthal.2026.03.005}, pmid = {41819216}, issn = {1879-3304}, abstract = {Mucosa-associated lymphoid tissue (MALT) lymphoma is a subtype of indolent extranodal B-cell non-Hodgkin lymphoma. Orbital and conjunctival MALT lymphomas (OAML) are the most common primary ocular adnexal lymphomas, while gastric MALT lymphoma remains a prototypical site linked to Helicobacter pylori infection. Despite the disparate anatomical locations, mounting evidence suggests a shared pathogenesis, including chronic antigenic stimulation, lymphoid accumulation, and genetic events. This review explores the epidemiologic, pathophysiologic, and molecular connections between OAML and gastric MALT lymphoma, with particular emphasis on the therapeutic implications. The role of H. pylori as a driver of gastric lymphomagenesis is well-established, and antibiotic eradication therapy has revolutionized treatment. By contrast, the evidence for microbial triggers and antibiotic responsiveness in OAML remains equivocal, although Chlamydia psittaci has been proposed in some populations. We comprehensively evaluate treatment modalities for OAML, including watchful waiting, antibiotic therapy, low-dose radiotherapy, immunochemotherapy (e.g., rituximab, bendamustine), and targeted agents. The differences in natural history, treatment response, and relapse patterns between gastric and ocular MALTomas are reviewed, and a proposed treatment algorithm is presented. Finally, we highlight knowledge gaps and future directions, including molecular profiling, predictive biomarkers, and microbiome-targeted interventions.}, }
@article {pmid41819204, year = {2026}, author = {Qi, Y and Zheng, X and He, X and Huang, K and Wang, D and Zhang, XX}, title = {Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124241}, doi = {10.1016/j.envres.2026.124241}, pmid = {41819204}, issn = {1096-0953}, abstract = {The escalating prevalence of benzotriazole (BTR), an emerging refractory organic pollutant, has drawn significant attention for the development of efficient bioremediation solutions. Although the construction of microbial consortia represents a promising strategy, the intrinsic relationship between community succession and functional features during artificial selection remains poorly understood. To address this, this study engineered two distinct microbial consortia from activated sludge using a top-down selection strategy in sequencing batch reactors fed with increasing BTR concentrations. While the two consortia evolved along divergent taxonomic pathways, they exhibited remarkable functional convergence, maintaining consistently high BTR transformation (>96%) and chemical oxygen demand (>75%) removal efficiencies. This robust performance under the stringent condition of BTR as the sole carbon source highlighted their significant adaptive potential. Metagenomic analysis further attributed this functional stability to the principle of functional redundancy, wherein taxonomically distinct keystone species (e.g., Nocardioides and Methylobacterium) harbored functionally analogous gene clusters. Additionally, multiple congeneric species (e.g., MAG.480 and MAG.17) within the Bacteroidota phylum exhibited significant divergence in their degradation gene repertoires. These findings not only advance ecological understanding of microbiome-mediated BTR biodegradation but also provide a foundation for the rational design and optimization of high-performance bioremediation consortia.}, }
@article {pmid41819101, year = {2026}, author = {Pérez Pañeda, L and Kadavá, T and Shamorkina, TM and Schulte, D and Pribil, P and Heidelberger, S and Narlock-Brand, AM and Yannone, SM and Snijder, J and Heck, AJR}, title = {Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101536}, doi = {10.1016/j.cels.2026.101536}, pmid = {41819101}, issn = {2405-4720}, abstract = {The ability to sequence proteins without reliance on a genomic template defines a critical frontier in proteomics. This approach, known as de novo protein sequencing, is essential for applications in antibody sequencing, microbiome proteomics, and antigen discovery, which require accurate reconstruction of target sequences. To advance this field, we here explore two hyperthermoacidic archaeal (HTA) proteases for de novo antibody sequencing, benchmarking them against trypsin and chymotrypsin. Each HTA-protease generated about five times more unique peptide reads than trypsin or chymotrypsin, providing high redundancy across all complementarity-determining regions. Combined with EAciD fragmentation on a ZenoTOF, this methodology enabled complete, unambiguous antibody sequencing. De novo analysis showed much higher alignment scores and reduced the sequence errors by using the HTA-generated data. With short digestion times, minimal sample cleanup, and analysis in just a single liquid chromatography-mass spectrometry (LC-MS/MS) run, this streamlined single-protease approach delivers a scalable and efficient strategy for de novo protein sequencing across diverse applications. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid41819083, year = {2026}, author = {Ponsioen, CY and Herrema, H}, title = {When phages fuel gut inflammation.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {3}, pages = {376-378}, doi = {10.1016/j.chom.2026.02.014}, pmid = {41819083}, issn = {1934-6069}, mesh = {Humans ; *Bacteriophages/physiology ; *Gastrointestinal Microbiome ; *Crohn Disease/microbiology/virology/pathology ; *Inflammation/microbiology/virology ; Bacteria/virology ; *Inflammatory Bowel Diseases/microbiology/virology ; Virome ; *Gastrointestinal Tract/virology/microbiology ; }, abstract = {Inflammatory bowel disease is associated with the gut microbiome, with many of its mechanistic underpinnings yet to be unraveled. In this issue of Cell Host &amp; Microbe, Wen and colleagues show that Crohn's disease pathology is amplified by phage-bacteria interactions and that the gut virome might be a driver of disease severity.}, }
@article {pmid41818936, year = {2026}, author = {Norfuad, FA and Mokhtar, MH and Zainuddin, AA and Chew, KT and Abu, MA and Nur Azurah, AG}, title = {The relationship between female genital tract microbiome and dysmenorrhoea: A systematic review of current evidence.}, journal = {Best practice &amp; research. Clinical obstetrics &amp; gynaecology}, volume = {106}, number = {}, pages = {102718}, doi = {10.1016/j.bpobgyn.2026.102718}, pmid = {41818936}, issn = {1532-1932}, abstract = {Dysmenorrhoea or painful menstruation is a common and challenging gynaecological condition affecting women of reproductive age, with a prevalence of between 45% and 93% worldwide. Despite its significant impact on quality of life, dysmenorrhoea has often been normalised as an integral part of the menstrual cycle. Recent advances in next-generation sequencing technology have opened new opportunities for exploring the microbial landscape of the female genital tract, providing new insights into the role of the microbiota in both healthy individuals and those with dysmenorrhoea. A growing body of research is addressing the complex interplay between dysmenorrhoea and the microbiome of the female genital tract. This systematic review aims to present an updated synthesis of current knowledge on this relationship. A comprehensive literature search was conducted across PubMed, Web of Science, and Scopus databases. Twelve articles were identified between 2018 and 2023, comprising a total of 397 cases of dysmenorrhoea that met the inclusion criteria. This review provides a detailed discussion of the microbiome findings of selected studies and offers the users the flexibility to choose the most appropriate indices. Therefore, this review would offer insights that hold promise for the development of targeted interventions aimed at modulation of the microbiome to alleviate symptoms, paving the way for a deeper understanding of women's reproductive health.}, }
@article {pmid41818927, year = {2026}, author = {Pawar, S}, title = {Low-grade chronic inflammation in young adults: An underrecognized epidicemic.}, journal = {Explore (New York, N.Y.)}, volume = {22}, number = {3}, pages = {103377}, doi = {10.1016/j.explore.2026.103377}, pmid = {41818927}, issn = {1878-7541}, abstract = {Low-grade chronic inflammation (LGCI) is increasingly recognized as a silent yet significant contributor to the global burden of non-communicable diseases. Traditionally associated with aging, emerging evidence indicates that LGCI is now prevalent among young adults due to modern lifestyle patterns. Factors such as sedentary behavior, ultra-processed food consumption, obesity, chronic psychological stress, sleep deprivation, environmental pollutants, and altered gut microbiota contribute to a persistent state of systemic inflammation. Unlike acute inflammation, which is protective and self-limiting, LGCI is characterized by subtle but continuous elevation of inflammatory biomarkers including C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α). In young populations, this chronic inflammatory milieu often remains clinically unnoticed but may predispose individuals to a range of metabolic, cardiovascular, neuropsychiatric, and reproductive disorders later in life. Recent epidemiological studies suggest that early exposure to inflammatory triggers accelerates the development of insulin resistance, endothelial dysfunction, and immune dysregulation. Additionally, lifestyle transitions associated with urbanization and digital dependence have intensified inflammatory risk factors among young adults worldwide. Recognizing LGCI as an early biological warning signal offers opportunities for preventive interventions. Dietary modulation, physical activity, adequate sleep, stress management, and gut microbiome optimization have shown promise in reducing inflammatory burden. Early screening of inflammatory biomarkers in high-risk young individuals may further aid in identifying subclinical disease risk. Increased awareness among clinicians and public health professionals is essential to address this emerging concern. This perspective highlights the importance of acknowledging low-grade chronic inflammation in young adults as an underrecognized epidemic and emphasizes the need for early preventive strategies to mitigate long-term health consequences.}, }
@article {pmid41818791, year = {2026}, author = {Johnson, A and O'Sullivan, EN and Valyasevi, P and Metras, B and Jang, S and Shields-Cutler, R and Hendel, KR and Harindhanavudhi, T and Teigen, L}, title = {The Potential for Complex Interplay Between GLP-1 Receptor Agonists, Gut Microbiome, and Obesity Management.}, journal = {Canadian journal of physiology and pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjpp-2025-0219}, pmid = {41818791}, issn = {1205-7541}, abstract = {Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are a class of medications used to treat and manage type 2 diabetes mellitus (T2DM) and obesity. The present narrative review explores potential interactions between the gut microbiome and GLP-1 RAs. Limited research has been conducted at the intersection of the gut microbiome and GLP-1 RA therapy. Therefore, this review focuses on potential relationships among GLP-1 RA, the microbiome, body weight, dietary changes, and gastrointestinal symptoms. The review of the current literature reveals significant gaps, particularly concerning the role of diet in mediating or confounding any impact of GLP-1 RA medications on the gut microbiome. Therefore, the body of the review is structured as a series of proposed directional and causal relationships. The limited available evidence suggests changes in behavior, diet, and weight loss resulting from GLP-1 RA treatment are the primary drivers of microbiome changes observed after GLP-1 RA treatment. The review concludes by proposing directions for future studies to clarify the complex interplay between GLP-1 RAs, the gut microbiome, diet, and obesity management.}, }
@article {pmid41818260, year = {2026}, author = {Sambanthan, R and Abu Kassim, NF and Abuelmaali, SA and Kamil, WMWA and Sabar, S and Zarkasi, KZ and Ishak, WRW and Webb, CE}, title = {Impact of sugar-based baits on midgut microbiome composition in Aedes mosquitoes: Implications for vector control.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0329341}, pmid = {41818260}, issn = {1932-6203}, mesh = {Animals ; *Aedes/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Mosquito Control/methods ; *Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Sugars/pharmacology ; Bacteria/genetics/classification ; *Microbiota/drug effects ; Female ; Mangifera/chemistry ; }, abstract = {The Aedes mosquitoes are responsible for the transmission of many severe diseases. Novel integrated vector management techniques like alginate hydrogel beads and appealing toxic sugar bait have strengthened control efforts. These techniques help to control mosquitoes by taking advantage of their attraction to sugar. Different types of sugar that mosquitoes ingest during feeding can affect the makeup of the microbiome in the midgut. The mosquito midgut microbiome maintains immune priming and baseline immune activity. Therefore, the current focus of this study is on utilizing microbial communities for vector control measures with a particular emphasis on how they consume various forms of sugars. Both wild and lab strains of Ae. aegypti and Ae. albopictus mosquito samples were reared, and attractive targeted sugar baits (ATSBs) infused with Chrysanthemum, mango, mix and control solutions. Then, the impact of bacterial communities was assessed using 16S rRNA gene sequences. According to our findings, the majority of the bacterial species in mango and mixed treatments belonged to the Enterobacteriaceae family. A total of 24 different bacterial species were found in Aedes mosquitoes that fed on mango ATSBs. The isolates were found to be members of three phyla from Actinobacteria (4.16%), Firmicutes (54.17%), and Proteobacteria (41.67%). Data reveals that different species, strains, and diets affect the midgut bacterial diversity in the mosquitoes. In addition to strengthening our knowledge concerning the way this bacterium shapes the microbial community, a thorough investigation of the prevalence of the midgut bacterial community is essential for alerting present and future mosquito and disease control initiatives.}, }
@article {pmid41818176, year = {2026}, author = {Thapa, M and Kumari, A and Chin, CY and Choby, JE and Akbari, E and Bogati, B and Jin, F and Furr, E and Chopyk, DM and Koduri, N and Pahnke, A and Burns, TL and Elrod, EJ and Burd, EM and Weiss, DS and Grakoui, A}, title = {Translocation of bacteria from the gut to the brain in mice.}, journal = {PLoS biology}, volume = {24}, number = {3}, pages = {e3003652}, pmid = {41818176}, issn = {1545-7885}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; *Brain/microbiology/metabolism ; Mice ; *Bacterial Translocation/physiology ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Male ; Enterobacter cloacae/physiology ; Vagus Nerve/microbiology ; Dysbiosis/microbiology ; }, abstract = {Recent advances suggest a correlation between gut dysbiosis and neurological diseases, however, relatively little is known about how gut bacteria impact the brain. Here, we reveal that bacteria can translocate directly from the gut to the brain in small numbers when mice are fed an atherogenic, high-fat diet (Paigen diet) that causes alterations in gut microbiome composition and gut barrier permeability. The bacteria were not found in other systemic sites or the blood, but were detected in the vagus nerve. Right cervical vagotomy reduced bacterial burden in the brain, implicating the vagus nerve as a conduit for bacterial translocation from the gut to the brain. Antibiotic treatment perturbed the composition of the gut microbiome and correspondingly changed the bacteria that localized to the brain in the setting of Paigen diet feeding. To further establish the gut as the origin of bacterial translocation to the brain, we gavaged exogenous Enterobacter cloacae into Paigen diet-fed mice, subsequently detecting the E. cloacae in the gut and brain. In addition, we monocolonized germ-free mice with E. cloacae and only cultured the bacteria from the brains of mice fed Paigen diet, but not those fed standard diet. Localization of bacteria to the brain in Paigen diet-fed mice was reversible with return to normal diet. Bacteria were also detected in the brain of murine models of Alzheimer's, Parkinson's, and autism spectrum disorder fed standard diet. These data reveal a bacterial translocation axis from the gut to the brain, impacted by environmental (diet) and genetic factors, and warrant further investigation to determine if this phenomenon also occurs in humans and to elucidate whether it may play a role in diverse neurological conditions.}, }
@article {pmid41817893, year = {2026}, author = {Matta, T and Bishnoi, M and Kumari, L and Dwivedi, S and Chopra, K and Kondepudi, KK}, title = {Beneficial Modulation of the Microbiota-Gut-Brain Axis by Supplementation with Modified Kodo Millet Bran and a GABA-Producing Bacterium in PTZ-Induced Kindling.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41817893}, issn = {1867-1314}, support = {Core Fund//National Agri-Food Biotechnology Institute/ ; }, abstract = {Beneficial modulation of the microbiota-gut-brain axis (MGBA) using dietary fibres and psychobiotics has emerged as a novel strategy for the management of various neurological conditions including epilepsy. Herein, we investigated the effects of supplementation of modified kodo millet bran (mKMB) along with GABA-producing Levilactobacillus brevis LAB6 MTCC 25662 in mitigating epileptic seizures, neuroinflammation and colonic aberrations in pentylenetetrazol (PTZ)-induced epilepsy in SD rats. Chronic PTZ kindling induced gut-brain dysregulation, whereas supplementation with mKMB and LAB6 reduced seizure severity, preserved neuronal spines, and restored hippocampal GABAergic function. It also effectively attenuated neuro- and systemic inflammation (~ 1.77-fold overall cytokine reduction), associated with enhanced FFAR2/3 expression and increased gut GABA and SCFAs. Microbiome analysis showed that supplementation mitigated kindling-induced dysbiosis by reducing Aerococcus, Clostridium, Enterococcus and enriching beneficial microbes; notably, Turicibacter abundance increased to 21.39% in Syn + PTZ compared to 13.6% in PTZ (log2FC = + 0.65, p = 0.056) and 17.21% in mKMB + PTZ (log2FC = + 0.56, p = 0.032), alongside an increase in Lactobacillus, particularly Levilactobacillus brevis. These findings highlight the protective potential of dietary fibres and rationale psychobiotics supplementation in modulating MGBA and developing an effective management strategy for epilepsy.}, }
@article {pmid41817831, year = {2026}, author = {Suryansh, S and Kannan, AB and Iyer, S and Jain, T}, title = {Bugging In: Rethinking Colorectal Cancer Pathogenesis Through the Gut-Tumor-Microbiota Axis.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {41817831}, issn = {1573-2568}, }
@article {pmid41817578, year = {2026}, author = {Pi, Y and Wei, Z and Xu, L and Yin, C and Li, Y and Li, X}, title = {Structural and functional characteristics of faecal, vaginal and colostrum microbiota in high-yielding sows.}, journal = {Microbial genomics}, volume = {12}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001627}, pmid = {41817578}, issn = {2057-5858}, mesh = {Animals ; *Colostrum/microbiology ; Female ; *Vagina/microbiology ; *Feces/microbiology ; Swine/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Recent studies have highlighted the critical roles of the microbiota in faeces, vagina and colostrum in reproductive success and piglet development. Understanding the structural and functional dynamics of these microbial communities is essential for optimizing the health and productivity of high-yielding (HY) sows. This study aimed to characterize the structural and functional features of these microbial communities in HY sows (litter size>10 piglets) vs. low-yielding (LY) sows (≤10 piglets) and to explore their associations with sow performance and piglet health. Fifteen Yorkshire sows from each group were selected, and fresh faecal, vaginal mucus and colostrum samples were collected post-parturition. Microbial composition was analysed using 16S rRNA gene amplicon sequencing, and functional potential was predicted via PICRUSt2. Results showed that HY sows exhibited higher alpha diversity in vaginal and colostrum microbiota and greater community stability (higher neutral community model R [2] values) compared to LY sows. In faeces, HY sows were enriched with Terrisporobacter and Romboutsia, while depleted in Ruminococcus_torques_group. In the vagina, Campylobacter and Peptoniphilus were increased, whereas Eubacterium_nodatum_group decreased. In colostrum, Lactobacillus, Bifidobacterium and Romboutsia were enriched, with reduced Peptostreptococcus, indicating a more beneficial profile for neonatal health. Functional predictions revealed distinct metabolic profiles: HY faecal microbiota upregulated cysteine/methionine metabolism and porphyrin and chlorophyll metabolism; vaginal microbiota enhanced oxidative phosphorylation and thiamine metabolism; colostrum microbiota showed enrichment in monobactam and novobiocin biosynthesis, which is associated with antimicrobial activity and stress response. These findings demonstrate that HY sows harbour a more stable and functionally advantageous microbiome across multiple biological niches, which may contribute to superior reproductive performance and improved offspring health. The results provide a foundation for developing microbiome-targeted strategies to enhance productivity and welfare in commercial pig production.}, }
@article {pmid41817458, year = {2026}, author = {Cable, J and Giuli, R and Fox, MR and Rosen, RL and Valdovinos-García, LR and Siboni, S and Clarke, JO and Johnston, N and Samuels, TL and Scarpignato, C and Stein, EM and Fass, R and Remes-Troches, JM and Khan, A and Rahman, AK and Lynch, K and Jodorkovsky, D and Vela, MF and Vandenberg, A and Kuo, B and Ergun, P and Jirapinyo, SP and Asti, E and Tolone, S and Sheu, EG and Salvador, R and Sozzi, M and Husain, IA and Wu, JC and Hobson, A and Sharma, NS and Lo, WK and Duncan, DR and Gyawali, CP and Chan, W and Sifrim, D and Savarino, E and de Bortoli, N and Rogers, BD}, title = {Gatherings in Esophagology: Innovations and Future Directions in the Diagnosis and Management of Reflux Disease.}, journal = {Annals of the New York Academy of Sciences}, volume = {1557}, number = {1}, pages = {e70225}, pmid = {41817458}, issn = {1749-6632}, support = {//Department of Otolaryngology and Communication Sciences, Medical College of Wisconsin/ ; }, mesh = {Humans ; *Gastroesophageal Reflux/diagnosis/therapy/physiopathology ; Proton Pump Inhibitors/therapeutic use ; Esophageal pH Monitoring/methods ; Fundoplication/methods ; }, abstract = {Recent advances in the diagnosis and management of reflux disease were the central focus of the inaugural Gatherings in Esophagology (GiE), which convened experts across gastroenterology, surgery, otolaryngology, pulmonology, and basic research. The sessions highlighted innovations in reflux monitoring-including high-resolution manometry, wireless pH monitoring, and novel salivary biomarkers-while critically evaluating their diagnostic accuracy and clinical utility. Presentations explored the limitations of traditional proton-pump inhibitor therapy, the emergence of potassium-competitive acid blockers as a new class of acid suppressants, and the evolving role of adjunctive treatments such as mucosal protectants, reflux reducers, and neuromodulators for refractory symptoms. The discourse extended to advanced interventional procedures, including transoral incisionless fundoplication, magnetic sphincter augmentation, and the RefluxStop device, with discussion of patient selection, efficacy, and complication management. Discussants emphasized the pathophysiology and management of extraesophageal manifestations of reflux, the interplay between reflux and pulmonary disease, and the diagnostic challenges in pediatric populations. The meeting also addressed the integration of behavioral therapies, the role of the microbiome, and the application of artificial intelligence in reflux diagnostics. Collectively, these insights underscore a shift toward precision medicine in reflux disease, emphasizing individualized diagnostic strategies and tailored therapeutic approaches to improve patient outcomes.}, }
@article {pmid41817438, year = {2026}, author = {Surve, SV and Valls, RA and O'Toole, GA}, title = {Draft genome sequences of 109 gut bacteria isolated from colonoscopy samples of individuals with and without cystic fibrosis.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0111425}, doi = {10.1128/mra.01114-25}, pmid = {41817438}, issn = {2576-098X}, abstract = {We report draft genome sequences of gut bacterial isolates recovered from colonoscopy samples obtained from individuals with and without cystic fibrosis. These genomes expand the representation of cultured gut microbes from distinct colonic regions and provide a resource for studying microbial diversity, adaptation, and host-microbe interactions in health and disease.}, }
@article {pmid41817287, year = {2026}, author = {Jeon, HW and Yang, KI and Yu, SJ and Kang, MS and Lee, WP}, title = {Clinical Efficacy of the Probiotic Weissella cibaria CMU in Adults with Gingivitis: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.}, journal = {Journal of medicinal food}, volume = {}, number = {}, pages = {1096620X261430298}, doi = {10.1177/1096620X261430298}, pmid = {41817287}, issn = {1557-7600}, abstract = {Periodontal disease results from dysbiotic oral biofilms and the host's inflammatory response. Given the limitations of conventional therapies, this study aimed to evaluate the efficacy and safety of Weissella cibaria CMU (OraCMU) in improving gingival inflammation in individuals with gingivitis and incipient periodontitis. In this randomized, double-blind, placebo-controlled trial, 80 participants received either OraCMU tablets (2.0 × 10[8] CFU/g; n = 40) or placebo (n = 40) twice daily for 8 weeks. The primary outcome was the gingival index (GI), and secondary outcomes included bleeding on probing (BOP), probing depth, clinical attachment level, gingival recession, plaque index, inflammation-related proteins, and oral microbiota. Clinical parameters were assessed at six preselected index teeth (#16, 12, 24, 32, 36, and 44). At week 8, the probiotic group showed significantly greater reductions in GI (-0.19 ± 0.03 vs. -0.08 ± 0.04; P = .035) and BOP (-7.74 ± 1.54 vs. -2.82 ± 1.60; P = .030) compared with the placebo group. Inflammatory markers, including fibroblast growth factor-5 (P = .003), thymic stromal lymphopoietin (P = .017), and the receptor activator of nuclear factor κB ligand/osteoprotegerin ratio (P = .021), were significantly decreased. The levels of Porphyromonas gingivalis (P = .001), Treponema denticola (P = .005), and Prevotella intermedia (P = .046) were also significantly reduced, while Weissella increased (P < .001) in the probiotic group. Eight-week supplementation with OraCMU improved gingival health and modulated the oral microbiota and inflammatory response. No serious adverse events were reported during the study period. These findings support the potential clinical utility of OraCMU as a probiotic adjunct for managing gingivitis.}, }
@article {pmid41817235, year = {2026}, author = {Anastasopoulou, M and Dereki, I and Sgourou, A and Lagoumintzis, G}, title = {Interactions between nutrition and the epigenome: how can it be harnessed for public health?.}, journal = {Future science OA}, volume = {12}, number = {1}, pages = {2641015}, doi = {10.1080/20565623.2026.2641015}, pmid = {41817235}, issn = {2056-5623}, abstract = {INTRODUCTION: A substantial body of evidence shows that dietary habits influence gene expression and epigenetic processes, holding significant implications for public health policies. Epigenetic modifications are increasingly associated with metabolic state, disease risk, and biological aging. Translating mechanistic results into scalable, efficient nutritional epigenetics treatments is difficult.<br><br>AREAS COVERED: This perspective article explores the influence of nutrition on epigenetic processes, focusing particularly on DNA methylation, histone modifications, and the significance of noncoding RNAs. It further clarifies the relationship between diet-induced epigenetic changes and increased risk for obesity, cardiovascular diseases, cancer, and neurocognitive impairments. Establishing causation, integrating multi-omics data, and creating ethical, equitable dietary advice are discussed when incorporating nutriepigenetic insights into public health. Recent studies demonstrate that dietary intake can influence epigenetics during pregnancy, adolescence, and adulthood, with long-term effects. However, individual variability, epigenome-wide association study confounders, and tissue specificity remain methodological challenges.<br><br>EXPERT OPINION/COMMENTARY: To advance the field, causal research, methodological rigor, and ethical governance must be prioritized. Using integrated microbiome, epigenomic, and metabolomic data can improve dietary risk assessment and intervention while assuring equal access and appropriate use of sensitive biological data.}, }
@article {pmid41817174, year = {2026}, author = {Moradi, D and Lotfi, A and Melnik, AV and Smirnov, A and Pobozhev, K and Monahan, H and Kopylova, E and Zhou, Y and Aksenov, AA}, title = {S'Wipe: user-friendly stool collection for high-throughput gut metabolomics and multi-omics.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0145925}, doi = {10.1128/msystems.01459-25}, pmid = {41817174}, issn = {2379-5077}, abstract = {UNLABELLED: The microbiome is increasingly recognized as a key factor in health. Intestinal microbiota modulates gut homeostasis via a range of diverse metabolites. In particular, molecules such as short-chain fatty acids (SCFAs), the microbial fermentation products of dietary fiber, have been established to be reflective of microbiome and/or dietary shifts, and SCFAs alterations have been linked to multiple gastrointestinal disorders, from cancer to colitis. Despite their potential as biomarkers, technical challenges in stool collection have limited clinical translation. Here, we present Stool Wipe (S'Wipe), an ultra-low-cost fecal collection method using lint-free, mass spectrometry (MS)-compatible cellulose wipes as toilet paper. Specimens are preserved in ethanol without refrigeration and can be shipped via regular mail. Mass spectrometry analysis demonstrated that S'Wipe captures both volatile and non-volatile metabolites with reproducibility and stability validated for diagnostically relevant molecules. We show that S'Wipe performs equivalently to direct stool collection, enabling interchangeable use and comparison with existing studies. This methodology is ideally suited for large-scale population studies, longitudinal tracking, and personalized medicine applications.<br><br>IMPORTANCE: Gut microbiome and intestinal metabolome present invaluable diagnostic and therapeutic targets. However, conventional stool testing has several barriers, limiting bioassessment from populations. Routine, high-temporal-resolution monitoring of stool metabolome, including extensively validated and broadly informative biomarkers such as short chain fatty acids (SCFAs), is not implemented due to relatively high cost and inconvenience of sampling, possible need for clinical setting for sample collection, difficulty in collecting samples reproducibly-especially due to potential for user errors-requirement for freezer storage and maintenance of the cold chain during shipment. We present a sampling strategy specifically designed to overcome these obstacles. We demonstrate how this method can enable capturing accurate molecular snapshots at massive scales, at ultra-low cost. The approach collapses complex medical-grade collection into easy self-administration. Individuals can thereby self-monitor therapeutic responses through routine metabolome tracking, including the volatilome, otherwise hindered by infrastructure restrictions. Ultimately, this sampling approach is intended to enable participatory wellness transformation through practical high-frequency self-sampling.}, }
@article {pmid41817170, year = {2026}, author = {Loeven, AM and Pacheco, FA and Brown, AN and Fadool, DA}, title = {Lack of Structural Change in Olfactory Circuitry Following Fecal Microbiome Transplant From Donors Subjected to Diet-induced Obesity.}, journal = {Journal of neurochemistry}, volume = {170}, number = {3}, pages = {e70396}, pmid = {41817170}, issn = {1471-4159}, support = {//Robinson Family and the Tallahassee Memorial Hospital/ ; F31 DC019867/NH/NIH HHS/United States ; R01 DK133464/NH/NIH HHS/United States ; T32 DC000044/NH/NIH HHS/United States ; }, mesh = {Animals ; Male ; Mice ; *Obesity/pathology/etiology/microbiology ; Female ; *Diet, High-Fat/adverse effects ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/physiology ; *Olfactory Bulb/pathology ; Olfactory Receptor Neurons/pathology ; }, abstract = {Obesity and fatty diets are known to damage the structure and function of chemosensory systems. Consumption of a moderately high-fat diet (MHF) induces loss of olfactory sensory neurons (OSNs) and reduces the density of associated axonal projections to the olfactory bulb that are central in the coding of odor information. Previous work has demonstrated reduced alpha diversity, as well as signature changes in microbiome composition when mice are challenged with a MHF diet that precipitates diet-induced obesity. Herein, we tested the hypothesis that a dysbiotic gut microbiome is sufficient to induce olfactory damage. Male and female donor mice were randomly assigned to a control-fat (CF) or MHF diet for 5 months duration, followed by baseline measurements of body weight, body composition (EchoMRI), glucose tolerance, and metabolic phenotyping via indirect calorimetry. We next performed fecal microbiome transplantation (FMT) from these donors to CF-maintained recipient mice. After 8 weeks post FMT, we observed no difference in body weight, glucose clearance, body composition, or fat pad weights as a consequence of transfer from MHF-maintained donors. Following FMT, recipient male mice exhibited increased Erysipelotrichaceae abundance and decreased Lactobacillaceae abundance, similar to MHF-fed donors. Recipient brains were processed for tissue clearing using immunolabeling-enabled three-dimensional imaging of solvent-cleared organs (iDISCO) and then imaged using high resolution light sheet microscopy. The volume of olfactory glomeruli expressing Olfr160 odor receptors could be visualized using genetic reporters; the FMT from MHF-maintained donors failed to evoke structural changes to these defined olfactory synapses. We conclude that diet-induced obesity, associated adiposity, and metabolic dysfunctions drive functional loss and structural changes to the olfactory system, but that gut microbiome dysbiosis alone is not sufficient to yield olfactory circuitry deficits.}, }
@article {pmid41817106, year = {2026}, author = {Jameson, GS and Roe, DJ and Borazanci, E and Hanna, DL and Roberts, CGP and Pelster, MS and Frank, RC and Alistar, AT and Miller, AM and Wiedmeier-Nutor, JE and Algaze, SD and Zoller, AR and Hallberg, SJ and Wertheim, BC and Lee, K and Cridebring, D and Rabinowitz, JD and Gately, S and Keppler, J and Sharma, S and Von Hoff, DD and Rasco, DW}, title = {A randomized phase II trial of gemcitabine, nab-paclitaxel, cisplatin with or without a medically supervised ketogenic diet for patients with metastatic pancreatic cancer.}, journal = {Cancer}, volume = {132}, number = {6}, pages = {e70343}, pmid = {41817106}, issn = {1097-0142}, support = {//Ludwig Institute for Cancer Research/ ; //John E Sabga Foundation/ ; //Purple Pansies/ ; //TGen's National Pancreatic Cancer Advisory Committee/ ; }, mesh = {Humans ; Gemcitabine ; Male ; Female ; Deoxycytidine/analogs &amp; derivatives/administration &amp; dosage/adverse effects ; *Pancreatic Neoplasms/pathology/drug therapy/therapy/diet therapy/mortality ; Middle Aged ; Aged ; Paclitaxel/administration &amp; dosage/adverse effects ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; *Diet, Ketogenic/methods ; Albumins/administration &amp; dosage/adverse effects ; Cisplatin/administration &amp; dosage/adverse effects ; Quality of Life ; *Carcinoma, Pancreatic Ductal/drug therapy/pathology ; Adult ; Progression-Free Survival ; }, abstract = {BACKGROUND: A randomized phase II screening trial of gemcitabine, nab-paclitaxel, and cisplatin with a medically supervised ketogenic diet (MSKD) versus usual diet (non-MSKD) was conducted in patients with treatment-naive metastatic pancreatic ductal adenocarcinoma (PDAC).<br><br>METHODS: Patients with untreated metastatic PDAC were randomized 1:1 to MSKD or non-MSKD while receiving gemcitabine, nab-paclitaxel, and cisplatin on days 1 and 8 of a 21-day cycle. The MSKD was guided by a remote health care team and daily ketone (beta-hydroxybutyrate) levels, with goal beta-hydroxybutyrate of 0.5 to 3.0 mM. The primary endpoint was progression-free survival (PFS) using a one-sided alpha level of 0.20. Secondary endpoints included overall survival (OS), safety, and quality of life (QOL). Changes in microbiome were an exploratory endpoint.<br><br>FINDINGS: Overall, there were 32 evaluable patients. In the MSKD arm, 15 of 16 patients achieved nutritional ketosis; the median proportion of days in ketosis was 39.4%. The median PFS was 8.5 months in MSKD patients and 6.2 months in non-MSKD patients: hazard ratio, 0.53 (95% CI, 0.21-1.37); one-sided p&#xa0;=&#xa0;.096. The median OS was 13.7 months with MSKD and 10.2 months in the non-MSKD arm: hazard ratio, 0.58 (95% CI, 0.25-1.37); one-sided p&#xa0;=&#xa0;.107). All MSKD-related adverse events were grade 1-2. There were no significant differences in grade &#x2265;3 chemotherapy-related adverse events between the arms. MSKD patients had no decline in QOL and had significant enrichment of beneficial taxa in the microbiome (p&#xa0;<&#xa0;.05, log-fold change &#x2265;2).<br><br>CONCLUSIONS: The MSKD is feasible in patients with PDAC and, although not powered for definitive outcomes, shows trends in improved PFS and OS when combined with gemcitabine, nab-paclitaxel, and cisplatin, without added toxicity or detriment to QOL. Larger studies are required to confirm these findings and establish the value of the MSKD in pancreatic cancer treatment.}, }
@article {pmid41816992, year = {2026}, author = {Rao, B and Jiang, J and Zhang, R and Zhang, D and Zhang, C and Li, A and Lu, H and Zhang, H and Zhou, L and Guo, W and Wen, P and Xue, J and Pan, J and Aji, T and Lan, Z and Jiang, X and Zheng, S and Yu, Z and Ren, Z}, title = {Multicohort Validation of Gut Microbiome Signatures for Cholangiocarcinoma Diagnosis and Functional Characterization of Bifidobacterium Pseudocatenulatum.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17658}, doi = {10.1002/advs.202517658}, pmid = {41816992}, issn = {2198-3844}, support = {82470654//National Natural Science Foundation of China/ ; 232300421124//Natural Science Foundation Key Project of Henan Province/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; ZYYC202301ZD//Henan Zhongyuan Medical Science and Technology Innovation and Development Foundation/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; }, abstract = {Growing evidence suggests a role for the gut microbiome in progression of cholangiocarcinoma (CCA), however, its diagnostic and therapeutic potential remains incompletely characterized. Here, metagenomic sequencing was performed on fecal samples (n = 785) from individuals across East, Central, and Northwestern China. Gut microbial dysbiosis in CCA was characterized by depletion of short-chain fatty acids-producing species and enrichment of potential pathobionts (Klebsiella aerogenes, Clostridium symbiosum). Diagnostic models built using species-level markers demonstrated superior performance, compared to pathway-based models, achieving area under the curve (AUC) values of 98.63% and 99.42% in the discovery cohort, with robust cross-regional validation (AUC = 80.89% and 80.43%). The model effectively distinguished CCA from hepatocellular carcinoma (AUC = 97.86%) and liver fibrosis (AUC = 98.73%) and nonalcoholic fatty liver disease (mean AUC = 96.86%). Analysis of public datasets encompassing 6847 samples across 31 studies and 11 disease states revealed moderate disease specificity influenced by biomarker overlap across conditions. Mechanistically, depleted Bifidobacterium pseudocatenulatum suppressed CCA progression, associated with inhibition of the PI3K-AKT-mTOR pathway. Collectively, this study supports the potential of fecal metagenomic signatures as a complementary noninvasive aid for CCA detection, and provides functional evidence for a candidate protective microbe.}, }
@article {pmid41816954, year = {2026}, author = {Wu, Q and Zhang, X and Zhang, J and Huang, G and Zhou, C and Li, C and Huang, X and Xiao, J and Feng, N and She, Y}, title = {Constraint of Lignin-Carbohydrate Complex Orchestrated on Polyphenol in Oil-Water Interface Targeting Ulcerative Colitis Therapy.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e24070}, doi = {10.1002/advs.202524070}, pmid = {41816954}, issn = {2198-3844}, support = {32472341//National Natural Science Foundation of China/ ; 21908048//National Natural Science Foundation of China/ ; 2024AFD281//Natural Science Foundation of Hubei Province/ ; F2023006//Science and Technology Program of Hubei Province/ ; JCZRJQ202500133//Science Fund for Distinguished Young Scholars of Hubei Province/ ; }, abstract = {The therapeutic potential of polyphenols in ulcerative colitis (UC), mediated through immune modulation and gut microbiota homeostasis. To enhance the oral bioavailability of polyphenols, we architected a colon-targeted W1/O/W2 emulsion system featuring a rationally designed lignin-carbohydrate complex (LCC) as a dual-functional emulsifier system for the first time. Based on the innate structural duality of LCC, which comprising hydrophobic lignin and hydrophilic carbohydrates, we employed LCC for O/W emulsifier. This inherent amphiphilicity was further engineered via laccase-mediated grafting of isovanillin, yielding a modified LCC with tailored lipophilicity for effective W/O interfacial stabilization. The W1/O/W2 emulsion ensured the stability of the encapsulated polyphenols with divergent polarity but also enabled pH-responsive payload release under colonic conditions (pH >7.0). In DSS-induced colitis, the system demonstrated a synergistic effect, the LCC itself acted as a prebiotic to modulate the gut microbiota, specifically enriching short chain fatty acid-producing bacteria, while the released polyphenols reinforced the intestinal barrier, which collectively accelerated mucosal healing. This research proposes a carbon-neutral therapeutic strategy for colitis, not only establishing a proof-of-concept for replacing synthetic emulsifiers with engineered biomass, but also as a multi-functional platform to stabilize colon-targeted co-delivery system and microbiome regulation in colitis.}, }
@article {pmid41816705, year = {2026}, author = {Xiang, Z and Wang, Z and Ghasemi, N and Wang, Y and Wen, J and Liu, Y}, title = {Interrogation of imaging-based interspecies dynamics in the oral microbiome.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2640344}, pmid = {41816705}, issn = {2000-2297}, abstract = {BACKGROUND: The oral cavity presents a highly dynamic environment where inter-microbial communications play a pivotal role. Understanding the spatial organization of microbial ecosystems has been highlighted on the microbiome and polymicrobial infection. Furthermore, cross-feeding and modulation by metabolites from the oral microbiota and host cells, such as lactate and reactive oxidative species, impact the stability and functionality of microbial communities. Traditional research focusing solely on the compositional aspects of these communities is insufficient to understand the sophisticated interactions.<br><br>METHODS: We evaluated recent advancements in imaging technologies, bolstered by multi-omics analyses and artificial intelligence (AI)-driven approachesinsights, to provide an more integrated understanding of the dynamics and function of the oral microbiome.<br><br>RESULTS: Real time imaging and resolution-enhancing methods at the single-cell level have unraveled the ecology and dynamics of microbial communities, indicating unique three-dimensional architectures and biogeographical patterns associated with disease status in polymicrobial interplays. Emerging computational techniques can account for the spatial features of oral microbiome by creating image-like representations that capture the complex relationships between host tissues and microbial communities. Spatial multi-omics, help address the limitations of single-cell sequencing, deciphering molecular mechanisms between species in these biogeographical patterns. To process the massive volume of imaging-based data, AI-assisted analysis enables complex dataset integration, predictive capacity, and personalized treatment, bringing a whole new level of understanding of the oral microbiome and its relationships with the host.<br><br>CONCLUSION: In this review, we highlight recent imaging-based technologies used to study the spatial biogeography of interspecies and interkingdom relationships within oral microbial communities, focusing on how these interactions and functional/metabolic alterations associated with health and disease. We further outline limitations of AI-generated predictions and imaging-based observational data. Finally, we elaborate on potential biomarkers for early diagnosis and new effective therapeutic strategies to reshape microbial dynamics.}, }
@article {pmid41816693, year = {2026}, author = {Xiao, X and Niu, Q and Zhou, K and Ma, L and Zhao, Z and Zhang, J and Chu, X and Shan, G}, title = {The invasion of Euphorbia jolkinii is mediated through the regulation of nitrogen transformation by functional microbial abundance in rhizosphere soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1757844}, pmid = {41816693}, issn = {1664-302X}, abstract = {INTRODUCTION: Euphorbia jolkinii Boiss. is a native invasive weed. Its invasion altered microbial composition, total nitrogen (TN) and available nitrogen (AN). However, the mechanisms influencing N transformation remain unclear. Particularly, the roles of the microbiome and genes in mediating N transformations to facilitate E. jolkinii invasion remain poorly understood. Therefore, the primary objectives of this study were to evaluate how E. jolkinii invasion affects N transformation, microbial interactions, and key genes associated with AN accumulation.<br><br>METHODS: We compared three patches (non-invaded, lightly, and heavily invaded patches of E. jolkinii) by analyzing rhizosphere soils of E. jolkinii and Poa crymophila Keng. Integrating soil physicochemical indices with metagenomic sequencing, we investigated the relationships among microbial communities, gene abundance, and N transformation.<br><br>RESULTS: With E. jolkinii increasing invasion intensity, N accumulation and transformation rates were significantly reduced in the rhizosphere of P. crymophila but enhanced in that of E. jolkinii, particularly for AN. Metagenomic analysis revealed that the invasion and expansion of E. jolkinii promoted functional adaptation of the microbial community, particularly by enriching the N cycling-related genes and increasing their relative abundance in the rhizosphere soil of E. jolkinii. Moreover, it inhibited the accumulation of N transformation functional genes in the rhizosphere soil of the companion plant, P. crymophila. Structural equation modeling identified Nitrospirota, Edaphobacter, Anaeromyxobacter, and soil N transformation rates as key drivers of AN accumulation.<br><br>DISCUSSION: E. jolkinii facilitated N accumulation in its rhizosphere by modulating N-transforming microbes and key functional genes, underscoring one of its invasive advantages.}, }
@article {pmid41816691, year = {2026}, author = {Yin, S and Cheng, J and Wang, M and Zhou, Y and Wei, H and Jiang, S and Peng, J}, title = {Maternal supplementation of functional fiber improves reproduction performance by modulating gut microbiota during pregnancy.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758091}, pmid = {41816691}, issn = {1664-302X}, abstract = {INTRODUCTION: This study aimed to investigate the impacts of gestation diets supplemented with functional fiber on performance and gut microbiome of sows.<br><br>METHODS: A total of 1,000 healthy sows of comparable body weight (DanBred Landrace &#xd7; DanBred Yorkshire, parities 1-2) were selected and randomly assigned to two dietary treatment groups after artificial insemination: a control group (CON, composed of beet pulp and barley as fiber sources) and a dietary fiber group [DF, supplemented with 1% functional fiber, consisted of 85.7% resistant starch (Hangzhou, China) and 14.3% guar gum (Yunzhou, China)].<br><br>RESULTS: DF treatment increased the numbers of total born, healthy piglets and litter birth weight (p&#x202f;<&#x202f;0.05), whereas markedly decreased (p&#x202f;<&#x202f;0.05) the number of intrauterine growth retardation (IUGR) compared with the CON group. Gut microbiota compositions underwent significant changes across gestation stages. Gut microbial diversity in DF group exhibited enhanced stability and resilience. Co-occurrence network analysis further demonstrated that the DF group maintained higher network stability at both G30 d and G109 d, with topological parameters consistently supporting these findings. In addition, Treponema showed a significant increase in the CON group starting from G30 d and persisted into late pregnancy (p&#x202f;<&#x202f;0.05), whereas NK4A214_group showed a significant increase in the DF group at G30 d, G109 d and L14 d (p&#x202f;<&#x202f;0.05). The abundance of Treponema was negatively correlated with the numbers of total born (p&#x202f;< 0.01) and healthy piglets (p&#x202f;<&#x202f;0.05). NK4A214_group showed a positive correlated with the numbers of total born and born alive (p&#x202f;<&#x202f;0.05), and a highly significant positive correlated with the numbers of healthy piglets (p&#x202f;<&#x202f;0.01). Fecal non-targeted metabolomics revealed that differential metabolites were significantly enriched in bile secretion and prolactin signaling pathways, with a series of bile acids, including hyodeoxycholic acid (HDCA), chenodeoxycholic acid (CDCA), glycochenodeoxycholic acid (GCDCA), cholic acid (CA), lithocholic acid (LCA), ursodeoxycholic acid (UDCA) and &#x3b3;-muricholic acid (&#x3b3;-MCA), were significantly increased in the DF group. And the abundance of NK4A214 was positively correlated with GCDCA (p&#x202f;< 0.05) and progesterone (p&#x202f;< 0.01).<br><br>CONCLUSION: The abundance of Oscillospiraceae, especially NK4A214_group of DF sows during gestation, may improve the numbers of total born and healthy piglets, with GCDCA likely playing a significant role in this process.}, }
@article {pmid41816689, year = {2026}, author = {Jian, Z and Qian, Y and He, S and Zhao, R and Li, K and Cha, J and Ning, Z and Ye, Y and Bao, Z and Wang, K and Ge, C and Jia, J and Dou, T and Hu, Y and He, X and Zi, X}, title = {The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768747}, pmid = {41816689}, issn = {1664-302X}, abstract = {Antibiotics remain central to modern poultry production, but their long-term and sometimes poorly managed use has markedly altered gut microbial ecology, effectively transforming the intestine into a substantial reservoir of antibiotic resistance genes (ARGs). In poultry, the composition of ARGs reflects not only resistant bacterial taxa but also the activity of mobile genetic elements, shifts in gut metabolic conditions, and features of the surrounding production system. This review synthesizes current understanding of both the structural and functional features of the poultry resistome, with particular attention to key bacterial hosts and the mobile genetic elements they carry. We further evaluate how different antibiotic-use patterns and additional co-selective pressures alter microbial communities and contribute to the persistence of ARGs. We also delineate the major transmission pathways that link breeder flocks, hatcheries, production facilities, and manure management, and interpret these connections within a One Health perspective. Particular emphasis is placed on microbial and nutritional interventions that influence gut microbial interactions, epithelial barrier integrity, and metabolic signaling. Drawing on these findings, we propose a resistome-microbiome-metabolome axis that links microbial taxa, resistance elements, and key metabolic signals, offering a conceptual framework for developing more targeted antimicrobial resistance mitigation strategies in poultry systems.}, }
@article {pmid41816687, year = {2026}, author = {Rosin, A and Krause, JL and Sprenger, H and Kissner, MS and Neuhaus, K and Tralau, T and Höper, T and Lemoine, L}, title = {Bacterial colonized melanoma skin models allow to study host-microbe interactions in situ.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736700}, pmid = {41816687}, issn = {1664-302X}, abstract = {INTRODUCTION: Melanoma represents the most lethal form of skin cancer, with the skin microbiome increasingly recognized as a potential risk factor. Previous studies demonstrated an altered microbiome composition at melanoma sites. However, the role of the microbiome remains elusive and technically challenging to investigate. Our proof-of-concept study aims to explore whether the contribution of skin bacteria to melanoma progression can be examined in situ.<br><br>METHODS: We utilized a commercial 3D melanoma model cultivated in an air-liquid interface configuration and apically inoculated it with a diverse bacterial community derived from healthy human skin.<br><br>RESULTS: During the 12-day co-cultivation period, bacterial counts were comparable to those found on human skin in vivo, with no significant induction of cytotoxicity, although a significant decline in bacterial diversity was observed. Nonetheless, microbial colonization had a clear impact on melanoma biology. This was evidenced by pronounced alterations in gene expression associated with pathways involved in melanoma progression, as well as cadherin switching and increased secretion of cytokines, such as VEGF and GM-CSF, along with the melanoma marker MIA.<br><br>DISCUSSION: This study is the first to demonstrate the feasibility of using 3D melanoma models to investigate the impact of skin bacteria on melanoma biology, thereby paving the way for elucidating causal mechanisms in situ.}, }
@article {pmid41816330, year = {2026}, author = {Zhang, X and Zhang, T and Geng, R and Wei, L and Liu, H and Shi, H}, title = {Interleukins in community-acquired pneumonia: from biomarkers to precision medicine.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1774731}, pmid = {41816330}, issn = {1664-3224}, mesh = {Humans ; *Community-Acquired Infections/immunology/diagnosis/metabolism ; Precision Medicine ; Biomarkers/metabolism ; *Interleukins/metabolism/immunology ; *Pneumonia/immunology/diagnosis/metabolism ; Animals ; Community-Acquired Pneumonia ; }, abstract = {Community-acquired pneumonia (CAP) is still a leading cause of death due to infection globally, yet precise severity assessment remains a significant clinical problem. More than any other group of cytokines, interleukins are central to the regulation of inflammation and shed light on this intricate pathology. In the present review we summarize the biological and clinical characteristics of some of the principal interleukins (ILs) in CAP, classified primarily according to their physiological activity as pro-inflammatory (IL-2, IL-6, IL-8 and IL-12), anti-inflammatory (IL-7, IL-10 and IL-37), dual-action (IL-4 and IL-17), and emerging factors (IL-3, IL-27 and IL-33). Additionally, recent multimodal approaches are discussed such as combining cytokines with organ dysfunction parameters (MR-proADM) or revealing host-response patterns to inform antibiotic and corticosteroid management. We propose that the field needs to transition to immunological endotyping, multi-omics (integrating genetics and lung microbiome), and artificial intelligence (AI) models based on dynamic patient data to achieve precision medicine in CAP management.}, }
@article {pmid41816110, year = {2026}, author = {Li, Z and Yan, J and Zeng, Z and Zhao, L}, title = {The role of gut microbiota and its metabolites in preventing oncogenesis.}, journal = {Frontiers in cell and developmental biology}, volume = {14}, number = {}, pages = {1790063}, pmid = {41816110}, issn = {2296-634X}, abstract = {The gut microbiota is increasingly recognized as a key determinant of cancer susceptibility, functioning as a dynamic interface between environmental exposures and host physiology. Dysbiosis disrupts immune homeostasis, epithelial integrity, and metabolic equilibrium, thereby fostering a microenvironment conducive to oncogenesis. Conversely, a balanced microbial ecosystem and its metabolites exert potent anti-tumor effects through immune modulation, maintenance of mucosal barrier function, and detoxification of carcinogens. This Review synthesizes emerging mechanistic insights into how commensal microbes and their metabolic products coordinate host defense pathways to suppress malignant transformation. We further discuss translational strategies-ranging from probiotics, prebiotics, and synbiotics to fecal microbiota transplantation and dietary interventions-that leverage microbiome modulation for cancer prevention. Despite compelling preclinical evidence, clinical translation remains constrained by inter-individual variability and incomplete mechanistic understanding. Integration of multi-omics analyses, gnotobiotic models, and precision microbial engineering offers a path toward microbiota-based interventions as a cornerstone of personalized cancer prevention and immunomodulation.}, }
@article {pmid41815495, year = {2026}, author = {Cottone, A and Seiter, K and Thomas, B and Schank, N and Wulf, M and Miller, L and Anderson, S and Munkhsaikhan, U and Verma, A and Abidi, AH and Kassan, M}, title = {The importance of prebiotics in managing colic in horses: focus on Akkermansia muciniphila and its anti-inflammatory potential.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1759381}, pmid = {41815495}, issn = {2297-1769}, abstract = {Colic remains one of the most frequent and costly causes of equine morbidity and mortality, with significant welfare and economic implications. Disturbances in the gut microbiome are increasingly recognized as an important contributing factor. In recent years, prebiotics, non-digestible substrates that promote beneficial microbes, have emerged as promising microbiome-targeted strategies. Akkermansia muciniphila (A. muciniphila) has gained attention for its unique ability to degrade mucin, maintain epithelial integrity, and exert potent anti-inflammatory effects. Although its benefits are well established in humans and rodent models, little is known about its abundance, function, and therapeutic potential in horses. This review evaluates current evidence on prebiotics and A. muciniphila in equine gut health and outlines their translational potential by examining biological mechanisms, feasibility of therapeutic application, and implications for equine colic prevention. Importantly, this review is intended as a hypothesis-generating synthesis rather than evidence of causality. Proposed mechanisms and therapeutic implications are based primarily on extrapolation from non-equine models and limited equine observational data, highlighting critical knowledge gaps and the need for controlled, hypothesis-driven studies in horses.}, }
@article {pmid41815191, year = {2026}, author = {Correia Gomes, D and Zamora-Briseño, JA and Camacho Morales, A and Cárdenas Tueme, M and Sarmiento, CC and Zepeda, RC and Viveros Contreras, R}, title = {Maternal Programming with a Cafeteria Diet Leads to Glucose Intolerance, Increased Insulinemia, Inflammation, and Intestinal Dysbiosis in Rat Offspring.}, journal = {Preventive nutrition and food science}, volume = {31}, number = {1}, pages = {}, pmid = {41815191}, issn = {2287-1098}, abstract = {The intake of diets high in fat and sugar but low in protein, fiber, and vitamins during pregnancy can contribute to metabolic imbalance, immunological disorders, and intestinal barrier disruption in the offspring. This study investigated the effects of a cafeteria (CAF) diet, high in fat and sugar, consumed throughout pregnancy and lactation, on metabolism, inflammation-related markers, and intestinal microbiota in rat offspring. Maternal programming was conducted for more than 9 weeks in 16 female Wistar rats aged 8－10 weeks. They were divided into two diet groups: control and CAF, each with n=8. On the 21st day after birth, the offspring were weaned, and fecal samples were collected. We conducted a series of glucose and insulin tolerance tests and analyzed serum metabolic markers [triglycerides (TGs), total cholesterol (TC), aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT)], inflammatory cytokines [monocyte chemoattractant protein-1 (MCP-1/CCL2) and interleukin 6 (IL-6)], and hormones (insulin, leptin, and active ghrelin). Gut microbial profiling was performed to assess compositional changes. The CAF offspring exhibited higher levels of serum glucose, insulin, TGs, MCP-1, and IL-6 compared with the control group. Moreover, the CAF diet altered the intestinal bacterial community structure, increasing the abundance of Prevotellaceae and Lachnospiraceae while reducing Lactobacillaceae. Our results suggest that ingesting a CAF diet during maternal programming promotes adverse impacts on the offspring metabolism homeostasis, inflammatory responses, and intestinal microbiota composition.}, }
@article {pmid41814894, year = {2026}, author = {}, title = {Yang Bai.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70928}, pmid = {41814894}, issn = {1469-8137}, }
@article {pmid41814750, year = {2026}, author = {Qian, ZX and Li, JX and Rao, XJ and Huang, GD and Liu, R and Wei, W}, title = {[Application progress of germ-free animal models in colorectal cancer and traditional Chinese medicine research].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {51}, number = {1}, pages = {32-39}, doi = {10.19540/j.cnki.cjcmm.20251011.708}, pmid = {41814750}, issn = {1001-5302}, mesh = {Animals ; *Colorectal Neoplasms/drug therapy/microbiology ; *Disease Models, Animal ; Humans ; *Medicine, Chinese Traditional/methods ; Gastrointestinal Microbiome ; *Germ-Free Life ; *Drugs, Chinese Herbal/therapeutic use ; }, abstract = {Colorectal cancer(CRC) is a highly prevalent malignant tumor worldwide, and its occurrence and development are closely related to gut microbiota disturbance. The germ-free(GF) animal model, by providing a unique environment free of indigenous microorganisms, has become a tool for precisely dissecting the causal role and mechanism of the gut microbiota in the occurrence and development of CRC and the therapeutic mechanisms of pharmaceuticals. This review aims to systematically elaborate on the application progress of GF animal models in CRC research, with a focus on the key mechanisms by which specific microorganisms promote the occurrence and development of CRC revealed by this model. Furthermore, this review focuses on the research dynamics of TCM in this field and systematically expounds the application of GF models in the research of TCM against CRC. Through in-depth analysis of the GF animal models of CRC, it is possible to develop precise diagnostic and therapeutic strategies based on TCM and the microbiome in the future, providing new directions and ideas for the prevention and treatment of CRC.}, }
@article {pmid41814663, year = {2026}, author = {Wang, T and Hu, W and Song, W and Liao, X and Zheng, H and Zhang, X and Xin, X and Singh, PK and Chen, Y and Xu, Y}, title = {From triangle to pyramid: Understanding host-microbiome-pathogen-environment interplay for enviromics-empowered sustainable plant disease management.}, journal = {Plant communications}, volume = {}, number = {}, pages = {101815}, doi = {10.1016/j.xplc.2026.101815}, pmid = {41814663}, issn = {2590-3462}, abstract = {Understanding plant disease development requires moving beyond the classical disease triangle, which considers host, pathogen, and environment. Recent advances in multiomics highlight the importance of disease pyramid that integrates host, pathogen, microbiome, and environment (HPME) to capture the complex interactions among these core biological/ecological components. This pyramid network emphasizes how host genetic architecture, pathogen traits, microbiome dynamics, and environmental conditions collectively and interactively shape disease outcomes, plant phenotypes, and adaptive potential. The conceptual expansion from the disease triangle into pyramid network reflects this shift, providing a more holistic and dynamic view of plant disease ecology. Environments regulate host susceptibility, and restructures both pathogen and non-pathogen microbial communities, thereby influencing infection severity and disease progression. Multi-omics approaches (hostomics, pathomics, microbiomics, and enviromics) hold promise for dissecting these interactions and enabling predictive disease modeling and sustainable management strategies. Moreover, integrating enviromic data into resistance breeding enables the identification of environmental factors and their interaction with host genotype and pathogen and non-pathogen microbes, and supports the deployment of durable resistance across diverse agroecosystems. Together, these perspectives advance a systems-level understanding of plant health and open new avenues for disease management through omics-driven breeding, microbiome-informed strategies, and environment-responsive interventions.}, }
@article {pmid41814632, year = {2026}, author = {Ferreti, JD and Ribeiro, B and Bonetti, JA and Camargo, LEA and Creste, S and Kuramae, EE and Monteiro-Vitorello, CB}, title = {Soil and Genotype Shape the Sugarcane Phytobiome for Enhanced Environmental Adaptation.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70314}, doi = {10.1111/1758-2229.70314}, pmid = {41814632}, issn = {1758-2229}, support = {2022/03962-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 405314/2021-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305961/2017-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Saccharum/microbiology/genetics/growth &amp; development ; *Soil Microbiology ; Genotype ; *Soil/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *Adaptation, Physiological ; Transcriptome ; }, abstract = {Soil properties critically shape sugarcane growth and its microbiome, yet their influence on gene expression remains unclear. We investigated the combined effects of soil type (clayey and sandy loam) and sugarcane genotype (IACSP-5503 and IACSP-6007) on microbiome composition and plant transcriptional profiles. Bacterial communities from soils and stalk tissues, as well as transcriptomes of 48-h sprouted buds grown for 10 months, were analysed. Results showed that IACSP-5503 (adapted to low-fertility soils) and IACSP-6007 (less adapted) recruited endophytic microbiota in a soil-genotype-dependent manner. In sandy loam, IACSP-5503 promoted diverse plant growth-promoting bacteria (PGPB) (including Burkholderia, Leifsonia and Mycobacterium), associated with nitrogen fixation, hormone production and stress tolerance, while IACSP-6007 displayed reduced PGPB diversity and transcriptomic signatures of nutrient deficiencies. Conversely, in clayey soil, IACSP-6007 recruited more PGPBs (such as Pseudomonas, Bacillus and Klebsiella) linked to nutrient acquisition and defence responses. Both genotypes exhibited enhanced expression of defence- and antioxidant-related genes in clayey soil, suggesting priming effects. Overall, our findings reveal soil-dependent, genotype-specific microbial recruitment strategies, particularly in IACSP-5503, reflecting adaptive responses to nutrient-poor conditions. The combined 16S metataxonomic and transcriptome data offered insights into how soil and genotype shape microbial recruitment and transcriptional plasticity in sugarcane.}, }
@article {pmid41814441, year = {2026}, author = {Stead, CE and Walker, L and Greco, C and Galloway, T and R Cousins, C and Nagel, F and Breitling, R and Takano, E and Björnsdóttir, SH and Nixon, SL}, title = {Exploring the biotechnological potential of terrestrial hot spring microbiomes for CO2 utilisation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00875-x}, pmid = {41814441}, issn = {2524-6372}, support = {ST/W002337/1//UK Space Agency/ ; BB/V00560X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RGS\R2\222350//Royal Society/ ; }, abstract = {BACKGROUND: Terrestrial hot springs are extreme environments shaped by geothermal heat, geogenic gases and extremes of pH and temperatures. Their gas fluxes, which include CO2, CO, H2S and SO2, mirror the chemical composition of CO2-rich waste streams. Microbial communities inhabiting these environments are typically thermotolerant or thermophilic and sustained by CO2 fixation and chemolithotrophic metabolism. Such communities may therefore provide a natural starting point for developing ex-situ, consortium-based biotechnologies capable of operating under elevated temperatures and chemically harsh conditions. Here, we assess the metabolic capabilities of hot spring microbiomes systematically through a biotechnological lens.<br><br>RESULTS: We conducted comparative analysis of 73 worldwide hot spring metagenomes, spanning a wide range of environmental conditions (pH 1.5-10.0, temperatures 25-98&#xa0;&#xb0;C). By taking a gene-centric approach to whole communities, we show that hot spring microbiomes ubiquitously encoded carbon fixation pathways and biosynthetic genes (and gene clusters) for the synthesis of value-added products, regardless of geographical location and pH-temperature conditions. Candidate value-added products include platform chemicals such as acetone, lactic acid, and 1,2-propanediol, as well as high-value biomolecules including B vitamins and alginate.<br><br>CONCLUSIONS: This first biotechnology-focused assessment of hot spring microbiomes demonstrates that these communities encode the genomic potential to support novel, ex situ microbial platforms for upgrading CO2 and transforming chemically complex gas mixtures.<br><br>SIGNIFICANCE: Industrial CO2 waste streams pose both an environmental challenge and an unutilised resource. Harnessing microbial consortia to valorise CO2, through a circular bioeconomy, remains underexplored and could offer an alternative to energy-intensive chemical methods. By reanalysing predominantly publicly available metagenomic data, we demonstrate how hot spring microbiomes can be mined for traits pre-adapted to CO2-rich, high-temperature, and chemically extreme conditions. In doing so, we provide proof-of-concept for their future biotechnological application and establish a blueprint for other microbiome-scale bioprospecting surveys.}, }
@article {pmid41814421, year = {2026}, author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {41814421}, issn = {2049-2618}, mesh = {*Gastrointestinal Microbiome/genetics/immunology ; Animals ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Songbirds/microbiology/immunology/genetics ; *Major Histocompatibility Complex/genetics ; Animals, Wild/microbiology/immunology ; Immunogenetics ; }, abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.<br><br>RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.<br><br>CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.}, }
@article {pmid41814394, year = {2026}, author = {An, Y and Xu, JZ and Ye, GC and Sun, JX and Xiang, JC and Gong, C and Zhang, SH and Miao, LT and Ma, SY and Ding, MX and Wang, SG and Xia, QD}, title = {Therapeutic translation of traditional Chinese medicine Huangqi derived exosome like nanoparticles: targeting prostate cancer through ferroptosis activation, immune reprogramming, and microbiome modulation.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04160-4}, pmid = {41814394}, issn = {1477-3155}, support = {2022ZHFY02//Tongji Hospital Medical Innovation and Transformation Incubation Project/ ; NSFC, 82370770//National Natural Science Foundation of China/ ; }, abstract = {Plant derived exosome-like nanoparticles (PELNs) are emerging as a powerful tool for treating cancers. Among them, PELNs derived from traditional Chinese medicines have shown great potential in treating various cancers. However, many Chinese medicines remain to be explored, and currently, there are no reports on the use of PELNs for treating prostate cancer. In this study, we extracted Huangqi derived exosome-like nanoparticles (HELNs) from fresh Huangqi (Astragalus membranaceus) and systematically explored the effects and mechanisms of HELNs in treating prostate cancer through an integrated approach of single-cell sequencing, 16 S rDNA sequencing, and bulk-RNA sequencing. We found that HELNs demonstrated robust cytotoxic effects against prostate cancer both in vitro and in vivo. HELNs reverse the polarization of M2 macrophages, promote their M1-like polarization, and increase the abundance of anti-tumor probiotics in the gut to exert anti-tumor effects. In terms of direct effects, HELNs downregulate the expression level of GPX4 protein in prostate cancer cells, thereby inducing ferroptosis. Finally, we loaded siGPX4 into HELNs to construct a new nanoparticle siGPX4@HELNs. siGPX4@HELNs induce more pronounced ferroptosis in prostate cancer cells, achieving better therapeutic outcomes while maintaining safety.}, }
@article {pmid41814359, year = {2026}, author = {Lai, C and Zhang, J and Xiong, Y and Wang, Y and Liu, Z and Shi, M and Ye, S and Zeng, J}, title = {Multi-omics analysis reveals the association of cesarean delivery with altered gut microbial profiles and a Th2-biased immune response in neonates.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07988-4}, pmid = {41814359}, issn = {1479-5876}, support = {Z-A20241044//Guangxi Zhuang Autonomous Region Health Department/ ; Z20210019//Guangxi Zhuang Autonomous Region Health Department/ ; Z-A20240946//Guangxi Zhuang Autonomous Region Health Department/ ; 2024GXNSFBA010112//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, }
@article {pmid41814018, year = {2026}, author = {Xiong, C and Ge, AH and Gao, M and Singh, BK}, title = {Impacts of climate extremes on plant pathogens, microbiomes and plant health.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41814018}, issn = {1740-1534}, abstract = {Plant diseases pose a great risk to global food security, and recent research indicates that pathogen pressures on plant productivity will substantially increase under ongoing climate change (that is, increasing CO2 levels and global warming). However, our mechanistic and predictive knowledge of the impacts of climate extremes, such as heatwaves and prolonged droughts, and their interaction with other climatic factors, on plant pathogens, hosts and microbiomes, remains largely unknown. This is an important knowledge gap that limits our ability to develop effective strategies to mitigate the socioeconomic impacts of climate change-induced plant disease outbreaks. This Review examines the impacts of key climate extremes on soil-borne pathogens, plant microbiomes and host physiology that ultimately determine disease outcomes. We explore evidence that suggests that the responses of pathogen-host-microbiome interactions to climate extremes may differ in many ways from those to long-term climate change. Climate extremes may increase the virulence and distribution of many pathogens, suppress certain plant immune responses, and weaken the core functions of host microbiomes within the disease triangle, thereby facilitating disease outbreaks. We propose an integrated pathway for harnessing microbiomes to address the critical challenges posed by climate extremes. These insights offer new approaches to mitigate disease risks by harnessing microbiomes and metabolites under climate extremes, with the potential to support climate-resilient and sustainable agricultural and natural ecosystems.}, }
@article {pmid41814006, year = {2026}, author = {Baldanzi, G and Larsson, A and Sayols-Baixeras, S and Dekkers, KF and Hammar, U and Nguyen, D and Graells, T and Ahmad, S and Gazolla Volpiano, C and Meric, G and Järhult, JD and Tängdén, T and Ludvigsson, JF and Lind, L and Sundström, J and Michaëlsson, K and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41814006}, issn = {1546-170X}, support = {20230687//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2023-0380//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2019-01471//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2025-02673//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-01460//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-00243//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-02784//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; Strategic Research Area Exodiab 2009-1039//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-00989//Svenska Forskningsr&#xe5;det Formas (Swedish Research Council Formas)/ ; IRC-0067//Stiftelsen f&#xf6;r Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; }, abstract = {Disruptions in gut microbiome are implicated in cardiometabolic disorders and other health outcomes. Antibiotics are known gut microbiome disruptors, but their long-term consequences remain underexplored. Here we combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. In multivariable confounder-adjusted regression models, antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1-4 and 4-8 years earlier. Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4-8 years earlier was associated with altered abundance of 10-15% of the species studied; penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Similar results were found comparing one antibiotic course 4-8 years before sampling versus none in the past 8 years. These findings indicate that antibiotics may have long-lasting consequences for the gut microbiome.}, }
@article {pmid41813961, year = {2026}, author = {Chen, E}, title = {Memory loss is fuelled by gut microbes in ageing mice.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41813961}, issn = {1476-4687}, }
@article {pmid41813891, year = {2026}, author = {Cox, TO and Devason, AS and de Araujo, A and Mason, S and Subramanian, M and Salvador, AFM and Descamps, HC and Kim, J and Zhu, Y and Litichevskiy, L and Jung, S and Song, WS and Cortés-Martín, A and Henderson, NT and Huang, KP and Nguyen, T and Sae-Lee, W and Umana, IC and Sacta, M and Rahman, RJ and Wisser, S and Nelson, JAD and Golynker, I and McSween, AM and Hohmann, EF and Patel, S and Bub, AL and Soekler, C and Blank, N and Hoxha, K and Boccia, L and Wong, AC and Bahnsen, K and Kim, J and Biderman, N and Abbasian, D and Shoffler, C and Petucci, C and McAllister, FE and Alhadeff, AL and Fuccillo, MV and Hill, C and Jang, C and Betley, JN and de Lartigue, G and Lee, VY and Levy, M and Thaiss, CA}, title = {Intestinal interoceptive dysfunction drives age-associated cognitive decline.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41813891}, issn = {1476-4687}, abstract = {Ageing is accompanied by declining memory function, with extremely heterogeneous manifestation in the human population[1]. Brain-extrinsic factors influencing cognitive decline, such as gastrointestinal signals, have emerged as attractive targets for peripheral interventions[2-6], but the underlying mechanisms remain largely unclear. Here, by charting a high-resolution map of microbiome ageing and its functional consequences throughout the lifespan of mice, we identify a mechanism by which inhibition of gut-brain signalling during ageing results in impaired neuronal activation in the hippocampus and loss of memory encoding. Specifically, accumulation of gut bacteria that produce medium-chain fatty acids, such as Parabacteroides goldsteinii, can drive peripheral myeloid cell inflammation through GPR84 signalling. As a result, the function of vagal afferent neurons is impaired, the interoceptive signal received by the brain is weakened and hippocampal function declines. We leverage this pathway to define interventions that enhance memory in aged mice, such as phage targeting of Parabacteroides, GPR84 inhibition and restoration of vagal activity. These findings indicate a key role for interoceptive dysfunction in brain ageing and suggest that interoceptomimetics that stimulate gut-brain communication may counteract age-associated cognitive decline.}, }
@article {pmid41813835, year = {2026}, author = {Homscheid, A and Moors, KA and Nap, B and Lieb, W and Franke, A and Laudes, M and Thiele, I and Kaleta, C and Marinos, G}, title = {Dietary patterns influence the in silico GABA production capacity of Bifidobacterium adolescentis HD17T2H and other human gut bacteria.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-43006-9}, pmid = {41813835}, issn = {2045-2322}, }
@article {pmid41813538, year = {2026}, author = {Abdoul Ahad, R and Joseph, N and Al Nabhani, Z}, title = {When infant microbes guide mom's milk.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.01.008}, pmid = {41813538}, issn = {1878-4380}, abstract = {In the Clinical and Translational Report in Cell Host &amp; Microbe, Deng et al. reveal that early infant gut microbiome states predict later changes in maternal milk nutrients and metabolites, uncovering developmentally timed feedback within the mother-infant dyad. This study challenges the prevailing unidirectional model of milk-driven microbial assembly.}, }
@article {pmid41812940, year = {2026}, author = {Tao, X and Wu, X and Wu, H and Tu, L and Dong, M and Xiao, Y and Yu, X and Zhong, T}, title = {A structural roadmap to gut health: A comprehensive review of edible insect chitin-protein complexes as alternative protein-derived, structure-specific prebiotics.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {151312}, doi = {10.1016/j.ijbiomac.2026.151312}, pmid = {41812940}, issn = {1879-0003}, abstract = {Edible insect chitin-protein complexes (CPCs) represent protein-associated biocomposites, where chitin nanofibrils are interwoven with cross-linked cuticular proteins, melanin and minerals, forming a natural protein-polysaccharide matrix that functions as both an alternative protein source and a structure-specific prebiotic substrate. This review first maps how extraction and processing alter degree of acetylation, crystallinity, lamellar spacing, particle size and surface chemistry. We then show that these structural parameters dictate hydration, enzyme accessibility, adsorption and fermentability within the gastrointestinal tract. Across in vitro fermentations, animal models and emerging human trials, CPCs behave as structure-specific prebiotics: they selectively expand saccharolytic taxa, boost short-chain fatty acid output and enrich butyrate producers, while suppressing opportunistic bacteria and systemic low-grade inflammation. Mechanistically, benefits arise through two converging pathways: (i) microbial degradation of CPCs into bioactive chitooligosaccharides and SCFAs, and (ii) direct, size- and charge-dependent pattern-recognition of chitinous particles by host immune receptors. Safety, allergenicity and regulatory status are scrutinised, highlighting cross-reactivity risks with shellfish and mite allergens, contaminant-binding propensity, and alignment with current novel-food frameworks. Finally, we outline rational design strategies that couple precision biorefinery to microbiome-guided nutrition. Overall, insect CPCs represent tunable, sustainable matrices able to co-deliver alternative protein and targeted prebiotic function, potentially offering a scalable approach to modulate gut microbiota and promote host health.}, }
@article {pmid41812714, year = {2026}, author = {Li, C and Gao, J and Shu, H and Zhao, G and Gu, X}, title = {Stereotypic behaviors across species: From neurobiological mechanisms to farm animal welfare.}, journal = {Neuroscience and biobehavioral reviews}, volume = {185}, number = {}, pages = {106637}, doi = {10.1016/j.neubiorev.2026.106637}, pmid = {41812714}, issn = {1873-7528}, abstract = {Stereotypic behaviors, characterized by repetitive, fixed, and seemingly functionless behavioral patterns, are critical indicator of compromised animal welfare and neuropsychiatric disorders. While stereotypic behaviors have been extensively studied in humans and laboratory animals, the neurobiological mechanisms of farm animals and their cross-species commonalities remain to be systematically elucidated. This review summarizes the progress in the research on stereotypic behaviors, with a particular focus on comparing the phenotypic similarities among humans, laboratory animals, and farm animals. It delves into key biological principles underlying stereotypic behaviors, including neurotransmitter system imbalances, basal ganglia circuit dysfunction, and the modulatory effects of environmental enrichment. Although these mechanisms have been thoroughly investigated in humans and laboratory animals, corresponding evidence in farm animals is still limited. Furthermore, this paper systematically analyzes the current limitations in farm animal stereotypic behaviors research, such as the lack of standardized quantification tools, inconsistent phenotypic descriptions, high economic costs, and insufficient interdisciplinary communication. However, several emerging opportunities promise to advance future developments, including the use of physiological and structural similarities across species for translational research, the application of computer vision, a focus on the potential regulatory mechanisms of the microbiome-gut-brain axis, and the integration of other advanced methods such as multi-omics and genetic marker screening. This review aims to provide new perspectives for a deeper understanding of the mechanisms underlying stereotypic behaviors in farm animals, offer a theoretical basis for developing precise behavioral welfare assessment and intervention strategies, and ultimately promote the advancement of farm animal welfare.}, }
@article {pmid41812701, year = {2026}, author = {Xu, L and Guo, L and Su, Q and Shao, Q and Lu, Y and Nie, Y and Yang, Y and Sun, Q}, title = {Dynamic impact of intermittent fasting and refeeding on metabolic health and microbiome-metabolome signatures in cynomolgus monkeys.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.03.004}, pmid = {41812701}, issn = {2090-1224}, abstract = {INTRODUCTION: Dietary intervention has emerged as a promising approach for improving metabolic health across species; however, its systemic effects in non-human primates (NHPs) remain insufficiently characterized.<br><br>OBJECTIVES: We sought to investigate the metabolic and physiological impacts of time-restricted intermittent fasting (IF) regimen that resulted in a net energy deficit in overweight female cynomolgus monkeys, both during the intervention and after dietary reversal, with particular focus on body weight, metabolic parameters, immune cell ratios, gut microbiota, and serum metabolomic profiles.<br><br>METHODS: Overweight monkeys underwent 20-hour fasting/4-hour feeding IF protocol for 84&#x202f;days, subsequently entering 42-day post-intervention phase where animals either continued IF (HW-IF-IF, n&#x202f;=&#x202f;8) or resumed normal feeding (HW-IF-NF, n&#x202f;=&#x202f;8). Normal-weight (Con-NF, n&#x202f;=&#x202f;8) and high-weight control (HW-NF, n&#x202f;=&#x202f;7) groups maintained standard feeding served as controls. We monitored body weight and measured serum triglycerides, insulin levels, and insulin resistance. Immune cell percentages were determined by flow cytometry. Gut microbiome was profiled via 16S rRNA sequencing. Serum metabolomic profiling was conducted using untargeted metabolomics.<br><br>RESULTS: IF promoted significant reductions in body weight (day126, p&#x202f;=&#x202f;0.0421), serum triglycerides (day126, p&#x202f;=&#x202f;0.0108), insulin levels (day126, p&#x202f;=&#x202f;0.0107), and insulin resistance (day126, p&#x202f;=&#x202f;0.0004) in overweight monkeys. The insulin-lowering effects and enhanced insulin sensitivity were maintained even after reintroduction of normal feeding. By day 126, the sustained increase in lymphocyte-to-neutrophil ratio was exclusive to the continuous intermittent fasting group (HW-IF-IF), suggesting a potential immunomodulatory effect of prolonged fasting. Longitudinal gut microbiota analysis indicated that the gut microbiota structure underwent limited compositional changes. Nevertheless, time-dependent enrichments emerged in several genera, including Ruminococcus, Eubacterium_hallii_group, and Monoglobus. Serum metabolomics unveiled pronounced time-dependent alterations in circulating metabolites.<br><br>CONCLUSION: These findings elucidate physiological and metabolic adaptations to specified IF-refeeding regimen in cynomolgus monkeys and establish a framework for mechanistic studies of fasting-induced metabolic responses in non-human primates.}, }
@article {pmid41812662, year = {2026}, author = {Rispal, J and Garcia, JR and Palikuqi, B and Vegesna, M and Vaka, D and Kang, SW and Trentesaux, C and Du, J and Realini, NR and Spencer, PN and Gardner, JM and Hausmann, A and Kattah, MG and Lau, KS and Boffelli, D and Klein, OD}, title = {Microbiome-produced nicotinic acid controls colon regional identity and injury susceptibility.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.02.007}, pmid = {41812662}, issn = {1097-4172}, abstract = {The regionalized structure of the intestinal epithelium is critical for its function, and the risk for certain diseases has a regional bias. However, how regionalization is established and how it influences disease susceptibility remain poorly understood. Here, we investigated the role of the gut microbiome-the regionalized community of microorganisms in the intestinal lumen-in promoting regionalization of the colon. We found that the proximo-distal identity of colonocytes along the organ's length is disrupted in mice lacking a microbiome and that the proximal colonic microbiome produces high levels of nicotinic acid, which induces Pparα expression to establish proximal colonocyte identity. Furthermore, we report that microbiome-driven proximal identity confers protection against tissue injury in the mouse. Finally, we determined that the human colon is regionalized and loses its proximal identity during certain disease states.}, }
@article {pmid41812606, year = {2026}, author = {Li, L and Tang, S and Liu, F and Yang, M}, title = {Role of lipid metabolites in mediating causal effects of gut microbiota on type 2 diabetes mellitus.}, journal = {Computational biology and chemistry}, volume = {123}, number = {}, pages = {108955}, doi = {10.1016/j.compbiolchem.2026.108955}, pmid = {41812606}, issn = {1476-928X}, abstract = {Using two-sample Mendelian randomization with genome-wide association study (GWAS) data from European-ancestry populations, we identified a significant mediation pathway linking genus Akkermansia to type 2 diabetes (T2D) via phosphatidylcholine (O-18:1_20:3). GWAS data were obtained from the Dutch Microbiome Project (gut microbiota), Finnish cohorts (lipid metabolites), and FinnGen (T2D). Lower levels of phosphatidylcholine (O-18:1_20:3), a protective lipid, mediated the association. The indirect effect was IE = 0.0206 (SE = 0.00187; 95% CI 0.01694-0.02428; P = 3.06 ×10[-28]; OR = e^IE = 1.0208), with a total effect TE = 0.0795 (SE = 0.00767; OR = 1.0827), corresponding to a mediation proportion of 25.9%. In contrast, higher-level Verrucomicrobiaceae taxa (phylum, class, order, and family aggregates) showed weaker, non-significant mediation (95% confidence intervals including zero). We also observed that the microbial pathway PWY.7221(de novo guanosine nucleotide biosynthesis) was inversely associated with T2D (OR = 0.903; 95% CI 0.852-0.957). ediation analyses further supported phosphatidylcholine (O-18:1_20:3) as a key lipid linking genus Akkermansia to T2D. Collectively, these findings support a causal gut microbiota-lipid-T2D axis and highlight phosphatidylcholine (O-18:1_20:3) as a potential target for therapeutic strategies that modulate lipid metabolism through microbiome interventions.}, }
@article {pmid41812343, year = {2026}, author = {Ricaurte-Fajardo, A and Garcia Gonzalez, K and Merino Campo, S and Alvarado-De la Hoz, C and Cardenas, AF and Zarco, L}, title = {Integrated determinants of multiple sclerosis susceptibility: Genetics, environment, infection and the microbiota.}, journal = {Journal of the neurological sciences}, volume = {484}, number = {}, pages = {125865}, doi = {10.1016/j.jns.2026.125865}, pmid = {41812343}, issn = {1878-5883}, abstract = {Multiple sclerosis (MS) arises from the convergence of polygenic immune susceptibility, environmental exposures, and infectious determinants, none of which alone is sufficient for disease expression. More than 200 genetic variants contribute to MS risk, with the HLA-DRB115:01 haplotype providing the strongest effect within a broader network of immune-regulatory loci. Functional genomic evidence shows that these variants primarily influence antigen presentation and lymphocyte activation, creating an immune landscape that can be further shaped by external factors. This review integrates epidemiological, genomic, and mechanistic data to outline the main determinants of MS susceptibility. Epstein-Barr virus infection emerges as the dominant infectious driver, with seroconversion preceding early neuroaxonal injury and clinical onset. In contrast, cytomegalovirus infection appears protective, likely through immune imprinting that counterbalances EBV-driven B-cell and T-cell activation. Environmental factors including cigarette smoking, adolescent obesity, vitamin D deficiency, circadian disruption, and gut microbiota dysbiosis further modify susceptibility by promoting proinflammatory immune programs and reducing regulatory stability. Many of these exposures interact synergistically with HLA-DRB115:01, amplifying risk beyond additive expectations. These determinants influence shared immunological pathways regulating antigen presentation, lymphocyte differentiation, and immune tolerance. Clarifying these biological interfaces highlights actionable domains including smoking avoidance, metabolic health optimization, vitamin D sufficiency, viral prevention strategies, circadian alignment, and microbiome-targeted interventions that may inform risk-reduction and early identification efforts.}, }
@article {pmid41812305, year = {2026}, author = {Gomes de Melo D'Elia, R and Saiuri de Aurélio Penteado, A}, title = {Letter to the Editor Regarding "Alterations of gut microbiome in chronic rhinosinusitis: insights from a mendelian randomization study".}, journal = {Brazilian journal of otorhinolaryngology}, volume = {92}, number = {3}, pages = {101783}, doi = {10.1016/j.bjorl.2026.101783}, pmid = {41812305}, issn = {1808-8686}, }
@article {pmid41811973, year = {2026}, author = {Martin, AN and Stuligross, C and Williams, NM and Noroian, HM and Vannette, RL}, title = {Floral microbes provisioned by Osmia lignaria establish in larval food stores, but do not affect bee development or survival.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag025}, pmid = {41811973}, issn = {1574-6941}, abstract = {Microbial dispersal and subsequent establishment among linked habitats can be used to examine drivers of community assembly and function. Flowers host microbial communities that can be acquired and vectored by bees to new flowers, establish within the adult bee gut, and enter food stores (e.g. pollen provisions) of developing larvae. Yet, whether microbes vectored by insects or applied for biocontrol can establish across these habitats and if they affect bee fitness remain unknown. Here, we applied microbes to flowers visited by blue orchard bees (Osmia lignaria) and compared microbial communities in flowers, adult bee guts, and pollen provisions before and after inoculation to determine microbial establishment, environmental filtering, and overlap across habitat types. We also inoculated provisions with microbes to test their effects on larval survival, development, and weight. Experimentally inoculated microbes were detected in all habitats, demonstrating that flowers are a source of microbial acquisition for adult and larval bees; however, the tested larval health metrics were largely unaffected by microbe supplementation.}, }
@article {pmid41816794, year = {2024}, author = {Merritt, J and Ferracane, JL}, title = {The oral microbiome: The next frontier in systemic preventative healthcare?.}, journal = {JADA foundational science}, volume = {3}, number = {}, pages = {}, pmid = {41816794}, issn = {2772-414X}, support = {R35 DE028252/DE/NIDCR NIH HHS/United States ; }, }
@article {pmid41811972, year = {2026}, author = {Berardi, S and Beltz, JK and Rudman, SM and Grainger, TN and Levine, JM and Oken, H and Schmidt, P}, title = {Seasonal evolution of Drosophila melanogaster abdominal pigmentation is associated with a multifarious selective landscape.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/evolut/qpag038}, pmid = {41811972}, issn = {1558-5646}, abstract = {Pigmentation has been widely studied by evolutionary biologists due to both ease of measure and relationship to fitness. Drosophila melanogaster pigmentation has represented a particularly useful avenue of investigation, as extensive genetic tools have enabled the characterization of the trait's complex architecture. Drosophila pigmentation also varies predictably across space and time in wild populations, suggesting pigmentation is a component of adaptation to local environmental conditions. Despite this, the impact of D. melanogaster pigmentation on fitness, and the environmental factors that drive the evolution of pigmentation, are not well understood. To address this gap, we experimentally evolved replicated D. melanogaster populations in field mesocosms to determine whether and how pigmentation evolves in response to environmental variation. We found that pigmentation rapidly and predictably adapted to a direct manipulation of temperature, supportive of melanization playing a role in thermoregulation. However, we also determined that pigmentation responded adaptively to direct manipulations of numerous additional factors, including intraspecific competition, diet, and the microbiome. These findings suggest that the selective landscape acting on pigmentation is complex and multifaceted, and that patterns of melanization may be driven, at least in part, by indirect selection due to correlations with other fitness-related traits.}, }
@article {pmid41811823, year = {2026}, author = {Bautista, J and Echeverría, CE and Maldonado-Noboa, I and Adatty-Molina, J and Suárez Urresta, S and Coral-Riofrio, EC and Araujo-Abad, S and Kyriakidis, NC and López-Cortés, A}, title = {Next-Generation Immune Checkpoints and Tumor Microenvironment Modulation in Cancer Immunotherapy.}, journal = {Journal of immunology research}, volume = {2026}, number = {1}, pages = {e7864229}, doi = {10.1155/jimr/7864229}, pmid = {41811823}, issn = {2314-7156}, support = {//Universidad de Las Am&#xe9;ricas Ecuador/ ; }, mesh = {Humans ; *Tumor Microenvironment/immunology/drug effects ; *Neoplasms/therapy/immunology/metabolism/etiology ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; Immune Checkpoint Proteins/metabolism ; }, abstract = {Immunotherapy has reshaped the oncology landscape by enabling the immune system to recognize and eliminate malignant cells. Although immune checkpoint inhibitors (ICIs) targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), programmed cell death-1 (PD-1), and programmed death-ligand 1 (PD-L1) have achieved durable responses in several cancers, their therapeutic benefit remains limited to a subset of patients, largely due to immune evasion, tumor heterogeneity, and immunosuppressive features of the tumor microenvironment (TME). This review comprehensively examines the expanding landscape of next-generation immune checkpoints, encompassing both co-inhibitory (lymphocyte activation gene-3 [LAG-3], T cell immunoglobulin and mucin-domain containing-3 [TIM-3], TIGIT, VISTA, and IGSF8) and co-stimulatory (ICOS, OX40, GITR, 4-1BB, CD40, and CD27) pathways that collectively regulate the balance between immune activation and tolerance. We discuss their molecular mechanisms, translational rationale, and emerging clinical evidence, highlighting their potential to reinvigorate antitumor immunity, particularly in ICI-refractory settings. Beyond checkpoint modulation, we explore complementary strategies aimed at remodeling the TME and enhancing immune responsiveness, including targeting immunometabolic pathways (IDO1 and CD73), innate immune sensing (toll-like receptors [TLRs]), cytokine signaling (IL-2), micronutrient immunoregulators (vitamin D), and the gut microbiota. The integration of these approaches into rational combination regimens, guided by predictive features such as T cell infiltration, tumor mutational burden (TMB), and microbiome composition, holds promise for extending the clinical impact of immunotherapy across malignancies. We further advocate for a precision immuno-oncology framework that leverages multiomic profiling, systems biology, and artificial intelligence (AI) to optimize therapeutic selection and mitigate immune-related toxicities. Emerging advances in nanomedicine, synthetic biology, and chronotherapy offer additional opportunities to enhance therapeutic specificity and durability, collectively charting a path from mechanistic insight to clinical translation toward realizing the full curative potential of cancer immunotherapy. Trial Registration: ClinicalTrials.gov identifier: LAG-3 (NCT03470922, NCT04082364, NCT05064059, NCT05352672, NCT02614833, NCT03625323, NCT01968109), TIM-3 (NCT03307785, NCT03680508, NCT02608268, NCT02817633), TIGIT (NCT03563716), VISTA (NCT02671955, NCT02812875), IGSF8 (NCT05669430), CD73 (NCT02503774), B7-H3 (NCT02475213, NCT01391143, NCT02628535, NCT03406949, NCT00089245, NCT01099644, NCT01502917), OX40 (NCT01862900, NCT02315066, NCT02410512, NCT02221960, NCT02528357, NCT02923349, NCT02705482), CD27 (NCT02335918, NCT02924038, NCT02302339, NCT02386111, NCT02543645), 4-1BB (NCT01307267, NCT02444793, NCT01471210, NCT02253992, NCT02554812), CD40 (NCT02588443, NCT03329950), ICOS (NCT02904226, NCT02723955, NCT03251924), GITR (NCT02583165, NCT02132754, NCT02697591, NCT03126110, NCT02740270, NCT02598960, NCT01239134, NCT02628574), IDO1 (NCT02752074, NCT02658890, NCT02077881, NCT01560923, NCT02073123, NCT02327078, NCT02178722), TLRs (NCT02556463, NCT02042781), and IL-2-based therapies (NCT02869295, NCT02983045).}, }
@article {pmid41811805, year = {2026}, author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L}, title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0344050}, pmid = {41811805}, issn = {1932-6203}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Adenoma/microbiology/metabolism/pathology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Case-Control Studies ; Aged ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.<br><br>OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.<br><br>MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.<br><br>RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K&#x2082;) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.<br><br>CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K&#x2082; biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.}, }
@article {pmid41811768, year = {2026}, author = {McGee, C and Jafari, AJ and Hebert, AA}, title = {Innovation in pediatric atopic dermatitis care: examining emerging topical treatment options.}, journal = {Expert review of clinical pharmacology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/17512433.2026.2641800}, pmid = {41811768}, issn = {1751-2441}, abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by pruritus, eczematous lesions, and a relapsing course. The pathophysiology of atopic dermatitis involves an interplay of skin barrier dysfunction, immune dysregulation, genetic predisposition, environmental triggers, and alterations in the skin microbiome. Pediatric AD is frequently associated with allergic comorbidities and imposes a substantial psychosocial burden on affected children and their families. This manuscript will describe recent innovations in topical, steroid-sparing therapies for pediatric AD, highlighting emerging agents such as roflumilast, ruxolitinib, and tapinarof, as well as investigational therapies.<br><br>AREAS COVERED: PubMed and Clinicaltrials.gov were used to identify the latest advancements in topical therapies available for pediatric AD treatment, as of November 2025. First-line therapies include topical corticosteroids, topical calcineurin inhibitors, and the phosphodiesterase-4 inhibitor crisaborole, all of which have demonstrated efficacy but are limited by safety considerations, tolerability, and acceptability for long-term use. In recent years, novel topical agents with distinct mechanisms of action have expanded the therapeutic landscape, representing important steroid-sparing alternatives for children with AD.<br><br>EXPERT OPINION: Emerging topical therapies for pediatric AD demonstrate substantial promise in addressing longstanding unmet needs, but long-term safety and practice-based effectiveness data remain critical for optimizing care.}, }
@article {pmid41811602, year = {2026}, author = {İşinibilir, M and Doğan, O and Bilgin, R and Çalıcı, SZ}, title = {Correction to: Microbiome dynamics linked to Aurelia aurita during bloom and post-bloom periods in the Golden Horn Estuary: a snapshot via eDNA metabarcoding.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, doi = {10.1007/s11356-026-37518-0}, pmid = {41811602}, issn = {1614-7499}, }
@article {pmid41811570, year = {2026}, author = {Zeng, L and Han, Y and Li, Q and Han, L}, title = {The co-fermentation water-dispersible granules of two PGPR strains enhances growth, yields and quality of pepper by increasing soil nutrients and changing soil bacterial community.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41811570}, issn = {1573-0972}, support = {QianKeHe Foundation - ZK[2022] Key 009//Natural Science Foundation of Guizhou Province/ ; }, }
@article {pmid41811526, year = {2026}, author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S}, title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.}, journal = {Cancer causes &amp; control : CCC}, volume = {37}, number = {4}, pages = {}, pmid = {41811526}, issn = {1573-7225}, support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Adult ; Metagenomics/methods ; Risk Factors ; Finland/epidemiology ; Metagenome ; Diet ; }, abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.<br><br>METHODS: Our data included 1,228 adults aged 25-64&#xa0;years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.<br><br>RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p&#x2009;<&#x2009;0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (&#x3b2; 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (<&#x2009;0.0001).<br><br>CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.}, }
@article {pmid41811452, year = {2026}, author = {Powell, CE and McSween, AM and Dohnalová, L and Kim, CH and Eisert, RJ and Sun, ZJ and Seo, HS and Marquardt, V and Dhe-Paganon, S and Thaiss, CA and Devlin, AS}, title = {Gut microbiome-produced bile acid metabolite lengthens the circadian period in host intestinal cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {11}, pages = {e2506313123}, doi = {10.1073/pnas.2506313123}, pmid = {41811452}, issn = {1091-6490}, support = {GM128618//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Humans ; *Circadian Rhythm/physiology/drug effects ; Mice ; *Bile Acids and Salts/metabolism ; *Lithocholic Acid/metabolism/pharmacology ; Mice, Inbred C57BL ; Male ; Cryptochromes/metabolism/genetics ; Colon/metabolism ; }, abstract = {Host circadian signaling, feeding, and the gut microbiome are tightly interconnected. Changes in the gut microbial community can affect the expression of core clock genes, but the specific metabolites and molecular mechanisms that mediate this relationship remain largely unknown. Here, we sought to identify gut microbial metabolites that impact circadian signaling. Through a phenotypic screen of a focused library of gut microbial metabolites, we identified a bile acid metabolite, lithocholic acid (LCA), as a circadian modulator. LCA lengthened the circadian period of core clock gene hPer2 transcription in a dose-responsive manner in human colonic cells. We found evidence that LCA modulates the casein kinase 1 δ/ε (CK1δ/ε)-protein phosphatase 1 (PP1) feedback loop and stabilizes core clock protein cryptochrome 2 (CRY2). Furthermore, we showed that LCA feeding alters circadian transcription in mouse distal ileum and colon. Taken together, our work identifies LCA as a molecular link between host circadian biology and the microbiome. Because bile acids are secreted in response to feeding, our work provides potential mechanistic insight into the molecular nature of the food-entrainable oscillator (FEO) by which peripheral clocks adapt to the timing of food intake. Given the association between circadian rhythm, feeding, and metabolic disease, our insights may offer an avenue for modulating host health.}, }
@article {pmid41811133, year = {2026}, author = {Thomassen, GGM and Olguin-Diaz, F and Kostopoulos, I and Preece, K and Wopereis, H and Jourdan, M and Knol, J and Abrahamse, E and Renes, IB}, title = {A Combination of Inulin and Long-Chain Fructooligosaccharides Enhances in Vitro Iron Bioavailability and Supports a Favorable Infant Gut Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c13296}, pmid = {41811133}, issn = {1520-5118}, abstract = {Iron deficiency is common during early life. Prebiotics may enhance iron bioavailability (IB) in the small intestine and in the colon. To study this, IMF was supplemented with inulin, lcFOS, their combinations (1:1 or 2:1), or scGOS:lcFOS (9:1). IMFs were digested in vitro, or fermented ex vivo yielding short-chain fatty acids (SCFA) and altering microbiota composition. Digested IMF containing either prebiotics or SCFA were incubated on Caco-2 cells to assess IB under simulated small-intestinal or colonic conditions respectively. Fermentation of inulin:lcFOS and scGOS:lcFOS increased Bifidobacteriaceae, reduced Enterobacteriaceae, and enhanced acetic acid (AA) production. Inulin:lcFOS increased small-intestinal IB (1.2-fold). SCFA from Inulin:lcFOS and scGOS:lcFOS increased colonic IB by 3.7- and 5.0-fold, respectively. When combining small-intestinal and colonic IB, overall IB increased ∼1.5-fold versus the control. Prebiotic-induced AA production played a key role in enhancing IB. Combining inulin or scGOS with lcFOS in IMF may improve iron absorption and support beneficial infant gut microbiota.}, }
@article {pmid41810990, year = {2026}, author = {Zhang, Y and Han, B and Wang, X and Li, Y and Zou, YR and Li, SH and Li, XQ and Li, YB and Huang, Y and Sun, DZ and Li, YH and Qian, ZQ and Song, SH and Shi, L and Li, X and Zhang, Y}, title = {Maternal microbiome-derived propionate regulates offspring myelination via histone lactylation.}, journal = {Brain : a journal of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1093/brain/awag034}, pmid = {41810990}, issn = {1460-2156}, abstract = {The maternal gut microbiome plays a crucial role in regulating offspring neurodevelopment through microbial metabolite signaling, yet its influence on CNS myelinogenesis, a pivotal process for neural circuit maturation, remains poorly understood. Here, using antibiotic-induced maternal dysbiosis models, we identify propionate (PA), a short-chain fatty acid (SCFA) derived from the maternal microbiome, as a key epigenetic modulator of oligodendrocyte precursor cell (OPC) differentiation. Maternal antibiotic-induced gut dysbiosis led to significant hypomyelination in offspring, an effect that could be rescued by postnatal PA supplementation. PA not only enhanced developmental myelination but also promoted remyelination following lysolecithin-induced demyelination by inducing OPC differentiation. Mechanistically, PA induced histone H4K12 lactylation (H4K12la), thereby activating transcription of cGMP-PKG signaling components (e.g., Gna12) and upregulating Sox family transcription factors essential for oligodendrocyte differentiation. Taken together, our findings delineate a PA-H4K12la-cGMP-PKG pathway that links maternal microbial metabolism to offspring myelination, offering a promising SCFA-mediated epigenetic strategy for the treatment of CNS demyelinating disorders.}, }
@article {pmid41810941, year = {2026}, author = {Aufiero, MA and Hohl, TM}, title = {Antibiotic-induced microbiota disruption impairs neutrophil-mediated immunity to respiratory Aspergillus fumigatus infection in mice.}, journal = {mBio}, volume = {}, number = {}, pages = {e0398225}, doi = {10.1128/mbio.03982-25}, pmid = {41810941}, issn = {2150-7511}, abstract = {Aspergillus fumigatus is an ubiquitous environmental mold that forms airborne conidia and can cause life-threatening infections in immunocompromised individuals. Invasive aspergillosis occurs in patients with quantitative or qualitative neutrophil defects who often receive systemic antibiotics to prevent or manage bacterial infections. Antibiotic-induced bacterial dysbiosis has been linked to impaired neutrophil bactericidal activity and to intestinal commensal bacteria escape during systemic candidiasis, though it remains unclear whether receipt of antibacterial antibiotics impairs neutrophil-dependent defenses against inhaled mold pathogens in the lung. Herein, we measured the outcome of A. fumigatus challenge in C57BL/6J mice that were treated with different antibiotics in the drinking water for 3 weeks prior to experimental infection. We found that ampicillin, but not neomycin or vancomycin treatment, significantly increased murine mortality and lung fungal burden. The heightened susceptibility was associated with impaired fungal killing by lung-infiltrating neutrophils and monocytes, as well as reduced neutrophil production of NADPH oxidase 2 (NOX2)-dependent reactive oxygen species (ROS). These findings demonstrate that systemic antibiotic treatment can compromise pulmonary immunity against A. fumigatus and suggest that the host microbiota can enhance neutrophil fungicidal activity by promoting NOX2-mediated ROS production.IMPORTANCEAspergillus fumigatus is an environmental mold that causes invasive pulmonary disease in immunocompromised individuals. Owing to limited diagnostic tools, a narrow arsenal of effective treatments, and rising antifungal resistance, the World Health Organization (WHO) has designated A. fumigatus as a critical priority fungal pathogen, highlighting the urgent need for further research. Patients with compromised immunity often receive broad-spectrum antibiotics to prevent or treat opportunistic infections, leading to significant disruption of the resident commensal microbiota. This antibiotic-induced dysbiosis has been linked to Clostridium difficile colitis and to intestinal overgrowth of vancomycin-resistant Enterococcus and Candida parapsilosis, preceding bloodstream infection. However, the impact of antibiotic treatment on susceptibility to invasive pulmonary aspergillosis remains undefined. In this study, we found that oral treatment with ampicillin, but not neomycin or vancomycin, significantly increased mortality in mice following A. fumigatus infection. Neutrophils from the lungs of ampicillin-treated mice also showed markedly impaired fungal killing. These findings raise the possibility that preserving microbiome integrity during antibiotic treatment could enhance immune protection against invasive aspergillosis in at-risk patient groups.}, }
@article {pmid41810937, year = {2026}, author = {Lee, J and Kim, H-J and Kim, E-H and Kim, S and Park, B and Hong, S and Kang, J and Lee, J-Y and Lee, S}, title = {Prediction model for periodontitis stage based on the salivary microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0110325}, doi = {10.1128/msystems.01103-25}, pmid = {41810937}, issn = {2379-5077}, abstract = {This study aimed to characterize salivary microbiome compositions that can classify periodontal health and various stages of periodontitis. We collected saliva samples from 250 study subjects, including 100 periodontally healthy controls and 150 periodontitis patients in stages I/II/III. We performed 16S ribosomal RNA gene sequencing to characterize their salivary microbiomes. Alpha diversities show significant differences between healthy and periodontitis. Differentially abundant taxa were identified by ANCOM. Random forest machine learning models were used to classify each periodontitis stage based on the centered log-ratio of differentially abundant taxa. We identified 20 differentially abundant taxa among the groups in the salivary microbiomes of all groups. Among these differentially abundant taxa, Porphyromonas gingivalis and Actinomyces spp. are the most important taxa on the random forest model to classify the periodontitis statuses. Our random forest model classified multiple periodontitis statuses with an area-under-curve of 0.829 ± 0.124, sensitivity 0.884 ± 0.022, and specificity 0.652 ± 0.065. Moreover, because it can be difficult to diagnose in dentistry practice, we performed our classifier model to distinguish healthy or stage I, providing an area-under-curve of 0.736 ± 0.168, sensitivity 0.789 ± 0.102, and specificity 0.622 ± 0.196. Furthermore, our random forest model detected periodontitis patients from healthy individuals with an area-under-curve of 0.924 ± 0.088, sensitivity of 0.862 ± 0.175, and specificity of 0.921 ± 0.061. Finally, we evaluated our classification model with external data sets from Spanish and Portuguese subjects. Some evaluations showed a slight decrease, but it might be due to different salivary microbiome compositions from ethnicity. Significant differences were identified in the differentially abundant taxa among healthy controls and the various stages of periodontitis.IMPORTANCEPeriodontitis is a common but complex oral disease that can lead to tooth loss and contribute to systemic health issues. Early and accurate diagnosis is essential for effective intervention, yet traditional diagnostic methods often rely on invasive clinical assessments that may miss early signs. This study demonstrates that salivary microbiome profiles can be used to classify both periodontal health and multiple periodontitis stages using a machine learning approach. By identifying the 20 key microbial taxa, including Actinomyces spp., we developed a non-invasive predictive model with high diagnostic accuracy. Importantly, the model was also able to detect early-stage disease and performed well across external data sets, highlighting its potential for broader clinical application. These findings suggest that a salivary microbiome-based diagnostic tool may support more precise, accessible, and early diagnosis of periodontitis in dental disease management.}, }
@article {pmid41810763, year = {2026}, author = {Pandey, VK and Tripathi, A and Choudhary, P and Thapliyal, S}, title = {Exploring the role of diet in modulating stress and emotional health: a review on mental nutrition and cognitive resilience.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70526}, pmid = {41810763}, issn = {1097-0010}, abstract = {The rise in mental-health-related disorders, including anxiety, depression, and cognitive impairment worldwide, has increased the demand for preventative non-pharmacological interventions and intervention aimed at modifiable lifestyle factors - particularly diet. Growing evidence shows that plant-based nutrition, with its anti-inflammatory and neuroprotective effects, is critically important for cognitive resilience, emotional stability, and mental wellbeing. Essential nutrient and bioactive compounds such as ω-3 fatty acids, polyphenols, B vitamins, magnesium, and probiotics themselves act on the gut-brain axis to alleviate neuroinflammatory stress. Functional and adaptogenic foods - for example, Ashwagandha, Rhodiola, and Holy Basil - are becoming the focus of interest as they play a significant role in cortisol control and stress adaptation. All plant-based dietary patterns, such as the Mediterranean, DASH (Dietary Approaches to Stop Hypertension), and plant-based diets, show comparable associations with lower risk for depression, anxiety, and cognitive deficits through enhancing gut microbiome richness and balancing neurotransmitters. This review outlines the scientific basis of mental nutrition, highlighting the interconnections between dietary patterns, gut microbiota composition, diet-mediated modulation of neurotransmitter levels, and neuroinflammatory pathways that collectively influence mental health. © 2026 Society of Chemical Industry.}, }
@article {pmid41810553, year = {2026}, author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ}, title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70264}, pmid = {41810553}, issn = {2045-8827}, support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Humans ; *Glycoside Hydrolases/metabolism/genetics ; *Polysaccharides/metabolism ; Infant ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; Substrate Specificity ; Infant, Newborn ; }, abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.}, }
@article {pmid41810506, year = {2026}, author = {Hirano, Y and Tomofuji, Y and Edahiro, R and Kishikawa, T and Miyawaki, S and Okada, Y}, title = {Association between autoimmune diseases and the gut microbiome.}, journal = {International immunology}, volume = {}, number = {}, pages = {}, doi = {10.1093/intimm/dxag013}, pmid = {41810506}, issn = {1460-2377}, abstract = {The gut microbiome has emerged as an important environmental factor in the pathogenesis of autoimmune diseases. Advances in high-throughput sequencing technologies have enabled comprehensive characterization of the gut microbiome, providing detailed insights into its composition and functional potential. These approaches have been widely applied in autoimmune disease research, revealing disease-associated alterations in the gut microbiome of patients with conditions such as rheumatoid arthritis and systemic lupus erythematosus. In addition, microbiome sequencing data can be leveraged to investigate the gut virome, including viruses residing in the intestinal ecosystem. This review summarizes current evidence linking autoimmune diseases and the gut microbiome, with a particular focus on studies employing microbiome sequencing-based analyses.}, }
@article {pmid41810379, year = {2026}, author = {Anzà, S and Rosa, BA and Herzberg, MP and Lee, G and Herzog, ED and Zhao, P and England, SK and Ndao, IM and Martin, J and Smyser, CD and Rogers, CE and Barch, DM and Hoyniak, C and McCarthy, R and Luby, J and Warner, BB and Mitreva, M}, title = {Simplifying Daily Cortisol Cycle Analysis: Validation and Benchmarking of the Cortisol Sine Score Against Cosinor and JTK_CYCLE models.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.23.26346831}, pmid = {41810379}, abstract = {UNLABELLED: The daily cortisol cycle is a critical indicator of hypothalamic-pituitary-adrenal (HPA) axis function. The current analytical approaches produce several outputs difficult to integrate into simple statistical models, clinical workflows, and ML/AI pipelines requiring single-value inputs. We developed the Cortisol Sine Score (CSS), a model-free scalar metric that quantifies daily cortisol exposure by computing a weighted sum of cortisol measurements across the day, using sine-transformed time-of-day weights. The CSS produces positive values for morning-dominant patterns, negative values for evening-shifted profiles, and near-zero values for flattened rhythms characteristic of chronic stress and circadian disruption. We validated the CSS performance in 3,006 samples from 501 pregnant women enrolled in the March of Dimes program, with cortisol values measured at 6 time points per day collected during the second trimester of pregnancy. The CSS showed strong correlations with observed and model-estimated amplitude and acrophase from Cosinor regression and JTK_CYCLE approaches, with excellent classifying performance (AUC=0.89, high versus low). The CSS successfully captured established associations between social disadvantage and cortisol dysregulation, and demonstrated utility in predicting gut microbiome composition in metagenomic analyses. Importantly, the CSS maintains excellent fidelity to the full 6-sample protocol with as few as 3-4 daily measurements. The 4-sample protocol achieves great performance (r = 0.952, MAE = 0.087) while reducing participant burden. The 06:00 time point was identified as essential for accurate CSS quantification. The CSS bridges the gap between circadian analysis and practical implementation by providing a simple, interpretable, and robust assessment of cortisol daily cycle in large-scale epidemiological studies, clinical screening, and biomedical sensors.<br><br>HIGHLIGHTS: Current state-of-the-art approaches estimating the daily cortisol exposures produce multi-output information difficult to implement in simple statistical analyses or ML/AI multi-omics approachesCortisol Sine Score is a novel model-free scalar metric expressing cortisol daily exposure and rhythmicity (morning vs evening exposure)Cortisol Sine Score was validated using 3006 salivary samples from clinical data and golden standards in circadian analyses such as Cosinor and JTK_CYCLECortisol Sine Score was the top performer in our benchmarking approach predicting association with social disadvantage and gut microbiome compositionReliable with 3-4 daily samples, reducing participant burdenOpen-source R package CortSineScore democratizes cortisol cycle analysis.}, }
@article {pmid41810375, year = {2026}, author = {Anderson, SM and Cing, Z and Drewes, JL and White, JR and Southward, T and Beauregard, H and Ferri, JT and Wanyiri, JW and Roslani, A and Vadivelu, J and Tang, SN and Queen, J and Sears, CL}, title = {Clostridioides difficile Detection in a Human CRC Cohort.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.20.26346702}, pmid = {41810375}, abstract = {BACKGROUND: The role of the gut microbiome and specific enteric bacteria in influencing the development of colorectal cancer (CRC) remains incompletely understood. Recently, it was shown that human CRC-derived strains of Clostridioides difficile were capable of inducing colonic tumorigenesis in a susceptible mouse model. We hypothesized that C. difficile contributes to the pathogenesis of human CRC and would be enriched in CRC tumors compared to paired normal tissues from the same individual.<br><br>METHODS: We analyzed matched tumor/normal tissue samples from a cohort of 108 individuals presenting to a tertiary care hospital in Kuala Lumpur, Malaysia for CRC resection between 2013-2014. We assessed the prevalence of C. difficile detection using 16S rRNA amplicon sequencing with high-resolution taxonomic assignment as well as culture and PCR.<br><br>RESULTS: We found that detection of C. difficile was prevalent (38% of individuals), but of low abundance (tumor median relative abundance 0.01%, paired normal 0.006% [p=0.4]). Detection of C. difficile was more prevalent in individuals with biofilm-positive tumor tissues than biofilm-negative (i.e., 81% of C. difficile -positive individuals were biofilm-positive vs. 63% of C. difficile -negative individuals [p=0.04]). Additionally, in exploratory analyses, we describe patterns of taxonomic and inferred functional pathway differences between C. difficile- positive and C. difficile -negative groups.<br><br>CONCLUSION: These findings suggest that C. difficile is frequently present in low abundance in the tumor microbiome with a potentially significant impact on community composition and function.}, }
@article {pmid41810263, year = {2026}, author = {Tan, Y and Wu, Y and Chen, Z and Zhang, Z and Huang, S and Li, Z and Huang, Y}, title = {Intestinal Flora Reconfiguration via Electroacupuncture: A Strategy to Counteract Depressive-Like Symptoms in Rats.}, journal = {Neuropsychiatric disease and treatment}, volume = {22}, number = {}, pages = {565614}, pmid = {41810263}, issn = {1176-6328}, abstract = {BACKGROUND: Depression is a global health concern, and acupuncture has emerged as an effective treatment. The role of intestinal microbiota in depression remains unclear. This study, utilizing 16S rRNA high-throughput sequencing, aimed to explore the relationship between electroacupuncture (EA) and depressive behavior by examining changes in the intestinal microbiota.<br><br>MATERIALS AND METHODS: Forty-eight male Sprague-Dawley rats were utilized, with 13 assigned to the normal control (NC) group. The remaining rats underwent a 28-day depression modeling process, and those exhibiting depressive symptoms were randomly divided into chronic unpredictable mild stress (CUMS) and EA groups. The EA group received 14 days of treatment. Behavioral analyses were conducted on rats from the NC, CUMS, and EA groups to assess EA's effectiveness. Additionally, 16S rRNA sequencing was performed on randomly selected rats from each group.<br><br>RESULTS: By examining the behavior of 39 rats and the intestinal microbiota of 18 rats, we found that EA may alter the composition of the intestinal microbiota community structure in CUMS rats, particularly modulating the abundance of Akkermansia in a manner potentially linked to gut-brain axis regulation, including stress- and inflammation-related pathways that may influence microbial composition.<br><br>CONCLUSION: The potential antidepressant impact of electroacupuncture (EA) might be linked to the modulation of Akkermansia abundance within the brain-gut axis.}, }
@article {pmid41810106, year = {2026}, author = {Yu, Z and Xu, Y and Li, W and Hu, Y and Zhang, C}, title = {Risk Factors and Biomarkers for Immune Checkpoint Inhibitor-mediated Hepatotoxicity: Emerging Insights and Future Perspectives.}, journal = {Journal of clinical and translational hepatology}, volume = {14}, number = {2}, pages = {215-231}, pmid = {41810106}, issn = {2310-8819}, abstract = {In the past decade, immune checkpoint inhibitors (ICIs) have dramatically changed cancer treatment, significantly improving outcomes for patients with various malignancies. Nonetheless, their widespread application has resulted in a rise in immune-related adverse events due to excessive immune activation, including immune-mediated hepatotoxicity (IMH). IMH can cause serious complications and even death, underscoring the need for early prediction and intervention. This review outlines the current understanding of risk factors and predictive biomarkers for IMH in cancer patients undergoing ICI therapy, with risk factors divided into patient-associated, tumor-associated, and agent-associated categories. Higher IMH risk is related to female sex, younger age, extreme BMI, Asian ethnicity, and chronic liver disease. Cancer type, prior ICI treatment, dual ICI combination therapy, and the concurrent use of chemotherapy, targeted agents, or other hepatotoxic drugs (e.g., acetaminophen, statins) also increase the risk of IMH. Potential predictive biomarkers encompass circulating blood cells, serum proteins, autoantibodies, cytokines, gene profiles, and the gut microbiome. Despite promising findings, the predictive value of these biomarkers remains inconsistent, and no definitive biomarker has been established for routine clinical use. Large-scale prospective studies are essential to verify the predictive value of these biomarkers and facilitate their integration into clinical practice, thereby providing deeper insights into the early identification and individualized management of IMH during ICI therapy.}, }
@article {pmid41810018, year = {2026}, author = {Ding, Q and Teng, Y and Zhu, H and Jia, Z and Xu, S and Hu, B and Chen, B and Dai, J and Sun, J and Nie, P and Liu, Z and Chen, Q and Wang, X and Xu, X and Zhang, X and Duan, S}, title = {Local periodontal injection, systemic heart repair: A dual-functional hydrogel for non-invasive concurrent treatment of periodontitis and myocardial infarction.}, journal = {Bioactive materials}, volume = {62}, number = {}, pages = {17-33}, pmid = {41810018}, issn = {2452-199X}, abstract = {Periodontitis and myocardial infarction (MI), the leading cause of mortality worldwide, represent globally prevalent inflammatory diseases with bidirectional pathophysiological links. Despite the urgent demand for non-invasive strategies capable of alleviating local periodontal destruction while mitigating associated systemic cardiovascular complications, no integrated treatment modality currently exists. To address this challenge, a protein-loaded antibacterial hydrogel, thiolated chitosan/AMP-PEG-maleimide (C1.5P4/BMP-2), with novel sustained protein release properties was developed. This hydrogel features an interconnected microporous architecture that: (1) enables high-efficiency BMP-2 protein encapsulation, (2) preserves protein bioactivity while ensuring sustained release, thereby addressing the recognized challenge of hydrogel-based protein delivery, (3) confers potent antibacterial properties, (4) facilitates remote cardiac function improvement by resolving periodontal inflammation. In murine models, locally, it attenuated alveolar bone loss (2-fold greater bone regeneration vs controls) while systemically improving post-MI cardiac function (75.6% higher ejection fraction). Mechanistically, the hydrogel's protein-protective microenvironment synergized with its antimicrobial action selectively inhibiting Gram-negative (G[-]) anaerobic pathogens (primary periodontal culprits) while enriching Gram-positive (G[+]) commensals, regulating biofilm G[-]/G[+] ratio. Concomitantly, this dual action modulates the oral-cardiac inflammatory axis, specifically downregulating B2 cell/TNF-α signaling to mitigate systemic inflammation associated with MI. Collectively, this study presents a novel non-invasive protein-stabilizing hydrogel that addresses periodontitis-MI comorbidity through sustained osteogenic factor delivery coupled with microbiome-immune modulation.}, }
@article {pmid41809991, year = {2026}, author = {Ma, L and Wang, W and Ma, S and Wang, Y and Li, H and Gao, Y and Xie, X}, title = {Association analysis of the differences in intestinal flora and clinical tumor indicators among colorectal cancer patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1742672}, pmid = {41809991}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; DNA, Bacterial/genetics ; Biodiversity ; Adult ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common malignant tumor globally, and its development is closely related to intestinal flora dysbiosis. However, the heterogeneity of cancerous tissues, paracancerous tissues, and fecal flora, and their clinical significance, has not been fully elucidated.<br><br>AIM: This study aimed to systematically analyze the diversity, composition, and functional differences of intestinal flora in patients with CRC compared to healthy individuals, and to reveal potential associations between the characteristics of these microbial communities and tumorigenesis and development.<br><br>METHODS: Thirty CRC patients (30 cancerous tissue samples, 30 paracancerous tissue samples, and 30 fecal samples) and 30 healthy volunteers (30 fecal samples) were enrolled in the study. The microbial communities were analyzed using 16S rRNA sequencing, and the status of the bacterial flora was evaluated by combining alpha and beta diversity, species difference analysis, the Gut Microbiome Health Index (GMHI), and the Gut Microbiome Dysbiosis Index (MDI). The correlation of these factors with clinical parameters was then analyzed.<br><br>RESULTS: The alpha diversity of the cancerous tissue from patients with CRC was significantly lower than that of the fecal samples (p < 0.05). The intestinal microbiota of patients with CRC was statistically different from that of healthy individuals (p < 0.01). Additionally, there was a statistically significant difference in beta diversity between the cancerous tissue and fecal gut microbiota of patients with CRC (p < 0.01). The microbiota of the paracancerous tissues exhibited significantly higher GMHIs than the cancerous tissues. Healthy individuals demonstrated better gut health than individuals with CRC. The fecal samples from CRC patients had a higher GMHI than the cancerous tissues. The difference was statistically significant (p < 0.001). For MDI, however, the trend was reversed. A statistically significant positive correlation was observed between Escherichia coli and tumor size (p < 0.05). Similarly, Methylobacterium/Methylorubrum exhibited a statistically significant positive correlation with tumor stage (p < 0.05).The research found that Blautia and Faecalibacterium had higher abundances in the feces of healthy individuals and the tissues adjacent to colorectal cancer, while Escherichia-Shigella, Bacteroides, Enterococcus, and Fusobacterium had higher abundances in colorectal cancer tissues.<br><br>CONCLUSION: The intestinal flora of CRC patients is characterized by decreased diversity, an enrichment of pathogenic bacteria, and a reduction in protective flora. these microbial alterations are associated with tumor progression, potentially via inflammatory and metabolic pathways, although causal mechanisms remain to be functionally validated. The flora health index and dysbiosis index have potential for use as adjunctive diagnostic tools. However, individualized preventive intervention strategies need to be developed in the future by combining multi-omics data.}, }
@article {pmid41809915, year = {2025}, author = {Karras, J and Schwab, F and Maechler, F}, title = {VRE and antibiotic use in German ICUs-an ecological analysis of 15 years of surveillance data.}, journal = {JAC-antimicrobial resistance}, volume = {7}, number = {6}, pages = {dlaf216}, pmid = {41809915}, issn = {2632-1823}, abstract = {BACKGROUND: This 15 years study reveals highlighting key differences in resistance trends and incidence of vancomycin-resistant Enterococcus faecium versus Enterococcus faecalis in German intensive care units (ICUs). By linking these patterns to antibiotic use, it uncovers crucial insights into the evolving battle against vancomycin-resistant enterococci (VRE) in critical care.<br><br>METHODS: A retrospective ecological cohort study using data from the German SARI (Surveillance of Antimicrobial Use and Antimicrobial Resistance in German ICUs) system was conducted from January 2006 to December 2020. Data from 79 ICUs were analysed. Incidence densities (ID) and resistance rates (RR) for E. faecium and E. faecalis were calculated, alongside antibiotic use densities in defined daily doses per 100 patient days. Generalized linear models and generalized estimating equations assessed temporal trends and associations with antibiotic consumption.<br><br>RESULTS: A total of 42&#x200a;701 Enterococcus isolates were analysed: 21&#x200a;672 E. faecium and 21&#x200a;029 E. faecalis. VRE was found in 17.0% of E. faecium and 0.2% of E. faecalis. VRE. faecium showed a significant increase in ID and RR, while vancomycin-sensitive E. faecium decreased. VRE. faecalis remained rare. Antibiotic use patterns showed a significant increase in carbapenem (184.9%), glycopeptides (131.7%), and vancomycin (93.9%).<br><br>CONCLUSIONS: This study highlights a sustained increase in the incidence and resistance of VRE. faecium. While glycopeptides are well-known contributors, carbapenem use may also play a role in VRE colonization, potentially through disruption of the microbiome. Further research is needed to clarify the complex relationship between antibiotic exposure, microbiome-related mechanisms, and resistance development.}, }
@article {pmid41809889, year = {2025}, author = {Kim, J and Sim, Y and Kim, D and Kwon, J and Lee, S and Rungratanawanich, W and Kim, J and Jung, J and Lee, Y and Hyun, S and Lee, S and Kwon, H and Song, B and Seo, K and Kim, D and Cho, Y}, title = {Ginseng-derived exosome-like nanovesicles protect against liver fibrosis by regulating TIMP2 pathways and gut dysbiosis.}, journal = {Asian journal of pharmaceutical sciences}, volume = {20}, number = {6}, pages = {101105}, pmid = {41809889}, issn = {2221-285X}, abstract = {Metabolic dysfunction-associated fatty liver disease (MASLD) and alcohol-associated liver disease (ALD) are prevalent chronic liver diseases that can progress to steatohepatitis, fibrosis, cirrhosis, and ultimately liver failure. Here, we demonstrated that oral administration of GNVs provided substantial protection against liver injury and fibrosis in MASLD and ALD mouse models. In a Western-style high-fat diet-induced MASLD model and a chronic binge alcohol-induced ALD model, GNVs treatment significantly reduced gut leakiness by restoring intestinal junctional complex proteins and rebalancing the gut microbiome. GNVs attenuated hepatic lipid accumulation, oxidative stress and fibrogenic markers. GNV treatment downregulated the fibrosis-associated tissue inhibitor of metalloproteinase-2 (TIMP2) pathway in hepatic stellate cells, which is linked to enhanced matrix degradation and reduced fibrogenesis. GNVs prevent MASLD- and ALD-associated gut barrier dysfunction and liver fibrosis through modulation of the gut-liver axis and the TIMP2 pathway. Edible GNVs represent a novel, multifaceted therapeutic strategy for managing chronic liver diseases.}, }
@article {pmid41809810, year = {2026}, author = {Qi, Y and Shi, J and Zhang, Q and Xuan, Y and Zhang, H and Duan, Y}, title = {Environmental and microbiome determinants of sperm quality: a narrative review on male health.}, journal = {Translational andrology and urology}, volume = {15}, number = {2}, pages = {64}, pmid = {41809810}, issn = {2223-4691}, abstract = {BACKGROUND AND OBJECTIVE: With the rapid development of modern production and daily life, human fertility has shown a declining trend, with male factors accounting for approximately half of the cases. Declining sperm quality is the primary issue in male infertility, and environmental factors play a significant role in its development. This paper aims to thoroughly explore the impact of environmental factors on male sperm quality and provide insights for the etiology and prevention of male infertility.<br><br>METHODS: A comprehensive literature search was conducted in PubMed from its inception to June 25, 2025, for articles on the effects of traditional environmental factors on male sperm quality. 84.9% of the references were published between 2020 and 2025, with most studies being recent and related to human male fertility. The search included all articles containing the following keywords: "sperm quality", "environmental factors", "temperature", "heavy metals", "pesticide", "phthalate", "viruses", "bacteria", "Radiofrequency Electromagnetic Radiation (RF-EMR)", "per- and polyfluoroalkyl substances (PFAS)", "air pollution", "Benzo[a]pyrene (BaP)", and "microbiome". The retrieved articles were reviewed to summarize the effects of environmental factors on male sperm quality.<br><br>KEY CONTENT AND FINDINGS: A total of 250 articles were identified with these keywords and later screened for inclusion. We finally included 82 publications that were relevant to our topic. Based on recent studies within China and international research, this paper not only examines the effects of traditional pollutants at the molecular mechanism level but also focuses on emerging environmental factors such as the synergistic toxicity of new environmental pollutants-PFAS, and heavy metals-as well as 5G radiofrequency radiation. These environmental factors significantly reduce sperm concentration, motility, morphological integrity, and DNA stability through multiple mechanisms and systemic effects-including reactive oxygen species (ROS), endocrine disruption, DNA damage, and inflammatory responses-thereby impairing male fertility.<br><br>CONCLUSIONS: Traditional and emerging environmental factors synergistically impair male sperm quality through multiple mechanisms, including oxidative stress, endocrine disruption, epigenetic alterations, and systemic inflammation. Future experimental research should shift from single-pollutant studies to real-world mixture exposure investigations, utilizing multi-omics technologies to deeply analyze epigenetic mechanisms and transgenerational effects. Clinically, environmental risk factors should be incorporated into routine screening and counseling for male infertility, with enhanced antioxidant intervention measures. At the policy level, there is an urgent need to improve chemical regulation to prevent potentially stronger reproductive toxicity from novel substitutes and to enhance air pollution control. Curbing the global decline in fertility at its source holds significant importance for advancing population reproductive health.}, }
@article {pmid41809656, year = {2026}, author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M}, title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {251}, number = {}, pages = {10894}, pmid = {41809656}, issn = {1535-3699}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration &amp; dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.}, }
@article {pmid41809655, year = {2026}, author = {Zhou, B and Parekh, Z and Phung, C and Rodriguez, SH and Skondra, D}, title = {The gut-retina axis in age-related macular degeneration: immune crosstalk and metabolite production.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {251}, number = {}, pages = {10847}, pmid = {41809655}, issn = {1535-3699}, mesh = {Humans ; *Macular Degeneration/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology/physiology ; Animals ; Dysbiosis/immunology ; *Retina/immunology/metabolism/pathology ; }, abstract = {Current therapies slow down advanced features but do not halt or reverse degeneration and neovascularization in dry and wet age-related macular degeneration (AMD). Recent research implicates the gastrointestinal microbiome as a potential critical modulator in AMD pathogenesis through the gut-retina axis. Dysbiosis, characterized by imbalanced microbial diversity, composition and function, can exacerbate systemic and retinal inflammation through microglial priming, inflammasome activation, and secretion of pro-angiogenic cytokines (IL-6, IL-1β, TNF-α, VEGF). Additionally, microbiome-derived metabolites such as short-chain fatty acids and bile acids may exert modulatory roles in host immunity and homeostasis. Their depletion in conjunction with enrichment of specific microbial taxa have been linked to progression of advanced AMD. Together, these complex systems of immune crosstalk in relation to dysbiosis highlight the gut-retina axis as a promising therapeutic target. Dietary modifications, particularly Mediterranean and high-fiber diets, enhance production of protective metabolites and are associated with decreased AMD progression risk compared to Western dietary patterns. Experimental strategies such as fecal microbiota transplantation in animal models and drug repurposing strategies show promise in modulating disease severity. This review synthesizes current mechanistic insights into microbial-immune crosstalk in AMD, emphasizing the interplay of dysbiosis, immune activation, and metabolite signaling.}, }
@article {pmid41809649, year = {2026}, author = {Kawano, A and Yamashiro, K and Takahashi, Y and Yoshida, Y}, title = {Effects of Initial Periodontal Therapy on Intraoral Bacterial Flora in Patients With Oral Contraceptive-Related Severe Gingivitis.}, journal = {Case reports in dentistry}, volume = {2026}, number = {}, pages = {5078642}, pmid = {41809649}, issn = {2090-6447}, abstract = {Gingivitis is a common inflammatory condition of the gingival tissues, influenced by microbial plaque and various systemic factors, including hormonal changes. Oral contraceptives containing estrogen and progestin are known to exacerbate gingival inflammation. We report the case of a 20-year-old Japanese woman who presented with gingival swelling and bleeding despite self-care, with a history of orthodontic treatment and oral contraceptive use. Clinical examination revealed probing pocket depths of ≥ 4 mm and bleeding on probing in more than half of the sites, a periodontal inflamed surface area (PISA) of 995.8 mm[2], and a plaque control record of 78%. Bacterial analysis identified elevated levels of Prevotella intermedia, Prevotella melaninogenica, and Fusobacterium nucleatum. Initial periodontal therapy-consisting of scaling and root planing, supported with systemic and topical antibiotics-was provided, followed by gingivectomy at sites lacking adequate gingival attachment. Posttreatment evaluation demonstrated marked reductions in probing depth, bleeding on probing, and PISA (44.9 mm[2]), with plaque control improving to 31.3%. Microbiome analysis revealed a decrease in pathogenic anaerobes and an increase in beneficial aerobic bacteria. The patient's oral hygiene practices improved substantially through targeted education and self-care instruction, supporting the maintenance of periodontal health. This case highlights that initial periodontal therapy, combined with patient education and regular monitoring, can effectively reduce gingival inflammation and favorably modify the oral microbiome in oral contraceptive-related gingivitis. Awareness of the potential impact of oral contraceptives on periodontal health and implementation of individualized oral hygiene measures are essential for preventing disease progression in similar patients.}, }
@article {pmid41809604, year = {2026}, author = {Srivastava, S and Mir, RA and Hussain, SJ and Mitra, S and Srivastava, S and Kumar, P and Kaur, H}, title = {Microbial engineering for pesticide degradation: current insights and future directions for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1751932}, pmid = {41809604}, issn = {1664-302X}, abstract = {Pesticides are synthetic agrochemicals widely used to protect crops from pests and diseases; however, their limited biodegradability and indiscriminate application pose serious risks to non-target organisms, soil fertility, human health, and overall environmental sustainability. Conventional physical and chemical remediation strategies often fall short in restoring contaminated ecosystems, highlighting the urgent need for effective and sustainable pesticide mitigation approaches. In recent years, in situ bioremediation has emerged as a promising, eco-friendly, and cost-effective strategy for pesticide degradation in agricultural soils. Under favourable conditions, microorganisms utilise pesticides as sources of carbon, sulphur, and electrons, facilitating their breakdown through diverse metabolic pathways, with enzymatic degradation playing a central role in chemical transformation. Microbial consortia exhibit enhanced degradation efficiency by leveraging functional diversity and synergistic interactions among their microbial members. For instance, a consortium comprising Azospirillum, Cloacibacterium, and Ochrobacterium achieved 100% degradation of 50 mg L[-1] glyphosate within 36 h. Advances in microbiome engineering have further expanded the scope of bioremediation by enabling the targeted manipulation of microbial communities to improve degradation specificity and performance. Notably, the recombined genomes of Psathyrella candolleana and Pseudomonas putida, generated through protoplast fusion, degraded 78.98% of pentachlorophenol in contaminated water. Additionally, engineering the rhizosphere with plant growth-promoting microorganisms, combined with microbial genetic modification, has demonstrated significant potential in enhancing pesticide degradation while simultaneously improving crop growth and productivity. Such integrative approaches represent a sustainable pathway towards resilient agroecosystems. This review synthesises current knowledge on the impacts of pesticides on crop physiology and metabolism, explores conventional and advanced microbe-mediated degradation strategies, and highlights the role of microbial engineering and consortia-based systems. Furthermore, it discusses emerging technologies, environmental and economic benefits, and recent patentable innovations, underscoring their relevance for sustainable agriculture and ecological restoration.}, }
@article {pmid41809465, year = {2026}, author = {Suarez, M and Martínez, R and González-Martínez, F and Torres, AM and Mateo, J}, title = {Artificial intelligence and digital transformation of gastroenterology and hepatology: A critical review of clinical applications and future challenges.}, journal = {World journal of hepatology}, volume = {18}, number = {2}, pages = {114834}, pmid = {41809465}, issn = {1948-5182}, abstract = {Artificial intelligence (AI) is reshaping modern medicine, and gastroenterology and hepatology are among the specialties where its impact is becoming increasingly evident. AI has demonstrated the ability to process and analyze large amounts of clinical, radiological, endoscopic, and multi-omics data, offering unprecedented opportunities to enhance diagnostic accuracy, optimize therapeutic decision-making, and reduce variability in clinical practice. In endoscopy, computer-aided detection and diagnosis systems have shown consistent improvements in adenoma detection rates and real-time polyp characterization, while in hepatology, machine learning models outperform traditional scores for non-invasive assessment of liver fibrosis. Furthermore, multimodal approaches integrating genomics, microbiome, and imaging data are paving the way for precision medicine in inflammatory bowel disease and other complex digestive conditions. Despite these promising advances, significant barriers remain. The quality and heterogeneity of training data, the lack of rigorous external validation, and the opaque "black box" nature of many algorithms limit their clinical reliability. Ethical challenges, including accountability in case of diagnostic errors, protection of patient privacy, cost, and equitable access, also need to be addressed. This narrative review summarizes the current applications of AI in gastroenterology and hepatology, critically examines methodological and ethical challenges, and outlines future perspectives. Responsible, transparent, and equitable implementation will be essential for AI to transition from an emerging promise to a consolidated tool that improves outcomes and advances personalized digestive care.}, }
@article {pmid41809456, year = {2026}, author = {Salamon, D and Krawczyk, A and Zapała, B and Duplaga, M and Kowalska-Duplaga, K and Gosiewski, T}, title = {Gut bacterial and fungal signatures in relation to human leukocyte antigen-DQ2/DQ8 in children with celiac disease and siblings.}, journal = {World journal of gastroenterology}, volume = {32}, number = {10}, pages = {116128}, pmid = {41809456}, issn = {2219-2840}, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/immunology/genetics ; *Celiac Disease/microbiology/immunology/genetics ; Male ; Female ; Adolescent ; *HLA-DQ Antigens/genetics/immunology ; Siblings ; Child, Preschool ; Feces/microbiology ; Genetic Predisposition to Disease ; Case-Control Studies ; *Fungi/isolation &amp; purification/genetics ; *Bacteria/isolation &amp; purification/genetics/classification ; Infant ; Mycobiome/immunology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The presence of human leukocyte antigen (HLA)-DQ2 and/or HLA-DQ8 alleles is necessary but not sufficient for the development of celiac disease (CeD). This suggests that additional environmental and biological factors, including bacteria and, above all, the still rarely studied fungal gut microbiota, play key roles in disease onset and progression.<br><br>AIM: To characterize and compare the intestinal bacteriobiota and mycobiota profiles of children with newly diagnosed CeD and their unaffected siblings, in comparison with a healthy control group.<br><br>METHODS: The study included children and adolescents aged 1 to 18 years. Participants were divided into three groups: (1) 14 patients with newly diagnosed CeD; (2) 16 asymptomatic siblings of CeD patients; and (3) 19 healthy children (control group). Stool samples were collected from all eligible participants. Next-generation sequencing was performed, followed by analysis of the relationship between the gut microbiota and genetic predisposition to CeD, with attention to the HLA DQ2/8 alleles.<br><br>RESULTS: Regarding alpha diversity, the CeD and sibling groups differed significantly from the control group (bacteria), and the CeD group differed from siblings (fungi). Significant dissimilarities in beta diversity were observed between siblings and both CeD and control groups. In comparisons between CeD group and their siblings, 13 indicator bacterial species were identified, whereas in comparisons between the CeD group and their siblings and controls, 8 indicator fungal species were detected. No significant correlation was found between bacterial species and the presence of the HLA DQ2.5 allele, or between fungal species and HLA DQ2.2. A strong (r = 0.8-0.9) positive relationship was found between Subdoligranulum variabile and several bacterial species. A moderate (r = 0.4-0.7) positive correlation was observed between the fungal species Microidium phyllanthi and Bifidobacterium longum, Clostridium leptum and Romboutsia timonensis.<br><br>CONCLUSION: While DQ2.5 plays a central role in disease pathogenesis, it appears to have less direct influence on microbial composition. The distinct fungal signatures observed in siblings may serve as early indicators of risk and warrant further investigation.}, }
@article {pmid41809269, year = {2026}, author = {Pei, J and Chen, L and Pushparaj, R and Huang, P and Pan, G and Sun, C and Gao, X and Zhang, L and Manirujjaman, M and Huang, CK and Ting, PS and Deng, Z and Chen, S and Zhang, X and Vatsalya, V and McClain, CJ and Feng, W}, title = {High-dose taurine supplementation exacerbates alcohol-associated liver disease by inducing gut microbiota dysbiosis and bile acid dysregulation in mice.}, journal = {eGastroenterology}, volume = {4}, number = {1}, pages = {e100321}, pmid = {41809269}, issn = {2976-7296}, abstract = {BACKGROUND: β-aminoethanesulfonic acid (taurine) is a conditionally essential amino acid that plays critical roles in bile acid (BA) conjugation, antioxidative defence and metabolic regulation. Previous studies showed that faecal taurine level was reduced in patients with alcohol-associated liver disease (ALD), suggesting that taurine supplementation may have beneficial effects. This study aimed to determine whether oral taurine supplementation prevents the development of ALD in mice and to elucidate the underlying mechanisms.<br><br>METHODS: A total of 8-week-old male mice were subjected to a chronic-plus-binge ALD model. Taurine was administered orally via the diet for ten days before and during ethanol exposure. Faecal 16S ribosomal RNA metagenomic analysis, liver RNA sequencing and BA profiling were performed.<br><br>RESULTS: High-dose taurine supplementation (3&#x2009;g/kg body weight/day) was associated with worsened ethanol-induced liver injury, as indicated by increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, hepatic steatosis, apoptosis and inflammation. At the molecular level, high-dose taurine treatment was associated with reduced Cpt1a expression, altered expression of genes involved in fatty acid &#x3b2;-oxidation and lipogenic gene Fasn, and decreased expression of Baat, accompanied by changes in taurine-conjugated BA profiles. These alterations were accompanied by changes in BA composition and intestinal FXR-associated gene expression. Taurine supplementation was also associated with shifts in gut microbial composition, including enrichment of hydrogen sulfide-producing bacteria, increased microbial H2S production, impaired intestinal barrier-related parameters and increased bacterial translocation to the liver, paralleling enhanced hepatic inflammatory responses. In contrast, low-dose taurine supplementation (0.2&#x2009;g/kg body weight/day) was associated with improved liver phenotypes, including reduced steatosis, lower serum ALT and AST levels, decreased Fasn expression and enhanced BA conjugation. Collectively, these results indicate a dose-dependent association between taurine supplementation and ALD-related outcomes.<br><br>CONCLUSIONS: Our findings suggest that high-dose taurine supplementation is associated with unfavourable alterations in gut microbiota composition, intestinal barrier integrity, BA metabolism and hepatic taurine-related pathways in ALD, coinciding with exacerbated liver injury. In contrast, low-dose taurine supplementation was associated with improved hepatic outcomes. These results highlight the importance of dose considerations in taurine supplementation and support the concept that taurine may exert divergent effects on ALD depending on the administered dose.}, }
@article {pmid41809178, year = {2026}, author = {Mundhra, SK and Kochhar, R}, title = {Methodological insights into fecal microbiota transplantation: Dissecting key approaches for success.}, journal = {World journal of methodology}, volume = {16}, number = {1}, pages = {108875}, pmid = {41809178}, issn = {2222-0682}, abstract = {Fecal microbiota transplantation (FMT) has emerged as a revolutionary treatment strategy for restoring gut microbiota in recurrent Clostridioides difficile infection and has also been explored across a broader range of dysbiosis-related diseases such as inflammatory bowel disease where it has demonstrated promising results and potential therapeutic benefits. The success of FMT largely depends on the careful implementation of best practices, which include selecting appropriate donors, preparing the stool properly, and choosing the right delivery methods. This mini-review explores the evolution of FMT methodologies, including donor screening protocols, advances in stool preparation, and innovations in administration routes. We also discuss emerging approaches, such as synthetic microbiota and microbiome engineering, alongside the challenges and future directions for standardizing FMT. These methodological advancements aim to enhance safety, efficacy, and accessibility of FMT, establishing it as a key player in microbiome-based therapies.}, }
@article {pmid41809042, year = {2026}, author = {Ratsika, A and Bergmann, CA and Valderrama, B and Bastiaanssen, TFS and Sharvin, BL and Renes, IB and Knol, J and Gunnigle, E and Clarke, G and Cryan, JF}, title = {Early-life microbiota disruption-induced deficits in the social brain are sensitive to diet.}, journal = {iScience}, volume = {29}, number = {3}, pages = {114968}, pmid = {41809042}, issn = {2589-0042}, abstract = {Diet is one of the major modulators of the microbiota-gut-brain axis across the lifespan. Milk bioactive components, including human milk oligosaccharides such as fucosyllactose and sialyllactose, and prebiotics, including GOS and FOS, promote the viability of commensal bacteria, fortify the intestinal barrier, and improve cognitive development. Here, we investigate the ability of these dietary components alone or in combination to counter the behavioral and physiological effects of early-life microbiota depletion via broad-spectrum antibiotics in mice. Microbiota depletion impaired social recognition in juvenile mice, which was reversed by supplementation with human milk oligosaccharides, GOS/FOS, and their combination. Transcriptomic analysis in brain areas linked to social memory (amygdala and prefrontal cortex), revealed that pathways for central nervous system development, learning, learning and memory are sensitive only to the combined supplementation. Together, our data show that prebiotics and milk bioactive components exert beneficial effects on the host by reversing microbiota depletion-related deficits on the brain and behavior.}, }
@article {pmid41809000, year = {2026}, author = {Pishchany, G and Fryling, KE and Vasukuttan, V and Shin, YH and Mortimer, TD and Grad, YH and Clardy, J}, title = {Aerocavin is an antibiotic with potent and specific anti-Neisserial activity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.23.707490}, pmid = {41809000}, issn = {2692-8205}, abstract = {Gonorrhea, caused by N. gonorrhoeae , is a widespread sexually transmitted disease that is becoming resistant to all currently used antibiotics. Therefore, new therapeutics against gonorrhea are desperately needed. Here, we show that a natural product - aerocavin, is highly potent and specific against Neisseria . Aerocavin accumulates in N. gonorrhoeae at high levels and inhibits bacterial RNA polymerase (RNAP) by binding the switch region. Aerocavin resistance mutations evolve in N. gonorrhoeae at a low rate and are absent in clinical isolates. Previously overlooked narrow-spectrum antimicrobials like aerocavin may enable microbiome-sparing treatments of gonorrhea.}, }
@article {pmid41808841, year = {2026}, author = {Huo, T and Huang, X and Liao, J and Zhang, H and Hu, L and Xie, M}, title = {The bidirectional effects and mechanisms of the oral and gut microbiomes: a narrative review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1697413}, pmid = {41808841}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Mouth/microbiology/immunology ; Dysbiosis/immunology/microbiology ; Animals ; *Microbiota ; }, abstract = {Among the microbial ecosystems of the human body, the gut and oral microbiota constitute the two largest communities, collectively harboring thousands of bacteria, fungi, and viruses. Under physiological conditions, these microbiotas maintain internal homeostasis and stability, thereby protecting the host against pathogenic colonization. However, when pathogens such as Porphyromonas gingivalis translocate from the oral cavity to the gut, disruption of gut microbial homeostasis may occur, increasing the risk of disease development. Potential mechanisms underlying this association include the establishment of new symbiotic relationships, the disruption of the intestinal barrier, the activation or suppression of inflammatory cells-particularly the balance between T helper 17 (Th17) cells and regulatory T cells (Tregs)-and the induction of systemic inflammation. Conversely, gut microbiota dysbiosis, as observed in patients with inflammatory bowel disease, irritable bowel syndrome (IBS), or colorectal cancer, is also associated with alterations in the composition and diversity of the oral microbiota. Factors such as immune cell migration, malnutrition, and taste disturbances may contribute to oral microbial imbalance. In this review, we summarize the bidirectional influences on the composition and diversity of the oral and gut microbiomes and propose potential mechanisms underlying their interactions. A deeper understanding of these processes will enhance our knowledge of microbiota-host interactions and systemic health, and may shed light on the prevention and treatment of systemic diseases related to oral and gut microbiota dysbiosis.}, }
@article {pmid41808840, year = {2026}, author = {Wang, X and Xiong, D and Cui, S and Duan, B and Ding, G and Huang, Y and Wang, Q}, title = {Artificial intelligence-enabled multi-omics biomarkers for immune checkpoint blockade: mechanisms, predictive modeling, and clinical translation.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1732079}, pmid = {41808840}, issn = {1664-3224}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Artificial Intelligence ; *Biomarkers, Tumor/genetics ; *Neoplasms/drug therapy/immunology/metabolism/genetics ; Genomics/methods ; Translational Research, Biomedical ; Machine Learning ; Metabolomics ; Proteomics ; Animals ; Multiomics ; }, abstract = {Immune checkpoint inhibitors (ICIs) have transformed oncology, yet durable benefit remains confined to a minority of patients, revealing the limitations of single biomarkers such as PD-L1 expression, tumor mutational burden, and microsatellite instability. Multi-omics profiling, spanning genomics, transcriptomics, epigenomics, proteomics, metabolomics, microbiomics, and imaging-derived radiomics/pathomics, enables a systems-level interrogation of tumor-immune interactions. It captures lineage plasticity, antigen-presentation defects, metabolic and epigenetic suppression, stromal remodeling, and microbiome-driven immune tone that collectively shape ICI sensitivity and resistance. Artificial intelligence (AI) and machine learning are increasingly indispensable for fusing these heterogeneous, high-dimensional data into deployable composite predictors and mechanistically grounded signatures, while explainability approaches (e.g., SHAP, Grad-CAM) help link model outputs to actionable biology. This review synthesizes emerging AI-enabled multi-omics biomarkers across major tumor types, highlights clinical applications in response stratification, combination-therapy selection, and longitudinal monitoring, and discusses key translational barriers, including cohort and platform heterogeneity, limited prospective validation, privacy constraints, model drift, and equity. We conclude by outlining future directions in single-cell and spatial multi-omics integration, federated learning, and generative modeling to accelerate robust, generalizable precision immunotherapy. Pragmatic implementation will require harmonized pre-analytics, clinically feasible assays or distilled panels, and decision-support interfaces that communicate calibrated uncertainty to oncologists.}, }
@article {pmid41808832, year = {2026}, author = {Zhou, S and Tang, J and Wang, Y}, title = {Trichuris suis ova in inflammatory bowel disease-clinical challenges and translational pathways.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1611690}, pmid = {41808832}, issn = {1664-3224}, mesh = {Animals ; *Trichuris/immunology ; Humans ; *Inflammatory Bowel Diseases/therapy/immunology ; Translational Research, Biomedical ; *Ovum/immunology ; Therapy with Helminths ; Gastrointestinal Microbiome ; }, abstract = {This article reviews the mechanisms and clinical trial findings of Trichuris suis ova (TSO) for inflammatory bowel disease (IBD).The results show TSO may exert potential effects on IBD via multiple pathways, yet no significant efficacy has been confirmed in clinical trials. Given its promising anti-inflammatory properties, further research is warranted. However, many knowledge gaps still exist in this field. Future trials should standardize study designs. Considering IBD complexity, priority should be given to precision medicine, with identifying TSO therapy's target populations as a core step. Additionally, enhanced safety monitoring is essential to fully assess short- and long-term risks of TSO treatment. Given the inherent uncertainties of live biotherapeutics, multi-omics and gene-editing tools should be adopted to clarify TSO's anti-inflammatory mechanisms and achieve its "artificial domestication", enabling stable therapeutic performance across diverse clinical settings. The breakthroughs will deepen insights into IBD pathogenesis and advance microbiome-based interventions from empirical practice to the precision medicine era.}, }
@article {pmid41808728, year = {2026}, author = {Pereira, MH and Tyagi, S and Mohanty, A and Garg, S and Kumar, A}, title = {Metagenomic studies reveal diverse microbial community in the developmental stages of highly adaptable malarial vector Anopheles stephensi liston.}, journal = {3 Biotech}, volume = {16}, number = {4}, pages = {124}, pmid = {41808728}, issn = {2190-572X}, abstract = {UNLABELLED: Anopheles stephensi, a highly adaptable malaria vector species, continues to expand its range from South Asia to Sub-Saharan Africa, posing a serious global public health concern. In India, it serves as the principal urban vector of both Plasmodium falciparum and P. vivax. Conventional control measures reliant on chemical insecticides have raised issues of resistance, highlighting the need for alternative strategies such as microbiota-mediated vector control. This study aimed to test the hypothesis that a subset of bacterial taxa persist across developmental stages of An. stephensi, representing potential candidates for transstadial transmission and future paratransgenic manipulation. Using both culture-based data and next-generation sequencing (NGS) approaches targeting the 16 S rRNA gene (V3-V4 region), we characterized bacterial communities from breeding water, larvae, pupae, and adult mosquitoes (male and female) collected in Goa, India. Across all developmental stages, Proteobacteria and Firmicutes were the dominant phyla, while 15 bacterial genera formed the putative core microbiome shared by ≥ 80% of stages at ≥ 0.1% abundance. Among these, Pseudomonas (adult males: 11.5%, pupae: 3.2%), Exiguobacterium, Acinetobacter, Psychrobacter, and Asticcacaulis were consistently detected, together contributing approximately 30% of total microbial composition. Alpha diversity indices indicated higher richness and evenness in pupae and adults than in larvae, suggesting microbial enrichment during metamorphosis. Beta diversity and PCoA analyses clustered pupal and adult stages distinctly from larvae and breeding water, confirming selective microbial retention through development. These findings reveal that An. stephensi harbors a stable, stage-spanning core microbiome dominated by metabolically versatile genera with potential for transstadial persistence. The dominance of Pseudomonas across life stages supports its candidacy for paratransgenic applications aimed at disrupting malaria transmission. This work provides the first integrated culture-NGS baseline of An. stephensi microbiota from India, offering essential insight for microbiome-based vector control strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04739-6.}, }
@article {pmid41808561, year = {2026}, author = {Ram, S and Corbin, M and 't Mannetje, A and Douwes, J and Kvalsvig, A and Eng, A}, title = {Antibiotic Exposure in Early Life and Risk of Type 1 Diabetes: A Meta-Analysis.}, journal = {Diabetes, obesity &amp; metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1111/dom.70636}, pmid = {41808561}, issn = {1463-1326}, support = {HD21/053//Health Research Council of New Zealand/ ; }, abstract = {BACKGROUND: Early-life antibiotic use may increase the risk of childhood type 1 diabetes (T1D), potentially through gut microbiota dysbiosis and associated effects on immune development. This meta-analysis evaluated associations between early-life antibiotic use and T1D.<br><br>METHODS: A systematic search of PubMed, MEDLINE, Scopus and Web of Science was conducted up to June 2025, which focused on studies reporting associations between antibiotic use in the pre- and postnatal periods and childhood T1D. Pooled effect sizes were assessed using random effects models separately for prenatal and postnatal antibiotic exposure, with subgroup analyses by antibiotic course, class and spectrum. Study quality was assessed using the Newcastle-Ottawa Quality Assessment Scale (NOS).<br><br>RESULTS: The analysis included 20 studies (11 cohort, 9 case-control), encompassing >&#x2009;1.5 million participants for prenatal and over 4 million for postnatal antibiotic exposure. A pooled effect size of 1.05 (95% CI 0.98-1.11) for prenatal exposure was found. Further analysis by antibiotic spectrum yielded no significant associations, likely due to the small number of studies. For postnatal antibiotic exposure, a pooled effect size of 1.07 (95% CI 1.01-1.14) was found, with estimates increasing with increased number of antibiotic courses: &#x2265;&#x2009;2 courses, 1.11, 95% CI 1.02-1.20; and &#x2265;&#x2009;5 courses, 1.14, 95% CI 1.00-1.30. Associations were stronger for broad-spectrum (1.13, 95% CI 1.03-1.23) than for narrow-spectrum antibiotics (1.08, 95% CI 0.93-1.26) but no significant associations were observed by antibiotic class. The impact of mode of obstetric delivery remained inconclusive across studies. The quality of the evidence was high.<br><br>CONCLUSION: This meta-analysis suggests that early-life antibiotic use is associated with an increased risk of T1D, particularly with repeated courses and broad-spectrum agents. However, confidence in these findings is constrained by variability in study design and exposure definitions, as well as the potential for confounding by indication. While the observed associations are modest, they highlight the importance of judicious antibiotic prescribing in early life. Further large, well-designed prospective cohort studies are needed to clarify causality and better disentangle the effects of antibiotics from those of underlying infections.}, }
@article {pmid41808525, year = {2026}, author = {Jiménez, DJ and Rosado, AS}, title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70272}, pmid = {41808525}, issn = {1462-2920}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; }, mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; }, abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.}, }
@article {pmid41808437, year = {2026}, author = {de Beer, JC and Alayande, KA and Pirk, CWW and Adeleke, RA and Sole, CL}, title = {Dietary Specialisation Shapes Gut Bacterial Diversity in Dung Beetles: Insights From Coprophagy to Millipede Carnivory.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70317}, pmid = {41808437}, issn = {1758-2229}, support = {98696//National Research Foundation of South Africa/ ; SRUG220326856//National Research Foundation of South Africa/ ; //South Africa Sweden University Forum/ ; }, mesh = {Animals ; *Coleoptera/microbiology/physiology/classification ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Diet ; Phylogeny ; *Arthropods/physiology ; Biodiversity ; Carnivory ; Coprophagia ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Dung beetles are ecosystem engineers, providing ecosystem services like nutrient cycling, waste degradation and parasite suppression. Their gut microbiome is essential for exploiting specialised diets, yet the eco-evolutionary factors driving microbial composition across diverse feeding strategies remain ambiguous. Here, we show that diet strongly influences gut bacterial composition across seven dung beetle species specialising in coprophagy, necrophagy, detritophagy, fungivory and carnivory. Most dietary specialisations grouped separately, though fungivores clustered with carrion and millipede feeders. The millipede-feeding species, Sceliages brittoni and S. hippias, hosted the most distinct and least diverse gut microbiomes. Taxonomically, differences were driven by distinct marker taxa, many of which are consistently isolated across taxonomic orders with similar diets. For example, the indicative bacterial species I. indica has been identified in various flesh-feeding insect taxa. Crucially, this pattern of shared bacterial communities suggests that diet is a dominant structuring factor which promotes community convergence regardless of host phylogeny. This study highlights the role of diet in shaping the dung beetle gut microbiome and provides the first characterisation of the gut microbiota in millipede-feeding dung beetles. Our findings underscore the critical role of diet, laying the foundation for functional studies into the eco-evolutionary significance of these host-microbe interactions.}, }
@article {pmid41808169, year = {2026}, author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J}, title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.}, journal = {Microbial cell factories}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12934-026-02977-0}, pmid = {41808169}, issn = {1475-2859}, support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; }, }
@article {pmid41808145, year = {2026}, author = {Bu, D and Yan, J and Yang, W and Zhang, X and Li, Q}, title = {Ensemble test for microbiome data.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02367-z}, pmid = {41808145}, issn = {2049-2618}, support = {12401359//National Natural Science Foundation of China/ ; 12325110//National Natural Science Foundation of China/ ; QNTD202303//Youth Academic Innovation Team Construction Project of Capital University of Economics and Business/ ; GZC20241867//Postdoctoral Fellowship Program of CPSF/ ; YSBR-034//CAS Project for Young Scientists in Basic Research/ ; }, abstract = {MOTIVATION: Recent research has revealed strong correlations between the human microbiome and various diseases. However, statistical analysis of microbiome data remains challenging due to its inherent sparsity and high dimensionality. PERMANOVA (Permutational multivariate analysis of variance using distance matrices) has been extensively employed to test the association between microbiome data and biological features. Its non-parametric nature makes it appealing, as it does not impose restrictions on data dimension or distribution. Despite its merits, several limitations have restricted its further application.<br><br>RESULTS: This paper introduces E-MANOVA (Ensemble multivariate analysis of variance using distance matrices), a method designed to address these limitations. Traditional PERMANOVA lacks consistent robustness across different distance metrics and association signals, which can lead to power reduction in specific scenarios. Leveraging the idea of ensemble learning, we construct base tests by taking the similarity matrix to the rth power and then combine these tests to build a final ensemble test. Our resulting test statistic exhibits high power and robustness compared to other existing methods. Furthermore, we employ direct moment approximation and the Pearson type III distribution to approximate the permutation null distribution, completely avoiding the computationally intensive permutation procedure. Finally, we utilize the Cauchy combination method to aggregate p-values from multiple distances, eliminating the need to pre-specify a single distance measure before analysis.<br><br>CONCLUSIONS: Our extensive simulations demonstrate that the proposed method outperforms existing methods across various situations. Further analysis of real data from cigarette smokers and curated microbiome data shows that our proposed method identifies the highest number of significant associations among all competing methods. Video Abstract.}, }
@article {pmid41808137, year = {2026}, author = {Dothard, MI and Caboni, M and Norment, D and Sigmund, N and Allard, SM and Gilbert, JA and Gavrish, E and Al-Ghalith, G and Der-Avakian, A and Strandwitz, P}, title = {A human-derived Bacteroides strain attenuates depressive-like behavior in a rat model of social defeat-induced stress.}, journal = {BMC medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12916-026-04787-y}, pmid = {41808137}, issn = {1741-7015}, support = {R44DK120181//National Institute of Health Small Business Innovation Research/ ; DGE-2038238//National Science Foundation Graduate Research Fellowship Program/ ; NNX16AO69A//Translational Research Institute for Space Health - Space Health Ingress Program (NASA)/ ; }, abstract = {BACKGROUND: The gut microbiome has been linked to mood disorders via communication along the gut-brain axis. We previously found levels of fecal Bacteroides were inversely associated with brain signatures of depression in the prefrontal cortex of human subjects. Bacteroides are important human commensals, playing a keystone role in regulating the immune system and producing bioactive metabolites, like the neurotransmitter gamma-aminobutyric acid and B vitamins.<br><br>METHODS: To better understand the link between Bacteroides and depression - and test a candidate novel next-generation probiotic - we administered a human-derived Bacteroides salyersiae strain, HB32, orally in rats that were subjected to the repeated social defeat model of stress-induced depression. The fecal microbiome and the prefrontal cortex transcriptome were then profiled for intervention-induced alterations.<br><br>RESULTS: Orally delivered B. salyersiae HB32 reduced depressive-like behavior in male rats comparable to the drug ketamine, independently of the strain being administered in its viable or inactivated (iHB32) form. Mechanistically, we observed that stress-induced anhedonia required the vagus nerve for its phenotype to develop, suggesting crosstalk between the gut and the brain. In support of this, we found HB32 and iHB32, but not ketamine, rescued stress-induced differential expression patterns in the prefrontal cortex, including those related to serotonin signaling and oxidative stress. In the gut, prolonged exposure to social defeat led to broad shifts in the composition of the gut microbiome, with a predominant reduction of the endogenous Bacteroides. Administration of HB32, iHB32, and ketamine attenuated the impact of stress on the microbiome, and intake of live HB32 resulted in a significant increase of the B. salyersiae species in the fecal microbiome.<br><br>CONCLUSIONS: Depressive-like behavior in male rats induced by repeated social defeat requires vagal signaling, suggesting gut-brain-axis crosstalk. In animals with an intact vagus nerve, oral administration of viable or inactivated B. salyersiae HB32 reversed behavioral changes induced by chronic stress at levels comparable to ketamine. Additionally, supplementation of HB32 and iHB32 was associated with attenuation of stress-related microbiome and prefrontal cortex transcriptional changes.}, }
@article {pmid41808045, year = {2026}, author = {Khogali, R and Bastos, A and Khamis, FM and Getange, D and Kabii, J and Yuko, E and Masiga, D and Villinger, J}, title = {Comparative tissue-specific microbiome analyses identify keystone endosymbionts shaping pathogen interactions in dromedary camel ticks.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04864-5}, pmid = {41808045}, issn = {1471-2180}, }
@article {pmid41807945, year = {2026}, author = {Morawski, BM and Morton, ER and Yunus, M and Muñoz-Zanzi, C and Mejia, R and Blekhman, R and Boulware, DR and Lofgren, SM}, title = {Bacterial fecal microbiome composition associated with HIV stage among rural and peri-urban adults living with HIV in Uganda.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12992-6}, pmid = {41807945}, issn = {1471-2334}, support = {Dissertation Funding//Graduate School, University of Minnesota/ ; }, }
@article {pmid41807808, year = {2026}, author = {Deng, C and Shang, X and Zhang, W and Liu, J and Zhang, H and Li, Z}, title = {Global research trends and hotspots in targeted therapy for IgA nephropathy: a bibliometric and visualization analysis (1999-2025).}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {41807808}, issn = {1432-1912}, abstract = {Targeted therapy has emerged as a promising precision medicine strategy for immunoglobulin A nephropathy (IgAN) through the modulation of specific pathogenic pathways. Although research in this area has accelerated, the literature remains scattered, and no bibliometric study has mapped its global knowledge structure or evolving hotspots. We conducted a bibliometric and visualization analysis of 678 publications indexed in the Web of Science Core Collection (1999-2025). CiteSpace 6.4R1, VOSviewer 1.6.20, and the R‑based bibliometric package were used to assess publication and citation trends; identify prolific countries, institutions, authors, and journals; and generate co‑authorship, co‑citation, and keyword co‑occurrence networks. Research frontiers were explored through thematic evolution mapping and keyword burst detection. Annual publications increased notably after 2015, indicating a shift from supportive care to molecularly targeted interventions. China and the United States produce over 60% of the global output, with expanding collaborations. The core themes clustered into three domains: complement inhibition (e.g., C5 blockade), B‑cell-directed therapy (including BAFF/APRIL modulation), and mucosal immune regulation. The gut-immune axis, particularly microbiome modulation, has emerged as a new frontier. Notably, recent trends highlight a growing interest in non-invasive biomarkers (e.g., urinary targets) to guide patient stratification, although clinical translation remains a challenge. This study delineates a rapidly evolving landscape of IgAN-targeted therapy. Precision approaches focusing on complement blockade, B‑cell pathways, mucosal immunity, and microbiome modulation hold substantial potential. While bibliometric data reflect a vibrant academic interest, future efforts should increasingly focus on translating candidate discoveries into clinical validation. Priority should be given to biomarker‑driven stratification and integrated diagnostic-therapeutic frameworks to accelerate translation and improve outcomes.}, }
@article {pmid41807803, year = {2026}, author = {Zhu, Y and Gao, W and Cheng, M and Li, X and Cai, K and Chen, L and Chu, H}, title = {Harnessing the power of the gut microbiome: a review of supplementation diagnosis and therapy for liver cirrhosis.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-026-06098-0}, pmid = {41807803}, issn = {1420-9071}, support = {No.&#xa0;2022YFA1305600//Key Technologies Research and Development Program/ ; No.&#xa0;82470584//National Natural Science Foundation of China/ ; No. 82000561//National Natural Science Foundation of China/ ; No.&#xa0;82400652//National Natural Science Foundation of China/ ; No. 82170678//National Natural Science Foundation of China/ ; No.&#xa0;2021xhyn005//Science Foundation of Union Hospital/ ; }, }
@article {pmid41807675, year = {2026}, author = {Karlsen, C and Meriac, A and Ytteborg, E and Johansson, GS and Timmerhaus, G and Alvestad, R and Noble, C and Kolarevic, J}, title = {Intestinal morphology and host‑ and system‑associated microbiome dynamics during short‑term fasting and refeeding of Atlantic salmon in recirculating aquaculture systems.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42939-5}, pmid = {41807675}, issn = {2045-2322}, }
@article {pmid41807560, year = {2026}, author = {Conroy, G}, title = {Forget SkinTok: the real science of skincare and why it matters for your health.}, journal = {Nature}, volume = {651}, number = {8105}, pages = {294-296}, pmid = {41807560}, issn = {1476-4687}, }
@article {pmid41807473, year = {2026}, author = {Cheng, L and Li, Y and Zhang, Y and Qin, C and Yang, L and Yan, X and Nie, G}, title = {Cetobacterium somerae as a microbial correlate of improved muscle quality after intestinal microbiota transplantation in Yellow River carp (Cyprinus carpio).}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00955-3}, pmid = {41807473}, issn = {2055-5008}, support = {U22A20532//National Natural Science Foundation of China/ ; HARS-22-16-S//Special Fund for Henan Agriculture Research System/ ; }, abstract = {Dietary faba bean enhances fish muscle quality but concurrently reduces growth performance. The gut microbiota critically modulates muscle growth and quality. However, the specific microbial taxa, metabolites, and regulatory mechanisms responsible remain to be elucidated. This study established a differential gut microbiota model in faba-bean-fed Yellow River carp (Cyprinus carpio), used whole-intestinal microbiota transplantation (WIMT) to directly test its effect on muscle quality, and supplemented the key bacterium and its metabolite to confirm their contribution. After a 6-week faba bean diet, growth performance declined, whereas muscle texture improved (P < 0.05). This improvement was concomitant with a higher abundance of the genera Aeromonas and Cetobacterium in the gut. Following 8 weeks of daily WIMT from faba-bean-fed donors, Yellow River carp maintained normal growth performance (P > 0.05) and simultaneously showed improved muscle texture, characterized by more small-diameter fibers, lower fat content, and higher collagen levels (P < 0.05), recapitulating the donor's key muscle phenotype. Meanwhile, WIMT reshaped the gut microbiome composition and its metabolic profile, and the marker species Cetobacterium somerae and its metabolite acetic acid showed associations with improvements in muscle quality. Further in vivo validation indicated that C. somerae reduced fat deposition and improved muscle texture, an effect possibly linked to activation of the AMPK-PGC-1α-FoxO pathway, and its metabolite acetic acid mirrored these changes. This study reveals the direct impact of gut microbiota on muscle quality through WIMT in Yellow River carp, provides novel evidence of the fish gut-muscle axis, and offers a scientific basis for improving muscle quality.}, }
@article {pmid41807415, year = {2026}, author = {Li, DZ and Li, Y and Wang, X and Feng, Y and Liu, Y and Yang, C and Zhang, W and Wen, X and Liu, Z and Yin, W and Zhang, X}, title = {An antifungal effector from a plant-parasitic nematode modulates host fungal community composition and supports ecological fitness.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00954-4}, pmid = {41807415}, issn = {2055-5008}, support = {2022ZD04016//STI 2030-Major Projects/ ; CAFYBB2020SZ008//Fundamental Research Funds of Research Institute of Forest New Technology, CAF/ ; NSFC 3237141290//National Natural Science Foundation of China/ ; }, abstract = {Host-associated microbiomes are increasingly recognized as key determinants of plant health, disease development, and ecosystem functioning. Plant pathogens, especially fungal pathogens, have been reported to secrete antimicrobial effectors to modulate the host microbiota and promote colonization. Plant-parasitic nematodes (PPNs) could also modulate host microbial communities, but the processes involved remain to be clarified. Here, we identify a secreted antifungal effector, BxylTLP6, from Bursaphelenchus xylophilus, the causal agent of pine wilt disease. BxylTLP6 degrades fungal cell walls and inhibits multiple plant-associated fungi, while the released oligoglucans serve as food-derived cues that guide nematode foraging toward fungal resources. In planta, silencing Bxyltlp6 significantly delayed disease progression. ITS-based mycobiome profiling revealed that BxylTLP6 modulates the pine endophytic fungal community by promoting Ascomycota, suppressing Basidiomycota, inhibiting wood-decaying fungi, and enriching pathogenic or parasitic taxa. These shifts are associated with enhanced nematode survival and pathogenicity. Our findings support the view that a TLP effector can modulate behavior and influence the host fungal microbiome, shedding light on how PPN may manipulate microbial environments to enhance their fitness.}, }
@article {pmid41807411, year = {2026}, author = {Zhang, W and Song, S and Zhang, Y and Pan, Y and Hu, D and Wang, Y}, title = {Emerging strategies in senotherapeutics: from broad-spectrum senolysis to precision reprogramming.}, journal = {npj aging}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41514-026-00355-z}, pmid = {41807411}, issn = {2731-6068}, support = {82172210//National Natural Science Foundation of China/ ; XJZT24CY38//Xijing Hospital Advancement Program/ ; }, abstract = {Cellular senescence, originally described as a finite proliferative arrest in cultured somatic cells, has since been recognized as a central mechanism underlying aging and the development of age-associated disorders. The progressive accumulation of senescent cells (SnCs) promotes chronic inflammation through the senescence-associated secretory phenotype (SASP) and circumvents immune-mediated clearance by upregulating pro-survival and immune checkpoint pathways. Early "first-generation" senolytics, including navitoclax (ABT-263) and the dasatinib-quercetin (D + Q) combination, provided proof-of-concept that selective removal of SnCs can alleviate certain fibrotic, metabolic, and cardiovascular pathologies in preclinical studies. However, these agents exhibited notable drawbacks, such as dose-dependent thrombocytopenia, variable therapeutic efficacy, and the emergence of resistance mechanisms. Consequently, current research has shifted toward precision senotherapy, though significant translational challenges remain. This review synthesizes three next-generation strategies developed to address limitations of early senolytic agents. (1) Immune-based senolysis: This approach applies immuno-oncology principles to counter immune evasion of SnCs. Strategies include blocking immunosuppressive ligands such as GD3 ganglioside, engineering chimeric antigen receptor (CAR) T cells to target senescence-specific surface markers like urokinase-type plasminogen activator receptor (uPAR), and exploiting metabolic vulnerabilities (e.g., glutaminolysis and ferroptosis) to sensitize SnCs to immune-mediated clearance. (2) Tissue-precision proteolysis-targeting chimeras (PROTACs): These agents recruit organ- or tissue-specific E3 ligases (e.g., von Hippel-Lindau (VHL)) to selectively degrade anti-apoptotic proteins such as BCL-xL. Localized activity may reduce systemic toxicity and mitigate dose-limiting effects observed with traditional inhibitors. (3) Microbiome-epigenetic interplay: This strategy modulates the gut-liver axis to enhance senolytic efficacy. Short-chain fatty acids (SCFAs), such as butyrate, epigenetically regulate drug transporter expression and suppress the SASP, while dietary interventions may create a microenvironment favorable to senolysis. These approaches offer potentially more targeted and personalized therapeutic options but face significant challenges, including immunopathology, manufacturing complexity, off-target effects, and long-term safety concerns. The ongoing shift from broad inhibition to precision reprogramming represents a promising but preliminary step in the treatment of age-related diseases.}, }
@article {pmid41688544, year = {2026}, author = {Murakami, Y and Hosomi, R and Tanaka, G and Murakami, H and Kanto, A and Kimura, T and Imamura, Y and Yoshida, M and Fukunaga, K}, title = {Fish (Alaska Pollock) protein intake attenuates age-related short-term memory decline through gut microbiota modulation.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41688544}, issn = {2045-2322}, support = {20K21587//Japan Society for the Promotion of Science/ ; }, abstract = {UNLABELLED: Dysbiosis leads to decreased intestinal barrier function, causing systemic inflammation and possibly the development of age-related cognitive decline. In this study, we investigated the effect of an Alaska pollack protein (APP) diet on cognitive function, gut microbiota composition, intestinal barrier function, and neuroinflammation in senescence-accelerated mouse prone8 (SAMP8) and senescence-resistant AKR/J (SAMR1) mice. The APP diet produced significant improvements across multiple parameters. It enhanced glucose tolerance in both strains and prevented short-term memory decline in SAMP8 mice. Microbiome analysis revealed that APP intake promoted beneficial bacteria growth, specifically increasing Lactobacillus in SAMR1 and butyrate-producing Lachnospiraceae in SAMP8. Notably, while APP diet increased butyrate-producing bacteria in SAMP8, short-chain fatty acids (SCFAs) analysis showed increased aetate but unchanged butyrate levels, suggesting complex metabolic interactions beyond simple bacterial abundance. Moreover, the APP diet significantly suppressed neuroinflammation in SAMP8, evidenced by decreased proinflammatory cytokine expression, microglia and astrocyte activation, and attenuated demyelination in the hippocampus. These findings suggest that APP intake prevents age-related short-term memory decline through beneficial gut microbiota modulation, and reduced neuroinflammation, supporting the role of the gut-brain axis in cognitive aging.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38717-y.}, }
@article {pmid41807298, year = {2026}, author = {Huang, J and Qin, Q and Li, X and Jiang, K and Xu, J and Mao, Y and Kang, W and Gao, R and Cheng, Y and Zhao, W and Ke, J and Mou, X}, title = {Bacteroides-associated NAD[+] depletion correlates with exacerbated radiation-induced colorectal injury and impaired mucosal proliferative capacity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2641260}, doi = {10.1080/19490976.2026.2641260}, pmid = {41807298}, issn = {1949-0984}, mesh = {Animals ; Humans ; *NAD/metabolism/deficiency ; *Bacteroides/metabolism/genetics/isolation &amp; purification ; Mice ; Male ; Female ; *Intestinal Mucosa/pathology/radiation effects ; *Radiation Injuries/microbiology/pathology ; Feces/microbiology/chemistry ; Mice, Inbred C57BL ; Middle Aged ; Gastrointestinal Microbiome ; Cell Proliferation ; Aged ; Nicotinamide Mononucleotide/metabolism/administration &amp; dosage ; Fecal Microbiota Transplantation ; Colon/radiation effects/pathology ; }, abstract = {Radiation proctitis (RP) is a frequent complication of pelvic radiotherapy that compromises treatment delivery and patient quality of life, yet the factors shaping injury severity remain incompletely defined. We prospectively profiled pretreatment fecal microbiomes and metabolomes from 55 patients and stratified them by outcome into mild versus severe RP. Baseline microbial composition showed Bacteroidales enriched in severe RP and Firmicutes enriched in mild cases. Multi-omics integration highlighted nicotinate/nicotinamide pathways; severe RP was characterized by concomitant reductions in both fecal and tissue NAD[+] levels, along with an enrichment of microbial nicotinate/nicotinamide metabolism genes, primarily contributed by Bacteroides ovatus, B. xylanisolvens, and B. fragilis. In mice, fecal microbiota transplantation from severe-RP donors exacerbated radiation-induced colorectal injury and decreased colorectal NAD[+], supporting a causal role for the microbiota. Gavage with Bacteroides similarly worsened pathology and lowered NAD[+], whereas nicotinamide mononucleotide (NMN) supplementation attenuated the injury. Mechanistically, Bacteroides gavage reduced mitochondrial membrane potential, decreased the Lgr5[+] stem-cell proportion and proliferative indices, associated with Wnt pathway modulation. NMN reversed these effects in parallel with NAD[+] restoration. Together, these results identify a microbiota‒metabolite association wherein Bacteroidales enrichment is associated with NAD[+] depletion, reduced mucosal proliferative capacity, and exacerbated radiation-induced colorectal injury. The work deepens insight into RP pathogenesis and suggests a potential basis for microbiome- and metabolite-targeted approaches to attenuate severe RP.}, }
@article {pmid41807185, year = {2026}, author = {Tsuji, H and Asahara, T and Sakai, T and Kado, Y and Moriyama-Ohara, K and Takahashi, A and Date, R and Atobe, S and Ishizuka, T and Takahashi, T and Ozaki, S and Shiono, Y and Fukada, Y and Kawashima, K and Yamashiro, K and Matsumoto, S and Yamashiro, Y}, title = {Early establishment of Bifidobacterium-dominant microbiome in planned cesarean-born infants via Bifidobacterium breve strain Yakult supplementation: A randomized, double-blind, placebo-controlled, parallel-group pilot study.}, journal = {Pediatrics and neonatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pedneo.2026.02.001}, pmid = {41807185}, issn = {2212-1692}, abstract = {OBJECTIVES: To investigate the effects of Bifidobacterium breve strain Yakult (BbrY) administration immediately after birth on the microbiome of cesarean-born full-term infants with an immature microbiota at birth.<br><br>METHODS: This single-center, placebo-controlled, randomized, double-blind, parallel-group intervention study included healthy, full-term Japanese infants born via planned cesarean section. Infants were administered either BbrY or placebo for the first month of life. The primary endpoint was the early establishment of a Bifidobacterium-dominant microbiome.<br><br>RESULTS: This study included 26 infants (14 in the BbrY group and 12 in the placebo group). Compared with the placebo group, the BbrY group showed significantly increased detection rates and counts of BbrY from day three to six months post-birth, with the level and proportion of Bifidobacterium and Bifidobacteriaceae remaining elevated until one month post-birth. Total bacterial counts and total organic acid concentrations, including acetic and lactic acids, were significantly higher in the BbrY group until the sixth day of life, concomitant with a decrease in fecal pH. At nine months, the BbrY group exhibited a significantly higher body weight than the placebo group, and the Kaup index remained within the normal range at six and nine months.<br><br>CONCLUSIONS: BbrY supplementation immediately after birth facilitated the early establishment of a Bifidobacterium-dominant microbiome and contributed to intestinal acidification in cesarean-born infants, indicating BbrY administration may support normal growth patterns during infancy.}, }
@article {pmid41806989, year = {2026}, author = {Marlicz, W and Krawczyk, M and Milkiewicz, P}, title = {Rifaximin in symptomatic uncomplicated diverticular disease: a stewardship perspective following the Fiesole Consensus.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338607}, pmid = {41806989}, issn = {1468-3288}, }
@article {pmid41806837, year = {2026}, author = {Mi, K and Cao, M and Zhang, L and Zhang, Q and Zhou, W and Deng, C and Zhang, Y and Zhao, Q and Wei, Y and Liu, X and Li, F}, title = {An integrative multi-omics approach identifies microbiome alterations linked to pathological and behavioral features in autism spectrum disorder.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102655}, doi = {10.1016/j.xcrm.2026.102655}, pmid = {41806837}, issn = {2666-3791}, abstract = {This study employs a multi-omics approach to investigate the gut-brain axis in 326 children with autism spectrum disorder (ASD) and 169 typically developing (TD) controls, aged 0-10 years. By analyzing neuroimaging, gut microbiome, and plasma metabolome data, we find that microbial features could accurately distinguish ASD from TD children. A key finding is that gut microbial abundance, particularly an increase in Clostridioides difficile, serves as the strongest predictor of both ASD symptom severity and brain structural variations. Crucially, these gut and brain differences are age dependent, diminishing as children with ASD aged and converging toward TD patterns. A mediation model suggests a potential pathway where specific microbes influence brain structure and behavior via metabolites. The findings establish the gut microbiota as a robust predictor of brain and behavioral phenotypes in pediatric ASD, underscoring the necessity for early, age-stratified therapeutic strategies via modulating the composition of the gut microbiome.}, }
@article {pmid41806833, year = {2026}, author = {Babdor, J and Patel, RK and Davidson, B and Koser, K and Noecker, C and Rahim, MK and Bisanz, JE and Tenvooren, I and Marquez, D and Calvo, M and Johri, V and McCarthy, EE and Shaheed, A and Ekstrand, C and Weakley, AM and Yu, FB and Krip, K and Shaikh, KA and Amatullah, H and Fiehn, O and Turnbaugh, PJ and Combes, AJ and Fragiadakis, GK and Spitzer, MH}, title = {Immune-microbiome coordination defines interferon setpoints in healthy humans.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.02.003}, pmid = {41806833}, issn = {1097-4172}, abstract = {Human immune systems are highly variable, with most variation attributable to non-genetic sources. The gut microbiome crucially shapes the immune system; however, its relationship with the baseline immune states of healthy humans remains incompletely understood. Therefore, we performed multi-omic profiling of 110 healthy participants through the ImmunoMicrobiome study. A factor-based integrative approach identified coordinated variation, revealing that the interferon response was amongst the most variable immune features in healthy participants. Microbiome composition, pathways, and stool metabolites varied concomitantly with interferon response pathways. Longitudinal data spanning more than a year indicated the significant stability of these parameters within individuals over time. Our study provides extensive data to examine the relationship between the immune states and microbiomes of healthy individuals at steady state, which paves the way for delineating inter-individual differences relevant for disease susceptibility and responses to therapy.}, }
@article {pmid41806724, year = {2026}, author = {Barril, PA and Brusa, V and Costa, M and Cap, M and Aguilera, P and Belforte, FS and Penas-Steinhardt, A and Leotta, G and Oteiza, JM}, title = {16S rRNA-based profiling of microbiota along the ground meat and sausage production lines in an Argentine meat processing facility.}, journal = {International journal of food microbiology}, volume = {453}, number = {}, pages = {111716}, doi = {10.1016/j.ijfoodmicro.2026.111716}, pmid = {41806724}, issn = {1879-3460}, abstract = {Microbial contamination in food processing environments can compromise both product quality and safety. This study aimed to characterize the microbiota present along the ground meat and sausage production lines of an Argentine meat processing facility, with a focus on microbial dynamics in raw materials, environmental surfaces, and final products. Using next-generation sequencing (NGS), we identified a total of 57 unique bacterial genera across both production lines (37 in ground meat samples and 34 in sausage samples) showing ≥5% relative abundance in at least one sample. The core microbiota across both lines included Pseudomonas, Acinetobacter, and Psychrobacter, consistently detected in raw materials, pre- and post-operational environments, and final products. Notably, raw materials introduced variable microbial communities that influenced both environmental and product microbiomes. In the ground meat line, Carnobacterium became dominant in final products, likely masking the detection of other genera. In the sausage line, Brochothrix and Vibrio were prominent in final products. Staphylococcus and Clostridium sensu stricto were detected at low relative abundances and were mainly associated with raw materials; however, because the NGS analysis was conducted at the genus level, these findings do not imply the presence of pathogenic species. The persistence of specific genera in the environment, despite cleaning and disinfection, is consistent with the potential presence of biofilms, which may contribute to increased tolerance to Sanitation Standard Operating Procedures (SSOP). This study highlights the importance of raw material microbiota in shaping the production environment and product composition.}, }
@article {pmid41806709, year = {2026}, author = {Hu, Z and Liu, Q and Song, H and Liu, J}, title = {Environmental factors outweigh seawater microbiomes in synergistically shaping epiphytic bacterial communities of Saccharina japonica.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119535}, doi = {10.1016/j.marpolbul.2026.119535}, pmid = {41806709}, issn = {1879-3363}, abstract = {Saccharina japonica is a commercially significant macroalgal species in coastal areas, where its growth and health are closely linked to epiphytic bacterial communities (EB). Previous studies have indicated that the structure of these EB communities is influenced by seawater microbiomes (SW) and various environmental factors. However, the mechanisms regulating these influences remain incompletely understood, particularly regarding their relative contributions throughout the life cycle, which are important for S. japonica production. To fill this gap, we investigated the diversity, composition, ecological networks, and functional predictions of EB and SW communities, as well as environmental factors from December 2022 to May 2023 in northern China. Mantel test results indicated that EB was significantly correlated with NO2[-], TN, NO3[-], and DIP, which was confirmed by Spearman's rank correlation coefficients and BIOENV analysis. Ecological network analysis revealed that the EB network was more simplified and clustered, with reduced robustness and increased vulnerability than SW. Only one keystone taxon identified in the EB network showed that the stability of the epiphytic microbiome may be highly dependent on the persistence of this key species. Environmental factors had a more substantial influence on EB communities compared to SW communities. Environmental factors uniquely explained 10.4% of the variation, while SW communities contributed only 2.4%. The combination effect accounted for 66.5% of the variation, indicating that their interplay is the key regulating driver of EB communities. Our findings provide a co-regulation framework between the environment and seawater microbiome for the sustainable development of kelp farming.}, }
@article {pmid41806697, year = {2026}, author = {Faisal, S and Ullah, I and Kambey, PA and Malik, A and Shakeel, M}, title = {Revolutionizing hepatic fibrosis staging: A machine learning approach combining clinical, biochemical, and microbiome insights.}, journal = {Computers in biology and medicine}, volume = {206}, number = {}, pages = {111584}, doi = {10.1016/j.compbiomed.2026.111584}, pmid = {41806697}, issn = {1879-0534}, abstract = {Non-alcoholic Steatohepatitis (NASH) is a common disease that not only affects adults but has also been seen to affect all ages. This includes young adults, children and even babies. Non-alcoholic fatty liver disease (NAFLD), NASH and the progression of it to fibrosis have been the subject of extensive research, as there still remains a great deal we do not understand. There are multiple factors that will influence how quickly and aggressively the progression of the disease occurs and also the way the disease is diagnosed or assessed, such as medical history, blood results and ultrasound imaging. This study aims to look at the use of machine learning (ML) to integrate clinical, biochemical and microbiome data to create a model to allow for non-invasive staging of hepatic fibrosis for NASH patients. A total of 1834 patients with biopsy-confirmed NASH were included in the retrospective analysis. The cohort was comprised of patients from multiple healthcare systems with known biopsy-confirmed NASH and a stated fibrosis stage (F0, F1, F2, F3, F4). A range of clinical variables, including liver function tests, demographics and microbiome profiles (via 16S rRNA gene sequencing), were included to train the machine learning models (Random Forest &amp; Extreme Gradient Boosting). The performance of these models were assessed using 10-fold cross-validation with the primary training cohort and external validation on an independent hospital database. The models demonstrated excellent classification accuracy, specifically a balanced accuracy of 99.1% for RF and an area under the curve (AUC) value of 1.0 for XGBoost. The addition of microbiome features (specifically, diversity indices and the relative abundance of certain taxa) enhanced the models' predictive capability, indicating that the gut-liver axis plays a significant role in the development of NASH. To interpret the machine learning models, we used SHapley Additive Explanations (SHAP) analysis to identify which of the clinical and microbiome features affected the models' predictions for the fibrosis stages. Advanced stages of fibrosis (F3 &amp; F4) were found to have significant dysbiosis in the microbiome with increased relative abundance of pathogenic bacteria including Escherichia-Shigella and Enterococcus, as well as decreased Akkermansia and Ruminococcus. The study provides evidence for the accuracy of a non-invasive method of determining hepatic fibrosis stage in NASH and demonstrates its superiority compared to traditional scoring systems (i.e. APRI, FIB-4) for the purpose of guiding clinical decision making and risk assessment for patients in clinical practice.}, }
@article {pmid41806586, year = {2026}, author = {Ji, Z and Hong, S and Zhang, Y and Su, Z and Wang, X and Yu, X and Zhu, Z and Shi, K and Wu, D and Hu, G and Jia, G}, title = {Reshaping the lung microenvironment: MSCs attenuate Cr(VI)-induced pulmonary fibrosis associated with metabolic and microbial modulation.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141708}, doi = {10.1016/j.jhazmat.2026.141708}, pmid = {41806586}, issn = {1873-3336}, abstract = {As a common environmental and occupational pollutant, hexavalent chromium [Cr(VI)] has been proved to induce pulmonary fibrosis. In recent years, mesenchymal stem cells (MSCs) have become a promising therapeutic strategy for pulmonary fibrosis. However, whether they can mitigate Cr(VI)-induced pulmonary fibrosis specifically through regulating the lung microenvironment and microbial homeostasis remains an open and critical question. This study aims to establish a Cr(VI)-induced lung fibrosis model in rats and investigate the protective mechanisms of MSCs through integrated metabolomic and microbiome analyses. MSCs attenuated lung structural destruction, reduced abnormal collagen fiber deposition, decreased the levels of TNF-α, IL6, MDA and 8-OHdG and increased T-AOC and T-SOD. In addition, Cr(VI) caused metabolic disorders in lung tissue, which was evidenced by the up-regulation or down-regulation of multiple phospholipid metabolites, down-regulation of immune-related pathways and up-regulation of arachidonic acid metabolism and glycerophospholipid metabolism pathways. Microbiome analysis revealed that Cr(VI) exposure significantly increased both the diversity and abundance of microbial communities in alveolar lavage fluid, promoting the enrichment of opportunistic pathogens and ultimately leading to microbial dysbiosis. After MSCs intervention, lipid metabolism disorder was alleviated, immune-related pathway was up-regulated, opportunistic bacteria was reduced, and dysbiosis was alleviated. Correlation analysis revealed that lung chromium and lipid-related metabolites were closely associated with microbial communities, suggesting that the pulmonary metabolism may interact with the lung microbiota to jointly maintain the homeostasis of the pulmonary microenvironment. Our study provides a new perspective on elucidating the role of MSCs in treating Cr(VI)-induced pulmonary fibrosis from the perspective of lung metabolism and microbiota.}, }
@article {pmid41806585, year = {2026}, author = {Li, H and Yang, Q and Liu, T and Liu, W and Ding, Y and Xu, Y and Wei, Z}, title = {Habitat-shaped microbial life-history strategies and host niche specialization govern soil ARG transfer potential.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141706}, doi = {10.1016/j.jhazmat.2026.141706}, pmid = {41806585}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) have been extensively studied in terms of their environmental sources and anthropogenic drivers. However, the ecological mechanisms by which soil microbiomes mediate ARG persistence and transfer remain poorly understood, even though microorganisms are the primary hosts, vectors, and regulators of resistance traits. We compared alpine plateaus and lowland plains, two habitats with contrasting ecological and anthropogenic conditions, to investigate how habitat-driven microbiome processes affect ARG transmission. We found that plateau soils harbored lower ARG abundance (6.2%∼86.3%) and reduced horizontal transfer capacity (94.12%) compared to plain soils. This difference was primarily driven by distinct microbial traits shaped by habitat differences. Plateau microbiomes were dominated by k-strategist taxa characterized by slower growth rates and reduced connectivity in co-occurrence networks, thereby limiting opportunities for ARG exchange. In addition, ARG-carrying hosts in plateau soils exhibited broader ecological niches and a higher proportion of generalist taxa (48.2%), which exerted stronger negative interactions on specialists, thereby constraining the spread of resistance traits. These findings highlight how habitat-shaped microbial traits restrict ARG transmission and offer new insights into the ecological containment of antibiotic resistance in agroecosystems.}, }
@article {pmid41806446, year = {2026}, author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C}, title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.}, journal = {The Science of the total environment}, volume = {1025}, number = {}, pages = {181655}, doi = {10.1016/j.scitotenv.2026.181655}, pmid = {41806446}, issn = {1879-1026}, abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.}, }
@article {pmid41806308, year = {2026}, author = {Liu, K and He, Q and Lin, Z and Huang, S and Zhong, Z and Zhu, P and Gao, M and Zhao, L and Jin, H and Wu, G and Geoff, GM and Han, Q and Pang, R}, title = {Genome-Wide Association Study Reveals Insect Genetics and Microbial Symbiont Effects on Susceptibility of Diaphorina citri to the Citrus Greening Pathogen, Candidatus Liberibacter Asiaticus.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17056}, doi = {10.1002/advs.202517056}, pmid = {41806308}, issn = {2198-3844}, support = {32001903//National Natural Science Foundation of China/ ; 2022ZDJS020//Guangdong Province Key Discipline Research Capacity Enhancement Project/ ; 2025A1515012591//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023KTSCX046//Guangdong Provincial Universities Characteristic Innovation Project/ ; 2024A04J4995//Guangzhou Science and Technology Plan Project/ ; }, abstract = {Insect-vectored pathogens pose a significant threat to global agriculture. The colonization efficiency of pathogens in vectors plays a central role in these pathosystems, yet studies of the factors that affect this aspect are limited. This study investigates the genetic and microbial symbiont factors influencing the susceptibility of Diaphorina citri to Candidatus Liberibacter asiaticus (CLas), the pathogen causing citrus greening disease (huanglongbing). Through a microbiome Genome Wide Association Study (mGWAS) based on 16S amplicon sequencing and genomic resequencing of 120 D. citri individuals from six populations, we identified 79 SNPs significantly associated with the relative abundance of CLas within insects. Additionally, some of these SNPs were also associated with the relative abundance of Candidatus Profftella armature, a key endosymbiont of D. citri. SNPs in the regulatory region of gene Dcitr04g11610.1 led to its overexpression in CLas-susceptible D. citri, and CLas infection further elevated its expression. Conversely, RNAi knockdown of Dcitr04g11610.1 reduced CLas infection rates and abundance, accompanied by increased abundance of Profftella. Phylogenetic analysis revealed Dcitr04g11610.1's high homology to Major Facilitator Superfamily-type transporter SLC18B1 proteins, suggesting a role in CLas polyamine utilization. These findings highlight the importance and potential interplay of insect genetics and symbiotic microbiota in insect-vectored plant pathogen systems.}, }
@article {pmid41806199, year = {2026}, author = {Li, H and Huang, X and Luo, Z and Zhou, F and Deng, Y and Tan, C and Jin, Y and Yan, J and Xiao, G}, title = {Prognostic prediction and immune microenvironment analysis in colorectal cancer using exosome-related lncRNA signatures.}, journal = {Discover oncology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12672-026-04755-1}, pmid = {41806199}, issn = {2730-6011}, abstract = {BACKGROUND: Exosomes play a crucial role in tumor microenvironment (TME) by mediating cell-cell communication, but their role in colorectal cancer (CRC) remains unclear. This study aimed to investigate exosome-related lncRNAs (ER-lncRNAs) in CRC.<br><br>METHODS: mRNA profiles and clinical data from TCGA and GEO, microbiome data from TCMAand exosome-related genes from ExoCarta were analyzed. Consensus clustering, ER-lncRNA-related risk signature, and nomogram were developed.<br><br>RESULTS: A total of 797 differentially expressed lncRNAs (DE-lncRNAs)were identified, with 490 ER-lncRNAs selected based on their correlation with exosome-related mRNAs. Consensus clustering stratified CRC samples into four molecular subtypes, with Cluster 2 exhibiting the most favorable prognosis and Cluster 1 the poorest. These subtypes showed significant differences in survival outcomes, immune cell infiltration, and therapeutic responses. Nine ER-lncRNAs were identified as prognostic biomarkers and used to develop a risk score model. Furthermore, a nomogram incorporating the risk score and clinical parameters was constructed to predict individual prognosis.<br><br>CONCLUSION: These findings highlight the clinical relevance of ER-lncRNAs as in CRC and underscores their potential as novel diagnostic and therapeutic targets.}, }
@article {pmid41806138, year = {2026}, author = {Köse, E and Ekren, BY and Doğulu, N and Yolcu, F and Eylem, CC and Nemutlu, E and Sezerman, U and Eminoğlu, FT}, title = {Dietary Protein Modulation, Gut Microbiota, and Metabolic Control in Methylmalonic Acidemia: A Prospective Longitudinal Study.}, journal = {Journal of inherited metabolic disease}, volume = {49}, number = {2}, pages = {e70172}, doi = {10.1002/jimd.70172}, pmid = {41806138}, issn = {1573-2665}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Amino Acid Metabolism, Inborn Errors/diet therapy/metabolism/microbiology ; Prospective Studies ; Male ; Female ; Longitudinal Studies ; *Dietary Proteins/administration &amp; dosage/metabolism ; Child, Preschool ; Child ; Metronidazole/therapeutic use ; Adolescent ; Infant ; Adult ; Amino Acids/blood ; Young Adult ; }, abstract = {Methylmalonic acidemia (MMA) is a rare inherited metabolic disorder caused by defective conversion of methylmalonyl-CoA to succinyl-CoA. Emerging evidence suggests that both dietary protein composition and intestinal microbiota influence metabolic stability and clinical outcomes. This study aimed to evaluate the effects of stepwise dietary modification and short-term metronidazole therapy on systemic and gut-derived metabolic profiles in MMA. In this prospective, longitudinal, single-center study, eight genetically confirmed MMA patients underwent four sequential phases: baseline mixed-protein diet (50% intact protein/50% medical formula), protein restriction, intact protein enrichment (80% intact protein/20% medical formula), and adjunctive metronidazole therapy (20 mg/kg/day, 10 days/month for 3 months). Plasma amino acids, urinary metabolites, stool microbiota (16S rRNA long-read sequencing), and untargeted/tandem metabolomic profiles were analyzed at each phase. Transition to an intact protein-enriched diet significantly reduced plasma leucine levels (p = 0.008) without affecting isoleucine or valine. Urinary methylmalonic acid, 3-hydroxypropionate, lactate, and pyruvate decreased, indicating improved propionyl-CoA clearance. Microbiota diversity progressively declined, accompanied by reductions in butyrate-producing genera (Novisyntrophococcus, Lacrimispora, Hespellia). Metronidazole further lowered urinary methylmalonic acid and 3-hydroxypropionate (p = 0.017 and p = 0.028), with parallel decreases in fecal 3-indolelactic acid and phytosphingosine, suggesting suppression of gut-derived propionate and tryptophan metabolism. Despite antibiotic-induced dysbiosis with expansion of Trabulsiella (Proteobacteria), systemic propiogenic burden decreased. A phased dietary regimen emphasizing intact protein, combined with intermittent metronidazole therapy, favorably modulated biochemical and microbial parameters in MMA. These findings support microbiome-informed dietary strategies and selective gut-targeted interventions to optimize metabolic control in organic acidemias.}, }
@article {pmid41805987, year = {2026}, author = {Kumar, SM and Ragupathy, TV and Dananjeyan, B and Thiyagarajan, C and Loganathan, A and Natarajan, S}, title = {Microbiome-assisted plant breeding: integrating host-microbiome interactions into crop improvement.}, journal = {Archives of microbiology}, volume = {208}, number = {5}, pages = {}, pmid = {41805987}, issn = {1432-072X}, mesh = {*Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth &amp; development ; *Microbiota ; *Host Microbial Interactions ; Seeds/microbiology/genetics ; Quantitative Trait Loci ; Genome, Plant ; }, abstract = {Conventional breeding and domestication have boosted crop productivity but have also narrowed plant genomic diversity and reduced the diversity of associated microbiota, contributing to domestication syndrome and limiting resilience under increasingly variable environments. Thus, genetic improvement remains essential for developing low-input, high-yielding, enhanced nutrient content and stress-tolerant crops. However, traditional breeding has largely focused on plant genomes, overlooking the microbial partners that influence plant performance. Plants function as holobionts where integrated units composed of the host and its microbiome. These microbial communities colonize all plant tissues and regulate nutrient acquisition, immunity, physiology, and yield, often generating novel phenotypes without altering the plant genome. Some beneficial microbial taxa can even restore plant traits lost during domestication, ascertaining their potential as heritable contributors to crop performance. Seeds play a major role in transmitting plant genes and vertically inherited microbiota, making them a strategic entry point for microbiome integration in breeding. Recent advances include seed microbiome inheritance, root-exudate-mediated microbial recruitment, microbiome-associated QTLs and synthetic microbial communities (SynComs) which can be harnessed to enhance crop traits. These insights provide the foundation for Microbiome-Assisted Plant Breeding (MAPB), a complementary breeding paradigm targeting both plant genomes and microbial partners. Hence, incorporating microbial inheritance, recruitment traits and holobiont performance into breeding pipelines positions MAPB as a promising path toward climate-resilient, resource-efficient, and sustainable crop varieties.}, }
@article {pmid41805839, year = {2026}, author = {Matarrita-Carranza, B and Weiss, B and Sandoval-Calderón, M and Koehler, S and Engl, T and Kaltenpoth, M}, title = {Defensive symbionts of European beewolves face competition from brood cell microbiota during vertical transmission.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag024}, pmid = {41805839}, issn = {1574-6941}, abstract = {Beewolf wasps rely on an ancient defensive symbiosis with Streptomyces bacteria that protect their larvae from fungal infection. Female beewolves apply the bacteria to the brood-cell ceiling, and larvae later transfer the symbionts onto the cocoon surface, where they produce antifungal metabolites. Here, we investigated the mechanism of symbiont transfer from the beewolf brood cell to the larval cocoon and characterized the microbial community dynamics across different beewolf life stages and during larval hibernation. Fluorescence in situ hybridization revealed that the symbionts are transiently taken up into the proximal midgut lumen and then regurgitated onto the cocoon during the spinning process. High-throughput sequencing showed that the bacterial community of beewolf feeding larvae resembles that of the honeybee prey, whereas that of adults and diapausing larvae is dominated by Wolbachia. Moreover, the cocoon bacterial community is initially dominated by the defensive Streptomyces philanthi symbiont, but when larvae excrete the gut content inside the cocoon, other bacterial taxa including Lactobacillus, Gilliamella and Bartonella shift the community composition toward dominance by Pseudomonadota. Our findings provide new insights into the transmission route of an ancient extracellular symbiont and its potential competition with other bacteria in this long-term defensive symbiosis.}, }
@article {pmid41805689, year = {2026}, author = {Xie, Y and Zhang, A and Wang, Y and Wang, R}, title = {Community-Acquired Pneumonia in Patients With Diabetes: Narrative Review.}, journal = {JMIR diabetes}, volume = {11}, number = {}, pages = {e82215}, pmid = {41805689}, issn = {2371-4379}, abstract = {BACKGROUND: Patients with diabetes carry a 1.5- to 2-fold higher risk of community-acquired pneumonia (CAP) and experience more severe outcomes, yet the mechanisms that integrate metabolic dysregulation, pathogen shifts, and novel cell death pathways remain fragmented.<br><br>OBJECTIVE: This study aimed to synthesize current evidence on epidemiology, pathophysiology, causative pathogens, clinical outcomes, and management of CAP in adults with diabetes and to identify research gaps for future trials.<br><br>METHODS: A narrative review (1999 to August 2025) of PubMed, EMBASE, the Cochrane Library, and Web of Science was conducted. GRADE (Grading of Recommendations Assessment, Development, and Evaluation) was used to rate evidence from 81 selected English-language studies (randomized controlled trials, cohorts, and meta-analyses).<br><br>RESULTS: Diabetes increases CAP incidence (relative risk 1.73, 95% CI 1.46-2.04), hospitalization (+30%-50%), and 30-day mortality (odds ratio 1.67, 95 % CI 1.45-1.92). Key drivers include hyperglycemia-induced immune paralysis, pulmonary microangiopathy, ferroptosis, glycation and methylation changes, and gut-lung dysbiosis that collectively favor multidrug-resistant Gram-negative bacilli (Klebsiella and Pseudomonas) and severe viral and fungal coinfections. Host-targeted therapy with moderate glycemic control (5-10 mmol/L), continued metformin, and pathogen-directed antibiotics improves survival, whereas single-dose PCV20 and annual influenza vaccination prevents approximately 45% of CAP admissions. Emerging strategies (nanozymes, ferroptosis inhibitors, probiotics, and proteolysis-targeting chimeras) are still preclinical.<br><br>CONCLUSIONS: CAP in patients with diabetes is a distinct, more severe entity mediated by metabolic-immune crosstalk. Multicenter randomized controlled trials integrating tight glucose monitoring, novel host-directed agents, and microbiome modulation are warranted to translate mechanistic insights into better outcomes.}, }
@article {pmid41805583, year = {2026}, author = {Unzueta-Martínez, A and Delaney, JA and Morkeski, K and Ross, A and Wang, ZA and Girguis, PR}, title = {Coexpression among eastern oyster host and microbiome genes suggests coordinated regulation of calcifying fluid chemistry.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {11}, pages = {e2521539123}, doi = {10.1073/pnas.2521539123}, pmid = {41805583}, issn = {1091-6490}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Calcification, Physiologic/genetics ; Hydrogen-Ion Concentration ; *Ostreidae/genetics/microbiology/metabolism ; Transcriptome ; Seawater/chemistry ; }, abstract = {Marine animals that build shells, such as oysters, carefully regulate the chemistry of their internal calcifying fluids, but the molecular mechanisms behind this control, as well as whether microbes play a role in calcification, are poorly understood. To better understand oysters' molecular mechanisms and the role of their calcifying-fluid microbes, we conducted experiments that simulated a tidal cycle, measured calcifying fluid pH and total dissolved inorganic carbon, and characterized host and microbial gene expression via transcriptomics. These experiments showed that calcifying fluid pH remained relatively stable throughout tidal pH fluctuations, with corresponding increases in oyster transcripts for ion transport and acid-base regulation. These data provide direct evidence that tidal fluctuations drive rapid changes in oyster calcifying fluid chemistry. Most surprisingly, increases in microbial transcripts related to nitrogen and sulfur cycling correlated to higher calcifying fluid DIC, and coexpression network analysis revealed patterns of gene expression that linked oyster immune and neural pathways to microbial redox processes, providing molecular evidence of potential host modulation of microbial metabolism. Together, these results reveal that oysters actively regulate their calcifying fluid pH over short timescales, and the endemic microbiome metabolic responses can yield metabolites that influence calcifying fluid pH, alkalinity, and ultimately calcification. These data offer a perspective on oyster physiological capacity and, most importantly, the potential role of microbes in oyster calcification. In light of ongoing changes in ocean pH and temperature, oysters provide a model for studying animal-microbial responses to environmental acidification and how their interactions may shape biomineralization.}, }
@article {pmid41805347, year = {2026}, author = {Song, L and Zhang, H and Wang, M and Li, S and Wang, F and Zhang, M and Qu, Y and Ma, Y and Ma, Q and Wen, C and Zhao, Y and Liu, M and Wang, F}, title = {Metacycloprodigiosin from Rhizosphere Streptomyces aurantiacus as a Natural Antifungal Agent against Fusarium oxysporum.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c15856}, pmid = {41805347}, issn = {1520-5118}, abstract = {Microbiome-guided crop protection increasingly emphasizes the chemical basis of disease suppression. Here, we identify Streptomyces aurantiacus YS-4, a rhizosphere-enriched actinobacterium selectively recruited by resistant cultivars of Salvia miltiorrhiza, as a producer of metacycloprodigiosin, a previously reported secondary metabolite that is reported for the first time in this strain and further investigated for its role in suppressing Fusarium oxysporum-induced root rot in S. miltiorrhiza. Metacycloprodigiosin inhibited Fusarium oxysporum growth by 81.66% at 200 μg mL[-1] and induced extensive cellular and transcriptional changes related to membrane function and virulence-associated pathways. Transmission electron microscopy confirmed severe hyphal damage, while transcriptomic profiling revealed broad downregulation of virulence-associated genes. Pot experiments demonstrated that YS-4 application alleviated root rot symptoms and enhanced plant biomass. Collectively, these findings establish a direct link between metabolite chemistry and pathogen suppression, advancing molecular understanding of plant-fungal interactions and highlighting metacycloprodigiosin as a promising biocontrol agent for sustainable management of crops.}, }
@article {pmid41805251, year = {2026}, author = {Zhou, H and Zhao, X and Li, Y and Wang, Y and Zhang, S and Xu, H and Sui, S and Wang, Q and He, Y and Gu, J}, title = {Nicotinamide mononucleotide supplementation modulates gut microbiota and metabolites to mitigate Alzheimer's disease pathology in APP/PS1 mice.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {}, number = {}, pages = {13872877261422502}, doi = {10.1177/13872877261422502}, pmid = {41805251}, issn = {1875-8908}, abstract = {BackgroundEmerging evidence indicates that gut microbiome dysbiosis may be linked to Nicotinamide adenine dinucleotide (NAD[+]) deficiency during Alzheimer's disease (AD) progression, a condition potentially alleviated by nicotinamide mononucleotide (NMN) supplementation.ObjectiveTo explore the therapeutic potential of NMN supplementation in regulating AD pathology as well as gut microbiome dynamics, APP/PS1 transgenic mouse models were employed in the research.MethodsMetagenomic and metabolomics analysis were conducted to assess modifications in the intestinal microbiota and metabolites of AD mice post-NMN treatment. Moreover, immunohistochemistry, immunofluorescence, western blot, and Morris water maze were applied to evaluate NMN's ameliorative effects on AD.ResultsNMN administration significantly altered gut microbial composition and fecal metabolite profiles, leading to improvements in colon damage and AD-related neuropathology. Key findings include the restoration of gut microbial balance, particularly increasing Bacteroides abundance, and the modulation of metabolites involved in lipid metabolism. Furthermore, NMN was found to regulate ferroptosis, improving gut barrier function in AD mice, which were mediated through gut-brain communication pathways. NMN supplementation also enhanced ATP production, mitochondrial function, and synaptic density in the hippocampus while reducing oxidative stress and Aβ accumulation in the brain. Ultimately, these multi-faceted improvements collectively alleviated cognitive deficits in AD mice.ConclusionsIn summary, NMN supplementation effectively modulated gut microbiota and metabolites, thus mitigating AD pathology in APP/PS1 mice. Our study offers novel perspectives on the mechanisms underlying NMN's therapeutic effects in AD and underlines its potential as a promising intervention strategy.}, }
@article {pmid41805178, year = {2026}, author = {Skolnick, S and Hall, B}, title = {Draft genome sequence of a family Acutalibacteraceae isolate, a human gut-derived cholesterol metabolizer.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0113725}, doi = {10.1128/mra.01137-25}, pmid = {41805178}, issn = {2576-098X}, abstract = {We report the draft genome sequence of a family Acutalibacteraceae isolate, which is an obligate anaerobe that converts cholesterol to coprostanol. The organism was isolated from a healthy adult's fecal sample, plated on cholesterol brain agar, and incubated anaerobically, yielding distinctive star-shaped colonies. This isolate is from an unclassified genus within the Acutalibacteraceae, highlighting the unexplored diversity within the gut microbiome.}, }
@article {pmid41805144, year = {2026}, author = {Zhou, B and Mokhashi, N and Skondra, D}, title = {Emerging strategies in drug repurposing for decreasing the risk of age-related macular degeneration.}, journal = {Expert opinion on drug discovery}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/17460441.2026.2635492}, pmid = {41805144}, issn = {1746-045X}, abstract = {INTRODUCTION: Vision loss in older adults is largely driven by age-related macular degeneration (AMD), characterized by progressive damage central visual field damage and functional decline. While current options for wet and dry AMD are limited and expensive, drug repurposing represents a promising strategy to accelerate the discovery of effective, accessible treatment by leveraging medications with established safety profiles. Notably, anti-diabetic agents including metformin, sulfonylureas, glucagon-like peptide-1 receptor agonists (GLP-1RAs), and insulin have emerged as modulators of the retinal pigment epithelium (RPE) function, photoreceptors, and retinal vascular integrity.<br><br>AREAS COVERED: This review highlights the roles of oxidative stress, inflammation, and complement-mediated immune dysregulation in AMD pathogenesis, alongside preclinical data demonstrating metformin's protective effects via AMP-activated protein kinase (AMPK) activation. Population-based studies and meta-analyses further suggest a modest reduction in AMD risk associated with metformin use in both diabetic and non-diabetic cohorts. Additional pharmacological agents include statins, glyburide, L-DOPA, fluoxetine, dimethyl fumarate, and nutraceuticals such as curcumin, melatonin, and N-acetylcysteine.<br><br>EXPERT OPINION: Early AMD prevention through repurposed therapeutics, guided by AI-driven design and systems biology, may enable personalized care via multimodal risk stratification incorporating genetic, metabolomic, and microbiome data. Rigorous, stratified clinical trials integrating bioinformatics and precision medicine are essential to validate the most effective candidates.}, }
@article {pmid41805117, year = {2026}, author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE}, title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c15254}, pmid = {41805117}, issn = {1520-5118}, abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.}, }
@article {pmid41804973, year = {2026}, author = {Mehl, A and Blacher, E}, title = {Gut microbiome and aging-A dynamic interplay of microbes, metabolites, and the immune system.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.70324}, pmid = {41804973}, issn = {1873-3468}, support = {03-23-24//The National Institute for Psychobiology in Israel/ ; 2023061//The United States-Israel Binational Science Foundation/ ; //Uncle Kory Foundation/ ; //Keren Shemesh: HUJI-STMC collaborative grant/ ; //The Abisch Frenkel Foundation for the Promotion of Life Sciences/ ; //ERA-Net NEURON MOODYGUT/ ; //The Azrieli Foundation Faculty Fellowship/ ; 888494//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, abstract = {Aging is accompanied by profound changes in both the gut microbiome and the immune system, which engage in continuous, bidirectional communication. Alterations in microbial diversity and metabolism, particularly reductions in short-chain fatty acid (SCFA) producers as well as shifts in bile acid and tryptophan-metabolizing species, can incite and worsen inflammation, damage barrier integrity, and accelerate immunosenescence. Concomitantly, immune aging and reduced mucosal IgA promote microbial dysbiosis, forming a self-reinforcing cycle that fuels chronic inflammation ("inflammaging"). Microbial metabolites such as SCFAs, secondary bile acids, and indole derivatives play central roles in this gut-immune dialog, influencing regulatory T-cell balance, epithelial repair, and neurological health through the gut-brain axis. Emerging evidence suggests that diet, probiotics, postbiotics, and microbiome transplantations can restore beneficial microbial and, consequently, immune functions, offering opportunities to promote healthy aging and potentially reverse adverse symptoms. Understanding and targeting the gut microbiome-immune feedback loops may reveal new strategies to modulate inflammaging and extend health span.}, }
@article {pmid41804971, year = {2026}, author = {Wang, Y and Cao, B and Liu, C and Ling, Q and Qiu, Z and Yan, W}, title = {Integrated Multiomics Analysis Indicates Seasonal and Geographical Drivers of Rhizosphere Microbiome-Metabolome Interactions and Dihydrochalcone Accumulation in Lithocarpus litseifolius (Hance) Chun.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c11982}, pmid = {41804971}, issn = {1520-5118}, abstract = {Lithocarpus litseifolius (L. litseifolius) is a valuable economic crop rich in dihydrochalcones (DHCs), with wide applications in medicines, tea, and sweeteners. By integrating multiomics approaches, the relationship between rhizosphere microecology and quality formation in L. litseifolius was systematically elucidated. Key bacterial groups, such as Burkholderia-Caballeronia-Paraburkholderia, Conexibacter, and Bradyrhizobium, were driven by soil physicochemical properties (available copper, exchangeable manganese, alkali-hydrolyzable nitrogen, and organic matter) and rhizosphere metabolome and were strongly associated with the up-regulation of key genes in phenylpropanoid biosynthesis (phenylalanine ammonia lyase, cinnamate 4 hydroxylase, chalcone synthase, phloretin 4'-O-glucosyltransferase), thereby promoting DHC accumulation. A pot experiment confirmed the functional contribution of Burkholderia in promoting the growth of L. litseifolius and the accumulation of its secondary metabolites. The mechanisms by which soil characteristics and microbial communities regulate DHC biosynthesis in L. litseifolius were elucidated, providing insights into the coupling mechanism of "soil-microbiome-metabolome-plant secondary metabolism".}, }
@article {pmid41804865, year = {2026}, author = {Ma, J}, title = {Inference for microbe-metabolite association networks using a latent graph model.}, journal = {Biometrics}, volume = {82}, number = {1}, pages = {}, doi = {10.1093/biomtc/ujag042}, pmid = {41804865}, issn = {1541-0420}, support = {R01 GM145772/GF/NIH HHS/United States ; }, mesh = {Algorithms ; Computer Simulation ; Humans ; *Models, Statistical ; Female ; *Microbiota ; *Metabolic Networks and Pathways ; Stochastic Processes ; }, abstract = {Correlation networks are commonly used to infer associations between microbes and metabolites. The resulting $p$-values are then corrected for multiple comparisons using existing methods such as the Benjamini &amp; Hochberg (BH) procedure to control the false discovery rate (FDR). However, most existing methods for FDR control assume the $p$-values are weakly dependent. Consequently, they can have low power in recovering microbe-metabolite association networks that exhibit important topological features, such as the presence of densely associated modules. We propose a novel inference procedure that is both powerful for detecting significant associations in the microbe-metabolite network and capable of controlling the FDR. Power enhancement is achieved by modeling latent structures in the form of a bipartite stochastic block model. We develop a variational expectation-maximization (EM) algorithm to estimate the model parameters and incorporate the learned graph in the testing procedure. In addition to FDR control, this procedure provides a clustering of microbes and metabolites into modules, which is useful for interpretation. We demonstrate the merit of the proposed method in simulations and an application to bacterial vaginosis.}, }
@article {pmid41804664, year = {2026}, author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B}, title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70278}, doi = {10.1111/1462-2920.70278}, pmid = {41804664}, issn = {1462-2920}, support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; }, mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; }, abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.}, }
@article {pmid41804655, year = {2026}, author = {Zhang, Y and Li, S and Li, Q and Wang, R and Sun, Y and Wang, Y and Yan, X and Wang, X and Wang, Y and Xue, Y and Ding, C and Gong, J and Ding, L and Ju, H}, title = {Synthetic Antibody Mimetics with ROS-Gated Saccharide Release for Targeted Colitis Therapy.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e05869}, doi = {10.1002/adhm.202505869}, pmid = {41804655}, issn = {2192-2659}, support = {22574077//National Natural Science Foundation of China/ ; 22274073//National Natural Science Foundation of China/ ; 5431ZZXM2504//State Key Laboratory of Analytical Chemistry for Life Science/ ; }, abstract = {Conventional targeted therapies for inflammatory bowel disease (IBD) often rely on unstable biological recognition elements. While molecularly imprinted polymers (MIP) offer robust synthetic alternatives, their utility is limited by an "always-on" binding state: even weak non-specific adsorption can significantly compromise their target-binding capacity. We convert static MIP into reactive oxygen species (ROS)-activated therapeutic actuators by conjugating mannose to transferrin-imprinted MIP via a ROS-cleavable linker. The saccharide acts dually as a therapeutic agent and a protective cloak. It sterically blocks non-specific binding during intestinal transit. At inflammatory sites, elevated ROS levels (higher than in healthy tissue) trigger simultaneous mannose release and activation of high-affinity targeting. This enables precise MIP anchoring to the inflamed epithelium for physical barrier formation and localized microbiome modulation. In murine colitis models, this achieved mucosal healing, mitigated inflammation, and microbiota rebalancing using a mannose equivalent dose of 27.2 mg/kg/d, benchmarking against free mannose and non-responsive MIP controls. This work establishes a generalizable paradigm for targeted recognition and drug delivery in complex physiological environments, paving the way for intelligent, disease-responsive nanomedicines.}, }
@article {pmid41804549, year = {2026}, author = {Tufvesson-Alm, M and Walsh, L and Pierce, S and Keohane, F and Clarke, G and O'Connor, K and Cryan, JF and Schellekens, H}, title = {Unravelling the role of the gut microbiome in antipsychotic-induced weight gain and metabolic dysfunction in humans and rodents: A systematic review.}, journal = {Dialogues in clinical neuroscience}, volume = {28}, number = {1}, pages = {131-144}, doi = {10.1080/19585969.2026.2637716}, pmid = {41804549}, issn = {1958-5969}, mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Humans ; *Antipsychotic Agents/adverse effects ; *Weight Gain/drug effects/physiology ; Animals ; *Metabolic Diseases/chemically induced/microbiology ; }, abstract = {Second-generation antipsychotics are frequently linked to weight gain and metabolic dysfunction, yet the mechanisms driving these effects remain elusive. The gut microbiome has been proposed as a potential mediator of these adverse outcomes. This study aimed to investigate the role of the gut microbiota in antipsychotic-induced weight gain. A systematic search of PubMed and Embase was conducted. In total, 24 publications were included in this review, including clinical and preclinical observational and intervention studies. Collectively, there is strong evidence that atypical antipsychotic-induced weight gain and metabolic dysfunction is accompanied by microbiota alterations. However, there is a lack of consensus with regards to the exact mechanisms and involvement of the microbiome in antipsychotic-induced weight gain. Nevertheless, a few patterns and common observations were found across studies, such as reduced diversity, increased Firmicutes/Bacteroidetes ratio and a reduction in Akkermansia species. While microbiota-targeted interventions had generally weak effects on weight gain and metabolic dysfunction in clinical cohorts, the use of specific probiotic strains and microbiota metabolites showed promise in preclinical studies. Thus, while the relationship between antipsychotic-induced weight gain, metabolic dysfunction, and changes in the gut microbiome are evident, further research is warranted to establish definitive causal relationships and to aid in the development of precision microbiota-targeted interventions to counteract these adverse effects.}, }
@article {pmid41804484, year = {2026}, author = {Rodríguez-Barreras, R and Suárez-Pérez, J and Godoy-Vitorino, F}, title = {Seasonality shapes gut microbiota composition in two sympatric sea urchins.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20918}, pmid = {41804484}, issn = {2167-8359}, mesh = {Animals ; *Seasons ; *Sea Urchins/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Puerto Rico ; Sympatry ; *Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The gut microbiota plays critical roles in digestion, immunity, and environmental adaptation in marine invertebrates. Its composition is shaped by both host traits and abiotic factors such as temperature and seasonality. In Caribbean reefs, sea urchins like Diadema antillarum and Echinometra lucunter are important grazers that regulate algal biomass and influence benthic community dynamics. This study used 16S rRNA gene sequencing to compare, for the first time, the gut microbiota of these two sympatric species across contrasting seasons.<br><br>METHODS: Adults of D. antillarum and E. lucunter were collected during summer and winter from three fringing reefs in Puerto Rico. Gut contents were extracted under sterile conditions, and bacterial DNA was extracted amplified for their 16S rRNA genes and sequenced. Microbial diversity and structure were assessed standard microbiota pipelines.<br><br>RESULTS: Microbial communities in both echinoids were dominated by Bacillota, Bacteroidota, Desulfobacterota, and Pseudomonadota. Core microbiota analysis revealed stable taxa across hosts and seasons, most notably Propionigenium, supporting host-driven selection mechanisms that maintain functional stability despite seasonal turnover. Core microbiome analyses revealed Bacillota, Bacteroidota, Desulfobacterota_G_459543, and Pseudomonadota as persistent phyla across seasons, and genera such as Desulfotalea, Photobacterium, and Propionigenium consistently present in both species. Alpha diversity was significantly higher in winter for both D. antillarum and E. lucunter, while species-level differences were not significant. Beta diversity analyses showed significant seasonal clustering, with no consistent segregation between species within seasons. Our findings demonstrate that shared environmental conditions, particularly seasonality, are the primary modulators of gut microbiota in sympatric sea urchins, while host selection preserves a conserved core community. This dual influence of environment and host highlights the ecological plasticity and resilience of sea urchin microbiotas under fluctuating reef conditions.}, }
@article {pmid41804293, year = {2026}, author = {Oringher, JL and Afruza, R and Chakraborty, M and Akiva, KL and Zhang, GY and Townsend, EC and Quinn, GM and Scheuing, L and Menkart, MG and Rai, A and Kleiner, DE and Levy, EB and Koh, C and Ali, RO and Etzion, O and Heller, T}, title = {Portal Vein Tryptophan Pathway Analysis Reveals Gut-Mediated Inflammatory Pathway Predominance in HCV Infection.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {46}, number = {4}, pages = {e70584}, doi = {10.1111/liv.70584}, pmid = {41804293}, issn = {1478-3231}, support = {DK054514/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Tryptophan/blood/metabolism ; Male ; Female ; Middle Aged ; Kynurenine/blood ; *Gastrointestinal Microbiome ; *Portal Vein/metabolism ; Adult ; Antiviral Agents/therapeutic use ; Cytokines/blood ; Sofosbuvir/therapeutic use ; Sustained Virologic Response ; Liver/pathology ; *Hepatitis C, Chronic/drug therapy/blood ; Xanthurenates/blood ; Inflammation ; *Hepatitis C/drug therapy ; Biomarkers/blood ; Aged ; Heterocyclic Compounds, 4 or More Rings/therapeutic use ; }, abstract = {BACKGROUND AND AIMS: The tryptophan pathway is an integral component of the gut-liver axis; however, the role in hepatitis C virus infection (HCV) and liver disease progression remains poorly understood. This study investigated tryptophan metabolites in portal and peripheral serum during and after HCV, and their relationship to inflammatory and clinical markers.<br><br>METHODS: HCV infected patients were evaluated during infection (HCVi, n&#x2009;=&#x2009;24) and 6&#x2009;months after sofosbuvir/velpatasvir mediated sustained virologic response (SVR, n&#x2009;=&#x2009;19) (NCT02400216). Liver biopsies, portal and peripheral blood collection, and stool sampling were performed at both time points. Statistical analyses assessed metabolite abundance during infection and recovery, and their associations with cytokines, clinical parameters, and the microbiome.<br><br>RESULTS: During infection, peripheral tryptophan and kynurenine were elevated while indolelactate and xanthurenate were reduced (p&#x2009;<&#x2009;0.05). In the portal blood, kynurenine/tryptophan ratio and kynurenine were increased, whereas indoleacetate and xanthurenate were decreased (p&#x2009;<&#x2009;0.05). Tryptophan metabolites positively correlated with hepatic activity index, gamma-glutamyl transferase, total bilirubin, spleen volume/height ratio, and pro-inflammatory cytokines including CXCL9, CXCL10, TNF&#x3b1;, IL6, and IL-12p40. Negatively, correlations were observed with gut microbes Dorea longicatena and Qiania dongpingenesis.<br><br>CONCLUSIONS: Elevated kynurenine in portal blood suggests upregulation of gut-mediated pro-inflammatory pathways during HCV infection. Integration of multi-omics data from the gut-liver axis highlights the contribution of the tryptophan pathway to inflammatory responses in HCV. However, small sample size, absence of quantitative values for all pathway metabolites, and reliance on correlative rather than causative associations limit mechanistic interpretation. Future studies with larger cohorts and functional analyses are needed to clarify causal mechanisms and evaluate therapeutic potential of targeting the tryptophan pathway.<br><br>TRIAL REGISTRATION: NCT02400216.}, }
@article {pmid41803943, year = {2026}, author = {Dai, W and Jiang, X and Liu, Y and Yu, Y and Hou, J and Xia, J and Li, SC and Li, C and Du, H and Wu, R}, title = {Integrated cross-sectional study and functional validation indicate the association of lactobacillus crispatus-derived D-lactic acid with cervical gene expression and precancerous cervical lesions.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07982-w}, pmid = {41803943}, issn = {1479-5876}, }
@article {pmid41803939, year = {2026}, author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M}, title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00544-x}, pmid = {41803939}, issn = {2524-4671}, }
@article {pmid41803924, year = {2026}, author = {Enokela, SO and Yergaliyev, T and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A}, title = {Towards standardization in pig microbiome research based on a comprehensive twenty-year review.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00541-0}, pmid = {41803924}, issn = {2524-4671}, support = {28N-2-051-01//German Federal Ministry of Food and Agriculture/ ; 28N-2-051-01//German Federal Ministry of Food and Agriculture/ ; }, }
@article {pmid41803907, year = {2026}, author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM}, title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02345-5}, pmid = {41803907}, issn = {2049-2618}, support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundaci&#xf3;n Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracci&#xf3;n de talento investigador C&#xe9;sar Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; }, abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.<br><br>RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs&#x2009;+&#x2009;BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs&#x2009;+&#x2009;BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p&#x2009;<&#x2009;0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.<br><br>CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.}, }
@article {pmid41803902, year = {2026}, author = {Liu, Q and Wang, C and Si, G and He, J}, title = {Integrated multiomics profiling predicts anti-tuberculosis drug-induced liver injury.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03608-3}, pmid = {41803902}, issn = {1465-993X}, support = {2023YFS0236//Sichuan Science and Technology Program Key R&amp;D Project/ ; }, }
@article {pmid41803738, year = {2026}, author = {Liu, G and Zhou, K and An, Q and Yang, C and Yang, S and Xu, L}, title = {Regulatory effects of winter Morchella esculenta cultivation on the summer maize phyllosphere microbiome and plant health-related traits.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08489-8}, pmid = {41803738}, issn = {1471-2229}, support = {202305AC160057//Project for Reserve Talents of Young and Middle-aged Academic and Technical Leaders/ ; 2023//Xingzhao Talent Support Program/ ; 2025//Yunnan Colorful Clouds Postdoctoral Program Innovation Project/ ; }, }
@article {pmid41803419, year = {2026}, author = {Liu, Y and Liu, R and Zheng, K and Wang, Z and Shao, H and McMinn, A and Wang, M and Liang, Y}, title = {Global genomic diversity of temperate P2-like viruses.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09823-4}, pmid = {41803419}, issn = {2399-3642}, support = {42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42120104006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025M770867//China Postdoctoral Science Foundation/ ; }, abstract = {P2-like viruses (P2Vs), temperate phages of the Peduoviridae family, possess a lysogenic lifestyle that renders traditional isolation unsuitable, hindering our understanding of their diversity and ecological roles. Utilizing profile-hidden Markov models to analyze public databases, this study achieved four major advances: (1) Identified 5945 P2V genomes and built the P2V Genome Dataset (P2VGD), expanding known genomes 48-fold; (2) Phylogenetic classification into 13 superclades and 4671 genus-level clusters, a 106-fold diversity increase; (3) Identification of 757 auxiliary metabolic genes with biome-specific metatranscriptomic activities: human gut P2Vs encode antibiotic efflux and cell-wall remodeling enzymes, while oligotrophic marine P2Vs express glycan-scavenging enzymes; (4) Uncovering their widespread distribution across diverse biomes, dominated by host-associated environments but extending to under-sampled natural ecosystems. These findings greatly expand the genomic and functional understanding of P2Vs, highlighting their biological strategies in host adaptation, virus-host co-evolution, and microbiome dynamics.}, }
@article {pmid41803343, year = {2026}, author = {Pal, SK and Davar, D}, title = {Microbiome modulation in cancer immunotherapy.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41803343}, issn = {1546-170X}, }
@article {pmid41803338, year = {2026}, author = {Tamang, KR and Mahdi, S and Koirala, P and Asiamah, JY and Sharma, S and Padyana, S and Carson, CB and Valliyodan, B}, title = {Soil Microbiome for Climate Smart Agriculture in Legumes: A Review.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41803338}, issn = {1432-0991}, support = {U.S. Department of Agriculture//U.S. Department of Agriculture/ ; }, abstract = {Climate-smart agriculture is a multidisciplinary farm model approach that helps reduce the impact of climate change not only on soil but on entire agricultural systems. One of the critical approaches of climate-smart agriculture is using the soil microbiome to help the crop adapt to the changing climate and increase crop production. The microorganisms that are present in the soil play a crucial role in ecosystem services, crop protection and performance, and productivity. Legumes are essential for their nutritional value and interaction with soil microbes, particularly in fixing atmospheric nitrogen and improving soil health through plant-microbe association. Beyond Rhizobium, a wide range of microorganisms and fungi assist legumes in adapting to climate stresses such as drought stress and salinity, which ultimately enhances biomass and legume yield. However, the molecular mechanisms behind the interactions between microbiomes and plant growth, ecosystem services, and carbon sequestration remain unclear in legumes. This review aims to explain the key roles of the soil microbiome, legume rhizobiome, and the microbial genes associated with functional plant traits that help plants adapt to a changing climate. Understanding how microbial populations shift due to climate variations and how these changes affect legume yields is crucial, given the ever-changing nature of ecosystems due to climatic shifts. Therefore, more research is warranted to explore plant microbial interactions, understand the dynamics of climatic shifts, and develop microbiome engineering tools for the improved health of crop and rhizobiome ecosystems. Furthermore, a parallel study is required to examine the harmful microbiome that causes crop destruction and antagonizes important bacteria.}, }
@article {pmid41803336, year = {2026}, author = {Mandal, S and Aran, KR}, title = {Symbiotic in Alzheimer's disease: modulating the gut-brain axis for neuroimmune homeostasis and cognitive protection.}, journal = {Inflammopharmacology}, volume = {}, number = {}, pages = {}, pmid = {41803336}, issn = {1568-5608}, abstract = {Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder defined by progressive cognitive impairment, neuroinflammation, oxidative stress, amyloid-β (Aβ) accumulation, synaptic dysfunction, mitochondrial impairment, and tau hyperphosphorylation. The gut-brain axis (GBA) is a crucial regulatory signaling cascade that links intestinal microbiome composition with both neural health and disease through the vagus nerve. Gut dysbiosis has increasingly been implicated in AD pathogenesis by exacerbating systemic and neuroinflammatory signaling, disrupting intestinal and blood-brain barrier (BBB) structural stability, and promoting microglial activation, thereby facilitating Aβ aggregation and neurodegeneration. Preclinical studies indicate that symbiotic interventions restore microbial balance and improve gut-brain communication, contributing to neuroprotective effects. Additionally, it has been demonstrated that symbiotics can restore synaptic plasticity and cognitive resilience by suppressing pro-inflammatory cytokines, as exemplified by interleukin-1β (IL-1β) and tumour necrosis factor-α (TNF-α), and by upregulating neurotrophic factors, particularly brain-derived neurotrophic factor (BDNF). These effects are associated with normalised glial reactivity, attenuation of oxidative stress, and improved mitochondrial bioenergetics, together contributing to enhanced synaptic function, reduced neuroinflammation, and preservation of cognitive performance. This review highlights a critical assessment of the treatment potential of symbiotic interventions in modulating the GBA in AD, emphasising mechanistic insights into neurodegenerative pathways and evaluating their capacity to mitigate symptoms and delay disease progression, as supported by current preclinical evidence.}, }
@article {pmid41803252, year = {2026}, author = {Jurry, AG and Sahoo, JP and Sharma, SS and Praveena, J and Hossain, SN and Sahu, N and Pradhan, S and Nayak, P and Tripathy, S and Vijayakumar, D and Dash, SS and Jena, B and Pradhan, P and Pradhan, SS}, title = {Morpho-biochemical and molecular identification of Bacillus licheniformis and Bacillus cereus isolates from sorghum (Sorghum bicolor L.) rhizosphere.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42932-y}, pmid = {41803252}, issn = {2045-2322}, abstract = {This study isolated, characterized, and identified rhizosphere-associated soil bacteria from sorghum-cultivated soils in Bhubaneswar, India, using serial dilution and spread plate techniques on Nutrient Agar. Morphological and biochemical analyses (Gram staining, catalase, oxidase, MR, and indole tests) identified 13 bacterial isolates, predominantly Gram-positive rods (Bacillus, Paenibacillus) and cocci (Staphylococcus, Micrococcus), with one Gram-negative isolate. Molecular characterization involved 16S rRNA gene amplification (~ 1500 bp), sanger sequencing, and phylogenetic analysis. BLASTN confirmed AG3 as Bacillus licheniformis (99.37% identity) (GenBank: PV590072), and AG11 as Bacillus cereus (100% identity) (GenBank: PV590099). The phylogenetic tress analysis of bacterial isolates AG3 and AG11 revealed distinct evolutionary rate variations. For AG3, site-specific rates ranged from 0.07 to 3.64 substitutions/site (nucleotide frequencies: A = 24.50%, T/U = 19.99%, C = 24.70%, G = 30.81%), while AG11 exhibited more uniform rates ranged from 0.90 to 1.10 substitutions/site (nucleotide frequencies: A = 25.79%, T/U = 20.86%, C = 22.71%, G = 30.64%). Maximum likelihood trees (log-likelihood: - 4077.853 for AG3, - 1928.562 for AG11) with 1,531 (AG3) and 1,402 (AG11) aligned positions resolved their phylogenetic relationships. This study provides valuable insights into the diversity and evolutionary dynamics of rhizosphere-associated Bacillus spp. in sorghum-cultivated soils, contributing to a better understanding of their ecological significance and potential application in sustainable agriculture and plant growth promotion.}, }
@article {pmid41803235, year = {2026}, author = {Chowdary, DD and Sridhar, Y and Rao, GR and Madhav, MS and Latha, PC and Malathi, VM and Padmakumari, AP and Sundaram, RM}, title = {Diversity of culturable gut bacteria associated with brown planthopper, Nilaparvata lugens (Stål) and their role in imidacloprid degradation.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41348-y}, pmid = {41803235}, issn = {2045-2322}, abstract = {The brown planthopper, Nilaparvata lugens (Stål), is a major pest of rice across Asia and has developed significant metabolic resistance to multiple insecticides. Microbiome-mediated insecticide resistance is of emerging interest in various insect pests, including N. lugens. In this study, we assessed the diversity of culturable gut bacteria in imidacloprid-susceptible (IMI-S) and imidacloprid-resistant (IMI-R) populations of N. lugens and their potential to degrade imidacloprid. Molecular characterization and phylogenetic analysis identified 13 bacterial isolates, representing ten families from three phyla: Proteobacteria, Actinobacteria and Firmicutes. The IMI-R population has contributed to nine of the 13 isolates. Screening for imidacloprid degradation identified four bacterial strains viz., Paenibacillus amylolyticus, Serratia marcescens, Acinetobacter soli and Brucella sp. associated with the IMI-R population were capable of growing in minimal salt medium supplemented with imidacloprid. Notably, S. marcescens and P. amylolyticus could utilize imidacloprid as a sole source of carbon and nitrogen, respectively. LC-MS/MS analysis revealed that P. amylolyticus and S. marcescens after 14 days of inoculation degraded 73.07 and 66.92% of imidacloprid (100 mg/L), respectively. These findings underscore a strong association between gut-microbial composition and insecticide resistance in N. lugens and highlight the potential of specific bacterial strains for microbiome-based pest and resistance management strategies.}, }
@article {pmid41803202, year = {2026}, author = {Kaczvinsky, C and Levy, H and Preston, S and Youngflesh, C and Clucas, G and Lynch, HJ and Christodoulou, MD and Hart, T and Smith, AL}, title = {Large-scale distribution of cestode infections in wild gentoo penguins and their impact on the host microbiome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-39642-w}, pmid = {41803202}, issn = {2045-2322}, }
@article {pmid41803165, year = {2026}, author = {Bearson, BL and Whelan, SJ and Encinosa, MPN and Neupane, DP and Bradshaw, DJ and Monson, MS and Anderson, CL and Bearson, SMD}, title = {Chicken vaccination reduces colonization and dissemination of Salmonella serovar Enteritidis with decreased susceptibility to ciprofloxacin.}, journal = {NPJ vaccines}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41541-026-01414-y}, pmid = {41803165}, issn = {2059-0105}, support = {CRIS project 5030-31000-007-000-D//United States Department of Agriculture (USDA), Agricultural Research Service (ARS) appropriated funds/ ; CRIS project 5030-32000-227-000D//United States Department of Agriculture (USDA), Agricultural Research Service (ARS) appropriated funds/ ; }, abstract = {Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of most common Salmonella serovars associated with human illness in the U.S. and worldwide. Surveillance from the U.S. National Antimicrobial Resistance Monitoring System indicates an increase in both chicken and human isolates of S. Enteritidis with decreased susceptibility to ciprofloxacin (DSC), a critical antibiotic prescribed for complicated human salmonellosis infections. S. Enteritidis reduction in chickens is a priority of poultry producers and public health agencies to improve food safety. In the current study, efficacy assessment of a live Salmonella vaccine (BBS 1134) revealed significant reduction of cecal and splenic colonization, and prevention of dissemination to the bone marrow by DSC S. Enteritidis in broiler chickens. Microbiome analysis indicated the cecal microbiota of vaccinated chickens is distinct compared to mock-vaccinated birds. The IDEXX SE Ab X2 Test did not detect antibodies to S. Enteritidis in vaccinated chicken serum, thereby permitting differentiation of infected from vaccinated animals (DIVA). Altogether, the Salmonella vaccine is a DIVA vaccine, afforded cross-protection, and significantly reduced intestinal colonization and dissemination to the spleen and bone marrow by DSC S. Enteritidis in chickens, thereby offering a prospective intervention for animal production to reduce food product contamination and improve food safety.}, }
@article {pmid41803145, year = {2026}, author = {Cazzaniga, M and Bra, KK and Herzog, MKM and Hardt, WD and Claesson, MJ and Mathur, H and Gahan, CGM}, title = {Impact of the defined Oligo-MM[12] microbiota on intestinal colonisation and dissemination of Listeria monocytogenes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41803145}, issn = {2045-2322}, support = {NCCR Microbiomes//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; Marie Sk&#x142;odowska-Curie grant agreement No 956279//H2020 European Institute of Innovation and Technology/ ; centres grant number SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Animals ; *Listeria monocytogenes/pathogenicity/physiology ; *Gastrointestinal Microbiome ; *Listeriosis/microbiology/immunology ; Mice ; Disease Models, Animal ; Feces/microbiology ; Specific Pathogen-Free Organisms ; Mice, Inbred C57BL ; Female ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of global concern, particularly for immunocompromised individuals at risk of severe disease. In mice, infection outcomes are strongly influenced by host immunity and gut microbiome composition. The Oligo-MM[12] defined microbiota mouse model, containing a simplified community of 12 bacterial strains, offers a controlled system to study L. monocytogenes pathogenesis and microbiome interactions. Defined or reduced-complexity microbiota models are increasingly used to investigate colonisation resistance and identify protective taxa. In this study, we compared Oligo-MM[12] mice with conventionally raised Specific Pathogen Free (SPF) mice to assess how microbiome complexity shapes infection. This allowed us to explore how microbiome complexity affects resistance to L. monocytogenes. We performed an in vivo infection study to assess host responses and pathogen-related outcomes, alongside an ex vivo fermentation assay that simulated the murine distal colon, to monitor microbial dynamics. Building on our earlier work, we now demonstrate that in vivo, Oligo-MM[12] mice showed significantly higher L. monocytogenes shedding in faeces during infection, whereas SPF mice progressively reduced L. monocytogenes levels. Despite this, L. monocytogenes dissemination to internal organs after three days of infection was similar in both models. Alterations to gut Prevotella, Akkermansia and Blautia species following L. monocytogenes infection were noteworthy. Ex vivo fermentation mirrored in vivo patterns, validating the Oligo-MM[12] system for mechanistic studies. Together, these results highlight the importance of microbiome complexity in modulating infection outcomes and establish a foundation for identifying protective taxa and mechanisms of colonization resistance.}, }
@article {pmid41803086, year = {2026}, author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L}, title = {Water mass specific genes dominate the Southern Ocean microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41803086}, issn = {2041-1723}, support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; }, mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; }, abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.}, }
@article {pmid41802805, year = {2026}, author = {Kim, M and Jo, MJ and Park, S and Lee, SB and Jang, SJ and Lee, C and Kim, WK and Ko, G}, title = {Lacticaseibacillus paracasei KBL382 contributes to the immunomodulation in THP-1 cells.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {2}, pages = {e2509016}, doi = {10.71150/jm.2509016}, pmid = {41802805}, issn = {1976-3794}, support = {2021R1I1A1A01048923//National Research Foundation of Korea/ ; //Ministry of Education/ ; RS-2022-NR067344//Ministry of Science and ICT/ ; }, mesh = {Humans ; THP-1 Cells/immunology ; *Immunomodulation ; *Probiotics/pharmacology ; Interleukin-1 Receptor-Associated Kinases/metabolism/genetics ; Lipopolysaccharides/immunology/pharmacology ; *Lacticaseibacillus paracasei/immunology/physiology/isolation &amp; purification ; Toll-Like Receptor 2/metabolism/genetics/immunology ; Monocytes/immunology/microbiology ; Interleukin-10/metabolism/immunology ; Interleukin-6/metabolism/immunology ; Suppressor of Cytokine Signaling 1 Protein/genetics/metabolism ; Signal Transduction ; Cytokines/metabolism ; Interleukin-12/metabolism ; Myeloid Differentiation Factor 88 ; }, abstract = {Gut microbiome imbalance can induce inflammatory responses via Toll-like receptor 2 (TLR2) signaling pathways. Lactobacillus spp., popularly applied as probiotics in both humans and animals, have come into the spotlight for their strong immunomodulatory effects. We aimed to evaluate the immunomodulatory potential of live or pasteurized Lacticaseibacillus paracasei (L. paracasei) KBL382, isolated from healthy Korean individuals, in an in vitro monocytic THP-1 cell model. Live L. paracasei KBL382 significantly increased TLR2 and MyD88 expressions and induced IRAK1 expression, irrespective of lipopolysaccharide (LPS) stimulation (p < 0.05). Under LPS stimulation, THP-1 cells treated with live L. paracasei KBL382 showed significantly increased interleukin (IL)-6 and IL-10 levels (p < 0.05). Pasteurized L. paracasei exhibited a decrease in IL-12 levels (p < 0.05). Moreover, live L. paracasei KBL382 also markedly elevated A20 and SOCS1 expressions, the critical negative regulators of inflammation, regardless of LPS stimulation (p < 0.05). The expression of IRAK3, another negative regulator of inflammation, was increased in THP-1 cells with live L. paracasei KBL382 under LPS stimulation (p < 0.05). Our findings demonstrate that L. paracasei KBL382 contributes to the immunomodulation in THP-1 cells by coordinating both positive and negative regulatory signaling. L. paracasei KBL382 could be used as a promising probiotic strain for attenuating chronic inflammation through the gut-immune axis mechanisms.}, }
@article {pmid41802666, year = {2026}, author = {Vashisht, E and Nguyen, H and Marques, FZ and Snelson, M}, title = {Diet, Gut Microbiota, and Intestinal Permeability: Emerging Mechanisms in Hypertension Pathogenesis.}, journal = {The Canadian journal of cardiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cjca.2026.03.005}, pmid = {41802666}, issn = {1916-7075}, abstract = {Hypertension is a leading contributor to global morbidity and mortality, arising from the interplay of genetic and environmental risk factors together with the dysregulation of multiple physiological systems involved in blood pressure control. Recent advances have established the gut as a central regulator, implicating the intestinal microbiota and barrier integrity in the modulation of blood pressure. Alterations in the gut microbial consortium, along with changes in levels of metabolites produced by the microbiota, have been associated with blood pressure regulation in both animal models and human studies. Key microbial metabolites, including short-chain fatty acids (SCFA), trimethylamine-N-oxide, and bile acids, influence endothelial function, immune activation, and renal signalling pathways. Concurrently, intestinal permeability facilitates the translocation of microbial products, such as lipopolysaccharides, triggering systemic inflammation, leading to renal and vascular dysfunction. Diet plays a pivotal role in shaping both microbiome composition and barrier integrity. Western-style diets rich in saturated fats, sugars, and processed additives promote gut dysbiosis and increased permeability, whereas fibre-rich, plant-based diets support microbial diversity, SCFA production, and tight-junction integrity. This review synthesises the current evidence linking diet, microbiota, and gut permeability to hypertension, integrating mechanistic insights from preclinical models with emerging human data. We propose a conceptual framework in which the gut serves as a modifiable target for the prevention and treatment of hypertension. By exploring dietary strategies that restore microbial balance and barrier function, this review underscores the potential of integrative, gut-targeted approaches to address a major global health burden.}, }
@article {pmid41802661, year = {2026}, author = {Hu, J and He, W and Liu, Z and Qiao, Q and Zhao, L and Li, Y and Ma, M and Yu, H and Shi, L and Huang, J}, title = {Differential effects of sulfide-induced transformation of biodegradable and conventional microplastics on sedimentary CO2 and CH4 emissions: Underlying microbiome-mediated mechanisms.}, journal = {Environmental research}, volume = {298}, number = {}, pages = {124216}, doi = {10.1016/j.envres.2026.124216}, pmid = {41802661}, issn = {1096-0953}, abstract = {The accumulation of microplastics (MPs) in sediments presents serious ecological risks. Although sulfidation is a key aging process in anoxic environments, its impact on sedimentary CO2 and CH4 emissions and underlying microbiome-mediated mechanisms remains unclear, particularly for biodegradable versus conventional MPs. Sediment incubation experiments with pristine and sulfidation-aged polyethylene (PE) and polylactic acid (PLA) revealed distinct carbon-related greenhouse gases patterns driven by material-specific microbial responses. Compared to controls, pristine PLA significantly enhanced cumulative CO2 and CH4 emissions by 4.47- and 2.59-fold, respectively, accelerating the CH4 emission peak due to its rapid carbon release. Conversely, sulfidation-aged PLA (PLA-S) reversed this trend, reducing CO2 emissions by 61.5%. This suppression was linked to an enriched microbiome (e.g., Acidobacteriota, ester-hydrolyzing Myxococcota) adapted to acidic stress, nitrogen fixation, and pathogenicity, likely diverted carbon flows. In contrast, sulfidation-aged PE (PE-S) exhibited surface oxidation, which led to a 36.7% increase in CH4 emissions, along with higher dissolved organic carbon (DOC) and microbial metabolic quotient (qCO2). This shift correlated with the enrichment of alkane-degrading Methylomirabilota and Bacillota, potentially converting plastic-derived carbon into methane. These findings emphasize the necessity of considering MPs' natural aging (e.g., sulfidation) and material types (degradable vs. conventional) when assessing their ecological risks and roles in CO2 and CH4 emissions, revealing key microbiome mechanisms linking MPs to the global carbon cycle.}, }
@article {pmid41802534, year = {2026}, author = {Darmadi, D and Muhame, AJ and Gerasimov, SG and Mirzaei, R and Karampoor, S}, title = {Microbiota metabolite lithocholic acid in cancer: Mechanisms and therapeutic potential.}, journal = {Experimental cell research}, volume = {}, number = {}, pages = {114981}, doi = {10.1016/j.yexcr.2026.114981}, pmid = {41802534}, issn = {1090-2422}, abstract = {The human gut microbiome is centrally implicated in host disease and health control via the production of a range of bioactive metabolites. Of these, lithocholic acid (LCA), a derivative of microbial metabolism secondary bile acid, has received attention owing to its multifaceted functions in cancer. LCA, a hydrophobic microbiota-derived bile acid, was implicated in carcinogenicity and hepatotoxicity even in the ancient era. In this sense, studies have found a contrasting role of LCA as a tumor promoter or tumor suppressor based on the molecular environment and type of tumor. Antitumor effects of LCA have also been observed in various cancers such as breast, prostate, colon, and neuroblastoma. Interestingly, LCA induces selective apoptosis of cancer cells through intrinsic and extrinsic pathways but without damaging normal cells, and the process is partly caspase-dependent. Mechanistically, LCA induces endoplasmic reticulum (ER) stress response, induces autophagy in certain cancer cell lines, and inhibits mitochondrial function, all contributing to its cytotoxic effect. It also causes oxidative and nitrosative stress through downregulation of nuclear factor erythroid 2-related factor 2 (NRF2)/Kelch-like ECH-associated protein 1(Keap1) pathway and induction of inducible nitric oxide synthase (iNOS) mediated through TGR5 and Chimeric antigen receptor (CAR) receptor activation. Besides its cytostatic action on itself, LCA was determined to have the capability to modulate the tumor microenvironment through immunomodulation and anti-inflammation, which are behind its therapeutic actions. Via its action on nuclear receptors like the vitamin D receptor (VDR), LCA has been shown to inhibit proteasome activity, create pores in membranes, and alter calcium uptake and epithelial integrity under conditions of oxidative stress. Because of its selective anticancer action, receptor-mediated signal activity, and microbiota origin, LCA is a good cancer drug candidate. This review discusses primarily the molecular processes through which LCA regulates cancer pathogenesis and determines its therapeutic potential based on preclinical and clinical data.}, }
@article {pmid41802308, year = {2026}, author = {Han, JY and Kim, MJ and Park, JW and Jeong, SY}, title = {Gut microbiome in colorectal cancer: recent advances and clinical implications.}, journal = {Annals of coloproctology}, volume = {42}, number = {1}, pages = {72-85}, pmid = {41802308}, issn = {2287-9714}, abstract = {The gut microbiome is not just a bystander of colorectal carcinogenesis but is an active driver of colorectal cancer (CRC). CRC-associated microbiome contributes in the tumorigenesis through chronic inflammation, formation of toxic metabolite and genotoxins, oncogenic signal activation, immune evasion, and barrier disruption-all reinforcing a tumor microenvironment. In contrast, beneficial microbiome supports the barrier-immune-metabolic axis by maintaining mucosal integrity and balanced immune tone. Despite extensive studies of microbiome-based CRC biomarkers, microbiome-based CRC biomarkers have not been yet ready for routine clinical use due to variation across populations and lack of standardization of key steps such as sampling, analysis, cutoffs, and interpretation. Microbiome-based therapies aim to change the overall intestinal ecosystem rather than simply adding or removing single strains. At present, dietary modulation and prebiotics are considered supportive measures, while probiotics or synbiotics are in preclinical stage. Fecal microbiota transplantation (FMT) still faces important challenges in effectiveness, standardization and safety. By its role in reshaping the tumor-host immune environment, FMT is viewed as a potential option for cancer therapy after further development through well-controlled clinical trials with careful safety monitoring.}, }
@article {pmid41802201, year = {2026}, author = {Pettersen, VK and Ponsero, AJ and Jian, C and Riumin, A and Kurilshikov, A and Moyo, SJ and Justine, M and Klingenberg, C and Debelius, J and Valles-Colomer, M and Noordzij, HT and Zhernakova, A and Korpela, K and Esteban-Torres, M and Brusselaers, N}, title = {Off to a good start: Current gaps and priorities in early-life microbiome research.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag010}, pmid = {41802201}, issn = {1574-6976}, abstract = {Early-life microbial exposures are essential for optimal development of human physiology. Yet, understanding of the human microbiome during pregnancy and childhood is still far from being complete. To identify knowledge gaps and establish research priorities, a multidisciplinary expert panel used the Delphi method for consensus development and conducted a literature search on early-life microbiome determinants. Responses from 55 researchers from an online survey were analyzed alongside keyword frequency from 20 501 publications. This approach enabled us to categorize existing evidence and highlight areas requiring investigation. While the main routes for mother-to-child bacterial transmission and their contributions to the newborn microbiome have been studied, many gaps remain. Priority areas include non-bacterial microbes, ecological principles of colonization, environmental and social influences, body sites beyond the gut, and factors affecting the maternal microbiome and its effects on the child's microbiome. Significance of factors such as hygiene habits, non-antibiotic medications, and pollution remains to be uncovered. Knowledge is also limited on postnatal microbial sharing via household contacts and shared environments (e.g. family members, peers) and the contribution of these pathways to microbiome assembly. We hope this report will guide and inspire future research into the early-life microbiome as a modifiable factor in reducing disease risk.}, }
@article {pmid41802195, year = {2026}, author = {Liu, GP and Li, ZC and Li, Q and Zheng, ZG and Lin, FB and Zhang, GY and Zhang, ZM and Li, S and Li, T and Zhao, JD}, title = {Microalgal delivery of recombinant fish interferon modulates gut microbiota and enhances antiviral immunity in fish.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {215}, number = {2}, pages = {}, doi = {10.1093/jimmun/vkaf304}, pmid = {41802195}, issn = {1550-6606}, support = {XDB0730300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 92251304//National Natural Science Foundation of China/ ; 202001539//Qidong-SLS Innovation Fund/ ; 32322086//Peking University, National Excellent Youth Science Fund/ ; 32073009//National Natural Science Foundation of China/ ; //Youth Innovation Promotion Association/ ; 2023YFD2400201//National Key Research and Development Program of China/ ; 32173023//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; Zebrafish/immunology ; *Fish Diseases/immunology ; *Interferons/genetics/immunology/administration &amp; dosage ; Recombinant Proteins/immunology/genetics ; *Microalgae ; *Antiviral Agents ; *Herpesviridae Infections/immunology/veterinary ; Herpesviridae/immunology ; Carps/immunology ; }, abstract = {Viral infections remain a challenge to aquaculture, resulting in severe economic losses and threatening fish health worldwide. As a key immunomodulatory and antiviral factor, interferon (IFN) plays a crucial role in regulating immune responses. We constructed a high-level expression strain of recombinant interferon (Rec-IFN) using Synechococcus sp. PCC 7002, which also served as a delivery system, and evaluated its efficacy as a dietary immunostimulant in gibel carp (Carassius gibelio) and zebrafish (Danio rerio). Analysis of the intestinal microbiome indicated that the Rec-IFN diet promoted beneficial bacteria such as Cetobacterium while reducing opportunistic pathogens including Aeromonas and Vibrio in gibel carp. Notably, after Cyprinid herpesvirus-2 (CyHV-2) infection, the Rec-IFN diet enhanced microbial connectivity, helping to preserve gut microbiota function. In zebrafish, the Rec-IFN diet increased species richness and evenness, while reducing opportunistic pathogens such as Vibrio. Transcriptomic analysis revealed specific activation of the Toll-like receptor signaling pathway and a reduction of immune overstimulation following infection in zebrafish. Our findings demonstrate that the Rec-IFN diet significantly enhanced the host IFN response and alleviated virus-induced damage to intestinal and immune organs, reduced viral load, and decreased mortality. This research offers a protective effect by reducing the severity of infections caused by both DNA virus (CyHV-2) and RNA virus (SVCV). It provides new insights into the application of Rec-IFN microalgae as an effective oral immunotherapeutic strategy for reducing losses from viral infections in aquaculture.}, }
@article {pmid41801733, year = {2026}, author = {Imam, IA and Morey, T and Jiang, Y and Wang, D and Xu, D and Shao, Q}, title = {Discovering naturally occurring antifreeze peptides from microbiome by integrating protein language models and molecular dynamics simulation.}, journal = {Journal of materials chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5tb02758f}, pmid = {41801733}, issn = {2050-7518}, abstract = {Antifreeze peptides inhibit ice crystal growth and recrystallization, and are promising components of cryoprotective formulations for cell, tissue, and food preservation, as well as anti-icing surface coatings. However, the discovery of new antifreeze peptides has been hindered by their sequence diversity and the limited scalability of experimental screening. In this study, we identify novel antifreeze peptide candidates from a microbiome-derived sequence library using ensemble machine learning and molecular dynamics (MD) simulations. We developed an ensemble classifier composed of 10 adapter-tuned protein-language models and a random forest meta-learner. After training on a curated dataset of 73 766 sequences, we applied this ensemble to 56 008 amino acid sequences from an Arctic microbiome library to identify antifreeze peptide candidates. Structural prediction yields a diverse range of conformations for six selected candidates, including α-helices, coils, and combinations of both. To evaluate their functional relevance, atomistic MD simulations were conducted to assess conformational stability and solvent interactions under freezing conditions. One candidate shows persistent helicity, surface amphipathicity, and an organized hydration pattern consistent with structural signatures reported for ice-binding helices. These findings expand the known landscape of antifreeze peptides and highlight a scalable strategy for discovering functional peptides from complex biological sources.}, }
@article {pmid41801404, year = {2026}, author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH}, title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {75}, number = {4}, pages = {}, pmid = {41801404}, issn = {1432-0851}, support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; }, mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; }, abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.}, }
@article {pmid41801284, year = {2026}, author = {Wang, J and Ge, H and Liu, Y and Huang, C and Zhang, L and Yu, Y and Xu, L and Fang, H}, title = {Earthworm gut microbiome promotes biodegradation of albendazole in soil.}, journal = {Crop health}, volume = {4}, number = {1}, pages = {}, pmid = {41801284}, issn = {2948-1945}, support = {2023YFD1902903//National Key Research and Development Program of China/ ; 42177252//National Natural Science Foundation of China/ ; 2023C02039-01//Leading Goose" R&amp;D program of Zhejiang Province of China/ ; }, abstract = {The excretion of the anthelmintic drug albendazole (ALB) from treated animals into the soil, as well as its widespread application as a fungicide, poses a serious ecological risk to the soil environment. In this study, we investigated the degradation of ALB in soil and its bioaccumulation in earthworms, changes in the microbiome and degradation genes, and the effect of zinc oxide nanoparticles on the degradation and enrichment behaviors of ALB and microbial community structure and function. Our findings showed that ALB selectively enriched specific albendazole degradation genes (i.e., hmr and ami) in the earthworm, preferentially activating the pathways associated with sulfur reduction, amination of ALB sulfone, and hydroxylation of ALB. Metagenomic analysis revealed that the relative abundances of ppo, xylA, cutC, and nfsl in the earthworm gut were 0.19-52.64-fold higher in the ALB treatment than in the control, indicating their potential dominance in ALB biodegradation. Network analysis further identified potential bacterial hosts carrying biodegradation genes and albendazole degradation genes. Notably, Sphaerobacter, Saccharothrix, Actinomadura, and Nocardia were recognized as potential dual hosts of biodegradation genes and albendazole degradation genes, displaying a 0.05-1.32-fold elevation in relative abundance in ALB-treated earthworm guts compared to the control. Additionally, ZnO nanoparticles were found to reduce ALB bioaccumulation in earthworms and accelerate its dissipation in soil. These findings provide novel insights into the bioremediation mechanisms of pesticides in soil-earthworm ecosystems.}, }
@article {pmid41801038, year = {2026}, author = {Manninen, J and Korhonen, A and Johnson, KL and Tahvonen, O and Luukkonen, A and Saarenpää, M and Puhakka, R and Uimonen, L and Kummola, L and Skevaki, C and Renz, H and Rajaniemi, J and Laitinen, OH and Roslund, MI}, title = {Playgrounds as microbial interfaces: strategies to enhance soil microbiomes and support healthy childhoods.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0166225}, doi = {10.1128/msystems.01662-25}, pmid = {41801038}, issn = {2379-5077}, abstract = {Emerging evidence suggests that reduced exposure to biodiversity, including rich environmental microbiota, is associated with negative outcomes in the health and well-being of children. Biodiversity loss not only impacts individual health but also poses significant threats to planetary health. It destabilizes systems that regulate climate, purify air and water, maintain soil fertility, and support plant and microbial life essential for environmental health. Here, we review the scientific evidence on microbiome-supportive strategies in eco-centric, child-friendly playground environments. Investigating how environmental features influence soil microbiomes and exposure pathways could provide insights into how playgrounds function as living interfaces. These are places where environmental microbes shape children's microbial colonization patterns, immune and endocrine regulatory systems, while also contributing to ecosystem services such as biodiversity support and pollutant mitigation-particularly relevant given that many pollutants are known to disrupt immune and endocrine functions in children. These dynamics have far-reaching implications for child well-being, preventive health strategies, physical activity, environmental literacy, and broader sustainability. A multi-omic systems approach offers a critical pathway to uncover the ecological and health-related impacts of nature-associated microbial exposure and characterize host-microbiome interactions underlying immune and endocrine regulation, brain development, cognition, and stress-related disorders. Our review highlights a lack of such integrative studies, underscoring the need to advance this line of research to inform evidence-based, sustainable, and health-promoting urban design.}, }
@article {pmid41801026, year = {2026}, author = {Starodubova, AV and Kislyak, OA and Demidova, TY and Nikitin, IG and Leonov, GE}, title = {[The gut microbiome in obesity: new horizons in personalized medicine].}, journal = {Terapevticheskii arkhiv}, volume = {98}, number = {2}, pages = {92-98}, doi = {10.26442/00403660.2026.02.203596}, pmid = {41801026}, issn = {0040-3660}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Obesity/microbiology/metabolism/therapy/physiopathology ; *Precision Medicine/methods ; *Dysbiosis/microbiology ; }, abstract = {Currently, disturbances in the composition and metabolic activity of the intestinal microbiota are considered a key modifiable factor in obesity and associated metabolic disorders. This review summarizes data on the characteristics and variability of the microbiota composition in individuals with obesity. The main mechanisms linking dysbiosis to metabolic disorders are discussed: changes in the production of short-chain fatty acids and other microbial metabolites, as well as the contribution of lipopolysaccharide-induced chronic inflammation. The influence of the microbiota on the regulation of appetite and eating behavior through the microbiota-gut-brain axis and intestinal hormones is discussed separately. Current approaches to the diagnosis of dysbiosis and potential strategies for correcting microbiome-associated disorders in obesity in the context of personalized medicine are presented.}, }
@article {pmid41800924, year = {2026}, author = {Palou, R and van der Sloot, AM and Fiebig, AA and Zangara, MT and Sangwan, N and Sánchez-Osuna, M and Ilyas, B and Zubyk, H and Cook, M and Wright, GD and Coombes, BK and Tyers, M}, title = {A yeast synthetic biotic platform for delivery of therapeutic nanobodies to ameliorate gastrointestinal inflammation.}, journal = {Disease models &amp; mechanisms}, volume = {19}, number = {2}, pages = {}, doi = {10.1242/dmm.052620}, pmid = {41800924}, issn = {1754-8411}, support = {//Weston Family Foundation/ ; //Genome Canada/ ; PJT-180315/CAPMC/CIHR/Canada ; FDN-167277/CAPMC/CIHR/Canada ; //Genome Quebec/ ; }, mesh = {Animals ; *Single-Domain Antibodies/therapeutic use/administration &amp; dosage/pharmacology ; *Saccharomyces boulardii/metabolism ; Colitis/pathology/drug therapy/microbiology ; *Inflammation/pathology/drug therapy ; Mice, Inbred C57BL ; Tumor Necrosis Factor-alpha/metabolism/immunology ; *Gastrointestinal Tract/pathology/microbiology ; Mice ; *Drug Delivery Systems ; }, abstract = {Protein-based pharmaceuticals, such as engineered antibodies, form a major drug class of steadily increasing market share. However, these biologic medicines are costly to manufacture, are subject to strict supply chain and storage constraints, and often require invasive administration routes. Engineered microbes that secrete bioactive products directly within the microbiome milieu may mitigate these challenges. Here, we describe a cell microfactory platform based on the probiotic yeast Saccharomyces boulardii for the production of nanobody biologics in the gastrointestinal (GI) tract. High-level secretion of nanobodies by S. boulardii was achieved by optimizing promoters, secretion signals and antibody formats. In mice, oral gavage of S. boulardii allowed efficient and transient colonization of the colonic compartment, and in situ production of a therapeutic nanobody directed against tumor necrosis factor (TNF). In a mouse model of chemical-induced colitis, GI-delivery of anti-murine TNF nanobody via live S. boulardii improved both survival and disease severity without causing overt perturbation of microbiome composition. These results position S. boulardii as a synthetic biotic platform for the in situ production and delivery of protein-based therapeutics to the GI tract.}, }
@article {pmid41800916, year = {2026}, author = {Vishnoi, V and Hoedt, EC and Zhao, M and Carroll, R and Kanakaratne, S and Lott, N and Pockney, P and Smith, SR and Keely, S}, title = {16S rRNA Amplicon Sequencing of the Intraoperative Surgical Site Demonstrates an Aberrant Microbiota Which Can Predict Colorectal Surgical Site Infection.}, journal = {ANZ journal of surgery}, volume = {}, number = {}, pages = {}, doi = {10.1111/ans.70578}, pmid = {41800916}, issn = {1445-2197}, support = {Doctor in Training Grant//Avant Foundation/ ; }, abstract = {INTRODUCTION: Surgical Site Infection (SSI) of an abdominal incision is a dreaded infectious complication following colorectal surgery. Understanding the intraoperative microbiology holds the key to prevention. Genomic sequencing has revolutionised culture-independent techniques, allowing for a more sensitive tool in microbial detection. The purpose of this study is to determine whether an aberrant microbiota is present within the intraoperative surgical site in patients that develop an SSI.<br><br>METHODS: The subcutaneous abdominal surgical site of patients undergoing elective bowel resection was opportunistically sampled, following fascial closure. DNA was recovered from the swabs and used for 16S rRNA gene amplicon sequencing. The intraoperative microbiota was compared in those with and without a subsequent SSI with focus on alpha diversity and beta diversity, as well as taxonomic composition.<br><br>RESULTS: 16/123 patients developed an SSI. The bacterial profile within the surgical site showed a strong presence of obligate anaerobes in all patients. Chao1, Shannon, and Simpson measures of alpha diversity from the intraoperative swabs were all significantly increased in SSI patients (p&#x2009;=&#x2009;0.05, 0.05 and 0.05, respectively). Beta diversity demonstrated no significant separation between patients (Bray-Curtis dissimilarity index, PERMANOVA p&#x2009;=&#x2009;0.394).<br><br>CONCLUSIONS: To the best of our knowledge this is the first study to demonstrate an aberrant intraoperative microbiota of the surgical site associated with subsequent infection. Pending validation studies, this provides a target for the strategic manipulation of the surgical site to reduce the burden of infection.}, }
@article {pmid41800893, year = {2026}, author = {Ge, T and Zhao, T and Ruan, Y and Ye, L and Xiao, Y and Xiao, F and Li, Y and Li, X and Wang, R and Hu, H and Lu, C and Sun, H and Zhang, C and Yu, G and Zhang, T}, title = {Dysbiosis of fecal virome in pediatric Crohn's disease and its dynamic changes during infliximab therapy.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0148925}, doi = {10.1128/msystems.01489-25}, pmid = {41800893}, issn = {2379-5077}, abstract = {UNLABELLED: The gut virome is an emerging but underexplored component of the human microbiota, especially in pediatric Crohn's disease (CD). This study aimed to characterize the fecal virome in children with CD and evaluate its association with clinical response to infliximab (IFX) therapy. A total of 85 participants, including 60 pediatric CD patients and 25 healthy controls (HC), were recruited. Among the CD patients, 53 received ≥3 IFX infusions, 41 achieved remission (IFX-R), and 12 did not (IFX-NR). Viral-like particles in fecal samples were enriched and profiled by metagenomic sequencing, while bacterial communities were assessed via 16S rRNA gene sequencing. Pediatric CD patients exhibited significantly reduced viral richness and altered viral community compared to HCs. Functional analyses revealed that CD patients exhibit a shift in fecal virome function from DNA repair to viral replication and assembly. Trans-kingdom correlations were disrupted in CD, particularly between Torque teno viruses and beneficial bacteria, such as Blautia. An integrated machine learning model combining viral and bacterial markers achieved a certain level of diagnostic accuracy for pediatric CD (area under the curve [AUC] = 89.3%). IFX treatment influences the gut virome, with remission associated with higher abundances of Microviridae and Siphoviridae, while Anelloviridae, Myoviridae, and Podoviridae were enriched in IFX-NR at baseline. These findings suggest the virome as a potential biomarker for predicting clinical outcome in pediatric CD, offering a novel avenue for disease diagnosis and personalized treatment strategies.<br><br>IMPORTANCE: Crohn's disease (CD) in children poses a growing clinical challenge, with increasing incidence and variable response to biologic therapies such as infliximab (IFX). While gut bacterial dysbiosis has been extensively studied, the role of the gut virome in pediatric CD remains largely unexplored. This study provides the first longitudinal characterization of the fecal virome in children with CD undergoing IFX therapy. We reveal distinct viral community patterns, functional alterations, and virus-bacteria interactions in pediatric CD patients. Notably, integration of virome and bacteriome profiles enhances diagnostic accuracy, offering a promising avenue for predictive biomarker development. Furthermore, virome changes may be associated with the IFX treatment outcomes in children with CD. These findings highlight the gut virome as a critical but overlooked dimension of host-microbiome interactions in pediatric CD, with potential implications for personalized therapy and mechanistic understanding of treatment resistance.}, }
@article {pmid41727074, year = {2026}, author = {Regan, MR and McDevitt, CJ and Robinson, LR and Issifou, S and Wadsworth, CB}, title = {Put your money where your mouth is: Surveillance of antibiotic resistance within the commensal Neisseria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41727074}, issn = {2692-8205}, abstract = {Commensal Neisseria species are major reservoirs of adaptive genetic variation, including antimicrobial resistance, for their pathogenic relatives, yet they remain poorly characterized. This gap limits our ability to anticipate resistance mechanisms that may ultimately emerge Neisseria gonorrhoeae and N. meningitidis. Here, we analyzed 166 novel commensal Neisseria isolates collected from 31 study participants and measured minimum inhibitory concentrations (MICs) for seven antimicrobials: azithromycin, cefixime, ceftriaxone, ciprofloxacin, doxycycline, and gentamicin. Resistance, defined using the Clinical and Laboratory Standards Institute (CLSI) guidelines, was highly prevalent for azithromycin (76%) and doxycycline (52%), while no resistance to gentamicin was observed. High-level doxycycline resistance was always associated with inheritance of tetM. Reduced susceptibility to azithromycin was linked to an MtrD K823E substitution, and reduced susceptibility to ciprofloxacin was associated with GyrA T91I (N. subflava) or S91V (N. mucosa). The PenA 312M mutation was associated with significantly elevated ceftriaxone and cefixime MICs. Across all antimicrobials, MICs varied widely, indicating the presence of additional modulating mutations. Finally, the genetic determinants underlying low-level doxycycline resistance and reduced penicillin susceptibility remain unresolved. Overall, here we continue to build on the foundation of surveillance efforts in the commensal Neisseria, and continue to flesh out what is known and unknown about this early warning system - or canary in the coal mine - for emerging resistance and clinically consequential evolution in pathogenic Neisseria.}, }
@article {pmid41800606, year = {2026}, author = {Kabir, K and Afzal, I and Haider, K and Naiem, F and Li, X and Zhang, H}, title = {Cuticle-associated microbiota in Bactrocera dorsalis suppress fungal infection through immune and chemical defenses.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70704}, pmid = {41800606}, issn = {1526-4998}, support = {//This study was supported by the National Natural Science Foundation of China (No. 32220103009), the China Agriculture Research System of MOF and MARA (CARS-26), and the Hubei Hongshan Laboratory./ ; }, abstract = {BACKGROUND: Cuticular microbial communities influence insect-pathogen interactions, yet their protective roles remain incompletely understood. These microbial defenses are critical in pest species like Bactrocera dorsalis, where microbial symbionts may shape resistance to biological control agents.<br><br>RESULTS: We show that the cuticular microbiota of Bactrocera dorsalis enhances resistance to the entomopathogenic fungi (EPF) Beauveria bassiana and Isaria fumosorosea through dual immune and chemical mechanisms. Gnotobiotic assays demonstrate that specific bacterial isolates (Microbacterium, Psychrobacter, and Staphylococcus) promote host survival and defense by stimulating Toll/IMD signaling pathway and up-regulating antimicrobial peptides (AMPs) such as defensin, attacin, and cecropin. In contrast, non-cuticle-associated bacteria (Escherichia coli and Staphylococcus aureus) failed to enhance survival and immune responses, indicating that protection is microbiota-specific rather than a result of general bacterial exposure. In parallel, bacterial volatiles, such as phenol, indole, and eicosane, along with extracellular enzymes including chitinase, cellulase, protease, and lipase, suppressed fungal germination and hyphal growth. Importantly, these protective effects were found to vary with host age, indicating age-dependent modulation of microbiota-mediated defense.<br><br>CONCLUSIONS: Our findings revealed that cuticle-associated bacteria protect their host through complementary immune and chemical pathways. These microbiota act as an active barrier, and microbial metabolism interacts with host immune signaling. By distinguishing specific cuticle-derived effects from non-specific bacterial stimulation, this study highlighted the role of microbiota in modulating fungal susceptibility and supports their application in developing next-generation biocontrol strategies in pest management. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid41800525, year = {2026}, author = {Pai, YC and Yu, LC}, title = {Application of Artificial Intelligence-Powered Research in Gastrointestinal Pathophysiology: Unveiling Intestinal Pathobionts and Microbiota Dysbiosis.}, journal = {Journal of physiological investigation}, volume = {}, number = {}, pages = {}, pmid = {41800525}, issn = {2950-6344}, }
@article {pmid41800490, year = {2026}, author = {Weng, YH and Chen, PC and Ruan, JW}, title = {Host-mediated Remodeling of the Gut Microbiota in Energy Homeostasis and Environmental Resilience.}, journal = {Journal of physiological investigation}, volume = {}, number = {}, pages = {}, doi = {10.4103/ejpi.EJPI-D-25-00028}, pmid = {41800490}, issn = {2950-6344}, }
@article {pmid41800457, year = {2026}, author = {Zhang, X and Fu, Y and Liu, S and Zhang, J and Xu, F and Zhang, C and Wang, Y and Huo, C}, title = {Carrier-free supramolecular architectonics of quercetin-berberine for safety-redefined therapy of ulcerative colitis.}, journal = {Materials today. Bio}, volume = {37}, number = {}, pages = {102970}, pmid = {41800457}, issn = {2590-0064}, abstract = {Ulcerative colitis (UC) poses significant clinical management challenges due to the limited efficacy and substantial safety burdens of existing treatments. This study develops a carrier-free supramolecular nanoassembly (QB) composed solely of quercetin (QU) and berberine (BBR), reshaping the safety-efficacy profile of these natural drugs at the nanoscale. Spectroscopic characterization and molecular dynamics simulations reveal that QU and BBR synergistically self-assemble into stable nanoparticles driven primarily by hydrogen bonding and π-π stacking, resulting in a highly negative surface charge and superior colloidal stability. In vitro and in vivo experiments demonstrate that QB markedly reduces BBR's cytotoxicity, expanding its therapeutic dose window by approximately 16-fold, while concurrently enhancing anti-inflammatory, antioxidant, and epithelial barrier repair effects in LPS-stimulated macrophages and DSS-induced UC mice. In vivo fluorescence imaging and tissue distribution indicate selective accumulation of orally administered QB in the inflamed colon and spleen, suggesting dual local intestinal and systemic immune modulatory capabilities. Transcriptomic and gut microbiome analyses further uncover QB's coordinated downregulation of inflammation-related signaling pathways, upregulation of metabolic and antioxidant modules, and restoration of microbial diversity and community homeostasis. Compared to QU or BBR monotherapy and 5-aminosalicylic acid, QB exhibits superior overall efficacy in alleviating colitis symptoms and tissue damage, with excellent biocompatibility, offering a scalable platform for safety-redefined, multidimensional precision interventions in UC based on natural small-molecule self-assembly.}, }
@article {pmid41800422, year = {2026}, author = {Bueno, CPAR and Domínguez, AC and Guyonnet, D and Pouteau, E}, title = {Health benefits of Bifidobacterium animalis subsp. lactis BB-12 in infants and children: a mini-review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773473}, pmid = {41800422}, issn = {1664-302X}, abstract = {The colonization of the infant gut microbiome during the critical window of 0-3 years is influenced by a multitude of prenatal, environmental and host factors, and may be crucial for life-long health. The infant gut microbiome is highly dynamic, with bifidobacteria-dominance generally established during birth and lactation, followed by transition to a more stable and adult-like composition reached around 3 years of age. Bifidobacteria-dominance in infancy is considered protective as they not only display both anti-inflammatory and immunomodulatory effects but also foster the establishment of other beneficial species via cross-feeding interactions. As predominance of bifidobacteria is considered the marker of a healthy breastfed infant, the use of bifidobacteria-based probiotics for the prevention of gut dysbiosis and related conditions has been investigated. This clinically oriented summary highlights the unmet research needs of Bifidobacterium animalis subsp. lactis, BB-12[®] (BB-12), a well-studied probiotic added to baby formulas, dietary supplements, and fermented milk products; several potentially beneficial attributes, including acid and bile tolerance, strong adherence properties, pathogen inhibition, and immune modulation are considered. Clinical studies have demonstrated the safety and beneficial effects of BB-12 in infants and children across multiple disorders and highlight the need for improved clinical and regulatory guidelines.}, }
@article {pmid41800418, year = {2026}, author = {Ye, H and Wong, A and Chen, X and Sun, W and He, H and Li, X and Wu, J}, title = {Dynamic remodeling of skin microbiota during healthy homeostatic and wound repair conditions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1781606}, pmid = {41800418}, issn = {1664-302X}, abstract = {The skin microbiota is a fundamental component of the cutaneous ecosystem and plays an important role in maintaining skin homeostasis through immune education, maintenance of the skin barrier, colonization resistance, and regulation of the physiological environment under healthy conditions. Skin injury disrupts this balanced microbial ecosystem, resulting in marked changes in the local microenvironment. However, the processes by which skin microbiota reorganise following injury and contribute to the restoration of a remodelled homeostatic ecosystem after wound repair are not fully understood. This review synthesizes current knowledge on host-microbiota interactions across the dynamic transition from healthy skin to wounded skin and to remodeled homeostatic skin. We highlight the functions of commensal microorganisms during the inflammatory, proliferative, and remodeling phases of wound healing, with a particular focus on their roles in the resolution of inflammation, tissue regeneration and barrier restoration. Finally, we discuss emerging microbiota-based therapeutic opportunities for wound management and outline key challenges and future research directions aimed at promoting long-term restoration of skin microbial homeostasis.}, }
@article {pmid41800416, year = {2026}, author = {Bustos, ML and Song, K and Brochu, HN and Zhang, Q and Iyer, LK and Icenhour, CR}, title = {Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1707004}, pmid = {41800416}, issn = {1664-302X}, abstract = {INTRODUCTION: The nasopharyngeal microbiome plays a critical role in respiratory health and disease and is a major focus of metagenomic research. However, inconsistent reporting practices across studies limit reproducibility, dataset usability, and cross-study integration, thereby reducing the overall scientific value of publicly available nasopharyn.<br><br>METHODS: A systematic review was conducted to evaluate the impact of non-standardized reporting on reproducibility, usability, and integration of nasopharyngeal metagenomic datasets. A total of 988 studies were screened, and 227 manuscripts met predefined inclusion and exclusion criteria for full-text review. Methodological reproducibility, metadata completeness, and compatibility between reported laboratory methods and deposited datasets were assessed. Reproducible datasets were further analyzed to evaluate the interchangeability of nasopharyngeal aspirates and nasopharyngeal swabs.<br><br>RESULTS: Only 78 studies (34%) contained methods sections sufficient for reproducibility, and of these, 33 studies (15%) provided analytically sufficient metadata to support secondary analysis. Mismatches between reported laboratory methods and deposited datasets were identified in 4% of studies. These deficiencies were primarily attributed to incomplete methodological reporting, inaccessible or insufficient metadata, and incompatible file formats. Comparative analysis of reproducible datasets demonstrated significant differences in microbial profiles between nasopharyngeal aspirates and nasopharyngeal swabs, confirming that these specimen types are not interchangeable within a study.<br><br>DISCUSSION: The findings demonstrate that inadequate reporting standards substantially impair the reproducibility, reuse, and integration of nasopharyngeal metagenomic data. The observed methodological and metadata inconsistencies limit the reliability of downstream analyses and cross-study comparisons. Standardized reporting guidelines are urgently needed to improve transparency, ensure reproducibility, and enhance the integrative potential of nasopharyngeal microbiome research. Adoption of comprehensive and consistent reporting practices would significantly strengthen the scientific rigor and utility of metagenomic studies in this field.}, }
@article {pmid41800415, year = {2026}, author = {Panek, J and Gryta, A and Maj, W and Mącik, M and Oszust, K and Pertile, G and Pylak, M and Siegieda, D and Hallama, M and Hatano, R and Kandeler, E and Pathan, SI and Pietramellara, G and Malusa, E and Weber, J and Turnau, K and Różalska, S and Frąc, M}, title = {Plant-soil-microbiome interactions: mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1762743}, pmid = {41800415}, issn = {1664-302X}, abstract = {The focus of this article is to summarize current knowledge of plant-associated microbiomes, which play a key role in plant health and in maintaining soil quality. Such microbiomes, comprising bacteria, fungi, archaea, algae, nematodes, and protists, perform various functions, including nutrient transformation, pathogen protection, and stress mitigation. Microbial communities are commonly used as an indicator of ecosystem health. Soil microbiome diversity depends on environmental factors (including biotic and abiotic stresses), which can alter microbial composition, thereby modifying microbial interactions and plant resilience. Biofertilizers, biopreparations, and microbial inoculants or consortia have been utilized in agriculture to enhance soil properties, such as microbial diversity and enzymatic activity, and to prime plant immune responses, thereby promoting plant growth and health. Biofertilizers can significantly help plants adapt to environmental stresses and climate change, mitigating drought stress and reducing greenhouse gas emissions. Recent advances in DNA sequencing technologies, the computing power available to scientists, and the development of bioinformatics tools have made microbial community studies widely accessible. These tools enable the research and modeling of changes in the soil microbiome, plant disease susceptibility, and soil health. Multi-omics approaches to microbiomes are key to characterizing the microbiome and predicting plant diseases. Future research should focus primarily on understanding the interactions among soil, plants, and microbiomes. This approach will help develop climate-resilient plants and improve the health and functionality of agroecosystems. Key efforts closely aligned with the European Union's goals and biodiversity strategies for sustainable agriculture and soil health restoration, as presented in this review, include studying the structures and functions of soil microbiomes, developing new assays, and designing and investigating microbial consortia to restore healthy communities. These strategies address contemporary challenges in agriculture, including vertical and urban farming and superfood production.}, }
@article {pmid41800413, year = {2026}, author = {Fang, J and He, X and Zhou, J}, title = {Multi-site microbiota crosstalk in the postmenopausal: from dysbiosis mechanisms to precision interventions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1702700}, pmid = {41800413}, issn = {1664-302X}, abstract = {Persistent estrogen deficiency in postmenopause reshapes the gut-vaginal-urinary ecosystems, contributing to multisystem dysfunction through interconnected dysbiosis. Cross-niche microbial interactions amplify systemic risks: gut-derived toxins are linked to vascular inflammation, vaginal dysbiosis facilitates urinary pathogen colonization, and bile acid disruption impairs bone-immune homeostasis. This review synthesizes current mechanistic evidence illustrating how microbial networks propagate postmenopausal comorbidities. We propose the framework of "Postmenopausal Microbiota Network Medicine" which integrates microbial dynamics with host omics to transition from symptomatic management toward root-cause interception by strengthening microbial network resilience.}, }
@article {pmid41800410, year = {2026}, author = {Kumar, S and Dutta, R and Auji, R and Wackchaure, GC and Jayalakshmi, K and Karuppaiah, V and Mahajan, V}, title = {Microbial succession and tissue-specific restructuring of bacterial and fungal communities during post-harvest onion bulb rotting.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1776996}, pmid = {41800410}, issn = {1664-302X}, abstract = {Despite being a relatively hardy bulb crop with a longer shelf life than many fresh vegetables, onions are susceptible to substantial postharvest losses due to microbial spoilage. This study used high-throughput amplicon sequencing to characterize the bacterial and fungal microbiomes associated with healthy (HB), mildly rotten (MRB), and severely rotten (SRB) onion bulbs. Microbial communities were analysed across three distinct bulb tissues comprising neck tissue (NT), outer scale (OS), and central tissue (CT), to generate stage-specific and tissue-specific microbiome profiles. The microbial community analysis based on over 2 million Illumina NGS reads revealed the presence of 85 bacterial OTUs and 53 fungal OTUs across nine bulb samples. Bulb deterioration was marked by pronounced microbial succession, with bacterial diversity increasing from healthy bulbs (8 genera) to mildly rotten bulbs (36 genera), followed by a sharp decline in severely rotten bulbs (11 genera). Several bacterial genera, including Lactobacillus, Novosphingobium, Sphingobium, Pluralibacter, Acetobacter, Gluconobacter and Pantoea, emerged exclusively in rotten bulbs and were absent in healthy tissues, indicating their association with the onion bulb rot. The microbiome of SRB was marked by an overwhelming dominance of Lactobacillus (33.2% in SRB-CT, 16.9% in SRB-NT, 10.8% in SRB-OS), Acetobacter (16.1% in SRB-CT, 15.6% in SRB-NT, 7.0% in SRB-OS), Carnimonas (57.0% in SRB-NT), and Gluconobacter (14.5% in SRB-OS). Fungal communities exhibited a similar successional pattern: healthy bulbs showed negligible fungal presence except in the neck tissue (HB-NT), whereas mildly rotten bulbs showed a sharp increase in fungal diversity dominated by Meyerozyma (21.7%), Blastobotrys (13.3%), and Penicillium (7.0%). In severely rotten bulbs, fungal diversity declined, with Pichia (48.3%) and Kazachstania (8.6%) becoming dominant. Differential abundance analysis using edgeR identified six bacterial genera (Lactobacillus, Novosphingobium, Acetobacter, Pluralibacter, Carnimonas, and Dysgonomonas) and two fungal genera (Pichia and Kazachstania) that exhibited significant stage-dependent shifts during bulb rot progression. Alpha- and beta-diversity analyses revealed strong tissue-specific structuring of fungal communities, identifying the neck region as the primary fungal succession zone. Overall, this study elucidates the ecological restructuring of bacterial and fungal communities during onion bulb deterioration, and would pave the way for devising microbiome-informed interventions to reduce postharvest losses in onions.}, }
@article {pmid41800399, year = {2026}, author = {Xiang, S and Tian, D and Chen, J and He, Z and Wei, L and Qin, L and Li, C and Li, B}, title = {Divergent sucker-corm endophytic microbiota underpins the progressive decline of Fusarium-wilt incidence in resistant bananas across ratoon cycles.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1676292}, pmid = {41800399}, issn = {1664-302X}, abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), threatens global banana production. Resistant cultivars exhibit reduced disease incidence after successive ratoon cycles, but the underlying micro-ecological mechanisms remain unclear. This study represents the first longitudinal analysis of corm endophytic microbiota across ratoon cycles in banana, revealing temporal dynamics that underpin progressive disease resistance. A three-cycle field trial with three biological replicates per cultivar per cycle was conducted in a Foc-infested orchard in Guangxi, China. Corm tissues were sampled from resistant ('Bao Dao Jiao' and 'Gui Jiao 9') and susceptible 'Williams B6' bananas (n = 3 biological replicates per group) at plant crop (cycle 1) and third ratoon (cycle 3). 16S rRNA amplicons were sequenced via Illumina NovaSeq. Alpha- and beta-diversity, taxonomic composition, and predicted functions (PICRUSt2) were analyzed. Resistant cultivars maintained significantly higher Chao1 and Shannon indices than the susceptible cultivar, with divergence intensified across ratoon cycles (p < 0.05). Community structure was shaped primarily by cultivar rather than maternal health status. Resistant genotypes enriched Proteobacteria and Actinobacteria, alongside beneficial genera (Halomonas, Nesterenkonia, Aliihoeflea). Functional predictions revealed enrichment in carbohydrate metabolism, membrane transport, and xenobiotic degradation pathways in resistant cultivars. Disease incidence declined significantly from 34-39% (cycle 1) to 4-8% (cycle 3) in resistant cultivars, whereas susceptible cultivars remained at 44-59%. Resistant bananas continuously recruit beneficial endophytes during ratooning, assembling a stable microbiome that reinforces Fusarium wilt resistance. These findings provide microbial targets for breeding and biocontrol strategies.}, }
@article {pmid41800398, year = {2026}, author = {Zhu, Q and Chen, B and Hu, W and Huang, Y and Wang, S and Feng, M and Zhao, J and Yu, M and Li, M and Gong, X}, title = {Trehalose-mediated reshaping of the rhizosphere microbiome drives tea root rot progression.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1787317}, pmid = {41800398}, issn = {1664-302X}, abstract = {Tea (Camellia sinensis [L.] Kuntze) is one of the most economically important crops and as a traditional medicinal plant in the world. The long-term continuous cropping and inappropriate management have led to frequent outbreaks of soil-borne diseases such as root rot, which pose a serious threat to the sustainable development of the tea industry. However, the pathogenesis of tea root rot remains poorly understood. In this study, two novel pathogen fungi, Paraconiothyrium cyclothyrioides F8 and Apiotrichum sporotrichoides F17, were isolated and identified from diseased tea roots. Microbiome analysis revealed significant restructuring of the rhizosphere microbial community in diseased tea plants, with a significant reduction in the abundance of Basidiomycota and marked enrichment of pathogen such as Fusarium and Apiotrichum. Meanwhile, the abundances of beneficial fungi (e.g., Saitozyma and Trichoderma) and bacteria (e.g., Bacillus and Sporosarcina) were significantly decreased. Further investigation demonstrated that root exudate trehalose exhibited prominent bidirectional regulatory effect through promoted the growth of pathogen, while simultaneously inhibiting biofilm formation, rhizosphere colonization at specific concentrations and weakened the biocontrol functions of the beneficial antagonistic bacteria Sporosarcina pasteurii T21 and Lysinibacillus sp. T23, facilitating the formation of a rhizosphere chemical environment that "aids enemies and harms allies" and thereby exacerbating disease occurrence. This study emphasized the dominant role of plant metabolites such as trehalose in driving the assembly of rhizosphere microbial communities from a disease-suppressive to a disease-conducive state, as well as in disease development. The findings provide a novel theoretical perspective for the microbiological regulation of tea root rot and offer theoretical and practical bases for tea root rot disease green prevention and control.}, }
@article {pmid41800387, year = {2026}, author = {Gupta, S and Quarato, V and Lai, W and Kobel, CM and Aho, VTE and Vera-Ponce de León, A and La Rosa, SL and Sandve, SR and Pope, PB and Hvidsten, TR}, title = {OmniCorr: an R-package for visualizing putative host-microbiome interactions using multi-omics data.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag057}, pmid = {41800387}, issn = {2635-0041}, abstract = {Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the prediction and interpretation of host-microbiome interactions. We present OmniCorr, an R package designed to: (i) manage the complexity of omics data by clustering co-varying features (e.g. genes, proteins, and metabolites) into modules, (ii) visualize correlations of these modules across different omics layers, host-microbiome interfaces, and metadata, and (iii) identify statistically significant associations indicative of putative host-microbiome interactions. OmniCorr's utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics to investigate methane emission variability. Availability and implementation: OmniCorr is freely available at https://github.com/shashank-KU/OmniCorr.}, }
@article {pmid41800386, year = {2026}, author = {Baum, S and Meshulam, I and Algavi, YM and Peleg, O and Borenstein, E}, title = {TAGINE: fast taxonomy-based feature engineering for microbiome analysis.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag056}, pmid = {41800386}, issn = {2635-0041}, abstract = {SUMMARY: TAGINE is a feature engineering algorithm that leverages the microbial taxonomic tree to optimize feature sets in microbiome data for predictive modeling. The algorithm starts with features at high taxonomic levels and iteratively splits them into lower-level clades in cases where it improves predictive accuracy, ultimately producing a feature set spanning multiple taxonomic levels. This approach aims to markedly reduce the number of features while preserving biological relevance and interpretability. We compare TAGINE's performance to other standard and taxonomy-based feature engineering methods on several different datasets, and show that TAGINE yields more compact feature sets and is orders of magnitude faster than other methods, while maintaining predictive accuracy.<br><br>TAGINE is freely available under the MIT license with source code available at https://github.com/borenstein-lab/tagine_fe.}, }
@article {pmid41800246, year = {2026}, author = {Liu, Y and Wang, S and Xiang, X and Du, Y and Xue, Q and Niu, Y and Peng, W and Ye, L and Zhou, Q}, title = {Gut-Lung Microbiota Axis Shapes the Immune Microenvironment and Immunotherapeutic Response in Lung Cancer.}, journal = {International journal of biological sciences}, volume = {22}, number = {5}, pages = {2265-2284}, pmid = {41800246}, issn = {1449-2288}, mesh = {Humans ; *Lung Neoplasms/immunology/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/immunology ; *Tumor Microenvironment/immunology ; *Immunotherapy/methods ; *Lung/microbiology/immunology ; Dysbiosis ; Animals ; }, abstract = {The gut-lung axis microbiota plays a pivotal role in shaping the tumor immune microenvironment (TIME) and regulating immunotherapeutic responses in lung cancer. This review highlights that pulmonary and gut microbial dysbiosis drives lung cancer development through inducing chronic inflammation, remodeling the immune microenvironment, and reprogramming metabolism. Lung cancer patients exhibit distinct microbial signatures characterized by altered microbiotal diversity and enrichment of specific taxa like Streptococcus, Veillonella, and Bacteroidetes in the airways, along with gut microbial shifts involving decreased Firmicutes/Bacteroidetes ratio. These microbial alterations promote tumor progression via activation of pro-inflammatory pathways (e.g., interleukin-17 (IL-17)/interleukin-23 (IL-23) axis) and suppression of antitumor immunity.Notably, the gut-lung microbiome exerts a profound impact on immunotherapeutic efficacy: responders are enriched with beneficial microbes like Akkermansia muciniphila and Bifidobacterium that enhance CD8[+] T cell responses, while non-responders show elevated levels of Gammaproteobacteria and Fusobacterium associated with immunosuppression. Regulatory mechanisms include systemic immune modulation by microbial metabolites such as short-chain fatty acids, as well as activation of key signaling pathways including cGAS-STING and CD40L-CD40/NF-κB. Emerging translational applications encompass lung cancer diagnosis and immunotherapeutic response prediction via microbial biomarkers, as well as therapeutic interventions including fecal microbiota transplantation (FMT) and probiotic supplementation. Future studies should clarify microbe-host interaction mechanisms and develop personalized microbiota-based strategies to overcome immunotherapy resistance, offering the potential to revolutionize precision oncology through integrating microbiota modulation with conventional therapies.}, }
@article {pmid41800020, year = {2026}, author = {Park, U and Heo, JY and Chun, SM and Lee, JC and Lee, SH and Lee, SW}, title = {Harnessing the Gut Microbiota to Improve Cancer Immunotherapy: Focus on Lung Cancer.}, journal = {Immune network}, volume = {26}, number = {1}, pages = {e7}, pmid = {41800020}, issn = {1598-2629}, abstract = {The gut microbiota has emerged as a key orchestrator of systemic immunity, capable of reshaping the tumor microenvironment and modulating responses to cancer immunotherapy via the gut-lung axis. While immune checkpoint blockade (ICB) has revolutionized lung cancer treatment, a significant proportion of patients fail to respond. Accumulating evidence suggests that intestinal microbial composition modulates antitumor immunity, yet clinical associations between specific microbial taxa and ICB outcomes often show inconsistencies across cohorts. In this review, we synthesize current mechanistic insights into how gut microbial metabolites and structural components modulate pulmonary immune surveillance. We critically examine the clinical landscape of microbiome signatures in non-small cell lung cancer (NSCLC), highlighting how species- and strain-level heterogeneity contributes to divergent findings. Finally, we discuss translational strategies-ranging from fecal microbiota transplantation to rationally designed bacterial consortia and engineered probiotics-and propose a roadmap for integrating multi-omics with microbiome engineering to overcome current limitations and optimize precision immunotherapy.}, }
@article {pmid41800013, year = {2026}, author = {Walia, T and Srivastava, N and Shetty, RM and Rana, V}, title = {Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review.}, journal = {International journal of clinical pediatric dentistry}, volume = {19}, number = {2}, pages = {278-284}, pmid = {41800013}, issn = {0974-7052}, abstract = {AIM AND BACKGROUND: The oral cavity harbors a diverse microbiota that significantly influences oral health and disease. Conventional microbiological techniques have limitations in detecting the full range of microbial species, particularly those that are uncultivable. Metagenomics, through culture-independent, high-throughput sequencing methods, offers a comprehensive approach to studying oral microbial diversity. This narrative review aims to evaluate the role of metagenomics in exploring the oral microbiome and its association with dental diseases.<br><br>METHODS: This review systematically synthesized current literature and research on metagenomic technologies, including 16S ribosomal RNA (rRNA) sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It highlighted their principles, diagnostic capabilities, and limitations in analyzing microbial communities in caries, endodontic infections, and periodontitis. It also reviewed auxiliary tools such as quantitative polymerase chain reaction (qPCR), microarrays, fluorescence in situ hybridization (FISH), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and discussed the integration of artificial intelligence (AI) in metagenomic data interpretation.<br><br>RESULTS: Metagenomic studies have expanded the scope of known microbial species involved in dental caries beyond Streptococcus mutans, highlighting the contributions of Lactobacillus, Veillonella, Actinomyces, and Candida albicans. In endodontics, resistant species such as Enterococcus faecalis, Porphyromonas endodontalis, and Fusobacterium nucleatum are implicated in persistent infections. In periodontitis, a dysbiotic microbial shift has been associated with the presence of complex microbial consortia, including red and orange complex bacteria.<br><br>CONCLUSION: Metagenomics is a powerful diagnostic tool that provides an in-depth characterization of the complex microbial ecosystem of the oral cavity. It offers diagnostic potential through early and accurate detection of pathogenic shifts, promotes personalized treatment planning, and opens avenues for the development of potential biomarkers of disease progression.<br><br>CLINICAL SIGNIFICANCE: The integration of metagenomics into dental practice can revolutionize caries risk assessment, treatment precision, and disease prevention strategies. Although challenges such as high cost, data complexity, and lack of standardization remain, ongoing advancements in sequencing technologies and bioinformatics are expected to enhance its accessibility and clinical relevance.<br><br>HOW TO CITE THIS ARTICLE: Walia T, Srivastava N, Shetty RM, et al. Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review. Int J Clin Pediatr Dent 2026;19(2):278-284.}, }
@article {pmid41799843, year = {2026}, author = {Fisk, AE and Dong, WX and Johnson, TA and Harlow, K and Scaff, TJ and DeDecker, AE and Hoogland, MJ and Parsley, MA and Richert, BT and Stewart, KR}, title = {Evaluation of Agolin® Pig on sow and piglet performance and sow fecal microbial communities during lactation.}, journal = {Translational animal science}, volume = {10}, number = {}, pages = {txag023}, pmid = {41799843}, issn = {2573-2102}, abstract = {Essential oils are increasingly evaluated as alternatives to antibiotics in swine nutrition. This pilot study investigated the effects of Agolin Pig, a blend of microencapsulated essential oils, on sow performance, piglet growth, and sow fecal microbiota during lactation. Twenty-five sows were randomly assigned to either a control group (CON; n = 13) or a treatment group supplemented with Agolin Pig (AGO; n = 12; 200 ppm) from two weeks pre-farrowing through lactation. Diets for both groups met NRC (2012) nutrient requirements. Sow average daily feed intake (ADFI), body weight, body condition score (BCS), and Knauer Caliper measurements were collected at baseline, one week post-farrowing, and weaning. Piglet average daily gain (ADG) was recorded throughout lactation. Sow fecal samples were collected on d-14, d-7, d0, d8, and d16 relative to farrowing for microbiome analysis. Performance data were analyzed using PROC GLM or MIXED (SAS 9.4), with parity, number nursed, number weaned, and lactation week included as covariates. Microbiota data were analyzed in QIIME2 (v2022.8) and R (v4.2.3). Agolin Pig supplementation did not affect sow ADFI, piglet ADG, or colostrum and milk composition. However, AGO sows lost significantly less body condition during lactation, as measured by the Knauer Caliper (P = 0.010). Beta diversity differed between treatments on d8 (P = 0.029) and tended to differ on d16 (P = 0.066). Additionally, Clostridium and Streptococcus increased in CON but not AGO sows on d8 and d16, respectively. In summary, Agolin Pig supplementation reduced body condition loss and altered sow fecal microbiota diversity during lactation. These findings highlight the potential of essential oils to support sow health and productivity and warrant confirmation in larger studies.}, }
@article {pmid41799813, year = {2026}, author = {Xian, J and Wang, L and Shang, R and Sun, M and Yua, HJ and Zhang, X and Cheng, B and Wang, SJ and Tan, QW}, title = {Gut microbiota and metabolic characteristics in subthreshold depression based on multi-omics.}, journal = {Frontiers in psychiatry}, volume = {17}, number = {}, pages = {1760479}, pmid = {41799813}, issn = {1664-0640}, abstract = {BACKGROUND: Subthreshold depression (SD) is an intermediate state between normal mood and major depressive disorder (MDD), but its biological underpinnings remain insufficiently understood. Increasing evidence suggests that gut microbiota and host metabolic alterations may contribute to early depressive pathophysiology.<br><br>METHODS: We performed full-length 16S rRNA gene sequencing and LC-MS-based untargeted metabolomics on stool and plasma samples obtained from SD subjects and healthy controls. Microbial diversity, taxonomic composition, metabolic pathway alterations, and gut microbiota-metabolite associations were analyzed using bioinformatics pipelines, KEGG annotation, and Spearman correlation analysis.<br><br>RESULTS: SD patients exhibited marked gut microbial disturbances, including reduced microbial diversity and altered abundances of key genera such as decreased Eubacterium hallii group, Blautia, Dorea, and Agathobacter, and increased Escherichia-Shigella, Monoglobus, and Lachnoclostridium. Metabolomic profiling identified widespread metabolic perturbations, mainly affecting lipid metabolism, steroid hormone biosynthesis, and amino acid pathways. Exploratory correlation analysis indicated that beneficial taxa (e.g., Eubacterium hallii group and Blautia) were positively associated with specific glycerophospholipid and steroid hormone metabolites, whereas inverse associations were observed for other lipid-related metabolites.<br><br>CONCLUSION: This integrative microbiome-metabolome analysis demonstrates that SD is accompanied by early disruptions in gut microbial composition and systemic metabolism, particularly within lipid-related pathways. These findings suggest that gut microbiota dysbiosis may reflect early metabolic dysregulation and depression-related biological vulnerability in SD and highlight the gut microbiota as a candidate biological target for early identification and intervention.}, }
@article {pmid41799794, year = {2026}, author = {Santhanakrishnan, S and Kannappan, K and Krithika, C and Sridhar, C and Mahendra, J}, title = {Periodontal disease and neuroinflammation in multiple sclerosis: a systematic review of current evidence.}, journal = {Frontiers in dental medicine}, volume = {7}, number = {}, pages = {1701357}, pmid = {41799794}, issn = {2673-4915}, abstract = {BACKGROUND: Multiple Sclerosis (MS) is a chronic, immune-mediated neurological disorder characterized by demyelination and neurodegeneration. Emerging evidence suggests a link between MS and Periodontal Diseases (PD) through shared immune-inflammatory pathways. This review assesses the association between periodontal diseases and multiple sclerosis, focusing on immune-inflammatory interactions and clinical correlations. Despite emerging evidence, the strength of association remains unclear due to methodological heterogeneity.<br><br>AIM: To review and evaluate the literature on the epidemiological association between PD and MS in adults.<br><br>MATERIALS AND METHODS: A systematic search was conducted in PubMed, Scopus, and Cochrane. Studies with full text articles that are available in English, without time restrictions, that assessed periodontitis, oral microbiome, and salivary biomarkers in relation to MS were included. Observational studies evaluating clinical, microbiological, or immunological associations were selected. Data extraction covered periodontal parameters, salivary biomarkers, periodontal pathogens and disease severity. The risk of bias was evaluated using Newcastle-Ottawa Scale.<br><br>RESULTS: The findings indicated that patients with MS had poorer periodontal health, when compared to healthy controls. Dysbiosis in the oral microbiome was observed, with a higher abundance of periodontal pathogens. Patients with MS exhibited elevated neutrophil-lymphocyte ratios and total oxidative stress, indicating a potential link between systemic inflammation and periodontal dysbiosis. While some studies established positive association between PD and MS, others highlighted the need for further investigation due to inconsistent findings in periodontal parameters between MS patients and controls.<br><br>CONCLUSION: Despite methodological heterogeneity, the available limited evidence indicates the association between periodontitis and MS. This highlights the need for standardized periodontal assessments in research involving MS and suggests that periodontal care may hold potential as an adjunct in management of MS.}, }
@article {pmid41799763, year = {2026}, author = {Zhou, Y and Wang, Z and Huang, C and Yu, X and Chen, J and Jiang, X and Dong, J and Peng, Q and Li, L and Song, X and Lu, X}, title = {Gut Microbiota Signatures and Potential Mediators in the Trajectory of Age-related Macular Degeneration: A Phased Atlas by Genetic Inference.}, journal = {International journal of medical sciences}, volume = {23}, number = {3}, pages = {950-962}, pmid = {41799763}, issn = {1449-1907}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/immunology ; *Macular Degeneration/genetics/microbiology/immunology/pathology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Disease Progression ; Polymorphism, Single Nucleotide ; }, abstract = {PURPOSE: To depict an atlas of stage-stratified gut microbiota (GM) signatures and intermediatory metabolites, inflammatory proteins, and immune cell traits, governing the AMD trajectory.<br><br>METHODS: We deployed bidirectional two-sample Mendelian randomization (TSMR) integrating GWAS data of 207 GM taxa from the Dutch Microbiome Project (N = 7,738), and multiple AMD stages/subtypes, including 'Macular degeneration (senile) of retina', 'Early AMD', 'Disease progression to GA/CNV', 'Dry AMD includes GA', and 'Wet AMD', encapsulating the disease trajectory (N > 410,000), complemented by multivariable MR (MVMR) mediation analysis of 1,400 circulating metabolites, 731 immune cell traits, and 91 inflammatory proteins.<br><br>RESULTS: We identified 12/8/5/2/9/8 genetically predicted causal GM taxa of various AMD stages/subtypes as a stage-stratified GM signature across the AMD trajectory, among which g.Ruminococcaceae and s.Ruminococcaceae_bacterium_D16 were the sole shared GM taxa in triple AMD stages, while s.Bacteroides eggerthii, c.Gammaproteobacteria, s.Dorea and s.Ruminococcus_obeum influence dual AMD stages. Bidirectional analysis revealed that f.Streptococcaceae, g.Erysipelotrichaceae_noname, g.Streptococcus, s.Streptococcus_thermophilus, g.Ruminococcaceae_noname, and s.Ruminococcaceae_bacterium_D16 exhibited genetically reciprocal causation with AMD. We also proposed that Firmicutes may exhibit stage-specific duality depending on their constituent members and AMD stages. Several understudied GM from p.Actinobacteria and p.Verrucomicrobia have been implicated as AMD-associated taxa for the first time. Key metabolites, immune cell traits, and inflammatory proteins were established as significant mediators of GM-AMD links.<br><br>CONCLUSIONS: This first phased atlas uncovers GM effects over the AMD course, identifying potential microbial and biochemical targets for intervening in disease development.}, }
@article {pmid41799697, year = {2026}, author = {Bulcão V C, L and Moreira, NCS and Carvalho, PC and Luz, IS and de S da G Fischer, J and Tsu, BL and Sejane, K and Savo, C and Martins, AMA and Bode, L and Muotri, AR}, title = {Human milk oligosaccharides promote synaptogenesis and neurite outgrowth in human cortical organoids.}, journal = {Biochemistry and biophysics reports}, volume = {45}, number = {}, pages = {102529}, pmid = {41799697}, issn = {2405-5808}, abstract = {The first 1000 days of a child's life represent a critical window for brain development, during which nutrition exerts profound effects on the trajectories of neurodevelopment. Human Milk Oligosaccharides (HMOs), a major component of human milk, are largely indigestible by infants and are known to influence immunity, microbiome composition, and gut-brain signaling, but their direct role in neurodevelopment remains poorly understood. Here, we investigated the impact of HMOs on human cortical organoids, a physiologically relevant in vitro model of early brain development. We found that HMO treatment significantly enhanced neurite outgrowth and synaptogenesis in a dose-dependent manner. Global proteomic profiling further demonstrated the upregulation of proteins associated with neuronal differentiation, synaptic maturation, and cytoskeletal remodeling. Our findings suggest that HMOs can influence neurodevelopmental processes and highlight a potential role for maternal milk components in early brain development.}, }
@article {pmid41799504, year = {2026}, author = {Santos, I and Liberal, J and Teixeira, P and Martins, D and Mendes, F}, title = {The Role of the Gut Microbiome in Clinical Outcomes of Colorectal Cancer: A Systematic Review (2020-2025).}, journal = {Oncology research}, volume = {34}, number = {3}, pages = {3}, pmid = {41799504}, issn = {1555-3906}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy ; *Gastrointestinal Microbiome ; Treatment Outcome ; Probiotics/therapeutic use ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: The Colorectal Cancer (CRC) pathogenesis and therapeutic efficacy are influenced by the gut microbiome, making it a promising biomarker for predicting treatment responses and adverse effects. This systematic review aims to outline the gut microbiome composition in individuals with CRC undergoing the same therapeutic regimen and evaluate interindividual microbiome profile variations to better understand how these differences may influence therapeutic outcomes.<br><br>METHODS: Key studies investigating the microbiome's role in therapeutic approaches for CRC were searched in both PubMed and Cochrane databases on 12 and 22 March 2025, respectively. Eligible studies included free full-text English-language randomized clinical trials and human observational studies reporting on gut microbiome composition and treatment outcomes. RoB 2 and ROBINS-I were employed in the evaluation of bias for randomized trials and observational studies, respectively. Data extracted was narratively analyzed.<br><br>RESULTS: Six studies involving a total of 361 individuals were included. Therapeutic interventions, either standard treatments and/or those targeting the gut microbiome, generally increased probiotic taxa and reduced pro-carcinogenic bacteria. However, no consistent pattern of improved clinical outcomes was observed, suggesting that treatment mechanisms, the tumor's nature, and individual characteristics play critical roles in microbiome modulation.<br><br>CONCLUSION: The gut microbiome holds significant potential in clinical settings. Nonetheless, further research is needed to better understand its functional aspects and to consider the influence of treatment mechanisms, the tumor's nature, and individual characteristics as modulators, in order to optimize clinical outcomes.}, }
@article {pmid41799378, year = {2026}, author = {Kaur, M and Babu, R and Baweja, S and Gupta, R and Singh, SP and Pamecha, V and Bihari, C}, title = {Human Leukocyte Antigen Alleles and Oral Microbiome Association With Antibody-mediated Rejection in Living-donor Liver Transplant Patients.}, journal = {Journal of clinical and experimental hepatology}, volume = {16}, number = {3}, pages = {103494}, pmid = {41799378}, issn = {0973-6883}, abstract = {BACKGROUND/AIMS: Antibody-mediated rejection (ABMR) is an important cause of graft dysfunction after liver transplantation, yet the combined influence of human leukocyte antigen (HLA) immunogenetics and the oral microbiome on ABMR risk is not well defined.<br><br>METHODS: In this prospective cohort of 180 living donor-recipient pairs, pre-transplant 16S ribosomal ribonucleic acid sequences and high-resolution HLA genotyping were done. The human leukocyte antigen epitope mismatch algorithm quantified amino acid and solvent-accessible mismatches. Oral microbiome profiles were generated using the Divisive Amplicon Denoising Algorithm (DADA2) and quantitative insights into microbial ecology version 2 (QIIME2). Associations between HLA alleles and microbial taxa were assessed using generalized linear models and linear discriminant analysis effect size (LEfSe). ABMR was diagnosed as per Banff criteria over one year.<br><br>RESULTS: ABMR was diagnosed in 15 patients. These patients had significantly higher mismatch burdens at HLA-DPB1, DQB1, and DRB1 than non-ABMR recipients. Across the cohort, 68 HLA alleles demonstrated distinct microbial associations at phylum, family, and genus levels. Alleles such as HLA-DRB108, HLA-DPB1575, and HLA-C05 were linked to differential abundance of Actinobacteriota, Campylobacterota, and Fusobacteriota, respectively. Genus-level analyses revealed strong allele-specific associations with Veillonella, Enterobacter, Streptococcus, and other immunomodulatory taxa. LEfSe identified HLA-DQB106 and HLA-DQB1&#x2217;104 as associated with enrichment of Enterobacter, Citrobacter europaeus, Bacteroides plebeius, Rothia dentocariosa, Megasphaera, and Burkholderiaceae-microbial signatures also prominent in ABMR cases.<br><br>CONCLUSION: Class II HLA mismatch burden and allele-specific oral microbial signatures are closely linked to ABMR. Combined HLA-microbiome profiling may enhance early risk stratification and inform targeted peri-transplant microbial interventions.}, }
@article {pmid41799196, year = {2026}, author = {Wang, D and Liang, S and Ai, Z and Kong, Q and Xing, D and Cao, Z and Geng, Z}, title = {Bacterial vesicles-initiated in-situ spray-polymerized coating enables synergistic antibacterial-photothermal functionality for accelerating wound healing.}, journal = {Theranostics}, volume = {16}, number = {9}, pages = {4566-4579}, pmid = {41799196}, issn = {1838-7640}, mesh = {Animals ; *Wound Healing/drug effects ; *Anti-Bacterial Agents/pharmacology ; Mice ; Humans ; *Extracellular Vesicles/chemistry/metabolism ; Escherichia coli/drug effects ; Human Umbilical Vein Endothelial Cells ; Polymers/chemistry/pharmacology ; *Photothermal Therapy/methods ; Staphylococcus aureus/drug effects ; Pyrroles/chemistry/pharmacology ; Disease Models, Animal ; Skin ; Neovascularization, Physiologic/drug effects ; Staphylococcus epidermidis/drug effects ; }, abstract = {BACKGROUND: Although microbial therapies can address the harm to beneficial bacteria and microbiome balance caused by traditional antibacterial treatments in skin damage and infection, their pathogenic potential limits clinical application. Bacterial extracellular vesicles (BEVs) offer a safer alternative by targeting microbes and modulating immunity.<br><br>METHODS: Lactobacillus reuteri-derived BEVs (LBEVs) are functionalized with Fe [3+] via electrostatic adsorption, and co-sprayed with pyrrole monomers onto wounds to initiate oxidative polymerization and then form conformal polypyrrole coatings (LBEVs-PPy). Thanks to the natural antibacterial activity of LBEVs, the LBEVs-PPy coating could inhibit the growth of pathogens efficiently. Furthermore, the mild hyperthermia induced by PPy's NIR-triggered photothermal activation significantly upregulates the expression of angiogenic regulators.<br><br>RESULTS: In vitro, LBEVs effectively inhibited the growth of S. aureus, E. coli, and S. epidermidis, demonstrating potent antibacterial efficacy. Following mild hyperthermia (42 &#xb0;C for 1 h), HUVECs showed elevated expression of angiogenic regulators, including VEGFA and ANGPT1. This treatment also activates HSP90/p-eNOS pathway in HUVECs, thereby accelerating angiogenesis. In a mouse model of skin damage and infection, LBEVs-PPy coating significantly accelerates wound healing through synergistic mechanisms that integrate the antibacterial activity of LBEVs and the photothermal effect of PPy.<br><br>CONCLUSIONS: Our research developed an in-situ spray-polymerized coating integrating antibacterial and photothermal modalities, thus presenting a promising biotherapeutic platform for clinical wound management and tissue regeneration.}, }
@article {pmid41798752, year = {2026}, author = {Lu, B and Zhang, A and Wu, M and Chen, S and Wang, Y and Wang, J and Huang, M and Zhu, Y and Liu, H and Zhu, F and Zeng, X and Chen, S and Zhou, X and Lin, R}, title = {Gut microbiome dysregulation is associated with segmental glomerulosclerosis in IgA nephropathy: insights from Oxford classification-based microbiome profiling.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1644626}, pmid = {41798752}, issn = {2235-2988}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/pathology ; *Gastrointestinal Microbiome ; Male ; RNA, Ribosomal, 16S/genetics ; Female ; Adult ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Glomerulosclerosis, Focal Segmental/microbiology/pathology ; Middle Aged ; Biomarkers ; Dysbiosis ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: IgA nephropathy (IgAN) is a common immune-complex-mediated glomerulonephritis with segmental glomerulosclerosis (S lesion, S1 in Oxford classification) being an independent predictor of poor renal prognosis, where 20%-40% of IgAN-S1 patients progress to end-stage renal disease, but its pathogenesis is unclear.<br><br>METHODS: This study enrolled 12 IgAN-S0 (without segmental sclerosis) and 19 IgAN-S1 (with segmental sclerosis) patients, performed 16S rRNA gene sequencing on fecal samples, and analyzed gut microbiota composition and functions.<br><br>RESULTS: S1 had enriched Firmicutes and Patescibacteria while S0 had more Proteobacteria, Campylobacterota, and Desulfobacterota; LEfSe analysis identified Subdoligranulum and unclassified_Erysipelotrichaceae_UCG-003 as S1-specific biomarkers and Phascolarctobacterium, Streptococcus_parasanguinis, and Proteobacteria as S0 biomarkers (P<0.05). Functional prediction showed S1 was enriched in pro-inflammatory pathways like endoplasmic reticulum stress and secondary bile acid biosynthesis, while S0 had activated protective pathways such as cytochrome P450 drug metabolism and ubiquitin system.<br><br>CONCLUSIONS: This study reveals gut microbiota dysregulation is closely associated with IgAN segmental sclerosis, with S1 showing pro-inflammatory microbial profiles and S0 retaining protective functions, providing new insights into gut-kidney axis mechanisms and potential microbiome-targeted therapies for IgAN.}, }
@article {pmid41798747, year = {2026}, author = {Natarajan, PM and Varma, SR and Kodangattil Narayanan, J and Odeh, R}, title = {Predicting inter-microbial host specificity in oral biofilms using a lightweight relation-aware knowledge graph model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1775191}, pmid = {41798747}, issn = {2235-2988}, mesh = {*Mouth/microbiology/virology ; *Biofilms/growth &amp; development ; Humans ; Microbiota ; *Bacteria/classification ; *Host Specificity ; Neural Networks, Computer ; Bacteriophages/physiology ; Periodontal Diseases/microbiology ; Dysbiosis/microbiology ; }, abstract = {INTRODUCTION: The human oral cavity hosts a complex microbial ecosystem of bacteria, viruses, bacteriophages, and other microorganisms forming biofilms in different niches. Phage-bacteria host specificity is crucial in shaping microbial community, stability, and dysbiosis. mapping this specificity is limited by experimental constraints and traditional methods can't capture ecological complexity. The goal is to create a graph-based model that treats inter-microbial host specificity as a relational learning problem, integrating taxonomic, ecological, and infection data into a knowledge graph. This improves phage-bacteria host predictions and reveals microbial hubs and interaction patterns related to periodontal disease dysbiosis.<br><br>METHODS: This study introduces a lightweight, relation-aware knowledge graph for predicting microbial host specificity in oral biofilms. We built a heterogeneous graph of the oral microbiome, incorporating microbial taxa, anatomical sites, taxonomic hierarchies, enrichment patterns, and INFECTS relationships. The dataset includes 500 viral taxa across four oral niches, with 21,338 significant co-occurrence relationships and various biological features. To learn meaningful representations, we combined graph embeddings with microbial features. We developed a relation-aware graph neural network, IK-BRNet, to efficiently encode ecological and interaction semantics.<br><br>RESULTS: Model performance was evaluated against a conventional Graph Attention Network (GAT) using stratified training, validation, and test splits with class imbalance correction. IK-BRNet demonstrated faster convergence and superior discrimination ability, achieving a higher AUC-ROC (0.929 vs. 0.904) and markedly improved sensitivity for disease-associated viral taxa (93.8% vs. 56.3%). While the baseline GAT achieved higher accuracy and specificity, IK-BRNet consistently reduced false negatives, thereby improving its ability to detect disease-related microbial signals. Site-specific predictions confirmed biological validity, with the highest disease scores for dental plaque-associated viruses and lower scores in healthy niches such as the tongue and buccal mucosa.<br><br>CONCLSUION: This study shows that relation-aware graph learning offers a meaningful and efficient way to model inter-microbial host specificity in oral biofilms. The framework improves oral microbiome network inference and supports disease screening, ecological analysis, and microbiome-based dentistry.}, }
@article {pmid41798687, year = {2026}, author = {He, Q and Zhao, Z and Jiang, D and Fei, A}, title = {Diabetes Mellitus Accelerates Alzheimer's Disease Development by Affecting the Gut Microbiome.}, journal = {BioMed research international}, volume = {2026}, number = {}, pages = {9974079}, pmid = {41798687}, issn = {2314-6141}, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; *Alzheimer Disease/microbiology/pathology/metabolism ; Animals ; Mice ; Brain/metabolism/pathology/diagnostic imaging ; Amyloid beta-Peptides/metabolism ; *Diabetes Mellitus, Experimental/microbiology/complications ; Male ; Butyrates/pharmacology ; Disease Models, Animal ; Positron Emission Tomography Computed Tomography ; Mice, Inbred C57BL ; Fatty Acids, Volatile/metabolism ; }, abstract = {Increasing evidence suggests a link between Alzheimer's disease (AD) and diabetes mellitus (DM). However, the precise mechanisms by which DM contributes to AD remain unclear. This study is aimed at elucidating the potential role of DM in the early stages of AD. Accordingly, a streptozotocin (STZ)-induced diabetic 5 × familial AD (FAD) mouse model was established. Immunohistochemistry and positron emission tomography/computed tomography (PET/CT) scanning were performed to examine amyloid beta (Aβ) deposition in the brain. The integrity of the colonic epithelium was assessed using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and immunofluorescence staining. Microbial diversity analysis was conducted for 5 × FAD mice with and without STZ-induced DM to determine shifts in intestinal flora profiles. After oral administration of butyrate to STZ-treated 5 × FAD mice, we observed that Aβ deposition in the brain was decreased, and the intestinal flora improved. Immunohistochemistry and PET/CT findings revealed a marked increase in Aβ formation in the brains of 5 × FAD mice treated with STZ. qRT-PCR and immunofluorescence staining revealed severe intestinal barrier dysfunction in these mice. Gut microbiota sequencing indicated significant dysbiosis in STZ-treated 5 × FAD mice, characterized by a reduction in short-chain fatty acid (SCFA)-producing species. After oral administration of butyrate, Aβ deposition in the brains of STZ-treated 5 × FAD mice was significantly reduced, and beneficial changes occurred in the intestinal flora, including increases in bacteria associated with SCFA production and neurological function. Dysregulation of the gut microbiome may exacerbate cerebral amyloidosis during AD pathogenesis. Microbes associated with SCFA production may play a beneficial role in AD treatment, and butyrate supplementation can significantly delay AD progression.}, }
@article {pmid41798257, year = {2026}, author = {Liu, J and Wu, X}, title = {Fecal microbiota transplantation in ulcerative colitis: evidence, mechanisms, and practice considerations.}, journal = {Therapeutic advances in gastroenterology}, volume = {19}, number = {}, pages = {17562848261426284}, pmid = {41798257}, issn = {1756-283X}, abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease strongly associated with intestinal dysbiosis, reduced microbial diversity, and disrupted microbial metabolite profiles. Fecal microbiota transplantation (FMT) aims to restore microbial homeostasis and has shown a signal of benefit for induction of remission in some trials, but results are heterogeneous and long-term maintenance efficacy remains uncertain. In this narrative review, we synthesize randomized controlled trials (RCTs), systematic reviews/meta-analyses, and recent guideline and regulatory updates on FMT in UC, and integrate mechanistic insights from microbiome and metabolomics research. Across RCTs, intensive lower-gastrointestinal regimens using pooled, multidonor material, and/or anaerobic processing have most consistently achieved modestly higher steroid-free clinical and endoscopic remission than placebo in mild-to-moderate UC (approximately 25%-32% vs 5%-10% in representative studies), whereas upper-gastrointestinal delivery or oral lyophilized formulations and highly restrictive donor selection have yielded mixed or negative results. Mechanistically, responders commonly demonstrate engraftment of short-chain fatty acid producing taxa and restoration of secondary bile acid pathways. Safety profiles in trials are generally comparable to placebo for common mild adverse events, but rare severe transmissions (e.g., multidrug-resistant Escherichia coli and SARS-CoV-2) have driven stricter donor screening and have limited routine use outside regulated programs. Current guidelines recommend against FMT for UC outside clinical trials. Future work should prioritize standardized protocols, biomarker-guided personalization, combination strategies (diet/priming), and development of defined microbial therapeutics to improve efficacy and safety.}, }
@article {pmid41797849, year = {2026}, author = {Jalalifar, S and Bajelan, B and Mohammadi, R and Ghafoury, R and Kalhori, Z and Pooshang-Bagheri, K and Nekouian, R and Faranoush, M}, title = {The impact of gut microbiota on leukemia and prospects for novel therapies.}, journal = {Infectious medicine}, volume = {5}, number = {1}, pages = {100239}, pmid = {41797849}, issn = {2772-431X}, abstract = {The Human Microbiome Project has underscored the pivotal role of the gut microbiome in human health, revealing its potential influence on leukemia development, progression, and treatment response. This review summarizes evidence on microbiome-targeted therapies such as probiotics, fecal microbiota transplantation, antimicrobial peptides, and nanoparticles. These approaches may improve leukemia treatment outcomes through immune and metabolic modulation and reduced toxicity. Although emerging data suggest beneficial effects, most findings remain correlative and limited by small, heterogeneous studies. Further mechanistic and clinical research is required to clarify causal pathways, standardize interventions, and evaluate long-term safety. Personalized microbiome-based strategies that integrate molecular and immunologic profiling may ultimately refine leukemia management and improve survival.}, }
@article {pmid41797814, year = {2026}, author = {Tetzlaff, EJ and Hancock, C and Waddell, L and Gagnon, SS and Mäkelä, KA and Karhu, T and Peltonen, JE and Herzig, KH and Gagnon, DD}, title = {Cold exposure and human metabolism: A heterogeneous response across tissues and organs.}, journal = {Temperature (Austin, Tex.)}, volume = {13}, number = {1}, pages = {15-50}, pmid = {41797814}, issn = {2332-8940}, abstract = {Cold-induced metabolic responses across human organs and tissues vary markedly and do not regulate metabolism uniformly. The magnitude and nature of these responses differ depending on the type of cold exposure, ranging from mild surface cooling and beta-adrenergic stimulation to deep tissue cooling impacting intracellular biophysical and metabolic properties. Upregulating brown adipose tissue (BAT) activity has been proposed to improve whole-body metabolism. Despite its high metabolic activity, BAT mass is typically only 50-100 g and may contribute less than 1% of total heat production during thermogenesis. In contrast, skeletal muscles and white adipocytes may play greater roles in thermogenic and metabolic regulation. Cold exposure triggers a cascade of metabolic responses across tissues, extending beyond fuel partitioning and the regulation of uncoupling proteins. It also alters gene expression, protein synthesis, and metabolic pathways. In response to cold, the body increases sympathetic nervous system activity, leading to peripheral vasoconstriction and energy substrate mobilization. Brown adipocytes increase mitochondrial uncoupling to produce heat, while skeletal muscle contributes through shivering and non-shivering thermogenesis. The liver adjusts glucose production and lipid metabolism, the heart and circulatory system adapt to altered hemodynamic demands, and the kidneys modify fluid balance. Endocrine systems, including the thyroid, amplify thermogenic capacity, and the brain integrates thermal sensing with behavioral responses. Cold exposure also modulates immune function, cytokine profiles and inflammatory pathways across tissues, and shifts in gut microbiome composition influence nutrient absorption, bile acid metabolism and energy homeostasis. These coordinated tissue-specific adaptations enable the maintenance of core temperature during cold stress.}, }
@article {pmid41797790, year = {2026}, author = {Carbone, RG and Puppo, F and Tapson, VF}, title = {Gut microbiota and sarcoidosis: a concise review.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1747012}, pmid = {41797790}, issn = {2296-858X}, abstract = {Microbial involvement in sarcoidosis pathogenesis is suggested by the observation that histological findings in sarcoid granulomas are like those of leprosy, tuberculosis and parasitic infection. Some studies have shown that the lung microbiome in patients with sarcoidosis is different from healthy individuals. Results are conflicting, reporting an abundance or decrease in bacterial and fungal species. The altered composition of the microbiome in sarcoidosis can contribute to the formation of granulomas, typical lesions of the disease, through interactions with the host immune system. However, no single microbe has been clearly demonstrated as a cause of sarcoidosis, several microorganisms have been involved in the formation of granulomas and are under study. In fact, various microorganisms have been detected in sarcoid granulomas and in the tissue of different organs. Microorganisms were demonstrated at the genomic level and only a few studies showed microbial presence using bacteriological or proteomic methods. A possible microbial involvement in sarcoidosis pathogenesis is further supported by studies reporting innate immune system activation and increased inflammatory cytokines secretion. Of note, a meta-analysis involving over 6,000 patients identified a strong association between Cutibacterium acnes and Mycobacterium tuberculosis and sarcoidosis. Interestingly, some studies have compared microbiomes in sarcoidosis with chronic respiratory conditions like chronic obstructive pulmonary disease, asthma, interstitial lung disease, and occupational lung diseases. Little is known whether gut microbiota alteration plays a causal role in the development of these diseases or is a consequence of a shared risk factor profile. However, current evidence does not conclusively support the causative role of microbes in sarcoidosis. Furthermore, research is studying the role of intestinal microbiomes in sarcoidosis with some studies showing that the restoration of the intestinal microbiome could be a possible therapeutic approach. The aims of the review are: (1) to clarify microbial involvement in sarcoidosis pathogenesis, (2) to describe microbiota in lungs of patients with sarcoidosis and to compare the data with other interstitial lung diseases.}, }
@article {pmid41797508, year = {2026}, author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W}, title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {6}, pages = {e71656}, pmid = {41797508}, issn = {1530-6860}, support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; }, abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.}, }
@article {pmid41797364, year = {2026}, author = {Peskett, ST and Grégoire, DS and Rand, AA}, title = {Human Intestinal Microbiota Composition Shapes Model Polyfluoroalkyl Substance Biotransformation.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {27}, number = {5}, pages = {e202500905}, pmid = {41797364}, issn = {1439-7633}, support = {RGPIN-2018-05330//Natural Science and Engineering Research Council/ ; NFRFE-2023-00695//New Frontiers in Research Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Biotransformation ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; *Organophosphates/metabolism/chemistry ; *Fluorocarbons/metabolism ; }, abstract = {6:2 polyfluoroalkyl phosphate diester (6:2 diPAP) is a prevalent environmental contaminant to which humans are regularly exposed. Environmental microbes can biotransform 6:2 diPAP, and the human gut microbiome can biotransform its congener, 8:2 monoPAP. While the human gut microbiome is highly variable between individuals, potential variability in PAP biotransformation has yet to be assessed. We address this gap using six cohorts (A-F) to examine in vitro biotransformation of 6:2 diPAP by the human gut microbiome. Biotransformation pathways of 6:2 diPAP and their connections to the composition of microbial taxa were assessed using gas chromatography mass spectrometry (GC-MS), liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing. All cohorts biotransformed 6:2 diPAP but differed in their downstream perfluoroalkyl acid (PFAA) profiles, suggesting diverse biotransformation pathways. Microbial community analysis showed similar alpha diversity across cohorts, while the degree of difference between cohorts varied. The analysis confirmed the initial composition of each cohort's microbial community had a bearing on products stemming from 6:2 diPAP transformation, likely driven by low-abundance microbial taxa. These findings underscore the complexity of microbe-mediated polyfluoroalkyl substance (PFAS) transformation and highlight the need for mechanistic studies that identify the genetic controls governing PFAS transformations in the gut microbiome.}, }
@article {pmid41797218, year = {2026}, author = {Wetzel, C and Bumm, CV and Becker, J and Schwendicke, F and Folwaczny, M and Werner, N}, title = {Infertility and Periodontitis: Are We Connecting the Right Dots?.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345261416502}, doi = {10.1177/00220345261416502}, pmid = {41797218}, issn = {1544-0591}, abstract = {Infertility is an increasing global health concern. Growing evidence suggests that systemic inflammatory conditions, including periodontal disease, may contribute to impaired reproductive outcomes. This narrative review highlights recent conceptual advances linking periodontal disease with male and female infertility, focusing on biological mechanisms (i.e., microbial translocation, chronic inflammation, immune dysregulation, oxidative stress, and epigenetic modifications). The review critically examines available studies focusing on scientific quality, design, and clinical relevance. In females, periodontal disease has been associated with idiopathic infertility and polycystic ovary syndrome. These conditions are characterized by immune dysregulation and low-grade systemic inflammation. In males, impaired semen parameters and idiopathic infertility have been linked to poor periodontal status. Despite growing interest, existing studies are largely associative and limited by methodological heterogeneity, insufficient control for confounders, and a lack of standardized outcome measures. This review proposes a framework for improved future research strategies addressing these shortcomings to clarify causality and therapeutic potential.}, }
@article {pmid41797118, year = {2026}, author = {Chen, YH and Du, H and Liu, YX and Xu, K and Ye, JC and Liu, BL and Feng, NX and Xiang, L and Li, YW and Cai, QY and Mo, CH and Zhao, HM}, title = {Silkworm excrement-immobilized bacteria for synergistic remediation of phthalate esters in agricultural soil.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141703}, doi = {10.1016/j.jhazmat.2026.141703}, pmid = {41797118}, issn = {1873-3336}, abstract = {The widespread contamination of agricultural soils by phthalate esters (PAEs) poses serious risks to ecosystem and human health. While microbial remediation is a promising solution, the poor survival and performance of free degrading bacteria in complex soil environments limit its practical application. To address this challenge, we develop a novel immobilized inoculant by leveraging silkworm excrement (SE), an agricultural by-product, as a carrier for the efficient PAE-degrader Pseudomonas aeruginosa PS1. This microbe-immobilized silkworm excrement (MSE) was thoroughly characterized and validated by pot experiments. The results showed that MSE treatment significantly reduced PAEs in both soil and choysum (Brassica parachinensis L.), with PAEs detected little in shoots (edible parts), significantly outperforming the treatments of free bacteria or SE alone. The enhanced remediation was linked to MSE-induced improvements in soil health, including increased pH, organic matter, and ammonium nitrogen. Crucially, high-throughput sequencing revealed that MSE application selectively enriched key PAE-degrading bacterial phyla, particularly Proteobacteria and Bacteroidetes, thereby reshaping the soil microbiome into a more effective remediation consortium. This study presents a sustainable and efficient bioaugmentation strategy for transforming a waste product into a functional inoculant, offering a viable solution for the in-situ remediation of PAE-contaminated soils.}, }
@article {pmid41796961, year = {2026}, author = {Bejaoui, S and D'Amico, F and Turroni, S}, title = {Role of the gut microbiome in shaping drug response in immunocompromised hosts.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.026}, pmid = {41796961}, issn = {1469-0691}, abstract = {BACKGROUND: There is an increasing amount of evidence on microbiome-drug interactions in several clinical settings, including in immunocompromised patients. The gut microbiome has been shown to directly and indirectly influence drug efficacy and toxicity, offering high potential for clinical translation.<br><br>OBJECTIVES: This narrative review aims to provide an up-to-date overview of the relationship between gut microbes and drugs, with a focus on immu1no-chemotherapy in immunocompromised hosts, including oncological and transplant patients.<br><br>SOURCES: We searched PubMed to identify relevant literature in English up to February 2026, as well as included articles known to the authors (prioritising clinical studies wherever possible).<br><br>CONTENT: For commonly used anticancer drugs in untargeted conventional chemotherapy, gut microbes may directly activate prodrugs, inactivate biologically active drugs, and/or interfere with their toxicity. Furthermore, indirect mechanisms of immune system modulation have been shown to enhance or worsen therapeutic outcomes, including in targeted immunotherapy. For immunosuppressants in transplant recipients, there is less available evidence overall. Nevertheless, existing studies support the role of the gut microbiome in influencing pharmacokinetics, including enterohepatic recirculation, also through modulation of host drug-metabolising enzymes. Notably, some studies have demonstrated the potential of targeted microbiome manipulation to improve therapeutic outcomes. However, most of this information derives from small, heterogeneous studies, including animal models and in vitro studies.<br><br>IMPLICATIONS: The translational implications of microbiome research in pharmacology are of paramount importance. Well-designed clinical studies and the integration of in vivo and ex vivo models will be essential for advancing knowledge and providing mechanistic insights into microbiome-drug interactions. In parallel, advanced computational approaches such as artificial intelligence and machine learning tools will facilitate the analysis of complex microbiome data. These approaches will help identify clinically relevant microbial signatures, including high-risk microbiome-drug interactions. This will enable the development of personalised precision strategies to improve clinical outcomes and prolong disease-free survival.}, }
@article {pmid41796931, year = {2026}, author = {Gondo, T and Abe, S and Hiraishi, N and Hayashi, F and Okazaki, Y and Abe, T and Shimabukuro, M and Moyes, D and Hill, RG and Shimada, Y}, title = {Effects of Fluoride Chemical Forms of Sodium Fluoride and Monofluorophosphate on Microbial Viability and Diversity in Saliva-Derived Biofilms.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {106615}, doi = {10.1016/j.jdent.2026.106615}, pmid = {41796931}, issn = {1879-176X}, abstract = {OBJECTIVES: Fluorides are widely used for caries prevention; however, knowledge of the differences in their chemical speciation and associated microbiological effects remains incomplete. This study aimed to elucidate the ionization behavior of sodium fluoride (NaF) and sodium monofluorophosphate (MFP) using [19]F NMR spectroscopy and to evaluate their effects on biofilm growth, viability, and microbial composition in saliva-derived polymicrobial biofilms.<br><br>METHODS: The chemical speciation of NaF and MFP solutions was characterized by [19]F NMR spectroscopy. Polymicrobial biofilms were established from human saliva using an in vitro biofilm model on hydroxyapatite discs. Biofilms were then exposed to NaF or MFP at an equivalent fluoride concentration (1450 ppm). Microbial viability was assessed using an ATP-based luminescence assay. Biofilm community composition was analyzed by 16S rRNA gene sequencing, followed by diversity and differential abundance analyses.<br><br>RESULTS: [19]F NMR analysis demonstrated that NaF fully dissociated into free fluoride ions, whereas MFP existed predominantly as monofluorophosphate ions, with only a small fraction of free fluoride. Both fluoride compounds significantly reduced microbial viability. NaF exerted a strong, non-selective inhibitory effect without significantly altering overall community structure or alpha diversity. In contrast, MFP caused selective suppression of specific taxa and significantly decreased Shannon diversity. Differential abundance analysis confirmed compound-specific shifts in bacterial genera, indicating distinct antimicrobial profiles.<br><br>CONCLUSIONS: NaF and MFP exhibited differential antibiofilm effects, with NaF causing a greater reduction in microbial viability than MFP. 16S rRNA analysis revealed that NaF had minimal impact on the overall microbial composition, whereas MFP induced selective changes in bacterial taxa.<br><br>CLINICAL SIGNIFICANCE: This study revealed that fluoride compounds exhibit different antibiofilm effects due to their distinct chemical forms. These forms were precisely identified using [19]F NMR rather than conventional fluoride ion-selective electrodes. These findings may help improve understanding of fluoride behavior and guide future research in caries prevention.}, }
@article {pmid41796720, year = {2026}, author = {Ye, J and Lan, Y and Li, W and Lv, H and Wen, C and Xu, Z}, title = {Vagus nerve stimulation in autoimmune diseases: Mechanisms, therapeutic potential, and clinical applications.}, journal = {Autoimmunity reviews}, volume = {}, number = {}, pages = {104023}, doi = {10.1016/j.autrev.2026.104023}, pmid = {41796720}, issn = {1873-0183}, abstract = {Autoimmune diseases characterized by dysregulated immune responses against self-antigens. Current pharmacotherapies are limited by like resistance, side effects, and high costs, highlighting the need for novel interventions. Vagus nerve stimulation (VNS) offers a promising alternative through three forms, including implantable, transcutaneous cervical, and transcutaneous auricular. Increasing clinical evidence demonstrates VNS benefits patients with autoimmune disorders, such as treatment-refractory rheumatoid arthritis, Crohn's disease, and systemic lupus erythematosus. Preclinical studies support that VNS attenuates inflammation primarily via the cholinergic anti-inflammatory pathway (CAP) through α7 nicotinic acetylcholine receptor (α7nAChR) activation. Emerging insights implicate β-adrenergic signaling, hypothalamic-pituitary-adrenal (HPA) axis modulation, and gut microbiome regulation. This review summarizes current clinical and preclinical evidence, synthesizes current mechanistic understanding, and addresses key gaps in clinical validation. Future research priorities include conducting large-scale randomized controlled trials to extend VNS applications to broader autoimmune diseases and advancing the neurostimulation efficacy of non-invasive vagus nerve stimulation devices.}, }
@article {pmid41796648, year = {2026}, author = {He, Q and Wu, H and Guo, M and Ye, R and Li, H and Zhang, Q}, title = {Functional and metabolic dysbiosis of the gut microbiome in the tumoral immune microenvironment of hepatocellular carcinoma.}, journal = {Cellular signalling}, volume = {143}, number = {}, pages = {112455}, doi = {10.1016/j.cellsig.2026.112455}, pmid = {41796648}, issn = {1873-3913}, abstract = {With its asymptomatic and heterogeneous nature, hepatocellular carcinoma (HCC) ranks as one of the most fatal malignancies globally, contributing to a deteriorating five-year overall survival. The gut microbiome, as the resident microorganism of the digestive tract, has been linked to a variety of hepatic disorders based on the internal "gut-liver" axis, accompanied by alterations in microbial components and derived metabolites. We found that patients with HCC had a greater abundance of Streptococcus salivarius (S. salivarius) and lithocholic acid (LCA), but its role in the tumor immune microenvironment remains elusive. Methodologically, we conducted 16S rRNA, 5R 16S rRNA sequencing and metabolomic analysis to discern the impact of S. salivarius in C-Myc/NRas-driven HCC mouse model and RNA-sequencing (RNA-seq) was performed to clarify the particular pathophysiological mechanism. In addition, the effect of S. salivarius on the efficacy of Anti-PD1 immunotherapy was evaluated as well. Mechanistically, S. salivarius was demonstrated to impede the cGAS/STING axis, consequently dampening the anti-tumor immune response by restricting the CD8[+] T cell trafficking to tumor microenvironment (TME) and triggering the immunosuppressive factor PD-1. Meanwhile, the integrative analysis indicated that the generated LCA facilitated the translocation of S. salivarius towards tumor site and activated the tumor-associated macrophages (TAMs), which altogether reshaped the immune TME in HCC. Our findings revealed perturbed microbial and metabolic features in the pathogenesis of HCC and offered a motivation for considering potential interventions during patient treatment.}, }
@article {pmid41796626, year = {2026}, author = {Minwuyelet, A and Atenafu, G}, title = {Exploring the gut micriobiome in Anopheles mosquitoes: A promising new approach to malaria control.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105917}, doi = {10.1016/j.meegid.2026.105917}, pmid = {41796626}, issn = {1567-7257}, abstract = {Malaria continues to pose significant public health issues globally. This disease is primarily spread through the bites of female Anopheles mosquitoes that are infected with the Plasmodium parasites. While conventional vector control strategies such as insecticide-treated bed nets (ITNs) and indoor residual spraying (IRS) have significantly reduced malaria burden, their long-term effectiveness is increasingly compromised by widespread insecticide resistance. Recent research has proposed manipulation of the Anopheles gut microbiome as a complementary malaria control strategy; however, the strength, consistency, and translational relevance of this evidence remain uneven. This review goes beyond descriptive synthesis by critically evaluating experimental approaches, identifying methodological limitations, highlighting contradictory findings, and assessing the robustness of current knowledge on mosquito microbiome Plasmodium interactions. We examine bacterial, fungal, and viral components of the Anopheles gut microbiome, emphasizing mechanisms such as immune modulation, nutrient competition, direct antiparasitic activity, and interference with mosquito physiology to inhibit pathogen transmission. Importantly, we identify key caveats, including laboratory bias, oversimplification of microbial consortia, context-dependent outcomes, and ecological uncertainties that challenge the deployment of microbiome-based interventions in the field. By integrating strengths and weaknesses of existing studies, this review provides a balanced and critical framework for future research and responsible translation of microbiome-based malaria control strategies.}, }
@article {pmid41796297, year = {2026}, author = {Shi, K and He, Q and Wang, S and Guo, J}, title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04922-y}, pmid = {41796297}, issn = {1471-2180}, support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; }, }
@article {pmid41796197, year = {2026}, author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M}, title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42270-z}, pmid = {41796197}, issn = {2045-2322}, }
@article {pmid41796087, year = {2026}, author = {Jiang, X and He, L and Han, Z and Zong, S and Du, S and Wu, H and Xiao, Y}, title = {Effects of Lactic Acid Bacteria on Fermentation Quality and Microbiome of Leymus chinensis Silage.}, journal = {MicrobiologyOpen}, volume = {15}, number = {2}, pages = {e70262}, pmid = {41796087}, issn = {2045-8827}, support = {202LHMS03022//Natural Science Foundation of Inner Mongolia/ ; BFGJ2024006//Northern Agriculture and Livestock Husbandry Technical Innovation Center/ ; }, mesh = {*Silage/microbiology/analysis ; *Fermentation ; *Microbiota ; *Poaceae/microbiology/metabolism ; *Lactobacillales/metabolism ; Lactiplantibacillus plantarum/metabolism ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics ; Lactobacillus ; }, abstract = {This study investigated the distinct effects of Lentilactobacillus buchneri (LB) and Lactiplantibacillus plantarum (LP) inoculants on the fermentation characteristics and bacterial community succession of Leymus chinensis silage. Treatments included distilled water (CON), LB, and LP, applied at a concentration of 1 × 10[6] cfu/g of fresh matter (FM). Compared with the CON group, the fermentation quality was improved by the inoculations, the markedly (p < 0.05) lower pH and NH3-N were found in the LB and LP treatments. The significantly (p < 0.05) highest LA and AA contents were detected in the LP and LB treatments, respectively. The bacterial diversity, reflected by Shannon and Chao1 indices, decreased throughout the ensiling process, with the LP group exhibiting the most pronounced reduction. Furthermore, beta-diversity analysis revealed distinct microbial community structures among the treatments. While fresh L. chinensis was dominated by Proteobacteria (48.03%), Firmicutes (26.23%), and Actinobacteriota (23.72%), the microbiome shifted dramatically after 60 days of ensiling to be predominantly Firmicutes (94.96%-99.79%), the genus Rhodococcus, Microbacterium, Enterococcus and Leuconostoc, Weissella, and Enterococcus were markedly (p < 0.05) enriched in the CK treatment during fermentation from 3 to 14 days, while from 30 days, the genus Lactobacillus as the dominant genus, especially in the LB and LP treatments. In conclusion, both additives facilitate L. chinensis ensiling by regulating the microbiome, yet L. plantarum demonstrates superior efficacy in optimizing fermentation quality.}, }
@article {pmid41795861, year = {2026}, author = {Malgesini, A and Marsiglia, MD and Borghi, E and Marzano, AV and Nazzaro, G}, title = {The Emerging Role of Gut Microbiota in Inflammatory Skin Diseases: A Systematic Review.}, journal = {Experimental dermatology}, volume = {35}, number = {3}, pages = {e70234}, pmid = {41795861}, issn = {1600-0625}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Psoriasis/microbiology/immunology ; *Hidradenitis Suppurativa/microbiology/immunology ; *Dermatitis, Atopic/microbiology/immunology ; Dysbiosis/microbiology ; }, abstract = {The human gut microbiota is involved in immune regulation, metabolism, and skin homeostasis. In recent years, gut microbiota alterations have been linked with several inflammatory skin disorders, such as atopic dermatitis (AD), psoriasis, and hidradenitis suppurativa (HS). This systematic review synthesises current evidence on gut microbiota composition and functional alterations in these dermatoses. A comprehensive literature search was conducted in the PubMed database, identifying studies from inception to January 2025. Eligible studies included human observational, interventional, and genetic studies investigating gut microbiota alterations in AD, psoriasis, or HS, using microbiome profiling or genetic causal-inference approaches. Studies lacking control groups or relying on culture-based techniques were excluded. Sixty-two studies were included: 38 on AD, 22 on psoriasis and 5 on HS, with three addressing more than one disease. In AD, most studies focused on paediatric populations, leaving a knowledge gap regarding adult-specific data. Reduced alpha-diversity and decreased abundance of Faecalibacterium prausnitzii, Bifidobacterium spp., and Akkermansia muciniphila were recurrent findings. In psoriasis, in addition to dysbiosis, microbial metabolic pathways were also found to be altered. In HS, data remain limited, but increased Ruminococcus gnavus and reduced alpha-diversity have been reported, mirroring findings in inflammatory bowel diseases. Gut microbiota has been increasingly implicated in skin inflammation. Despite advances in microbiota analysis, significant gaps remain-especially in adult AD and HS. Future research should prioritize standardised methodologies, larger and more diverse cohorts, and leverage emerging tools such as Mendelian randomization and AI-based models to develop precision medicine interventions.}, }
@article {pmid41795836, year = {2026}, author = {Wray, C and Castañeda-Monsalve, V and Engelmann, B and Rolle-Kampczyk, UE and Schweiger, N and Gutsfeld, S and Ghosh, D and Kader, S and Tyler, CR and Jehmlich, N and Tal, T}, title = {Integration of human microbiota (SIHUMIx) and zebrafish models reveals microbiome-mediated host responses to azoxystrobin.}, journal = {Toxicological sciences : an official journal of the Society of Toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1093/toxsci/kfag022}, pmid = {41795836}, issn = {1096-0929}, abstract = {The gut microbiome is essential for neurodevelopment via bidirectional gut-brain axis signaling, yet environmental chemicals can potentially disrupt this communication by altering community structure and xenobiotic metabolism. In this study, we investigated whether the fungicide azoxystrobin, a known metabolic disruptor, modulates microbiome composition and function to influence neurobehavior. We utilized a simplified human gut microbiota model (SIHUMIx) and a vertebrate host model (larval zebrafish) to elucidate microbiome-mediated mechanisms of xenobiotic neurotoxicity. SIHUMIx was exposed to azoxystrobin for 7 days at 10% of the acceptable daily intake, followed by recovery. Integrated metaproteomic and metabolomic analyses revealed functional reprogramming of the microbiota, characterized by upregulation of vitamin and cofactor biosynthesis, nutrient acquisition, and detoxification pathways, and decreased carbohydrate fermentation and amino acid turnover, consistent with reduced short-chain fatty acid levels. Microbiome-depleted and SIHUMIx-inoculated larvae were exposed to azoxystrobin at 4 days post fertilization and neurobehavioral outcomes were assessed after 24 h using the Visual and Acoustic Motor Response assay. Azoxystrobin exposure disrupted non-associative habituation learning independent of microbiome status but induced dark phase-hyperactivity only in colonized larvae, indicating a microbiome-dependent phenotype. Targeted metabolomics revealed lower serotonin levels in microbiome-depleted larvae relative to colonized controls, and that azoxystrobin exposure reduced serotonin in colonized larvae toward depleted levels. These results suggest that microbiota-dependent serotonergic signaling may modulate host responses to azoxystrobin. This integrated ex vivo-in vivo approach supports the concept that the microbiome is a key determinant of neurotoxic responses and underscores the importance of incorporating microbiome-mediated effects into chemical risk assessment frameworks.}, }
@article {pmid41795238, year = {2026}, author = {Sasia, S and Ortiz, M and Peña, M and Lumpkins, B and Arguelles-Ramos, M}, title = {Microbial dynamics in sorghum-based diets: impact of phase feeding and phytase superdosing vs. corn-based diets.}, journal = {Research in veterinary science}, volume = {204}, number = {}, pages = {106130}, doi = {10.1016/j.rvsc.2026.106130}, pmid = {41795238}, issn = {1532-2661}, abstract = {This study evaluated the cecal microbiome of broilers fed sorghum- or corn-based diets with standard or superdosed phytase across different feeding phases. A total of 1500 male broiler chicks were reared for 42 days in a floor pen facility and assigned to three dietary treatments. Birds received a corn-based diet with standard phytase, a sorghum-based diet with standard phytase, or a sorghum-based diet with phytase superdosing. Cecal samples were collected at the end of the starter, grower, and finisher phases for 16S rRNA sequencing. Microbial diversity increased as birds matured, with the lowest diversity observed in the starter phase and the greatest richness in the finisher phase. Microbial community structure clustered distinctly by feeding phase, confirming that age and diet progression were the main drivers of microbiota composition. Grain type and phytase level had minimal influence on alpha or beta diversity, although sorghum inclusion was associated with shifts in specific taxa, such as increased Muribaculaceae and reduced Ruminococcaceae. Overall growth performance and microbiome profiles were similar across dietary treatments, reinforcing the potential of sorghum as an effective substitute for corn in broiler diets. The findings highlight the importance of diet phase progression in shaping gut microbial communities and demonstrate that phytase superdosing does not substantially alter microbiome dynamics under these conditions.}, }
@article {pmid41795148, year = {2026}, author = {Shabana, H and Rodriguez-Wallberg, KA}, title = {The microbiome research in obstetrics and gynecology is getting attention-Some reasons why.}, journal = {Acta obstetricia et gynecologica Scandinavica}, volume = {}, number = {}, pages = {}, doi = {10.1111/aogs.70184}, pmid = {41795148}, issn = {1600-0412}, }
@article {pmid41795122, year = {2026}, author = {Kerr, EN and Yu, L and Hesse, RD and Roberts, CN and Bulone, V and Meyer, L and Edwards, RA and Doane, MP and Dinsdale, EA}, title = {Interactions of Mucus Monosaccharides and the Epidermal Microbiome in Four Benthic Elasmobranchs.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70303}, pmid = {41795122}, issn = {1758-2229}, support = {//Royal Society for South Australia/ ; RC2DK116713/NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; }, mesh = {Animals ; *Mucus/chemistry/metabolism/microbiology ; *Monosaccharides/metabolism/analysis ; *Microbiota ; *Epidermis/microbiology ; *Elasmobranchii/microbiology/metabolism ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Skin Microbiome ; }, abstract = {Epidermal mucus is a complicated mixture of macromolecules which acts as the first line of defence for organisms against abrasions and infections. We quantified the carbohydrate (monosaccharide) composition of the mucus from four Elasmobranchii hosts, including eagle rays (Myliobatis tenuicaudatus), Port Jackson sharks (Heterodontus portusjacksoni), Australian angelsharks (Squatina australis) and whitespotted skates (Dentiraja cerva). Elasmobranchii had low amounts of mucus and a low proportion of carbohydrates (< 10%) compared with other marine organisms. Four key monosaccharides: glucose, glucosamine, galactose and fucose, were identified in mucus samples. Hosts exhibited distinct, species-specific monosaccharide signatures. We identified key carbohydrate microbial genes from host and water microbiomes. Elasmobranch microbiomes had a higher relative abundance of carbon utilisation genes compared to the water column and contained gene pathways for the utilisation of specific monosaccharides found in host mucus, suggesting that the host mucus was a regulator of the microbiome. Elasmobranch epidermal microbiomes have the genetic machinery required for detecting, transporting and metabolising monosaccharides and other carbohydrates present in the host mucus, demonstrating the selective nature of Elasmobranch epidermal mucus.}, }
@article {pmid41794853, year = {2026}, author = {Zhang, Z and Yu, L and Wu, C and Guo, J and Zhu, L and Wang, J and Zhou, C}, title = {Soil acidification dismantles a citrulline-mediated microbe-metabolite-host defense axis in watermelon, exacerbating Fusarium wilt.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00951-7}, pmid = {41794853}, issn = {2055-5008}, support = {20250586//where they are referenced/ ; 2023AH020024, gxyq2022053//Natural Science Foundation of Universities in Anhui Province/ ; XK-XJGY003//University-Level Advanced Discipline/ ; DTR2024033//Discipline (Major) Leader Development Program/ ; }, abstract = {Soil acidification disrupts the structure and function of soil microbiomes, resulting in increased vulnerability to soil-borne pathogens. While the link between soil acidification and disease susceptibility is well-established, the mechanisms underlying the suppression of plant defense remain poorly understood. In this study, we found that soil acidification perturbed the co-evolved assembly process of endophytic microbiomes in watermelon roots, leading to the collapse of a critical microbe-metabolite-host defense axis essential for resistance against Fusarium oxysporum f. sp. niveum (FON). Integrated field surveys and multi-omics analyses revealed that acidification-induced dysbiosis in the root endophytic microbiomes, characterized by the depletion of keystone Pseudomonas species (Pseudomonadaceae), strongly correlated with increased Fusarium wilt incidence. Central to this interaction was citrulline, a metabolite produced by root Pseudomonas endophytes that functioned as a symbiotic effector promoting bacterial colonization and a defense modulator inhibiting FON-induced oxidative burst. Disruption of citrulline biosynthesis abolished these protective effects, whereas exogenous citrulline application restored disease resistance. These findings underscored the role of root endophyte-derived citrulline in sustaining microbial fitness and plant defense, revealing a tripartite interaction impacted by soil acidification. Collectively, this study provides insights for developing microbiome-based strategies to enhance sustainable crop protection in degraded agroecosystems.}, }
@article {pmid41794812, year = {2026}, author = {Müller, F and Wang, H and Reinhard, A and Omirbekova, A and Berzhanova, R and Mukasheva, T and Urich, T and Mikolasch, A}, title = {The hydrocarbon-degrading bacteria and fungi in oil contaminated soils of Kazakhstan: microbiome composition, enrichment, isolation and bioremediation potential.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00866-y}, pmid = {41794812}, issn = {2524-6372}, abstract = {BACKGROUND: Oil contamination in soils causes significant environmental impacts and risks to human health. Oil components can be naturally reduced by indigenous microorganisms, that are able to degrade such substrates. We used culture-independent and culture-dependent methods to examine the prokaryotic and the eukaryotic microbiome of different heavily oil contaminated soils in Kazakhstan. Bacteria and fungi were enriched and isolated from four soils contaminated with crude oil or hydrocarbons. Aliphatic, aromatic and condensed aromatic model hydrocarbons of crude oil and crude oil itself were used as substrates for the enrichment and the isolation experiments. The enrichment process was accompanied by culture-independent tests.<br><br>RESULTS: The results of the Illumina sequencing of the contaminated soils and the enrichment cultures were compared with the results of the culture-dependent isolation and determination of bacterial, yeast and filamentous fungal strains. The majority of these 110 strains from 45 different genera belong to well-described hydrocarbon degraders like Bacilli and Rhodococci as well as to Achromobacter, Gordonia, Pseudomonas, Stenotrophomonas, Aspergillus, Exophiala, Fusarium, Meyerozyma, Penicillium and Trichoderma species. The most abundant species was the ascomycetal yeast Meyerozyma guilliermondii followed by strains of the bacterial genus Peribacillus. Furthermore, we combined the microbiome insights on the enrichment procedures and the isolation of bacteria, yeasts and filamentous fungi with the in-fact degradation potential of the isolated species based on substrate consumption and metabolite formation. In addition to the well-described hydrocarbon degraders, the utilization spectrum of less-studied strains of the genera Leifsonia, Neorhizobium, Purpureocillium, Rhodotorula and Sarocladium could be broadened.<br><br>CONCLUSION: In the end a complex overview of the indigenous microorganisms and their degradation ability of crude oil components emerged and demonstrates the great potential of bioremediation for Kazakhstan soils.}, }
@article {pmid41794696, year = {2026}, author = {Amsalu, A and Haidari, H and Mirco, B and Rudolph-Stringer, V and Walter, S and Antipov, A and Murrell, DF and Kopecki, Z}, title = {Characterisation of the wound microbiome and antimicrobial resistance profiles in clinical isolates from epidermolysis bullosa patients.}, journal = {Orphanet journal of rare diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13023-026-04295-5}, pmid = {41794696}, issn = {1750-1172}, support = {Channel 7 Children's Research Foundation//Channel 7 Children's Research Foundation/ ; DEBRA Australia//DEBRA Australia/ ; Epidermolysis Bullosa Medical Research Foundation//Epidermolysis Bullosa Medical Research Foundation/ ; }, }
@article {pmid41794620, year = {2026}, author = {Iftikhar, N and Konig, I and Brammer-Robbins, E and Kozuch, M and Bisesi, JH and Hashmi, I and Martyniuk, CJ}, title = {Corrigendum to "Environmentally relevant levels of sulfamethoxazole (SMX) alter the skin and gastrointestinal microbiome of adult male and female zebrafish (Danio rerio)" [Aquatic Toxicology, Volume 288 (2025) 107546].}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {}, number = {}, pages = {107767}, doi = {10.1016/j.aquatox.2026.107767}, pmid = {41794620}, issn = {1879-1514}, }
@article {pmid41794500, year = {2026}, author = {Hua, Q and Meng, Y and Hu, J and Wei, Y and Yi, H and Liang, X and Zhang, L and Zhang, Z}, title = {ILA-producing bifidobacterium bifidum ameliorates chronic kidney disease via AHR signaling by modulating the gut-kidney axis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118638}, doi = {10.1016/j.foodres.2026.118638}, pmid = {41794500}, issn = {1873-7145}, mesh = {Animals ; *Renal Insufficiency, Chronic/therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; *Gastrointestinal Microbiome ; Signal Transduction ; Mice ; *Probiotics/pharmacology ; *Bifidobacterium bifidum/metabolism/genetics ; *Indoles/metabolism ; Kidney/metabolism ; Male ; Disease Models, Animal ; *Lactic Acid/metabolism/analogs &amp; derivatives ; Dysbiosis ; Mice, Inbred C57BL ; *Basic Helix-Loop-Helix Proteins/metabolism ; }, abstract = {Chronic kidney disease (CKD) is associated with gut microbiota dysbiosis and disruption of the gut-kidney axis, making probiotics-which can modulate host metabolism and the gut microbiome-a highly promising intervention strategy. Building on this premise, this study used High-Performance Liquid Chromatography (HPLC) to screen 39 candidate strains and successfully isolate two high indole-3-lactic acid (ILA)-producing strains of Bifidobacterium bifidum: FL228.1 and ZL.1. Whole-genome sequencing subsequently confirmed that both strains possess the aromatic lactate dehydrogenase (Aldh) gene, which is essential for ILA biosynthesis. The strains were then evaluated in an adenine-induced CKD mouse model. ZL.1 exhibited pronounced efficacy: it not only improved renal injury, restored gut barrier function, and corrected dysbiosis, as evidenced by an increased relative abundance of Muribaculaceae and a decreased abundance of Dubosiella, but also significantly elevated the level of the key metabolite ILA. In-depth mechanistic analysis revealed that ILA exerts its effects by activating the aryl hydrocarbon receptor (AHR) signaling pathway, which in turn inhibits NLRP3 inflammasome activation, thereby achieving the dual benefit of mitigating intestinal inflammation and alleviating renal fibrosis. Targeted metabolomics analysis supported the conclusion that high ILA production is a critical characteristic for B. bifidum's modulation of the gut-kidney axis. In contrast, the FL228.1 strain showed moderate effects, with its specific mechanism remaining unclear. In conclusion, our study suggests that ILA-producing B. bifidum may ameliorate CKD by regulating the gut-kidney axis via ILA and AHR signaling. This indicates a potential probiotic strategy targeting tryptophan metabolism for CKD.}, }
@article {pmid41794479, year = {2026}, author = {Baheti, R and Deshkar, S and Jadhav, S and Mule, K and Jha, A and Giram, P and Mahore, J}, title = {Interplay of probiotics, prebiotics, synbiotics and postbiotics: a review of their therapeutic potential for gastrointestinal inflammation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118598}, doi = {10.1016/j.foodres.2026.118598}, pmid = {41794479}, issn = {1873-7145}, mesh = {*Prebiotics/administration &amp; dosage ; Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Synbiotics/administration &amp; dosage ; Gastrointestinal Microbiome ; Animals ; *Inflammation ; *Inflammatory Bowel Diseases/microbiology/therapy ; *Gastrointestinal Diseases/therapy ; }, abstract = {Gastrointestinal inflammation is a multifaceted condition deeply connected to the gut microbiota. The prebiotics, probiotics, synbiotics and their metabolites, termed postbiotics, have been explored extensively in the past as a novel approach in managing inflammatory bowel disorders. Prebiotics, probiotics, and postbiotics derived from food sources play crucial roles in modulating the gut microbiota and significantly impact gastrointestinal inflammation. Prebiotics are non-digestible, selectively fermented dietary fibers found in foods such as inulin-type fructans and galacto-oligosaccharides that promote the growth of beneficial gut bacteria like bifidobacteria and lactobacilli. These prebiotics contribute to the production of short-chain fatty acids which possess anti-inflammatory properties and enhance immune regulation in the gut. Together, prebiotics, probiotics, and postbiotics synergistically maintain and restore gastrointestinal health by modulating the gut microbiome composition, enhancing production of anti-inflammatory metabolites, strengthening the intestinal barrier, and regulating immune responses. These interventions show promise in preventing and managing gastrointestinal inflammatory conditions such as irritable bowel syndrome, Crohn's disease, and ulcerative colitis by counteracting dysbiosis and mucosal inflammation. Drawing from recent preclinical and clinical studies, these strategies have shown promising results in managing gastrointestinal inflammation. Despite the compelling evidence, significant challenges remain. These include the considerable variability of host responses, the necessity for standardized strains and precise dosages, and a lack of a unified regulatory framework. This comprehensive review integrates the current understanding of prebiotics, probiotics, synbiotics, and postbiotics, highlighting their mechanistic interplay and highly promising role in managing gastrointestinal inflammation. It provides an in-depth discussion on current limitations and future directions for research and clinical application.}, }
@article {pmid41794478, year = {2026}, author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V}, title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118597}, doi = {10.1016/j.foodres.2026.118597}, pmid = {41794478}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.}, }
@article {pmid41794466, year = {2026}, author = {Huang, S and Ding, H and Su, Y and Chen, Z and He, W and Chen, ZY and Zhu, H}, title = {Alpha-lipoic acid improves intestinal homeostasis and ameliorates colitis through modulation of gut microbiota and production of short chain fatty acids in mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118582}, doi = {10.1016/j.foodres.2026.118582}, pmid = {41794466}, issn = {1873-7145}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fatty Acids, Volatile/metabolism ; *Thioctic Acid/pharmacology ; *Colitis/chemically induced/drug therapy/microbiology ; Mice, Inbred C57BL ; Male ; *Homeostasis/drug effects ; Mice ; Dextran Sulfate ; Fecal Microbiota Transplantation ; Oxidative Stress/drug effects ; NF-kappa B/metabolism ; Disease Models, Animal ; Antioxidants/pharmacology ; Cytokines/metabolism ; }, abstract = {α-Lipoic acid (ALA) is a natural antioxidant present in both plants and animal foods. It has attracted growing attention for its potential role in maintenance of intestinal homeostasis. This study was to investigate the protective effects of dietary ALA on experimental colitis, and to evaluate its modulating effect on gut microbiome in mice. Male C57BL/6 J mice with dextran sulfate sodium (DSS)-induced acute colitis were administered ALA (40 or 80 mg/kg) dissolved in corn oil. Results showed that dietary ALA ameliorated colitis severity, improved intestinal barrier integrity, and attenuated inflammation by reducing oxidative stress and suppressing NF-κB pathway activation and pro-inflammatory cytokines expression. Moreover, dietary ALA increased the microbial diversity (Shannon index), reshaped gut microbiota composition by suppressing pathogenic bacteria and promoting beneficial taxa such as Akkermansia, and elevated levels of short chain fatty acids (SCFA). Fecal microbiota transplantation (FMT) further confirmed that ALA could modulate gut microbiota and protect against colitis in mice. In conclusion, ALA could effectively maintain the intestinal homeostasis and ameliorate colitis at least in mice. Such protective effect of ALA in gut health was mediated through modulation of gut microbiota and enhancement of SCFA production.}, }
@article {pmid41794462, year = {2026}, author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V}, title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {230}, number = {}, pages = {118577}, doi = {10.1016/j.foodres.2026.118577}, pmid = {41794462}, issn = {1873-7145}, mesh = {*Fermentation ; *Vitis/microbiology ; *Wine/microbiology/analysis ; *Mycobiome ; Italy ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metagenomics/methods ; Food Microbiology ; Metabolome ; Kluyveromyces/metabolism ; Multiomics ; }, abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.}, }
@article {pmid41794383, year = {2026}, author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G}, title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {110327}, doi = {10.1016/j.jnutbio.2026.110327}, pmid = {41794383}, issn = {1873-4847}, abstract = {BACKGROUND: Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains scope for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden.<br><br>METHODS: We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45).<br><br>RESULTS: Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. Eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population.<br><br>CONCLUSIONS: Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.}, }
@article {pmid41794297, year = {2026}, author = {Wang, T and Binion, B and Alves, JMP and Ridlon, JM}, title = {Characterization of an NADPH-dependent 17ɑ-hydroxysteroid dehydrogenase encoded by the desF gene from the gut bacterium Clostridium scindens VPI 12708.}, journal = {The Journal of steroid biochemistry and molecular biology}, volume = {}, number = {}, pages = {106982}, doi = {10.1016/j.jsbmb.2026.106982}, pmid = {41794297}, issn = {1879-1220}, abstract = {Epitestosterone (epiT) is the isomer of the androgen testosterone. Historically, the role of epiT has remained unclear. Recently, it has been reported that epiT promotes nuclear androgen receptor (AR)-dependent prostate cancer cell proliferation. The gut bacterium Clostridium scindens VPI 12708 was shown to convert androstenedione (AD) to epiT over three decades ago. The bacterial enzymatic pathways involved in epiT formation have only recently been reported. The desF gene encodes 17α-hydroxysteroid dehydrogenase which converts AD to epiT using NADPH as a cofactor. In this study, we quantitatively characterized DesF kinetic parameters and substrate specificity. The results revealed that the optimal pH for the reductive reaction is 7.0, and for the oxidative reaction it is 7.5 and 8.0. The kinetic analysis showed that for the reductive reaction, the KM was 8.1 ± 1.8µM and the Vmax was 6.4 ± 0.3 µmol·min[-1]·mg[-1]; for the oxidative direction, the KM was 27.3 ± 3.3µM and the Vmax was 7.2 ± 0.3 µmol·min[-1]·mg[-1]. Moreover, the substrate specificity analysis revealed that 11-keto-AD is the most favourable substrate for DesF, and the 17-keto group of 11-keto-AD can be converted to the 17α-hydroxy group. The phylogenetic relation between DesF and other characterized hydroxysteroid dehydrogenases reveals common ancestry with human HSD17B10 and Eggerthella lenta 3β-HSDH. These results are a significant advance in understanding epiT formation by the gut microbiome.}, }
@article {pmid41794153, year = {2026}, author = {Ma, Y and Ni, Z and Zhu, L and Yang, J and Zhang, Y and Liu, W and Wang, R and Sun, Y and Liu, J and Zhang, P and Yu, L and Huangfu, C and Gao, Y and Zhou, W}, title = {Skin commensal Cutibacterium acnes alleviates UVB-induced solar dermatitis via ceramide-mediated TLR4-MyD88-NF-κB.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2026.02.074}, pmid = {41794153}, issn = {1873-4596}, abstract = {BACKGROUND: The high-altitude environment is characterized by hypobaric hypoxia and intense ultraviolet B (UVB) radiation, contributing to increased incidence of UVB-induced skin injuries, including plateau solar dermatitis (PSD). The role of commensal skin microbiota in mediating photoprotection under such extreme conditions remains poorly understood. This study aimed to identify UVB-protective skin microbiota in high-altitude populations and to elucidate their potential mechanisms in mitigating UVB-induced skin damage.<br><br>METHODS: Skin microbiota profiles were analyzed by 16S rRNA gene sequencing in healthy plateau residents and PSD patients. Protective effects were evaluated using a murine model of UVB-induced skin injury and an in vitro UVB-exposed HaCaT keratinocyte model. Integrated transcriptomic, proteomic, and metabolomic analyses were performed to identify candidate bioactive microbial metabolites, followed by functional validation.<br><br>RESULTS: Cutibacterium acnes (C. acnes) was significantly enriched in healthy plateau residents compared with PSD patients. Topical application of C. acnes alleviated UVB-induced skin inflammation, collagen degradation, and DNA damage in mice. Multi-omics analyses revealed dysregulation of sphingolipid metabolism following UVB exposure and highlighted bacterial-derived ceramides as candidate protective metabolites. Two representative ceramides, CER2 and CER14, significantly reduced UVB-induced apoptosis, oxidative stress, and DNA damage in keratinocytes. These effects were associated with suppression of TLR4-MyD88-NF-&#x3ba;B signaling activity.<br><br>CONCLUSION: This study identifies C. acnes as a commensal bacterium with photoprotective potential against UVB-induced skin damage in high-altitude environments. Ceramide-related lipid metabolites derived from C. acnes contribute to attenuation of UVB-triggered inflammatory signaling and cellular injury, providing new insights into microbiome-based strategies for photoprotection.}, }
@article {pmid41794001, year = {2026}, author = {Noor, S and Qureshi, A and Parvez, S and Ahmad, B}, title = {The dual binding of pantoprazole mitigates ceftriaxone-mediated misfolding of human serum albumin.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {355}, number = {}, pages = {127661}, doi = {10.1016/j.saa.2026.127661}, pmid = {41794001}, issn = {1873-3557}, abstract = {Proton pump inhibitors (PPIs) like pantoprazole are often prescribed alongside antibiotics to prevent antibiotic-induced gastritis, ulcers, and microbiome disturbances. In this study, we provide the first evidence of pantoprazole's (PTP) distinct protective role in preventing ceftriaxone (CTX) induced structural alterations and aggregation of human serum albumin (HSA). We have found strong binding of pantoprazole at domain-I and domain-III, whereas ceftriaxone binds in domain-II of HSA. The ceftriaxone binding was found to disrupt the tertiary structure of the protein and induces the non-native β-structures without affecting the thermal stability of the protein. Moreover, it was found to promote the thermal-induced formation of protofibrils. However, the addition of pantoprazole in HSA-CTX complex efficiently restored the structural alterations and aggregation reaction. This study highlights a previously unrecognized protective role of PPIs, particularly pantoprazole, in preserving protein structure and aggregation caused by antibiotic overuse.}, }
@article {pmid41793943, year = {2026}, author = {Burns, GL and Roberts, F and Wark, JA and Fowler, S and Jones, MP and Duncanson, K and Talley, NJ and Keely, S}, title = {Serological and faecal markers of irritable bowel syndrome: a systematic review and meta-analysis.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106198}, doi = {10.1016/j.ebiom.2026.106198}, pmid = {41793943}, issn = {2352-3964}, abstract = {BACKGROUND: The irritable bowel syndrome (IBS) has long been considered a functional disorder, but recent work has demonstrated clear biological signatures in immune, microbiome and enteric nervous systems of patients with IBS. Despite this new knowledge, there is still no clear biological marker of IBS, with patient symptom reporting and exclusion of organic disease the main criteria for diagnosis. We aimed to perform a systematic review and meta-analysis to identify consistent biomarkers for IBS in serum and stool samples.<br><br>METHODS: We searched Medline, EMBASE, Cochrane Library, Web of Science and Scopus to obtain all relevant publications published between 1992 and January 2026. Original, peer-reviewed research articles including adults with IBS and healthy or outpatient controls, and/or patients with organic gastrointestinal conditions (e.g. IBD) were included. All articles had quantification of blood and faecal markers between IBS and controls. Descriptive data presented as median and range or median (interquartile range) was converted to mean &#xb1; SD. To account for methodological assay differences between studies, standardised mean difference (SMD) with 95% confidence interval was used as the primary outcome measure for the meta-analyses, with a random effects model fitted to the data.<br><br>FINDINGS: The search strategy identified 55,444 citations across all databases. 124 studies were included encompassing 14,930 patients with IBS, 7544 healthy/asymptomatic controls and 4317 patients with organic diseases. The top serum discriminators between IBS and healthy controls were TNF-&#x237a; (13 studies, 1025 controls and 1244 IBS, SMD = 2.74, 95% CI = 0.70, 4.70, p = 0.006), IL-6 (13 studies, 736 controls and 1022 IBS, SMD = 1.87, 95% CI = 0.13, 3.61, p = 0.035) and IFN-&#x263; (4 studies, n = 195 controls, n = 372 IBS, SMD = 2.79, 95% CI = 1.07, 4.51, p = 0.002). For faecal markers calprotectin was significantly higher in patients with IBS over controls (11 studies, 1624 controls and 1383 IBS, SMD = 0.75, 95% CI = 0.30, 1.21, p = 0.001), while faecal valerate levels were lower in IBS versus controls (4 studies, 290 controls and 488 IBS, SMD = -0.79, 95% CI = -1.48, -0.11, p = 0.02). For discriminating IBS overall from organic diseases, serum albumin (4 studies, 282 IBS and 312 organic, SMD = 2.15, 95% CI = 0.20, 4.11, p = 0.031) and faecal calprotectin (16 studies, 1591 IBS and 1685 organic, SMD = -1.13, 95% CI = -1.51, -0.75, p < 0.0001) were significantly different. In discriminating IBS subtypes from controls, only diarrhoeal IBS (IBS-D) could be distinguished by albumin (3 studies, 248 controls and 219 IBS-D, SMD = -0.39, 95% CI = -0.68, -0.11, p = 0.007) and IL-6 (4 studies, 153 IBS-D and 169 controls, SMD = 2.53, 95% CI = 0.86, 4.21, p = 0.003). Heterogeneity across the studies ranged from moderate to high, but few overly influential studies were identified between comparisons.<br><br>INTERPRETATION: Patients with IBS exhibit increased peripheral cytokine levels that are consistent with reports of increased epithelial permeability and may be important in distinguishing subgroups of IBS patients. Patients with IBS also demonstrated higher faecal calprotectin levels than healthy individuals, although these levels were still significantly lower than patients with organic diseases. Similarly, patients with IBS-D have lower serum albumin levels compared to healthy controls, while patients with organic disease had lower levels compared to patients with IBS, irrespective of subtype. There are clear biological signatures at play in IBS patients that may be useful clinically in establishing IBS diagnosis and may indicate the mechanisms of disease symptoms.<br><br>FUNDING: National Health and Medical Research Council Centre for Research Excellence in Digestive Health (NJT, SK) G180219.}, }
@article {pmid41793899, year = {2026}, author = {Amin, H and Cramer, C and Finster, K and Real, FG and Gislason, T and Holm, M and Janson, C and Jögi, NO and Jogi, R and Malinovschi, A and Modig, L and Norbäck, D and Shigdel, R and Sigsgaard, T and Svanes, C and Thorarinsdottir, H and Wouters, IM and Šantl-Temkiv, T and Schlünssen, V and Bertelsen, RJ}, title = {Indoor airborne bacterial communities and adult lung health: A cross-sectional study.}, journal = {International journal of hygiene and environmental health}, volume = {274}, number = {}, pages = {114780}, doi = {10.1016/j.ijheh.2026.114780}, pmid = {41793899}, issn = {1618-131X}, abstract = {BACKGROUND AND OBJECTIVE: Indoor microbial exposures influence respiratory health, yet how men and women respond differently to airborne bacterial communities remains unclear. This study aimed to assess sex-specific associations between indoor airborne bacteria, and lung function, and airway inflammation in adults.<br><br>METHODS: Airborne dust was collected from the bedrooms of 1038 adults (463 men, 575 women) across five Nordic cities as part of the European Community Respiratory Health Survey (ECRHS) III. Bacterial communities were profiled using 16S rRNA amplicon sequencing. Bacterial and endotoxin loads were quantified via quantitative PCR (qPCR) and the Limulus amebocyte lysate (LAL) assay, respectively. Multivariable linear regression models stratified by sex were used to examine associations with lung function and airway inflammation.<br><br>RESULTS: Greater indoor bacterial diversity was associated with higher lung function in men (FEV1 &#x3b2;&#xa0;=&#xa0;0.17, 95% CI: 0.05 to 0.29, P&#xa0;=&#xa0;0.003) and higher FeNO levels in women (&#x3b2;&#xa0;=&#xa0;2.44, 95% CI: 0.73 to 4.15, P&#xa0;=&#xa0;0.005). Endotoxin load was positively associated with FeNO in women (&#x3b2;&#xa0;=&#xa0;0.37, 95% CI: 0.05 to 0.70, P&#xa0;=&#xa0;0.02), but not in men. Genera from Actinobacteriota and Bacilli were associated with higher lung function, while Clostridia was linked to lower lung function and reduced FeNO. In contrast, several genera from Actinobacteriota and Gammaproteobacteria were positively associated with FeNO.<br><br>CONCLUSIONS: Indoor bacterial exposures were associated with respiratory health in a sex-specific pattern. These findings highlight the importance of microbial composition in shaping adult lung health and underscore the need for sex-specific approaches in future epidemiological research.}, }
@article {pmid41793893, year = {2026}, author = {Narla, T and Nudurupati, U and Ou, Y}, title = {Developing fast scan cyclic voltammetry at carbon fiber microelectrodes to quantify short chain fatty acids in situ.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {171}, number = {}, pages = {109266}, doi = {10.1016/j.bioelechem.2026.109266}, pmid = {41793893}, issn = {1878-562X}, abstract = {Acetic, propionic, and butyric acids are short chain fatty acids (SCFAs) and the most abundant metabolites produced by gut bacteria. To uncover mechanistic insights of their function throughout the body, it is critical to measure rapid SCFA fluxes in sites of action such as brain, muscle, and skin. Current approaches have focused on fecal and plasma measurements, where SCFA levels are low and not representative of tissue-specific concentrations or fluxes. Thus, a rapid, in situ methodology is needed. Fast scan cyclic voltammetry (FSCV) at carbon fiber microelectrodes (CFMs) has the spatiotemporal resolution to fill this need. However, the electrochemical response of CFMs to SCFAs have not been explored until now. By coupling FSCV at CFMs with flow injection analysis of each SCFA, we demonstrate there are distinct peaks in the cyclic voltammograms for each fatty acid. Some of these peaks display faradaic behavior in scan rate, holding potential, and switching potential experiments. Interestingly, we identify several peaks that are concentration-sensitive and therefore are promising quantifiable markers of SCFA dynamics and fluxes. This work lays the foundation in understanding the response of CFMs to fatty acids and demonstrate the utility of FSCV at CFMs for the in situ quantitation of SCFAs.}, }
@article {pmid41793548, year = {2026}, author = {Shahadha, MH and Voigt, A and Gruner, D and Marschner, U and Le Floch, M and Hampe, J and Brauer, F and Schostek, S and Luniak, M and Bock, K and Richter, A}, title = {Ingestible active capsule for gastrointestinal microbiome sampling.}, journal = {Biomedical microdevices}, volume = {28}, number = {1}, pages = {}, pmid = {41793548}, issn = {1572-8781}, abstract = {UNLABELLED: Various gastrointestinal disorders have been linked to gut microbiome dysbiosis, as it plays a critical role in immune regulation, metabolism, nutrient digestion, and pathogen suppression. However, the microbiome’s spatial variability across gastrointestinal segments and its intra- and interindividual differences complicate its study and clinical interpretation. While fecal DNA analysis is commonly used, stool samples only capture an accumulated signal and miss the spatial dynamics of microbial populations. To address this, we propose a modular sampling capsule capable of wirelessly collecting liquid. The capsule consists of two main modules: (i) an actuator module integrating a polymer-based microfluidic system with meltable wax-based opening valve, screen-printed microheater, cellulose membrane-based closing valve, evacuated sampling chamber with dried sample preservative material, filter membrane (size exclusion 150 μm), and sample extraction channel; and (ii) a control electronic module with communication, localization, and power supply units. The actuator module was validated in vitro using a diluted stool simulant (330 mg/mL) and an uncleaned porcine intestine. The opening valve activated within 3.6 ± 0.5 s at 120 ± 10 mA and 0.8 V. The sample was then filtered and aspirated into the sampling chamber within 1–2 s, and the closing valve sealed the inlet completely within 10 min. We overcame design, material, and fabrication challenges to construct an actuator module that functions effectively in liquids with variable physicochemical conditions (pH, chemical composition, viscosity, and particle size). These results demonstrate the feasibility of a controlled, segment-specific intestinal sampling capsule, representing a step towards precise and accurate microbiome profiling.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10544-026-00802-4.}, }
@article {pmid41793273, year = {2026}, author = {Britos, M and Pellegrini, E and Hernández-Ríos, P and Garrido, M and Fernández, A and Tomás, I and León, R and Arredondo, A and Álvarez, G and Teuche, AH and Ríos, MH}, title = {Subgingival Microbial Signatures Associated With Apical Periodontitis Identified by Next Generation Sequencing and Predictive Modelling.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70131}, pmid = {41793273}, issn = {1365-2591}, support = {1200098//FONDECYT/ ; 1251739//FONDECYT/ ; ID24I10282//Vice-Rectorate for Research and Development (VID), University of Chile/ ; //Chilean Government/ ; }, abstract = {AIMS: To assess the relationship between endodontic and subgingival bacterial communities in individuals with apical periodontitis (AP), and to identify disease-associated subgingival microbial signatures. We propose that subgingival microbial communities exhibit a dysbiotic profile, defined by distinct bacterial signatures, which may provide complementary biological insights into AP.<br><br>METHODS: In this cross-sectional study, DNA was extracted from paired endodontic and subgingival samples from mesiobuccal sites of first molars in patients with AP (n&#x2009;=&#x2009;25 sample pairs), and from subgingival samples from the same sites in healthy individuals (n&#x2009;=&#x2009;34). Microbiota was explored using 16S rRNA sequencing. Alpha and beta diversity metrics were calculated. Differentially abundant taxa were identified using LEfSe. Random forest models based on the bacterial counts observed in the subgingival samples were trained to classify the individuals with AP from the controls.<br><br>RESULTS: Within AP individuals, the subgingival communities differed from those present in root canals. Subgingival communities exhibited higher alpha diversity than root canal communities, irrespective of the clinical diagnosis (p&#x2009;<&#x2009;0.001). Subgingival microbial communities in AP individuals exhibited a dysbiotic profile associated with enrichment of anaerobic and inflammophilic species (p&#x2009;<&#x2009;0.05). Beta diversity analyses showed compositional differences between AP and control individuals, with Jaccard distance reaching statistical significance (p&#x2009;<&#x2009;0.05), and Bray-Curtis indicating a borderline effect (p&#x2009;=&#x2009;0.07). The best predictive model (Streptococcus sanguinis and Prevotella maculosa) achieved an accuracy of 89.8%, sensitivity of 80%, specificity of 97%, precision of 95.2%, and an AUC of 0.98.<br><br>CONCLUSIONS: Subgingival profiles from AP individuals are distinct from those in healthy controls, showing AP-associated dysbiosis. Specific subgingival bacterial signatures achieved high diagnostic accuracy, supporting the potential broader impact of AP on the subgingival microbiota.}, }
@article {pmid41793176, year = {2026}, author = {Zheng, L and Zhao, G and Zheng, L and Zou, Y and Zhang, S and Dong, J}, title = {Insights Into Highly Associated Co-Factors on HPV-Related Cervical Cancer.}, journal = {Reviews in medical virology}, volume = {36}, number = {2}, pages = {e70131}, doi = {10.1002/rmv.70131}, pmid = {41793176}, issn = {1099-1654}, mesh = {Humans ; *Uterine Cervical Neoplasms/virology/epidemiology/etiology ; Female ; *Papillomavirus Infections/complications/virology/epidemiology ; *Papillomaviridae/genetics/classification ; Prevalence ; Microbiota ; }, abstract = {Cervical cancer ranks among the most prevalent malignancies, representing a substantial threat to women's health. The incidence of cervical cancer is strongly correlated with persistent infections by high-risk human papillomavirus (HPV) types. Overall, the prevalence of HPV infection is high, with most cases being classified as recessive, latent, and subclinical. The predominant HPV types and overall infection rates exhibit variability across different tissue types, individuals, and regions. Numerous co-factors contribute to the processes underlying persistent HPV infection and carcinogenesis, including the microbiome, individual immune characteristics, and geographical population differences. Moreover, these factors affect the efficacy of chemotherapy and immunotherapy in cancer treatment. This review aims to summarise several key factors associated with HPV-related cervical cancer and discuss their mechanisms in promoting carcinogenesis in HPV-related malignancies. The insights gained may inform the development of more effective preventive and therapeutic strategies.}, }
@article {pmid41793016, year = {2026}, author = {Yin, J}, title = {Mechanistic Insights for Microbiome Application in Plant Disease Resistance.}, journal = {Molecular plant pathology}, volume = {27}, number = {3}, pages = {e70233}, pmid = {41793016}, issn = {1364-3703}, support = {//Xinyang Normal University Scientific Research Start-up Fund./ ; 5250046//2025 Key Pilot Research Projects in Natural Sciences, Xinyang Normal University/ ; }, mesh = {*Microbiota/physiology ; *Disease Resistance/physiology ; *Plant Diseases/microbiology/immunology ; *Plants/microbiology ; }, abstract = {Plant diseases caused by biotic and abiotic stresses pose a great threat to both plant health and yield. Plant microbiomes play a crucial role in improving disease resistance, representing a sustainable approach to enhance crop performance. Plant host factors, including genetic variation, metabolites and microRNA, shape the assembly and function of the plant microbiome, thereby augmenting disease resistance. This interplay presents opportunities for plant-mediated manipulation of microbiome to promote plant health. Multiple mechanisms are involved in the microbiome-mediated plant disease resistance, such as direct and indirect pathogen antagonism, niche pre-emption, alteration of microbiota and activation of plant defences. Nevertheless, the application of plant microbiome in the field remains limited due to the intrinsic complexity of plant-microbiome and environment-microbiome interactions. This review synthesises current knowledge on the roles of plant microbiomes in plant disease resistance. I further summarise the mechanisms underlying plant-guided microbiome modulation and probiotic-mediated disease suppression. I also raise work and challenges that should be addressed, with the ultimate goal of informing more efficient microbiome application in sustainable agriculture.}, }
@article {pmid41792922, year = {2026}, author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD}, title = {Microbially Derived Essential Amino Acids Compensate for Dietary Deficiencies in an Ecologically Relevant Mammalian Host.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag044}, pmid = {41792922}, issn = {1751-7370}, abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.}, }
@article {pmid41792460, year = {2026}, author = {Imre, A and Kovács, R and Jakab, &#xc1; and Harmath, A and Németh, B and Nagy, F and Forgács, L and Balázsi, D and Majoros, L and Benkő, Z and Crook, N and Pócsi, I and Pfliegler, WP}, title = {ENA1 deficiency attenuates Saccharomyces 'boulardii' probiotic yeast virulence in immunosuppressed mouse fungaemia model.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09763-z}, pmid = {41792460}, issn = {2399-3642}, abstract = {Recently, fungal infections originating from the probiotic Saccharomyces 'boulardii' yeast are increasingly reported. Here, we aimed to reveal the background of and to diminish the virulence of this yeast, mitigating infection risks in vulnerable patient groups. Product and human isolates of S. 'boulardii' were subjected to in-host selection and their subclone lineages were compared phenotypically to identify target phenotypes and associated genes. More virulent isolates showed signs of selection for high osmotic tolerance in immunosuppressed mouse model, hence the genes NHA1 and ENA1 were deleted in six different 'boulardii' backgrounds. Only ENA1 deletion diminished virulence in our mouse fungemia model and it retained the ability for gut colonization and its probiotic characteristics, including similar effects on the gut microbiome in gavaged mice. We also demonstrated the successful substitution of the ENA1 gene with an antilisterial bacteriocin, opening a strategy for safe strains with therapeutic effect. Our strain development approach highlighted the importance of testing various genetic backgrounds and resulted in engineered strains with drastically reduced capability to cause bloodstream infections even in immunosuppressed hosts, establishing the groundwork for safer probiotic yeast therapies in the future.}, }
@article {pmid41792406, year = {2026}, author = {Llirós Dupré, M and Buxó, M and Virolés, S and Pujolassos, M and Serra, I and Martínez, J and Lluansí, A and Bahí, A and Calle, M and Aldeguer, X}, title = {Preliminary insights into gut microbiome shifts as screening proxy for MASLD disease progression.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42368-4}, pmid = {41792406}, issn = {2045-2322}, support = {2015 Research Initiation Grant #3//Societat Catalana de Digestologia/ ; Girona Townhall, 2017//Joan Bruguera Fund/ ; }, }
@article {pmid41792366, year = {2026}, author = {Ikram, S and Ullah, M and Lee, J and Hasan, N and Yoo, JW and Khan, R and Naeem, M}, title = {Fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis of randomized controlled trials (2020-2025).}, journal = {Inflammopharmacology}, volume = {}, number = {}, pages = {}, pmid = {41792366}, issn = {1568-5608}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has emerged as a therapeutic strategy for Inflammatory Bowel Disease (IBD) including ulcerative colitis (UC) and Crohn's disease (CD). Although multiple randomized controlled trials (RCTs) have been published in recent years, evidence remains fragmented regarding safety and efficacy. This systematic review and meta-analysis evaluated the efficacy and safety of microbiome-based interventions in Inflammatory Bowel Disease (IBD).<br><br>METHODS: A systematic search of PubMed, Cochrane CENTRAL and Embase was conducted for randomized controlled trials (RCTs) published between January 2020 and May 2025. Eligible studies compared donor FME with placebo, autologous FMT or standard therapy in adult patients with IBD. Primary outcomes were clinical remission and endoscopic improvement; secondary outcomes included maintenance of remission and adverse events. Risk of bias was assessed using the Cochrane RoB-2 tool. Meta-analyses were performed in R using the meta and meta for packages. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated using common-effects and random-effects models.<br><br>RESULTS: Six RCTs involving 220-230 patients were included (majority UC patients, two trials CD). For induction of clinical remission, FMT was associated with significantly higher rates vs controls (OR&#x2009;=&#x2009;3.24, 95% CI 1.43-7.41, p&#x2009;=&#x2009;0.005) under a common-effect model; random-effects model showed similar point estimate but wide CI overlapping unity. Endoscopic response was strongly increased with FMT (OR&#x2009;=&#x2009;6.80, 95% CI 2.96-15.63, p&#x2009;<&#x2009;0.0001). Serious adverse events were more common in FMT arms but not statistically significant (common-effects OR&#x2009;~&#x2009;2.05, 95% CI 0.72-5.81, p&#x2009;=&#x2009;0.18). Evidence for maintenance of remission from two trials was limited and inconsistent.<br><br>CONCLUSION: Microbiome-based therapies, particularly FMT, significantly improved clinical and endoscopic remission in IBD (especially in UC) compared with control interventions, but safety signals and maintenance efficacy remain uncertain. Larger and strictly designed UC and CD-specific RCTs are needed to confirm long-term efficacy, clarify safety and define the role of microbiome-targeted therapies in IBD management.}, }
@article {pmid41792350, year = {2026}, author = {Gan, Y and Zhang, J and Yao, K and Jiang, R and Li, Z and Yang, Y}, title = {The microbiome of interstitial cystitis revealed by 2bRAD-M.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42249-w}, pmid = {41792350}, issn = {2045-2322}, support = {82103239//National Natural Science Foundation of China/ ; 7244419//Beijing Municipal Natural Science Foundation/ ; }, }
@article {pmid41792309, year = {2026}, author = {Ntekas, I and Takayasu, L and McKellar, DW and Grodner, B and Holdener, C and Schweitzer, P and Park, YS and Sauthoff, M and Shi, Q and Brito, IL and De Vlaminck, I}, title = {Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41792309}, issn = {2058-5276}, abstract = {Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong intermicrobial interactions at short length scales and tumour-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.}, }
@article {pmid41792269, year = {2026}, author = {Ray, K}, title = {HIV-associated gut microbiome influences gut mucosal immunity.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {41792269}, issn = {1759-5053}, }
@article {pmid41792267, year = {2026}, author = {Almeida, AP and Moncau-Gadbem, CT and Goes, CP and Garcia, IS and da Silva, TR and Clemente, LG and Coutinho, LL}, title = {Characterization of bacterial microbiome and molecular detection of rickettsiosis in free-living ticks (Amblyomma sculptum Berlese, 1888).}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-38069-7}, pmid = {41792267}, issn = {2045-2322}, abstract = {Amblyomma sculptum is a major tick species in southeastern Brazil and an important vector in the epidemiology of Brazilian Spotted Fever (BSF). This study characterized the bacterial microbiome of free-living A. sculptum ticks in a BSF-endemic area, focusing on differences among developmental stages and sexes, and investigated rickettsial agents using 16S rRNA gene (V3-V4) sequencing. A total of 154 ticks were collected and analysed as 13 pooled samples grouped by stage and sex. Sequencing identified a diverse bacterial community of 180 genera, dominated by Sphingomonas, Nocardioides, Actinomycetospora and Methylobacterium, alongside genera of potential zoonotic relevance such as Rickettsia, Anaplasma, Ehrlichia and Coxiella, mainly in nymph pools. Alpha and beta diversity analysis showed that microbial community composition differed among stages and sexes, with adult males exhibiting higher richness and compositional dispersion, whereas nymphs showed reduced diversity and tighter clustering. Because 16S sequencing does not allow species-level identification of rickettsiae, positive samples were further analysed by PCR amplification and sequencing of the gltA gene, which identified Rickettsia bellii. Together, these results highlight stage- and sex-associated patterns in the microbiome of free-living A. sculptum and support the use of integrated microbiome profiling and targeted rickettsial detection in ecological and epidemiological studies of tick-borne diseases.}, }
@article {pmid41792233, year = {2026}, author = {Wu, Q and Hu, K and Wang, Q and Luo, T and Hu, L and Liu, J and Zou, D and Hu, J and Guo, Z}, title = {Proline/serine-rich coiled-coil 1 alleviates atherosclerosis via remodeling tryptophan metabolism mediated by Akkermansia muciniphila.}, journal = {Experimental &amp; molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {41792233}, issn = {2092-6413}, abstract = {Genome-wide association studies have implicated proline/serine-rich coiled-coil 1 (PSRC1) in coronary artery disease (CAD) pathogenesis. Our previous studies demonstrated that Psrc1 deficiency accelerates atherosclerosis via gut microbial dysbiosis, characterized by a substantial depletion of Akkermansia muciniphila. Recent studies implicate microbiome-dependent tryptophan metabolism as a novel checkpoint in atherosclerosis, with specific microbial taxa regulating metabolite-driven immune responses. The mechanism by which Psrc1 modulates atherosclerosis through A. muciniphila and its regulation of tryptophan metabolism remains unclear. Here Psrc1 knockout mice exhibited reduced colonic mucin content, altered tryptophan metabolic enzyme expression and diminished levels of Trp metabolites including indoleacetic acid (IAA), with concomitant suppression of Ahr signaling in macrophages. In vivo analysis revealed that Psrc1 knockout diminishes Ahr through A. muciniphila-dependent IAA depletion. In vitro experiments further uncovered that Psrc1 stabilizes Ahr protein via ubiquitin carboxyl terminal hydrolase L3 (Uchl3)-mediated deubiquitylation. In addition, we identified plasma IAA levels positively correlating with decreased PSRC1 expression in peripheral blood mononuclear cells from patients with CAD. Furthermore, therapeutic restoration of a live A. muciniphila-IAA axis through oral supplementation reversed atherosclerosis in Psrc1 knockout mice. Notably, oral IAA supplementation substantially ameliorated atherosclerosis in Psrc1 knockout mice by suppressing plaque macrophage apoptosis. Crucially, co-administration of the Ahr antagonist CH-223191 abolished these benefits, confirming Ahr dependence. Our findings position PSRC1 as a critical regulator of the A. muciniphila-IAA-Ahr axis and nominate microbiome-targeted Ahr activation as a precision therapeutic strategy for patients with CAD with PSRC1 loss-of-function variants.}, }
@article {pmid41791848, year = {2026}, author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and ,  and Stewart, CJ and Rees, CJ}, title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337478}, pmid = {41791848}, issn = {1468-3288}, abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.<br><br>OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.<br><br>DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.<br><br>RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and &#x3b2;-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).<br><br>CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.}, }
@article {pmid41791791, year = {2026}, author = {Corona, M and García-Vicente, R and Saez-Marin, AJ and Ancos-Pintado, R and Rodríguez-Garcia, A and Arroyo, A and Blanco, A and Chari, A and Martin, T and Wolf, J and Rey-Bua, B and Mateos, MV and Kortüm, KM and Riedhammer, C and Tamariz-Amador, LE and Valencia, E and Rodríguez-Otero, P and San Miguel, J and Ibarra, G and Oriol, A and Cedena, MT and López-Muñoz, N and Alonso, R and Calbacho, M and Sanchez-Pina, JM and Linares, M and Martínez-López, J}, title = {Antibiotic-associated dysbiosis and bispecific antibody outcomes in multiple myeloma.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {3}, pages = {}, doi = {10.1136/jitc-2025-014224}, pmid = {41791791}, issn = {2051-1426}, mesh = {Humans ; *Multiple Myeloma/drug therapy/mortality/immunology ; Male ; Female ; *Dysbiosis/chemically induced ; *Antibodies, Bispecific/therapeutic use/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Middle Aged ; Aged ; Retrospective Studies ; Gastrointestinal Microbiome/drug effects ; Adult ; Treatment Outcome ; }, abstract = {BACKGROUND: The gut microbiota plays a critical role in regulating immune homeostasis and modulating responses to cancer immunotherapies. However, the impact of antibiotic-induced dysbiosis in patients with multiple myeloma (MM) treated with bispecific antibodies (BsAbs) remains unexplored. This multicenter, international study investigated whether antibiotic exposure prior to BsAb initiation alters the gut microbiome and affects clinical outcomes in patients with relapsed or refractory MM.<br><br>METHODS: We retrospectively analyzed 237 adult patients with MM treated with CD3-engaging BsAbs across six academic institutions. Antibiotic exposure was defined as the administration of any broad-spectrum, non-prophylactic antibiotic within 30 days before BsAb initiation. Clinical outcomes included overall survival (OS), progression-free survival (PFS), and cumulative incidence of relapse, evaluated using Kaplan-Meier estimates, log-rank tests, and multivariable Cox and competing-risk regression models. Additionally, in a subset of 24 patients, peripheral blood samples were collected prior to BsAb infusion for immunophenotyping, cytokine profiling, and serum short-chain fatty acid (SCFA) quantification, while stool samples for 16S ribosomal RNA (rRNA) sequencing were collected in a subset of 19 patients.<br><br>RESULTS: Broad-spectrum antibiotic exposure prior to BsAb therapy was associated with significantly inferior 1-year OS (60% (95% CI 44% to 81%)&#x2009;vs 77% (95% CI 71% to 83%), p=0.004) and PFS (26% (95% CI 14% to 47%)&#x2009;vs 53% (95% CI 46% to 61%), p<0.001), and higher relapse incidence (68% (95% CI 48% to 82%)&#x2009;vs 43% (95% CI 36% to 50%), p=0.004). In multivariable analyses, antibiotic exposure remained independently associated with poorer OS, PFS, and higher relapse risk. These associations were also observed within the subgroup of patients treated with CD3/B-cell maturation antibody-targeted BsAbs (n=155). Immunoprofiling revealed lower CD4[+] T-cell counts (p=0.017) and reduced circulating cytokine levels among antibiotic-exposed patients. 16S rRNA sequencing demonstrated a marked depletion of SCFA-producing genera, including Roseburia and Eubacterium, accompanied by lower serum SCFA concentrations. Moreover, microbiota composition before BsAb treatment correlated with therapy response and treatment-related toxicity.<br><br>CONCLUSIONS: Antibiotic-induced dysbiosis prior to BsAb therapy is associated with impaired immune reconstitution and inferior clinical outcomes in MM. These findings underscore the importance of antibiotic stewardship and suggest that microbiota-preserving strategies could enhance the efficacy of BsAb therapy in MM.}, }
@article {pmid41791749, year = {2026}, author = {Ribeiro, B and Duarte, G and Thomas, T and Reeves, S and Suggett, DJ and Peixoto, RS}, title = {Exploring the transformative potential of multi-trophic strategies to enhance coral restoration and mitigate disease.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1945}, pages = {}, doi = {10.1098/rstb.2024.0323}, pmid = {41791749}, issn = {1471-2970}, mesh = {Animals ; *Coral Reefs ; *Anthozoa/physiology/microbiology ; *Conservation of Natural Resources/methods ; Climate Change ; *Environmental Restoration and Remediation/methods ; *Food Chain ; Microbiota ; }, abstract = {Unprecedented coral reef degradation from climate change, local impacts and disease requires time-critical development of innovative, cost-effective and ecologically grounded restoration strategies. Conventional restoration strategies to recover coral reef ecosystems largely focus on coral propagation, often de-prioritizing the broader ecological interactions that underpin reef resilience. However, coral reefs are complex ecosystems where other reef-associated organisms have fundamental and connected roles in nutrient cycling, biofiltration, pathogen control and microbiome stewardship. Integrating these key functional groups into restoration efforts in both the production phase (co-cultivation) and ecological recovery phase (ecological reconstruction) is required to advance coral restoration efforts toward more holistic coral reef ecological restoration frameworks. Integrating multi-trophic strategies provides a multifunctional, nature-based solution to enhance coral survival, mitigate disease outbreaks and promote overall ecosystem health. Here, we discuss the benefits of such a multi-trophic approach, where filter feeders, suspension feeders, detritivores and grazers are incorporated into the processes of reef restoration efforts. By leveraging positive species interactions based on facilitation theory, a multi-trophic approach provides a tool that not only enhances microbiome stewardship and coral reef restoration success but also reinforces the long-term sustainability of reef ecosystems in a changing climate. This article is part of the theme issue 'Managing infectious marine diseases in wild populations'.}, }
@article {pmid41791695, year = {2026}, author = {Chandra, QM and Clister, D and Halim, P and Dalimunthe, A and Ichwan, M and Sari, DK and Umaya, C and Aktary, N and Rani, A and Park, MN and Kim, B and Syahputra, RA}, title = {Harnessing the gut-heart axis for cardiovascular drug innovation: microbiome, metabolites, and personalized treatment strategies.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {587}, number = {}, pages = {120941}, doi = {10.1016/j.cca.2026.120941}, pmid = {41791695}, issn = {1873-3492}, abstract = {Cardiovascular disease (CVD) remains the leading cause of mortality worldwide despite major advances in pharmacotherapy. Emerging evidence reveals a pivotal role for the gut-heart axis, wherein gut microbiota are and their metabolites influence CV physiology, pathology, and drug responsiveness. Dysbiosis in conditions such as hypertension, atherosclerosis, and heart failure has been associated with altered production of bioactive metabolites including trimethylamine N-oxide, short-chain fatty acids, bile acids, and tryptophan derivatives. These metabolites have been shown to modulate inflammation, endothelial function, lipid metabolism, and myocardial remodeling. This review synthesizes current knowledge on microbiome-drug interactions in CV pharmacology, including how gut bacteria may metabolize drugs (e.g., digoxin, aspirin, warfarin) and how CV agents can shape microbial communities. We further explore microbiome-targeted therapeutic strategies-probiotics, prebiotics, postbiotics, fecal microbiota transplantation, and small-molecule inhibitors of harmful metabolites-highlighting their mechanisms, preclinical evidence, and translational potential. Integrating microbiome profiling with multi-omics platforms and artificial intelligence may enable personalized treatment strategies that optimize CV outcomes. While the gut-heart axis presents an exciting frontier for drug innovation, challenges remain in establishing causality, addressing inter-individual microbiome variability, managing confounding factors such as diet and medication use, and meeting regulatory requirements. Harnessing this bidirectional relationship holds promise for transforming CV pharmacotherapy from a one-size-fits-all approach to precision medicine grounded in host-microbe interactions.}, }
@article {pmid41791635, year = {2026}, author = {Laojun, S and Changbunjong, T and Bunchu, N and Chaiphongpachara, T}, title = {Microbial communities and wing variation associated with ectoparasitic mites in medically important Mansonia mosquitoes (Diptera: Culicidae) from coconut plantation habitats in central Thailand.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108042}, doi = {10.1016/j.actatropica.2026.108042}, pmid = {41791635}, issn = {1873-6254}, abstract = {This study presents the comprehensive assessment of the bacterial microbiome and the effects of ectoparasitic mites on wing morphometry in Mansonia mosquitoes, namely, Ma. annulifera, Ma. indiana, and Ma. uniformis from coconut-growing areas in central Thailand. High-throughput sequencing of the 16S ribosomal RNA gene (V3-V4 regions) generated 1,813,140 raw reads. Following quality control with the DADA2 pipeline, including filtering, denoising, merging, and chimera removal, 681,766 non-chimeric sequences were retained across nine libraries, yielding 467 unique amplicon sequence variants (ASVs). Distinct, species-specific bacterial community profiles were identified: Fructobacillus fructosus dominated Ma. annulifera (28.85% relative abundance), whereas Wolbachia was predominant in Ma. indiana (57.94%) and Ma. uniformis (80.87%). Although alpha diversity showed no significant interspecific differences (p > 0.05), beta-diversity analyses revealed clear species-specific clustering. Differential abundance testing further identified Rosenbergiella sp. as a biomarker for Ma. annulifera and Wolbachia sp. as highly enriched in Ma. indiana and Ma. uniformis. Geometric morphometric analysis revealed significant differences in mean centroid size among all mite infestation groups in Ma. annulifera (p < 0.05), but not in Ma. indiana or Ma. uniformis (p > 0.05). Shape analysis indicated that Ma. annulifera differed significantly only between the no-mite and high-intensity groups, Ma. indiana across all pairwise comparisons, and Ma. uniformis between the no-mite and high-intensity groups and between the low- and high-intensity groups (p < 0.05). This study provides new insights into Mansonia microbiome diversity and mite-associated morphological variation, with implications for mosquito ecology and disease transmission.}, }
@article {pmid41791375, year = {2026}, author = {Shane, J and Evans, M and Rigas, Y and Shanks, RMQ and St Leger, AJ}, title = {Genetically engineered eye-colonizing microbes that deliver the anti-inflammatory cytokine interleukin-10 enhance corneal tissue repair.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117064}, doi = {10.1016/j.celrep.2026.117064}, pmid = {41791375}, issn = {2211-1247}, abstract = {Barrier surfaces harbor tissue-colonizing microbes that can shape local physiology and immunity. During corneal injury, inflammation can delay healing, resulting in loss of visual acuity. Standards of care include topical applications of therapies, which are quickly washed away, requiring a laborious treatment regimen to maintain efficacy. To address this problem, we engineered an eye-colonizing microbe, Corynebacterium mastitidis, to act as a long-term therapeutic delivery vehicle by secreting bioactive interleukin (IL)-10 using a native secretion signal that we identified using transposon mutagenesis. Engineered microbes stably colonize the eye and release mouse (mIL-10) or human IL-10 (hIL-10) that modulates local immunity and accelerates wound repair after an initial inoculation event. Further, hIL-10 producing C. mast can regulate inflammatory cytokine production in immune cells, highlighting the immune-regulatory capabilities of this live biotherapeutic product. These findings demonstrate that genetically engineered eye-colonizing bacteria can serve as a self-sustaining therapeutic platform to control inflammation and promote tissue repair.}, }
@article {pmid41791329, year = {2026}, author = {de Vicente, M and Tomás-Pejó, E and González-Fernández, C}, title = {From conventional to adapted microbiomes: Promoting high short-chain fatty acid yields and productivities from agricultural waste.}, journal = {Journal of environmental management}, volume = {403}, number = {}, pages = {129216}, doi = {10.1016/j.jenvman.2026.129216}, pmid = {41791329}, issn = {1095-8630}, abstract = {Microbial consortia play an essential role in anaerobic fermentation (AF) devoted to the production of short-chain fatty acids (SCFAs) from organic wastes. AF is usually performed by a conventional anaerobic microbiome (CM) sourced from anaerobic digestion reactors. During AF, the microbiome undergoes an adaptation period to the imposed operational conditions and substrate characteristics, leading to the bio-enrichment of certain microorganisms. This work compared the use of CM and a bio-enriched microbiome (BM) as inoculum for AF of agricultural wastes in continuous stirred tank reactors (CSTR) with hydraulic retention time (HRT) of 8 d. The novelty of this study lies in demonstrating that using a BM enhances the production rate of SCFAs when compared to CM. BM, composed of adapted microorganisms previously working at an HRT of 10 d, allowed the highest SCFAs productivity (1.97 g/L·d) and concentration (15.6 g/L). Bioconversion efficiencies achieved with BM and CM (60.1 % and 71.8 %, respectively) were among the highest reported in literature. Microbiome analysis revealed inoculum-driven changes in the microbial community. However, Clostridium and Megasphaera, which are involved in the hydrolysis and acidification steps of AF and are associated with acetic acid formation and chain elongation, predominated in all cases (up to 48 % of the microbial abundance within the total community). These results evidenced the feasibility of operating CSTRs at an HRT of 8 d with diverse inoculum sources to maintain exceptionally high SCFA productivity and bioconversion. The outcomes also highlighted the robustness of the microbial community, even under short HRT, providing a novel strategy for AF processes optimization.}, }
@article {pmid41791313, year = {2026}, author = {Filippini, G and Bugnot, AB and O'Connor, W and Gribben, PE and Varkey, DR and Paulsen, IT and Dafforn, KA}, title = {Marine heatwaves alter shell microbiomes and denitrification capacity: An oyster family-specific response.}, journal = {Marine pollution bulletin}, volume = {227}, number = {}, pages = {119503}, doi = {10.1016/j.marpolbul.2026.119503}, pmid = {41791313}, issn = {1879-3363}, abstract = {Marine heatwaves (MHWs) are increasing in frequency and intensity, significantly affecting biodiversity and ecosystem processes. However, the impact of MHWs on microbiome structure and function, and whether such changes are influenced by intraspecific differences among hosts, remains unclear. This study investigated the effect of a simulated MHW on external shell microbiomes (alpha diversity, community and taxonomic compositions, and denitrification capacity) of four oyster families (1, 11, 14 and 15), with different levels of disease resistance and growth rate. Oysters were exposed to 29 °C (MHW) and 24 °C (control) temperatures for 6 days, followed by a 21-day recovery period. The MHW shifted bacterial community composition and decreased alpha diversity in Family 14, together with reductions in the relative abundance of Pseudomonadota and Planctomycetota, and in denitrification genes (nirK and nosZ). In Family 15, MHW exposure decreased the abundance of Rhizobiaceae and the denitrification gene nirS, which recovered within three weeks. Reduction in denitrification genes suggests a potential decline in nitrogen removal capacity, which could negatively affect coastal systems, as bioavailable nitrogen may accumulate and lead to eutrophication. Conversely, in Families 1 and 11 the shell microbiomes remained stable under heat stress. Although mechanisms were not directly assessed, these faster-growing families may possess physiological traits (e.g. efficient metabolism and filtration) that support the resilience of nitrogen-cycling microbes during thermal stress. This study highlights the importance of intraspecific differences among hosts in shaping microbiome responses to MHWs, suggesting that selecting certain oyster families could help maintain key microbial-driven processes like denitrification under climate stress.}, }
@article {pmid41790992, year = {2026}, author = {Berendse, R and Verkleij, M and Daams, J and Hemmings, S and Lindauer, R and Korosi, A and Zantvoord, JB and Lok, A}, title = {The microbiome and PTSD: a scoping review across preclinical and clinical studies.}, journal = {European journal of psychotraumatology}, volume = {17}, number = {1}, pages = {2627060}, doi = {10.1080/20008066.2026.2627060}, pmid = {41790992}, issn = {2000-8066}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Stress Disorders, Post-Traumatic/microbiology/physiopathology ; Disease Models, Animal ; }, abstract = {BACKGROUND: Posttraumatic Stress Disorder (PTSD) is a psychiatric condition that substantially impairs quality of life and global health. Emerging evidence implicates that the human microbiome contributes to PTSD pathophysiology via gut-brain-immune interactions, although the underlying mechanisms and therapeutic implications remain unclear.<br><br>OBJECTIVE: This review aimed to systematically map the evidence linking microbiome alterations to PTSD, with a focus on mechanistic pathways, therapeutic potential, and research gaps.<br><br>METHODS: This scoping review was conducted in Medline, Embase, and PsychINFO from inception to 18-03-2025. Eligible studies included human participants with PTSD and preclinical rodent models employing validated PTSD paradigms. Outcomes of interest included microbiome diversity and composition, gut-brain axis biomarkers, and effects of microbiome-targeted interventions.<br><br>RESULTS: Fifty studies were included, comprising 20 human, 29 preclinical and one cross-species study. Human observational studies frequently observed reduced overall microbial diversity, along with a loss of short-chain fatty acid (SCFA)-producing bacteria, such as Ruminococcaceae and Lachnospiraceae, and an increased abundance of Veillonella, Odoribacter, and Catenibacterium&#xa0;linked to gut permeability and inflammation. Human intervention studies testing probiotics, prebiotics, fermented soy, and dietary fibre showed preliminary evidence for symptom and related metabolic and inflammatory marker improvements; however, microbiome effects were inconsistent. Preclinical models revealed stress-induced reductions in Bifidobacteria, Verrucomicrobia, and Parabacteroides, and increases in Coprobacillus&#xa0;and Anaeroplasma. Functional consequences included impaired barrier integrity, altered SCFA levels, and heightened immune activation. Preclinical interventions, particularly Mycobacterium vaccae, as well as probiotics, synbiotics, acetate, and MDMA, mitigated microbial alterations, reduced anxiety-like behaviours, and modulated neuroimmune pathways.<br><br>CONCLUSION: Current evidence supports an association between PTSD and microbiome alterations, with convergent human and preclinical findings. However, human research remains limited by small, cross-sectional designs, which preclude causal inferences. Rigorous longitudinal and interventional studies are required to establish causality and assess microbiome-targeted therapies as adjuncts in PTSD treatment.}, }
@article {pmid41790682, year = {2026}, author = {Xie, RX and Ci, XY and Xue, YB and Liu, M and Zhang, MJ}, title = {Association between oral microbiota and inflammatory bowel disease: A 2-sample Mendelian randomization study in East Asian populations.}, journal = {Medicine}, volume = {105}, number = {10}, pages = {e47909}, doi = {10.1097/MD.0000000000047909}, pmid = {41790682}, issn = {1536-5964}, mesh = {Humans ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Asia, Eastern/epidemiology ; *Microbiota/genetics ; *Crohn Disease/microbiology/genetics ; *Mouth/microbiology ; Asian People/genetics ; *Inflammatory Bowel Diseases/microbiology/genetics/epidemiology ; *Colitis, Ulcerative/microbiology/genetics/epidemiology ; Saliva/microbiology ; Male ; Female ; East Asian People ; }, abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is increasingly prevalent in East Asia. Its pathogenesis is linked to microbiota dysbiosis via the oral-gut axis, but population-specific causal evidence remains scarce. This study aimed to clarify the causal associations between oral microbiota and UC/CD in East Asian populations using Mendelian randomization (MR), providing evidence for IBD etiology and precise prevention/treatment. A 2-sample MR approach was adopted, using genome-wide association study data of East Asian populations. Single nucleotide polymorphisms associated with tongue dorsum and salivary microbiota were selected as instrumental variables after rigorous screening (F-statistic > 10, linkage disequilibrium R2 = 0.001). Inverse variance weighted was the primary analysis method, supplemented by sensitivity tests (MR-PRESSO, MR-Egger intercept test, etc) and Benjamini-Hochberg multiple testing correction (false discovery rate < 0.05). A total of 82 oral microbiota taxa (22 families, 35 genera) were significantly causally associated with UC (FDR < 0.05), and 21 taxa (10 families, 12 genera) with CD (FDR < 0.05). High-risk taxa included Aggregatibacter and Streptococcus (OR > 1), while protective taxa included Fusobacterium_periodonticum_C_mgs_3022 and TM7x_unclassified_mgs_1084 (OR < 1). A distinct "mixed effect" was identified: the Streptococcus genus was risky for UC but protective for CD; genera such as Streptococcus (UC), Oribacterium (CD), and TM7x (CD) exhibited bidirectional risk/protective associations within a single IBD subtype; and the TM7x genus was risky for UC and showed bidirectional effects in CD. Other genera (e.g., Fusobacterium, Aggregatibacter) only had unidirectional associations. This study is the first to confirm the causal association between oral microbiota and IBD in East Asian populations, revealing the heterogeneity and "mixed effect" of this association. Identified high-risk and protective oral microbiota taxa provide new insights into IBD etiology and potential targets for clinical precise prevention and treatment.}, }
@article {pmid41790596, year = {2026}, author = {Srivastava, H and Sehgal, T and Sharma, V and Narang, H and Berinstein, J and Sood, A and Bishu, S and Goyal, MK}, title = {Beyond the binary: understanding inflammatory bowel disease in the context of HIV-Induced immunodeficiency.}, journal = {Expert review of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1080/1744666X.2026.2642832}, pmid = {41790596}, issn = {1744-8409}, abstract = {INTRODUCTION: The coexistence of inflammatory bowel disease(IBD) and human immunodeficiency virus(HIV) represents a clinical paradox in which immune hyperactivity coexists with persistent immunodeficiency. Improved survival with antiretroviral therapy(ART) has led to increasing co-diagnoses, creating complex diagnostic and therapeutic challenges.<br><br>AREAS COVERED: A comprehensive literature search of PubMed/MEDLINE, Embase, Scopus, and the Cochrane Library from inception through December 2024 was conducted, supplemented by major gastroenterology and infectious disease conference proceedings through April 2025. This review synthesizes contemporary evidence on epidemiology, immunopathogenesis, clinical presentation, and management of IBD in people living with HIV. Key themes include immune reconstitution and Th17-cell depletion, diagnostic differentiation from infectious and noninfectious mimickers, underutilization of advanced IBD therapies despite emerging safety data, bidirectional interactions between intestinal inflammation and HIV viral dynamics, and clinically relevant ART - IBD interactions requiring multidisciplinary care.<br><br>EXPERT OPINION: Accumulating evidence supports the safe and appropriate use of immune-modulating therapies in virologically suppressed HIV-positive patients with IBD, challenging historical risk-averse approaches. Optimal management requires precision-based strategy incorporating CD4[+] cell thresholds, mucosal and inflammatory biomarkers, and individualized risk stratification. Future priorities include standardized diagnostic algorithms, longitudinal registries integrating immunological and virological parameters, and improved access to advanced therapies, moving beyond the traditional autoimmunity - immunodeficiency binary.}, }
@article {pmid41790425, year = {2026}, author = {Kim, E and Kim, H and Lee, M and Kim, B and Kim, B and Kim, H and Kim, D and Kang, D and Shatta, A and Kim, JY and Holzapfel, WH and Yoon, H}, title = {Saccharomyces cerevisiae 48338 Suppresses Antibiotic-Induced Clostridioides difficile Infection in a Murine Model.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41790425}, issn = {1867-1314}, support = {RS-2025-16070149//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 202400440001//Handong Global University Research Grants/ ; }, abstract = {Clostridioides difficile infection (CDI) is a major cause of antibiotic-associated diarrhea and colitis, driven by toxin-mediated epithelial injury and inflammation. While antibiotics such as vancomycin remain the primary treatment, they can further disrupt the gut microbiota and promote recurrence. Probiotics, including yeast strains, have emerged as potential adjunctive therapies for mitigating CDI. In this study, several Saccharomyces cerevisiae strains were evaluated for their probiotic potential, and strain 48338 was identified as the most promising candidate based on its gastrointestinal tolerance, auto-aggregation ability, and antioxidant activity. Using a CDI mouse model, we found that treatment with S. cerevisiae 48338 reduced disease severity, as reflected by lower clinical sickness scores. Quantitative PCR analysis confirmed that the expression of the toxin gene tcdA was significantly decreased following 48338 treatment, whereas total C. difficile burden remained unchanged. In addition, 48338 treatment might enhance intestinal barrier integrity by upregulating occludin gene expression and also might attenuate production of pro-inflammatory cytokines, particularly the expression of IL-1β. The strain also increased the proportions of Foxp3[+] regulatory T cells and macrophages in both the spleen and mesenteric lymph nodes, as determined by flow cytometry, suggesting a shift towards an anti-inflammatory immune profile. Collectively, these findings suggest that the primary mechanism by which S. cerevisiae 48338 exerts its protective effect against C. difficile infection is not through direct reduction of C. difficile colonization, but primarily through modulation of the microbiome, host immune response, and maintenance of epithelial cell integrity. This study highlights the potential of yeast-based probiotics as adjunctive agents for the prevention or mitigation of CDI.}, }
@article {pmid41790398, year = {2026}, author = {Sutton, S and Voskamp, S and Le, K and Hafez, A and Nelson, J and Palomo, P}, title = {Malondialdehyde Drives a Feed-Forward Reactive Oxygen Species Loop in Pediatric Crohn's Disease.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {41790398}, issn = {1573-2568}, abstract = {PURPOSE: Crohn's disease (CD) is a chronic, relapsing inflammatory bowel disease with multifactorial etiology. Recent studies implicate reactive oxygen species (ROS) in pediatric CD. Expression of malondialdehyde (MDA), a biomarker of oxidative stress, is elevated in inflammatory diseases, including CD. This study aimed to evaluate genes driving ROS production in pediatric CD and MDA's role in shaping downstream gene expression.<br><br>METHODS: Using the Search Tag Analyze Resource for NCBI's Gene Expression Omnibus (STARGEO), we performed a tagged meta-analysis of publicly available gene expression data comparing pediatric CD with controls. Differentially expressed genes were restricted to p&#x2009;<&#x2009;0.05 and absolute experimental log ratio of 0.2 for further analysis with Ingenuity Pathway Analysis (IPA), to explore biologic relationships.<br><br>RESULTS: Fifty-two pediatric CD samples and 24 healthy pediatric intestinal samples were identified and analyzed via STARGEO, yielding 1968 genes that met inclusion criteria. DUOX2, MMP3, and NOD2 were significantly upregulated in pediatric CD (log ratios of 2.521, 1.823, 0.524, respectively). Upstream regulators include TNF (z-score 11.195), TGFB1 (5.945), IFNG (9.983), and TLR4 (5.989). MDA was identified as a strongly activated regulator with a z-score of 10.909 and downstream targets including TGFB1, MMP3, TNF, and IL-6.<br><br>CONCLUSION: Our findings enhance the current understanding of the role of immune dysregulation, ROS, the gut microbiome, and epithelial barrier dysfunction in pediatric CD. DUOX2 functions as one of the central mediators of ROS-driven dysregulation, with TLR4-driven DUOX2 activity potentially overriding the NOD2 regulation. MDA formation stimulates inflammation and tissue injury, upregulating MMP3, which in turn increases ROS production to generate more MDA. This feed-forward inflammatory loop may accelerate fibrosis and chronic inflammation. This meta-analysis provides a preliminary framework of ROS-related gene programs in pediatric CD.}, }
@article {pmid41790338, year = {2026}, author = {Shibuki, T and Yamashita, R and Hashimoto, T and Fujisawa, T and Imai, M and Yuda, J and Kuwata, T and Misumi, T and Nakamura, Y and Bando, H and Kojima, K and Tokioka, S and Chiba, I and Nakaya, N and Hozawa, A and Koshiba, S and Fuse, N and Saito, S and Shimizu, R and Park, WY and Kinoshita, K and Yoshino, T}, title = {Clinical development of molecular residual disease (MRD) and multi-cancer early detection (MCED) using liquid biopsy multiomics with artificial intelligence (AI).}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {41790338}, issn = {1437-7772}, support = {23tk0124005h0001//Japan Agency for Medical Research and Development/ ; 24tk0124005h0002//Japan Agency for Medical Research and Development/ ; 25tk0124005h0003//Japan Agency for Medical Research and Development/ ; }, abstract = {BACKGROUND: Early detection of cancer and precise recurrence monitoring remain major unmet needs in oncology. Conventional screening is limited to a few cancer types, leaving nearly half of cancers without established programs. Multi-cancer early detection (MCED) tests based on circulating tumor biomarkers have shown promise, but sensitivity for early-stage remains a challenge. In parallel, detection of molecular residual disease (MRD) using circulating tumor DNA (ctDNA) has emerged as a powerful prognostic and predictive tool, though current assays remain limited in sensitivity and specificity. This study aims to integrate multi-omics data to develop more refined and highly sensitive MCED and MRD assays.<br><br>METHODS: This study leverages clinical information and biospecimens from patients with cancer and cancer-na&#xef;ve individuals. Samples from patients with cancers will be derived from the MONSTAR-SCREEN-3 study, while those from cancer-na&#xef;ve individuals will be obtained from the Tohoku Medical Megabank Project. Comprehensive analyses will include whole-genome sequencing (WGS), whole-exome sequencing (WES), whole-transcriptome sequencing (WTS), proteomics, metabolomics, and microbiome profiling using stool and saliva. Artificial intelligence (AI)-based multi-omics integration will be performed to develop novel MCED and MRD assays and to evaluate their clinical performance. The primary endpoints are the sensitivity and specificity of MCED and MRD assays.<br><br>DISCUSSION: This is the first large-scale study to integrate comprehensive multi-omics profiling with AI for MCED and MRD assay development. The findings are expected to advance precision oncology by improving early diagnosis and recurrence monitoring.<br><br>TRIAL REGISTRATION: UMIN000053815, approved by the Institutional Review Board of the National Cancer Center Hospital East.}, }
@article {pmid41790238, year = {2026}, author = {Zhao, S and Liu, B and Shi, Y and Zhou, Z and Chen, S and Saiding, Q and Xu, Q and You, X and Zhen, X and Chen, Q and Zhang, Y and An, S and Tao, N and Ouyang, J and Tao, W}, title = {Sprayable Lactococcus lactis-Nanocatalyst Gel for Postsurgical Immunomodulation in Preclinical Oral Squamous Cell Carcinoma.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.6c01542}, pmid = {41790238}, issn = {1520-5126}, abstract = {Oral squamous cell carcinoma (OSCC) is one of the most prevalent and aggressive head and neck cancers. Emerging evidence shows that distinct microbiomes coexist with tumor and immune cells in the tumor microenvironment (TME), shaping tumor progression and antitumor immunity. Harnessing probiotic-based immune modulation therefore represents a promising strategy to improve postoperative outcomes. Here, we develop a dual-channel sprayable Lactococcus lactis probiotic-nanocatalyst gel (L. lactis@Co4N/C@Gel) to potentiate postoperative immune reconstruction in OSCC. L. lactis can activate antitumor responses through Toll-like and NOD-like receptor pathways. However, its therapeutic benefit is constrained by lactate overproduction, which promotes tumor aggressiveness, immunosuppression, and therapy resistance. The incorporated Co4N/C nanoparticles efficiently scavenge L. lactis-derived lactate, thereby amplifying downstream immune activation. Benefiting from the thixotropic properties of calcium alginate, a sodium alginate solution containing L. lactis and CaCl2 solution containing Co4N/C nanoparticles can be cosprayed to achieve uniform wound coverage and rapid in situ gelation. In an orthotopic OSCC mouse model, L.lactis@Co4N/C@Gel effectively reconstructs postoperative antitumor immunity and markedly suppresses tumor recurrence. These findings highlight a microbiome-nanocatalyst synergistic strategy for improving postoperative immunotherapy in OSCC.}, }
@article {pmid41789971, year = {2026}, author = {Zhang, D and Tian, S and Feng, B and Yang, F and Zhu, P and Wu, Q and Xu, J and Wang, H and Zhang, X}, title = {Rapid Classification of Pantoea spp. via Raman Flow Cytometry.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.6c00276}, pmid = {41789971}, issn = {1520-6882}, abstract = {Microorganisms play pivotal roles in ecosystems, where precise taxonomic identification is fundamental to understanding and harnessing their functions. Conventional microbial classification, however, relies on pure-culture techniques that suffer from prolonged cultivation cycles, low throughput, high costs, and limited resolution. To address these constraints, we developed an integrated platform combining positive dielectrophoresis-activated Raman-activated cell sorting (pDEP-RACS) with deep ResNet. Using the ecologically versatile and taxonomically challenging genus Pantoea as a model, we constructed a reference Ramanome database by pDEP-RACS that consists of 180 000 single-cell Raman spectra (SCRS) from 12 Pantoea species (22 strains) and two phylogenetically related species and established a classification model by ResNet-18. The model achieved optimal performance 96.9% mean accuracy and 97.3% recall for 24 SCRS colony isolates. Cross-batch validation shows the highest reproducibility in nutrient-starved samples, with 87.9% accuracy postpreprocessing with reduced batch effects. For optimal accuracy (97.6% ± 2.0%), classification accuracy plateaus at >1,500 SCRS of Raman detection depth. In synthetic communities, the model shows ≤3.21% absolute abundance error for species identification. For the rice seed microbiome, a good consistency was observed between Raman-derived Pantoea abundance (34.8%) and 16S rRNA sequencing results (45%). This platform enables species- and strain-level classification of Pantoea spp. cultures, acquiring >7,200 SCRS per hour to facilitate rapid identification in both synthetic microbial communities and field-derived samples.}, }
@article {pmid41789898, year = {2026}, author = {Sharma, N and Singh, M and Radeny, J and Mukherjee, A and Sullivan, RF and Boyd, JM and Carabetta, VJ and Yang, JH and Yadavalli, SS}, title = {Insights into bacterial stress adaptation, host interactions, and drug resistance: key findings from the fall 2025 ASM Theobald Smith Society meeting.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0087825}, doi = {10.1128/msphere.00878-25}, pmid = {41789898}, issn = {2379-5042}, abstract = {The annual fall meeting for the Theobald Smith Society (TSS), the New Jersey Branch of the American Society for Microbiology (ASM), took place in November 2025 at Cooper Medical School of Rowan University in Camden, New Jersey. A total of 72 branch members from across New Jersey participated, including undergraduate and graduate students, postdoctoral trainees, faculty, and professionals from government and industry. This report highlights the scope and diversity of research carried out by TSS members and celebrates their impactful discoveries.}, }
@article {pmid41789894, year = {2026}, author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N}, title = {Gut virome and metabolic associations in patients with acute pancreatitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0140025}, doi = {10.1128/msystems.01400-25}, pmid = {41789894}, issn = {2379-5077}, abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.}, }
@article {pmid41789806, year = {2026}, author = {Nair, AV}, title = {Friend and Foe: Microbes in Orchestrating Immunity and Shaping Infection Dynamics.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.5c00709}, pmid = {41789806}, issn = {2373-8227}, abstract = {Microbial communities, or microbiota, are fundamental regulators of host immunity and infection outcomes across diverse body sites, including the gut, skin, respiratory tract, and vagina. Despite advances, infectious diseases remain a global challenge, exacerbated by antimicrobial resistance and emerging pathogens. This review explores the dynamic interplay between microbiota, host immune responses, and pathogens, highlighting how microbial interactions shape immune homeostasis and colonisation resistance. The review discusses therapeutic approaches leveraging probiotics, prebiotics, defined microbial consortia, and fecal microbiota transplantation to enhance resistance against bacterial, viral, fungal, and parasitic infections. These microbiome-based strategies represent promising, sustainable alternatives to conventional antibiotics, offering scalable and mechanism-driven interventions. This review further underscores the potential of microbiota-informed therapies to contribute to effective infectious disease prevention and management while addressing global health challenges.}, }
@article {pmid41789608, year = {2026}, author = {Marginean, SS and Radu, PA and Zurzu, M and Garofil, D and Paic, V and Tigora, A and Bratucu, M and And, FP}, title = {Advances and Ongoing Challenges in Colorectal Cancer.}, journal = {Chirurgia (Bucharest, Romania : 1990)}, volume = {121}, number = {1}, pages = {27-42}, doi = {10.21614/chirurgia.3262}, pmid = {41789608}, issn = {1221-9118}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/therapy/epidemiology/genetics ; Early Detection of Cancer/methods ; Biomarkers, Tumor/blood ; Prognosis ; Treatment Outcome ; }, abstract = {Colorectal cancer (CRC) remains a major global health concern, with a rising incidence among younger adults and persistently high mortality in advanced stages, despite significant scientific and technological progress. Its etiology is multifactorial, involving lifestyle factors, genetic susceptibility, chronic inflammation, and gut microbiome dysbiosis. Recent advances in screening, molecular profiling, surgery, and systemic therapies have substantially reshaped CRC management. This narrative review was conducted through a comprehensive literature search of PubMed/MEDLINE, Scopus, and Web of Science databases, covering publications from January 2015 to June 2025. Peer-reviewed articles addressing CRC epidemiology, molecular pathways, screening and diagnostic strategies, surgical management, systemic therapies, and emerging treatment modalities were selected. Evidence was qualitatively synthesized and organized into clinically relevant thematic domains. Recent progress in CRC screening, including advanced endoscopic imaging, fecal DNA testing, and blood-based biomarkers, has improved early detection, although implementation remains uneven. Molecular characterization such as MSI-H/dMMR status, RAS/RAF mutations, HER2 amplification, and consensus molecular subtypes â?" guides prognostic assessment and personalized therapy. Surgical resection remains the cornerstone of curative-intent treatment, with minimally invasive and robotic approaches reducing morbidity while maintaining oncologic safety. Techniques such as complete mesocolic excision and total mesorectal excision, along with multimodal strategies for advanced disease, have expanded therapeutic options. Despite these advances, challenges persist, including therapeutic resistance, tumor heterogeneity, limited immunotherapy efficacy in microsatellite-stable disease, and rising early-onset CRC. Future progress relies on precision medicine, ctDNA-guided monitoring, microbiome-targeted strategies, and optimized surgical selection.}, }
@article {pmid41789481, year = {2026}, author = {Stevenson, E and Susic, D and Craig, ME and Henry, A and Gow, M}, title = {Maternal antenatal health and infant growth outcomes: a Microbiome Understanding in Maternity Study.}, journal = {Journal of developmental origins of health and disease}, volume = {17}, number = {}, pages = {e15}, doi = {10.1017/S2040174425100378}, pmid = {41789481}, issn = {2040-1752}, mesh = {Humans ; Female ; Pregnancy ; Infant ; Adult ; *Child Development/physiology ; Infant, Newborn ; *Maternal Health/statistics &amp; numerical data ; Longitudinal Studies ; Australia/epidemiology ; Male ; Life Style ; *Microbiota/physiology ; Weight Gain ; }, abstract = {The influence of the maternal antenatal environment on infant growth and development beyond the neonatal period is not well understood. This study investigated associations between maternal cardiometabolic health and lifestyle on infant growth during the first year of life. This sub-study of the longitudinal Microbiome Understanding in Maternity Study included 87 mother-infant dyads. Maternal anthropometrics were collected at each trimester. Lifestyle was assessed through the Australian Eating Survey (Trimester T1 and T3) and International Physical Activity Questionnaire (T1, T2 and T3). Infant anthropometrics were measured at birth, 6 weeks, 6 months and 12 months. Changes in weight, weight-for-age z-score, length-for-age z-score, rapid weight gain and conditional weight gain (CWG) were determined. Multiple linear regression was used to assess associations between maternal parameters and infant growth, adjusting for common confounders. Maternal T1 weight (CWG: p = 0.03), T3 weight (CWG: p = 0.03) and GWG (weight z-score change: p = 0.031) were positively associated with increased infant growth from 0 to 6 months. Greater maternal fat mass was associated with increased CWG (p = 0.042) from 6 weeks to 6 months. Higher quality maternal T1 diet was associated with increased infant growth (weight z-score change: p = 0.022, CWG: p = 0.013) from 0 to 12 months. Increased maternal physical activity was associated with increased CWG (p = 0.022) and length z-score change (p = 0.024) from 0 to 12 months in T1, and increased CWG from 6 to 12 months in T2 (p = 0.014) and T3 (p = 0.047). Markers of maternal cardiometabolic health risk and healthier lifestyle were associated with increased infant growth. Further investigation is required to confirm findings and investigate links with future health sequelae.}, }
@article {pmid41789431, year = {2026}, author = {Priya, C and Jain, A and Shetty, DC and Pai Khot, AJ and Yadav, S and Jain, M and Gulati, N and Almalki, SA and Gowdar, IM}, title = {Analysis of Fusobacterium nucleatum Driven Modulation of c-Myc Pathways in Oral Carcinogenesis.}, journal = {F1000Research}, volume = {15}, number = {}, pages = {176}, pmid = {41789431}, issn = {2046-1402}, mesh = {Humans ; *Fusobacterium nucleatum/physiology ; *Mouth Neoplasms/microbiology/metabolism/pathology ; *Proto-Oncogene Proteins c-myc/metabolism ; Female ; Male ; *Carcinogenesis/metabolism/pathology ; Middle Aged ; Aged ; *Carcinoma, Squamous Cell/microbiology/metabolism/pathology ; Adult ; Fusobacterium Infections ; Signal Transduction ; }, abstract = {OBJECTIVE: To evaluate the association between Fusobacterium nucleatum and c-Myc expression in Oral Potentially Malignant Disorders (OPMDs) and Oral Squamous Cell Carcinoma (OSCC) and to explore its potential role in oral carcinogenesis.<br><br>MATERIALS AND METHODS: A total of 32 histopathologically confirmed cases (18 OPMDs and 14 OSCC) were analyzed. Anaerobic cultures and polymerase chain reaction (PCR) were used to detect F. nucleatum. Immunohistochemistry (IHC) was performed to assess c-Myc expression. Statistical analysis was conducted using Mann-Whitney and Chi-square tests, with p < 0.05 considered significant.<br><br>RESULTS: F. nucleatum was detected in eight OSCC and two OPMD cases, with higher colony counts in OSCC. All samples were positive for c-Myc, but their expression levels varied. In OPMDs, positivity was mainly observed in the basal and suprabasal epithelial layers, whereas OSCC showed both peripheral and central tumor cell localization. F. nucleatum-positive OSCC cases demonstrated strong nuclear c-Myc staining (50-75% positive cells). Tobacco habits, particularly combined smoking and smokeless use, were more common in F. nucleatum-positive OSCC cases.<br><br>CONCLUSION: F. nucleatum colonization correlates with increased c-Myc expression in OPMDs and OSCC, supporting its possible role in microbially driven oral carcinogenesis. These findings suggest its potential as a prognostic biomarker and a therapeutic target.}, }
@article {pmid41789326, year = {2026}, author = {Yu, H and Li, F}, title = {Multi-Omics Mechanisms of Trimethylamine Oxide and Cardiovascular Disease: A Review.}, journal = {Reviews in cardiovascular medicine}, volume = {27}, number = {2}, pages = {44420}, pmid = {41789326}, issn = {2153-8174}, abstract = {Cardiovascular diseases (CVDs) rank among the most prevalent conditions globally, encompassing coronary heart disease, hypertension, cardiomyopathy, and heart failure. The global prevalence of CVD continues to rise despite available therapies such as interventional procedures and pharmacotherapy, which remain associated with high rates of recurrence and mortality. In recent years, with a deepening understanding of the human gut microbiome, researchers have discovered that gut microbiota and their metabolites play a significant role in the development and progression of cardiovascular diseases. Among these, trimethylamine N-oxide (TMAO), a major metabolite of gut microbiota, has garnered extensive attention. Thus, this review leverages a multi-omics perspective to compare the commonalities and differences in TMAO-related mechanisms across various cardiovascular diseases. Moreover, this review aims to construct a TMAO-driven pathogenic network and critically evaluate the translational potential of this metabolite as a disease biomarker and therapeutic target, alongside current challenges.}, }
@article {pmid41788774, year = {2026}, author = {Patel, E}, title = {Dietary interventions for modulating the gut microbiome in PCOS management.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1713408}, pmid = {41788774}, issn = {1664-2392}, mesh = {Humans ; *Polycystic Ovary Syndrome/diet therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; Insulin Resistance ; Dysbiosis/diet therapy ; }, abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) is a multifactorial endocrine disorder affecting about 10% of reproductive-age women. It is defined by insulin resistance, androgen excess, and chronic inflammation, which drive both reproductive and metabolic complications. Growing evidence suggests that gut microbiome dysbiosis contributes to PCOS by altering intestinal permeability, promoting endotoxemia, and worsening hormonal and metabolic dysfunction. Diet, as a modifiable factor, may offer a therapeutic route to restore microbial balance and improve outcomes.<br><br>OBJECTIVES: This review aims to (1) synthesize evidence on how diet shapes gut&#xa0;microbiome composition in PCOS; (2) evaluate the effects of specific dietary patterns on microbial diversity, insulin sensitivity, lipid metabolism, and hormonal regulation; and (3) identify dietary components that may improve clinical outcomes.<br><br>METHODS: Evidence from observational studies, randomized trials, and meta-analyses was reviewed to assess how dietary interventions influence gut microbiome modulation and PCOS outcomes. Dietary patterns-including the Mediterranean diet, low-glycemic index diets, anti-inflammatory diets, time-restricted eating, and probiotic supplementation-were examined for their effects on microbiota and metabolic or hormonal measures.<br><br>RESULTS: Dietary interventions can beneficially alter gut microbiota, reduce systemic inflammation, improve insulin sensitivity, and lower androgen levels. The Mediterranean diet enhances microbial diversity and is associated with reduced PCOS risk. Low-glycemic index diets improve metabolic and hormonal profiles by lowering insulin demand. Anti-inflammatory diets and time-restricted eating may restore microbial rhythmicity and reduce inflammatory and endocrine imbalances. Probiotic supplementation, particularly with Lactobacillus and Bifidobacterium, strengthens gut integrity and benefits metabolic and hormonal outcomes. A multi-component dietary plan integrating high-fiber foods, probiotics, anti-inflammatory nutrients, low glycemic load, and structured eating patterns is proposed.<br><br>CONCLUSION: Modulating the gut microbiome through diet is a promising, non-invasive, cost-effective strategy for PCOS management. By targeting insulin resistance, androgen excess, and inflammation, nutrition-based interventions can improve metabolic and reproductive outcomes. Long-term randomized trials are needed to strengthen causal evidence and guide personalized dietary approaches.}, }
@article {pmid41788695, year = {2026}, author = {Xu, J and Cheng, C and Yu, K and Wang, Q and Peng, Y and Li, Y and Yao, W and Pi, Y and Yu, S and Han, Z and Wei, J and Chen, T and Yu, Y}, title = {Ocular Surface Microbiota Alterations Following FS-LASIK and Their Association With Postoperative Dry Eye.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2026}, number = {}, pages = {2148587}, pmid = {41788695}, issn = {1712-9532}, abstract = {PURPOSE: Given the limited evidence on ocular surface microbiota (OSM) changes after femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and their link to dry eye (DE), this study aimed to compare microbial profiles in patients with and without postoperative DE, offering a basis for early detection and targeted treatment.<br><br>METHODS: Patients undergoing FS-LASIK were evaluated 3&#x2009;months postoperatively and stratified into DE (N&#x2009;=&#x2009;30) and non-DE groups (N&#x2009;=&#x2009;30) based on ocular surface disease index (OSDI), TBUT, and the Schirmer I test. Corneal nerve alterations were assessed using IVCM. Conjunctival sac samples were collected pre- and postoperatively, and microbiota profiles were analyzed via 16S rRNA sequencing.<br><br>RESULTS: Comparative analysis of the OSM revealed significantly higher &#x3b1;-diversity in the DE group compared to the NDE group. At the phylum level, a decrease in Proteobacteria and an increase in Bacteroidetes were observed. At the genus level, Veillonella, Streptococcus, and Aggregatibacter were enriched, whereas Pseudomonas and Lactobacillus were depleted. The abundance of Staphylococcus was positively correlated with OSDI scores and negatively correlated with corneal nerve fiber length (CNFL), corneal nerve branch density (CNBD), corneal nerve fiber area (CNFA), and corneal nerve fractal dimension (CFracDim) (all p < 0.05). In contrast, Lactobacillus was positively associated with the Schirmer I test values and corneal nerve fiber density (CNFD) (p < 0.05). At baseline, patients in the DE group exhibited lower abundances of Cyanobacteria and Acinetobacter but higher levels of Verrucomicrobia and Akkermansia. Postoperative within-group comparisons further showed that, relative to baseline, the DE group had increased abundances of Staphylococcus, Veillonella, Ralstonia, and Aggregatibacter, along with decreased levels of Pseudomonas, Corynebacterium, and Helicobacter.<br><br>CONCLUSIONS: In summary, dysbiosis between the Staphylococcus and Lactobacillus genera may represent both a biomarker of DE susceptibility and a therapeutic target. Additionally, the preoperative microbial composition may influence postoperative dynamics and DE risk.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT06448468.}, }
@article {pmid41788690, year = {2025}, author = {Kozik, AJ and Henderson, K and Salameh, L and Mahboub, B and Al Bataineh, MT and Huang, YJ}, title = {Respiratory Microbiota Associations with Asthma Across American and Emirati Adults: A Comparative Analysis.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {41788690}, issn = {2673-8007}, support = {R01 AI129958/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Clinical features of asthma are associated with differences in the lower airway microbiome. However, knowledge is limited on whether airway microbiota composition differs between individuals residing in different geographic regions and if asthma-associated differences in lower airway microbiota are similar between distinct populations.<br><br>METHODS: Existing 16S rRNA gene sequence data, generated from sputum collected from adults with or without asthma (n = 74) from two single-center cohort studies in the U.S. and United Arab Emirates, were re-processed for merged computational analysis using standard available tools. Potential differences between study sites, asthma status and specific clinical factors (inhaled corticosteroid use, ICS; obesity) were examined.<br><br>RESULTS: Differences in sputum bacterial composition, assessed by alpha- and beta-diversity measures, were associated with study site. Despite this, asthma-related differences were discerned in both cohorts. Specifically, sputum microbiota of asthmatic patients on ICS treatment displayed reduced bacterial phylogenetic diversity, compared to those not on ICS treatment (p = 0.006). Sputum bacterial composition also differed by obesity status (unweighted Unifrac distance PERMANOVA, p = 0.004). Specific genera were identified in both cohorts that were differentially enriched between obese vs. non-obese subjects, including Rothia and Veillonella (obesity-associated) and Campylobacter (non-obesity-associated).<br><br>CONCLUSIONS: Our findings suggest clinical factors associated with differences in the lower airway microbiome in asthma may transcend variation related to geographic area of residence.}, }
@article {pmid41788459, year = {2026}, author = {Gadara, D and Schwaiger-Haber, M and Jackstadt, MM and Song, MG and Guo, Q and Barr, M and Bakulski, KM and Shriver, LP and Patti, GJ}, title = {Transient exposure to bisphenol F in early life affects the metabolic health of adults.}, journal = {Exposome}, volume = {6}, number = {1}, pages = {}, pmid = {41788459}, issn = {2635-2265}, support = {R35 ES028365/ES/NIEHS NIH HHS/United States ; }, abstract = {Although bisphenol F (BPF) is widely used in plastic products, there are concerns about its potential health risks. Here, we aimed to understand the long-term effects of a brief BPF exposure during development. We treated zebrafish larvae 7 days post-fertilization with 1 mg/L BPF for 48 hours. We then maintained the animals under standard conditions for 5 months and compared them to control adults never exposed to BPF. In addition to sequencing the gut microbiome, we profiled six different tissues and serum by metabolomics and lipidomics. Strikingly, we found widespread alterations in metabolites and lipids throughout the animal that were both sex and tissue specific. For example, over 60 lipid species were depleted in the livers of BPF-treated females but no changes were observed in male livers. At the tissue level, BPF treatment altered fatty acid oxidation uniquely in skeletal and cardiac muscle. This study shows that transient exposures limited to the developmental phase of life can induce metabolic abnormalities later in adulthood. Our findings highlight the importance of profiling specimens from early life by exposomics and suggest that, even with the introduction of regulatory measures, the adverse effects of BPF could persist in the population for a generation.}, }
@article {pmid41726958, year = {2026}, author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41726958}, issn = {2692-8205}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid39344767, year = {2024}, author = {Slobodnikova, L and Halasa, AI and Kalmanova, S and Calkovsky, B and Juricek, R and Malachovsky, I and Repiska, V and Skerenova, M and Janickova, M}, title = {Genetic factors affecting susceptibility to dental caries.}, journal = {Bratislavske lekarske listy}, volume = {125}, number = {10}, pages = {635-647}, doi = {10.4149/BLL_2024_98}, pmid = {39344767}, issn = {0006-9248}, mesh = {Humans ; *Dental Caries/genetics ; *Genetic Predisposition to Disease ; Dental Caries Susceptibility/genetics ; }, abstract = {Dental caries remains the most prevalent chronic, oral biofilm-associated disease affecting majority of the globe's population in all age categories. Despite enormous and revolutionary progress in omics technologies, it´s aetiology is not fully understood. The interest of current research is primarily focused on the identification and understanding of the crosstalk between main players such as host cell genome, oral microbiome´s genome, factors of immune response, saliva content and nutrition. For accurate, multi-omix analyses, it is essential to know which patient´s genes enter into crucial interactions. Identifying genes and understanding the mechanism of their action is the key for deeper understanding of their involvement in the pathogenesis of this disease. Serious alterations of these genes should be consequently used as markers to determine the extent of genetic predisposition to dental caries and identify susceptible patients. That should significantly improve the prevention, diagnostic and therapy of the disease with an individual approach and provide more efficient and effective implementation of newer preventive measures and novel therapeutic approaches in the management of the disease. This review focuses on contemporary evidence on genetics factors affecting dental caries and to provide an up-to-date comprehensive description and classification of the genes and their alterations influencing the disease. It also aims to delineate and discuss evidence gaps and potential novel applications of genetics in the context of recent advances (Tab. 2, Ref. 113). Text in PDF www.elis.sk Keywords: dental caries, candidate gene, genetic variation, multifactorial disease.}, }
@article {pmid41788329, year = {2026}, author = {Wang, M and Huo, Y and Zhao, Y and Du, X and Yun, BW and Wu, J and Ying, X and Wei, F and Wang, Y and Lu, R and Chen, J and Wang, X and Yang, Q and Liu, L}, title = {Responses of Panax notoginseng (Burk.) F.H. Chen to cadmium stress: hormetic effects on growth, antioxidant systems, and rhizosphere microbial dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741415}, pmid = {41788329}, issn = {1664-302X}, abstract = {BACKGROUND: Cadmium (Cd) contamination poses a major threat to Panax notoginseng (Burk.) F.H. Chen cultivation, yet the dose-dependent thresholds separating adaptive responses from toxicity remain poorly understood, particularly at the level of rhizosphere microbial processes.<br><br>METHODS: A 75-day pot experiment was conducted using eight soil Cd concentrations (0-100 mg kg[-1]). Plant growth traits and antioxidant enzyme activities (SOD, POD, CAT) were measured. Rhizosphere microbial communities were characterized in terms of alpha and beta diversity, co-occurrence network structure, and predicted functional potential using PICRUSt2 and FAPROTAX.<br><br>RESULTS: Moderate Cd exposure (&#x223c;30 mg kg[-1]) enhanced plant growth and antioxidant enzyme activities, whereas high Cd (&#x2265; 80 mg kg[-1]) caused physiological inhibition, consistent with a hormetic response. Microbial alpha diversity also peaked under moderate Cd but declined sharply at high Cd levels. Beta diversity differentiation was primarily driven by shifts in relative abundance rather than taxonomic turnover. Severe Cd stress reduced co-occurrence network connectivity and increased negative correlations, although several persistent core taxa (e.g., Granulicella) were maintained. Functional predictions indicated substantial functional redundancy, with key nutrient-cycling pathways largely retained despite pronounced network simplification.}, }
@article {pmid41788326, year = {2026}, author = {Yin, X and Zeng, J and Li, Z and Chen, S and Xie, C and Li, X and Zhang, L and Pan, Y and An, J}, title = {Gut bacteriome alterations during high altitude exposure: a comprehensive analysis of different species.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1762563}, pmid = {41788326}, issn = {1664-302X}, abstract = {With the increase of high-altitude sojourn population, more and more studies on hypoxia have been conducted, but the associated changes in gut bacteriome in different hypoxic environments need to be further investigated. Gut bacteriome plays an important role in host adaptation to high-altitude hypoxia, but the contribution of gut bacteriome in high-altitude hypoxia adaptation is still controversial and may be influenced by multiple factors. In this study, we reviewed the changes in diversity and composition of the gut bacteriome of different populations of animals in different highland hypoxic environments, clarified the dynamics of the gut bacteriome during exposure to high altitude, identified the core bacteriome that may contribute to host adaptation to hypoxic environments, and comprehensively considered the effects of multiple factors on the gut bacteriome.}, }
@article {pmid41788296, year = {2026}, author = {Guo, ZL and Cui, MW and Dong, YL and Wang, S}, title = {The oral microbiome as a regulatory hub for systemic health: a systematic review of mechanistic links and clinical implications.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2635233}, pmid = {41788296}, issn = {2000-2297}, abstract = {BACKGROUND: The human oral microbiome is a highly diverse ecosystem with important roles in oral and systemic health. Beyond dental caries and periodontitis, oral dysbiosis has been increasingly implicated in the development of multiple non-communicable diseases.<br><br>OBJECTIVE: To systematically synthesize evidence on the mechanisms linking oral dysbiosis to systemic diseases and to summarize its diagnostic and therapeutic implications.<br><br>DESIGN: A systematic review was performed using major electronic databases. We screened 1,128 records and included 104 studies that met predefined eligibility criteria.<br><br>RESULTS: Evidence indicates that oral dysbiosis may influence systemic health through several mechanisms, including hematogenous dissemination of oral pathogens and virulence factors (e.g. lipopolysaccharide), chronic systemic inflammation, molecular mimicry in autoimmune disorders, and microbial metabolic byproducts. The reviewed studies support associations between oral microbiome alterations and atherosclerotic cardiovascular disease, type 2 diabetes, Alzheimer's disease, rheumatoid arthritis, and gastrointestinal cancers. The literature also highlights the promise of non-invasive oral microbiome-based biomarkers for early detection and disease monitoring. Emerging microbiome-modulating interventions, including probiotics, prebiotics, and bacteriophage therapy, show potential for restoring oral eubiosis and improving systemic outcomes.<br><br>CONCLUSIONS: Oral dysbiosis is an important regulator of systemic disease processes and a promising target for diagnosis, prevention, and therapy. Integrating oral health and oral microbiome assessment into broader disease management may improve outcomes, although methodological standardization and stronger causal evidence are still needed.}, }
@article {pmid41788258, year = {2026}, author = {Keles, E and Celik, O}, title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.}, journal = {Microbial cell (Graz, Austria)}, volume = {13}, number = {}, pages = {117-130}, pmid = {41788258}, issn = {2311-2638}, abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.}, }
@article {pmid41788170, year = {2026}, author = {Koh, YC and Pan, MH}, title = {Pterostilbene-mediated microbiota shifts: Implications and opportunities.}, journal = {Journal of traditional and complementary medicine}, volume = {16}, number = {2}, pages = {131-142}, pmid = {41788170}, issn = {2225-4110}, abstract = {Pterostilbene, a natural stilbene compound present in blueberries and several medicinal plants, has been increasingly studied for its ability to influence gut microbiota composition across different disease contexts. In a variety of animal and cell-based models, researchers have observed notable shifts in microbial profiles following pterostilbene supplementation. These changes are thought to be, at least in part, responsible for the compound's health-promoting properties, especially in relation to disease prevention and immune regulation. Despite these findings, no in-depth review has yet compiled the specific bacterial taxa most consistently affected by pterostilbene, nor analyzed the broader physiological significance of such changes. In this narrative review, we aim to address that gap by synthesizing current knowledge on the gut microbiota-modulating effects of pterostilbene. Particular focus is placed on beneficial genera that are frequently enriched, such as Akkermansia, Bifidobacterium, Faecalibacterium prausnitzii, Roseburia, and Lactobacillus. These microbes are often associated with key functions like intestinal barrier support, immune homeostasis, and the production of short-chain fatty acids. By linking microbial alterations to potential host benefits, we hope this review will inform future studies that explore pterostilbene as a microbiota-targeted therapeutic agent. Moreover, considering that this compound is found in many herbal medicines, our discussion may also offer valuable insights for research at the intersection of microbiome science and traditional medicine.}, }
@article {pmid34333553, year = {2022}, author = {Howard, MM and Bass, E and Chautá, A and Mutyambai, D and Kessler, A}, title = {Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {5-9}, pmid = {34333553}, issn = {1751-7370}, mesh = {Plant Roots ; Plants ; *Rhizosphere ; *Soil Microbiology ; }, abstract = {The perception of airborne chemical signals by plants can trigger reconfigurations of their metabolism that alter their biotic interactions. While plant-to-plant chemical communication has primarily been studied in the context of eliciting defenses to herbivores and pathogens, recent work suggests that it can also affect plants’ interactions with their rhizosphere microbiomes. In this perspective, we discuss the potential for integrating the fields of plant-to-plant communication and microbial ecology to understand the chemical ecology of plant−microbiome interactions. As an introduction for microbial ecologists, we highlight mechanistic knowledge gaps in plant volatile organic compound (VOC) perception and provide recommendations for avoiding common experimental errors that have plagued the plant communication field. Lastly, we discuss potential implications of plant VOCs structuring rhizosphere microbiomes, particularly effects on plant community and evolutionary dynamics. As we continue to discover links between plant metabolism and their microbiomes—from molecular to community scales—we hope that this perspective will provide both motivation and words of caution for researchers working at the intersection of these two fields.}, }
@article {pmid41788069, year = {2026}, author = {Fedosova, N and Symchych, T and Gogol, S and Cheremshenko, N and Virych, P and Voyeykova, I and Chekhun, V}, title = {INFLUENCE OF BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BB-12 AND LACTOBACILLUS RHAMNOSUS GG ON POLARIZATION OF TUMOR-ASSOCIATED MACROPHAGES.}, journal = {Experimental oncology}, volume = {47}, number = {4}, pages = {451-458}, doi = {10.15407/exp-oncology.2025.04.451}, pmid = {41788069}, issn = {2312-8852}, mesh = {Animals ; *Lacticaseibacillus rhamnosus ; Female ; Mice ; *Carcinoma, Ehrlich Tumor/pathology/immunology/microbiology ; *Probiotics/pharmacology ; Mice, Inbred BALB C ; *Bifidobacterium animalis ; Nitric Oxide/metabolism ; *Tumor-Associated Macrophages/immunology/metabolism ; Reactive Oxygen Species/metabolism ; Arginase/metabolism ; }, abstract = {BACKGROUND: The microbiota has a significant impact on the host's immune system. However, the influence of the microbiome is heavily dependent on species, strain, and context. The aim of this study was to evaluate the influence of Bifidobacterium animalis subsp. lactis BB-12 (BB-12) and Lactobacillus rhamnosus GG (LGG) supplementation on the polarization of tumor-associated macrophages (TAMs) in mice with Ehrlich carcinoma.<br><br>MATERIALS AND METHODS: Female Balb/c mice bearing solid Ehrlich carcinoma were administered via gavage with BB-12, LGG, or 0.9% NaCl. On days 14, 21, and 28 of tumor growth, macrophages from tumor tissue were isolated and subjected to functional analysis. The nitric oxide (NO) production was measured using the standard Griess reaction. The arginase activity was determined based on the urea measurements. The reactive oxygen species (ROS) production was checked using flow cytometry. The cytotoxic activity was estimated by an MTT assay.<br><br>RESULTS: The application of different probiotic bacteria elicited different TAM polarization states. The TAMs in the group supplemented with LGG demonstrated M1 polarization with low arginase activity but high production of NO and ROS, as well as cytotoxic activity toward Ehrlich carcinoma cells. The TAMs of BB-12-treated mice exhibited M2 (supposedly M2b) polarization, characterized by high arginase activity alongside the preserved cytotoxic activity toward Ehrlich carcinoma cells in vitro.<br><br>CONCLUSION: The results indicate that the consumption of two probiotics, BB-12 and LGG, affects the polarization of TAMs in distantly located experimental tumors.}, }
@article {pmid41788021, year = {2026}, author = {Mezera, CC and Steffan, S and Holland, LA}, title = {Pollinator Visitation Alters Cranberry Flower Fungal Communities in Wisconsin Cranberry Agroecosystems.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70310}, pmid = {41788021}, issn = {1758-2229}, support = {AWD00000457//U.S. Department of Agriculture/ ; }, mesh = {*Vaccinium macrocarpon/microbiology/physiology ; Animals ; *Flowers/microbiology ; *Pollination ; *Fungi/classification/isolation &amp; purification/genetics ; Wisconsin ; Bees/microbiology/physiology ; *Mycobiome ; Plant Diseases/microbiology ; Diptera/microbiology ; }, abstract = {Pollinators are known dispersal agents of microbial communities between flowering plants, although the role of insect-mediated microbial assembly in flowering agricultural crops is not well understood. In cranberry (Vaccinium macrocarpon Ait.) agroecosystems, the blossom period is a vulnerable time for infection from pathogens within the cranberry fruit rot fungal disease complex, and understanding the components and assembly dynamics in cranberry flower fungal communities may provide important insights to the relationship between the cranberry microbiome and crop health. This 2-year study uses a combination of culture-dependent and next-generation sequencing approaches to compare the community structure of cranberry flowers, honey bees (Apis mellifera), bumble bees (Bombus sp.), wild solitary bees, hover flies (Syrphidae), and nearby wildflowers to identify shared fungal associates. Compared to a tenting treatment in cranberry flowers used to prevent insect visitation, cranberry flowers with access to pollinators have higher detection of fungal genera in culture, as well as more fungal genera identified through culture-independent methods. Fungi associated with the cranberry fruit rot complex were identified in several insect groups, with the highest proportion of identified fruit rot fungi detected in Toxomerus fly samples. This research provides the first evidence of shared fungal communities between pollinators and managed cranberry flowers.}, }
@article {pmid41788004, year = {2026}, author = {Kumar, D and Gupta, V and Jaiswal, NK and Tanwar, R}, title = {Antibiotics and Metabolic Dysregulation After Surgery: Exploring an Overlooked Connection.}, journal = {Current diabetes reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115733998425015260116113449}, pmid = {41788004}, issn = {1875-6417}, abstract = {Hypertension and hyperglycemia are common in patients without metabolic disease even after surgery and are generally considered to have been caused by surgical stress and inflammation. Nonetheless, in the case of long-term or repeated exposure to perioperative antibiotics, this can be a hidden cause of disturbances. Broad-spectrum antibiotics may interfere with gut microbiota, decrease short-chain fatty acid synthesis, and impair mitochondrial function and vascularity, thereby facilitating the development of insulin resistance and metabolic instability. Observational cohort evidence associates cumulative exposure to antibiotics with the risk of developing type 2 diabetes, whereas experimental models show that antibiotics cause glucose intolerance via the mechanism of dysbiosis. There are also clinical observations that, in certain patients, suitable parameters of the metabolic condition return to normal only on removal of antibiotics. These mechanisms can interact with surgical stress, especially in metabolically vulnerable individuals. This hypothesis-generating editorial demonstrates the need to explore antibiotic-related metabolic changes during postoperative care and to implement microbiome-informed interventions in perioperative practice and antibiotic stewardship.}, }
@article {pmid41787837, year = {2026}, author = {Orozco-Mosqueda, MDC and Flores-Piña, A and Kumar, A and Parra-Cota, FI and de Los Santos-Villalobos, S and Mitra, D and Babalola, OO and Santoyo, G}, title = {Impact of Fire and Heat Stress on Soil Microorganisms: A Review of Community Changes, Molecular Responses and Plant-Beneficial Roles.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70247}, pmid = {41787837}, issn = {1758-2229}, mesh = {*Soil Microbiology ; *Fires ; Fungi/genetics/classification/metabolism ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Soil/chemistry ; *Heat-Shock Response ; Plants/microbiology ; Hot Temperature ; }, abstract = {Fire, whether occurring on the surface or underground, significantly influences soil microbial dynamics by reshaping community composition, functional diversity and overall soil and plant health. This review examines the effects of fire on soil-beneficial microbial communities, with particular attention to how surface and underground fires drive shifts in microbial diversity and functional roles within the agroecosystems. These changes impact key processes such as nutrient cycling, soil physicochemical structure and organic matter decomposition, ultimately affecting crop production. Bacterial groups such as Firmicutes and Actinobacteria often increase in abundance following fire events, while others lacking survival strategies tend to decline. Resilient fungal groups, including Ascomycota (such as Aspergillus, Penicillium and Trichoderma), frequently play pivotal roles during the recovery process. Fire can also enhance microbial metabolic activity, particularly in pathways involved in organic matter degradation, leading to short-term increases in nutrient availability that support plant regrowth. Finally, the review discusses the molecular responses of microbes to fire and outlines perspectives for better understanding this type of stress and how it affects the beneficial soil microbiota in agricultural edaphic systems.}, }
@article {pmid41787816, year = {2026}, author = {Shi, Y and Lin, X and Wang, L and Ou, Y and Wu, Q and Song, M}, title = {Engineered Biomimetic Nanoparticles With Targeted Delivery of Chlorothiazide for the Treatment of Inflammatory Bowel Disease.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e25914}, doi = {10.1002/anie.202525914}, pmid = {41787816}, issn = {1521-3773}, support = {82201873//National Natural Science Foundation of China/ ; 2408085QH239//Natural Science Foundation of Anhui Province/ ; 2025AHGXZK31379//University Natural Science Research Key Project of Anhui Province/ ; 2025AHGXZK31514//University Natural Science Research Key Project of Anhui Province/ ; BK20241589//Natural Science Foundation of Jiangsu Province/ ; BK20220202//Natural Science Foundation of Jiangsu Province/ ; 2022M723510//Project funded by China Postdoctoral Science Foundation/ ; 2022ZB294//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; LH250104002//Longhu Talent Project of Bengbu Medical University/ ; bsqd202427//Research Foundation for Advanced Talents from Bengbu Medical University/ ; 2025SYKFD15//Anhui Provincial Engineering Research Center for Biochemical Pharmaceuticals/ ; }, abstract = {While conventional treatment strategies for inflammatory bowel disease (IBD) focus primarily on suppressing overactive immunity, there is still a lack of definitive interventions targeting key pathological mechanisms, such as intestinal barrier dysfunction, dysbiosis of the gut microbiome, and disrupted mucosal immune regulation. Using a high-throughput drug screening platform, the present study successfully identified chlorothiazide (Chl), a lead compound with anti-inflammatory potential, from a library of 3152 natural compounds. To further increase the bioavailability of Chl and mitigate its potential toxicity, we constructed a biomimetic delivery system based on engineered bacterial membrane-encapsulated reactive oxygen species (ROS)-responsive biomimetic nanoparticles (CHM NPs). This delivery system achieved targeted accumulation in inflamed colonic tissue in a mouse model of acute colitis and effectively facilitated the restoration of epithelial barrier function. Moreover, CHM NPs significantly altered the gut microbiome, increasing overall microbial abundance and diversity while increasing the abundance of gut Lactobacillus, which plays a crucial role in maintaining gut microecological homeostasis. We systematically elucidated the multifaceted mechanisms by which CHM NPs regulate gut homeostasis, remodel the microbial composition, and modulate innate immunity. These findings provide novel theoretical foundations and potential intervention strategies for the treatment of IBD and other related inflammatory conditions.}, }
@article {pmid41787616, year = {2026}, author = {Stoehr, MC and Martin, EM and Babalola, JT and Xue, J and Kern, MJ and Li, NY and Winters, MF and Bhagwagar, S and Smith, CJ}, title = {Effects of combined prenatal exposure to air pollution and maternal stress on social behavior and oxytocin and vasopressin systems in male and female mice.}, journal = {Journal of neuroendocrinology}, volume = {38}, number = {3}, pages = {e70151}, pmid = {41787616}, issn = {1365-2826}, support = {R00ES033278/ES/NIEHS NIH HHS/United States ; }, abstract = {Prenatal exposures to air pollution and maternal psychosocial stress are each associated with increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), and epidemiological work suggests that concurrent exposure to these risk factors may be particularly harmful. This is important given that the same populations often bear the brunt of both toxicant and psychosocial stress burdens. Social impairments are a defining symptom in ASD. Previous work modeling combined prenatal exposure to diesel exhaust particles (DEPs) and maternal stress (MS) in rodents has found male-biased social deficits in offspring, as well as changes to neuroimmune processes and the gut microbiome. However, the precise neural circuits on which these exposures converge to impact social behavior are unclear. Oxytocin (OXT) and vasopressin (AVP) are neuropeptides critical to the regulation of social behavior across species, signaling primarily at the oxytocin receptor (Oxtr) and vasopressin V1a receptor (V1aR) in the brain. Here, we hypothesized that OXT and/or AVP expression would be reduced in the brain following DEP/MS exposure. Following prenatal exposure to DEP/MS or the vehicle/control condition (VEH/CON), we measured maternal and offspring outcomes during the perinatal period, social and anxiety-like behavior during adolescence, OXT and AVP cell/fiber density, and Oxtr and Avpr1a mRNA expression in early adulthood in several brain regions in both males and females. We observed a decrease in interaction time in DEP/MS males as compared to VEH/CON in the sociability assay and a decrease in social novelty preference in DEP/MS females as compared to VEH/CON. No effects of sex or treatment were observed on OXT or AVP cell number or fiber density in the hypothalamic regions assessed. However, numerous sex differences were observed in Oxtr and Avpr1a mRNA. Moreover, Avpr1a mRNA was significantly increased following DEP/MS exposure in the nucleus accumbens in both sexes and trended towards increasing in the dorsal hippocampus. Together, these findings suggest that DEP/MS exposure has a stronger impact on female social behavior than previously observed. Moreover, while DEP/MS exposure does not appear to impact OXT or AVP expression in the brain, V1aR expression is modulated by DEP/MS exposure in the nucleus accumbens.}, }
@article {pmid41787564, year = {2026}, author = {Luo, F and Cai, Y and Cui, Y and He, X and Xu, J and Tang, W and Wang, X and Cai, Y and Xie, H and Chen, W and Li, W and Ding, X}, title = {Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02359-z}, pmid = {41787564}, issn = {2049-2618}, support = {CARS-01-09//the earmarked fund for the China Agriculture Research System/ ; 32260023, 31560041//National Natural Science Foundation of China/ ; 20232ACB205006//Key Project of Jiangxi Natural Science Foundation/ ; }, abstract = {BACKGROUND: Crop wild relatives and their microbiomes are essential for sustainable crop production. However, the co-evolution of wild rice species and their microbiomes remains poorly understood. Herein, we investigated microbiome assembly across 17 wild rice and one cultivated rice species under controlled conditions spanning ~15 million years of evolution.<br><br>RESULTS: Our data reveal distinct eco-evolutionary patterns for bacteria and fungi. Host divergence time was the predominant driver of root microbiota structure, outweighing polyploidy and life cycle, and exerted a stronger effect on bacteria than fungi. Bacterial community exhibited a significant phylosymbiosis with its host, but fungi did not. Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased. Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly. Potentially functional taxa, including nitrogen-fixing and methane-cycle bacteria, were differentially enriched across evolutionary time and polyploidization events. Notably, co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution. Using a synthetic community (SynCom) derived from the wild rice core microbiome and four nitrogen-fixing&#xa0;strains enriched in early- and medium-diverging Oryza species, we demonstrated that the SynCom strongly promoted rice growth, with the removal of key members markedly reducing its impact.<br><br>CONCLUSIONS: These results reveal co-phylogenetic patterns between Oryza and root-associated bacteria, highlighting the closer functional linkage between rice traits and bacteria than fungi, likely due to their co-evolution. Our findings provide new insights into crop-microbiome symbiosis from an eco-evolutionary perspective and underscore the importance of co-speciating microbiomes from wild relatives in supporting crop growth. Video Abstract.}, }
@article {pmid41787488, year = {2026}, author = {Gu, C and Qi, Y and Xie, Y and Yang, L and Wang, G and Zhou, J and Ren, J and Liu, S and Zhu, G and Li, W and Hu, W and Chen, Y and Liu, D}, title = {A lung microbial signature for postoperative recurrence in stage I-II non-small cell lung cancer.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03609-2}, pmid = {41787488}, issn = {1465-993X}, support = {82300011//National Natural Science Foundation of China/ ; 82173182//National Natural Science Foundation of China/ ; 2024ZD0529501 / 2024ZD0529500//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2023NSFSC1939//Science and Technology Program of Sichuan Province/ ; }, }
@article {pmid41787302, year = {2026}, author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W}, title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12725-8}, pmid = {41787302}, issn = {1471-2164}, support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; }, }
@article {pmid41787261, year = {2026}, author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N}, title = {Lifestyle associates with unique resistome and microbiome signatures in children.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-025-04665-2}, pmid = {41787261}, issn = {1471-2180}, }
@article {pmid41787031, year = {2026}, author = {Jiang, EX and Quarta, G and Delau, O and Shaukat, A}, title = {Mutations in Exon 29 of Ring Finger Protein 213 Are Associated with Early-Onset Colorectal Cancer.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {41787031}, issn = {1573-2568}, abstract = {BACKGROUND AND AIMS: Growing evidence suggests that the gut microbiome plays a role in carcinogenesis for early-onset colorectal cancer (EOCRC). The novel Ring Finger Protein 213 (RNF213) gene has broad antimicrobial properties. Our study aimed to compare RNF213 mutation rates in EOCRC and late-onset colorectal cancer using data from the cBioPortal for Cancer Genomics.<br><br>METHODS: All participants from the cBioPortal with CRC samples that profiled the RNF213 gene were included. Multivariable logistic regression was used to assess the association between EOCRC and primary tumor RNF213 mutation. Cox proportional hazards models were used to evaluate the influence of RNF213 mutation on all-cause mortality risk. All tests were two-sided.<br><br>RESULTS: 1594 participants with CRC from six cohorts were included, of which 7.8% (N&#x2009;=&#x2009;125) had EOCRC. Participants with EOCRC were more likely to have late-stage CRC (p&#x2009;<&#x2009;0.001) and left-sided tumors (p&#x2009;<&#x2009;0.001). Participants with a mutation in exon 29 of RNF213 had significantly increased odds of EOCRC diagnosis (adjOR 3.82, 95% CI 1.82, 7.54) compared to participants with wild-type RNF213, while mutations in other exons did not confer significantly increased odds of EOCRC diagnosis (adjOR 1.61, 95% CI 0.72, 3.22). There was no significant difference in all-cause mortality risk by RNF213 mutation status.<br><br>CONCLUSIONS: Primary tumor mutations in exon 29 of the RNF213 gene are associated with significantly increased odds of EOCRC diagnosis in a multicohort sample of participants with CRC. Future studies of germline and precancerous RNF213 mutations are needed to elucidate its possible role in EOCRC tumorigenesis.}, }
@article {pmid41786774, year = {2026}, author = {Moiseyenko, A and Antonello, G and Schonhoff, AM and Boktor, JC and Long, K and Dirks, B and Oguienko, AD and Winnett, AV and Simpson, P and Daeizadeh, D and Ismagilov, RF and Krajmalnik-Brown, R and Segata, N and Waldron, LD and Mazmanian, SK}, title = {Faecalibacterium prausnitzii, depleted in the Parkinson's disease microbiome, improves motor deficits in α-synuclein overexpressing mice.}, journal = {NPJ Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41531-026-01287-x}, pmid = {41786774}, issn = {2373-8057}, support = {ASAP-020495; ASAP-000375//Aligning Science Across Parkinson's/ ; }, abstract = {Gut microbiome composition is altered in Parkinson's disease (PD), the fastest-growing neurological condition, that is characterized by neurodegeneration, motor dysfunction, and is frequently accompanied by gastrointestinal (GI) symptoms. Notably, microbial taxa with anti-inflammatory properties are consistently depleted in PD patients compared to controls. To explore whether specific gut bacteria may be disease-protective, we assembled a microbial consortium of 8 human-associated taxa that are reduced in individuals with PD. Treatment of α-synuclein overexpressing (Thy1-ASO) mice, an animal model of PD, with this consortium improved motor and GI deficits. A single bacterial species from this consortium, Faecalibacterium prausnitzii, was sufficient to correct gut microbiome deviations in Thy1-ASO mice, induce anti-inflammatory immune responses, and promote protective colonic gene expression profiles. Accordingly, oral treatment with F. prausnitzii robustly ameliorated motor and GI deficits and reduced α-synuclein aggregates in the brain. These findings support the emerging hypothesis of functional contributions by the microbiome to PD outcomes, and embolden the development of potential probiotic therapies to treat motor and non-motor symptoms.}, }
@article {pmid41786764, year = {2026}, author = {Franciosa, I and Castelnuovo, G and Cantele, C and Cardenia, V and Bo, S and Ponzo, V and Goitre, I and Pontonio, E and Tortarolo, D and Verni, M and Bugianesi, E and Cordero, F and Beccuti, M and Cocolin, L and Ferrocino, I}, title = {Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00785-9}, pmid = {41786764}, issn = {2396-8370}, support = {D17G22000150001//NODES funding from the MUR - M4C2 1.5 of PNRR, funded by the European Union - NextGenerationEU, Mission 4 Component 1.5 - ECS00000036/ ; }, abstract = {Entomophagy is increasingly popular, and Acheta domesticus offers an ecologically sustainable protein alternative, but the effects on the human gut microbiome need further investigation. In this study, we investigated the impact of the intake of three isolated proteins: pea (plant), whey (animal), and cricket (insect) on gut microbiome of a single-donor using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Cricket protein intake was associated with potential beneficial taxa such as Bifidobacterium and Lactobacillus, genes related to vitamin biosynthesis and bacteriocin transport, and short and medium-chain fatty acids. Pea protein intake was associated with Faecalibacterium and Slackia, while whey protein with Butyricimonas and Lactobacillus. Metagenomic analysis revealed that pea intake led to increased lysine degradation genes, promoting SCFAs production. Each protein has its own unique characteristics that may contribute positively to gut health. Specifically, cricket protein intake appears to have beneficial effects, promoting the growth of potentially beneficial taxa and enhancing short-chain fatty acid production. The results of this study indicate that cricket protein does not exhibit any detrimental effects compared to pea and whey proteins.}, }
@article {pmid41786749, year = {2026}, author = {Chechi, K and Chakaroun, R and Myridakis, A and Forslund-Startceva, SK and Fromentin, S and Nielsen, T and Aron-Wisneswky, J and Belda, E and Prifti, E and Lassen, PB and Falony, G and Vieira-Silva, S and Chilloux, J and Sonomura, K and Hoyles, L and Martinez-Gili, L and Pallotti, F and Andrikopoulos, P and Puig-Castellví, F and Tapia, RP and Castro-Dionicio, I and Roume, H and Pons, N and Le Chatelier, E and Quinquis, B and Galleron, N and Berland, M and Olanipekun, MT and Jia, M and Manolias, A and Holmes, B and Adriouch, S and Blüher, M and Coelho, LP and Da Silva, K and Galan, P and Ji, B and Neves, AL and Rouault, C and Salem, JE and Tremaroli, V and Hansen, TH and Søndertoft, NB and Lewinter, C and Pedersen, HK and ,  and Mark, PD and Goetze, JP and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Sato, TA and Hercberg, S and Bäckhed, F and Letunic, I and Oppert, JM and Nielsen, J and Raes, J and Tzoulaki, I and Dehghan, A and Zuber, V and Bouzigon, E and Lathrop, M and Raina, P and Froguel, P and Matsuda, F and Demenais, F and Gauguier, D and Stumvoll, M and Bork, P and Pedersen, O and Ehrlich, SD and Clément, K and Dumas, ME}, title = {A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69405-0}, pmid = {41786749}, issn = {2041-1723}, support = {HEALTH-F4-2012-305312//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; }, abstract = {Cardiovascular diseases (CVD) remain a major global health challenge. Early markers of disease initiation and progression are urgently needed. We, and others, have previously shown changes in the gut microbiome in association with metabolic and CVD. Here, we demonstrate that gut microbiome-related changes can be detected in association with subclinical variations in heart and kidney function. Markers related to gut microbial metabolism of aromatic amino acids, phenylalanine and tyrosine, associate with circulating pro-atrial natriuretic peptide and estimated glomerular filtration rate in a metabolically healthy European population. Observational and genetic evidence further identify microbiome-related metabolites as mediators of this gut microbiome-kidney axis, with their baseline levels associating with incident CVD in an external Canadian population. Altogether, our work suggests that the gut microbiome interacts with the cardiorenal axis and participates in an interorgan crosstalk affecting host physiology and risk of CVD.}, }
@article {pmid41786640, year = {2026}, author = {Santana, AE and Torres, SMF and Costa, MO}, title = {Skin Commensal Microbiota Does Not Influence the Clinical Course of Dermatophyte Infection in Persian Cats.}, journal = {Veterinary dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/vde.70058}, pmid = {41786640}, issn = {1365-3164}, support = {//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {BACKGROUND: Dermatophytes can be isolated from both symptomatic and asymptomatic cats, yet the role of skin commensals in modulating disease expression remains unclear. This study investigates whether microbial skin communities influence the clinical presentation (symptomatic or asymptomatic) of dermatophyte infection in Persian cats.<br><br>HYPOTHESIS/OBJECTIVES: We hypothesised that the fungal and bacterial skin microbiota differ between Persian cats with and without clinical signs of dermatophytosis. The objectives of this study were to compare the fungal and bacterial skin microbiota among healthy, symptomatic, and asymptomatic cats with dermatophytosis and to evaluate the performance of two skin sampling methods (carpet and toothbrush) for microbiome analysis.<br><br>ANIMALS: Forty-five cats.<br><br>MATERIAL AND METHODS: Cats were grouped according to clinical presentation: Persian cats with skin lesions characteristic of dermatophytosis (multifocal alopecia and scaling) and a positive fungal culture (symptomatic group; n&#x2009;=&#x2009;15), Persian cats with no skin lesions and a positive fungal culture (asymptomatic group; n&#x2009;=&#x2009;15), and domestic short hair cats with no history and clinical signs of skin disease and negative fungal culture (negative group; n&#x2009;=&#x2009;15). Hair and scale samples were collected using carpet and toothbrush techniques from all animals. Fungal and bacterial communities were investigated using high-throughput sequencing targeting internal transcribed spacer (ITS)1 and 16S ribosomal (r)RNA genes.<br><br>RESULTS: Our data showed that the taxonomic composition of fungal and bacterial communities was similar between symptomatic and asymptomatic cats, regardless of the sampling method used. No notable differences were identified in the relative abundance of Microsporum spp. between symptomatic and asymptomatic cats.<br><br>Our findings suggest that the commensal microbiota may not influence the clinical presentation of dermatophyte infection. Instead, other factors, such as the host immune response, appear to play a pivotal role in determining disease outcomes.}, }
@article {pmid41786560, year = {2026}, author = {Albright, JD and Haug, LI}, title = {Bidirectional Communication: The Gut-Brain Axis in Companion Animal Health.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cvsm.2026.01.008}, pmid = {41786560}, issn = {1878-1306}, abstract = {The microbiome-gut-brain axis (MGBA) is a complex network of gastrointestinal (GI) microbiota and host enteric, immune, neural, endocrine, and metabolic pathways. Disruptions to homeostasis promote dysbiosis, immune dysregulation, inflammation, and vagal signal disruption. Many disease states and behavioral disorders are associated with a change in GI microbial composition and diversity. Psychoactive treatments may specifically target the MGBA to reduce systemic and neuroinflammation linked to the pathogenesis of many GI and neuropsychiatric conditions.}, }
@article {pmid41786542, year = {2026}, author = {Kobayashi, S and Nakagawa, H and Komai, M}, title = {Comprehensive analysis of tonsillar gene expression and the tonsillar microbiota in patients with palmoplantar pustulosis and pustulotic arthro-osteitis.}, journal = {Journal of dermatological science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jdermsci.2026.01.006}, pmid = {41786542}, issn = {1873-569X}, abstract = {BACKGROUND: Tonsillectomy improves symptoms in patients with palmoplantar pustulosis (PPP) and suppresses disease progression in patients with pustulotic arthro-osteitis (PAO), highlighting the important role of tonsils in the pathogenesis of PPP/PAO.<br><br>OBJECTIVE: To identify inflammatory pathways involved in the tonsil tissue of patients with PPP/PAO, and to clarify the characteristics of tonsillar microbiota.<br><br>METHODS: We assessed gene expression in tonsil tissue obtained from PPP/PAO or recurrent tonsillitis (RT)/sleep apnea syndrome (SAS) patients using microarray and quantitative reverse transcription polymerase chain reaction analysis. We also performed a comprehensive analysis of the tonsillar microbiota using next-generation sequencing. Potential associations between tonsillar gene expression and bacterial composition or disease activities were evaluated.<br><br>RESULTS: Twenty-five tonsils from PPP/PAO patients and 15 tonsils from RT/SAS patients were included. The gene expression of inflammatory cytokines and molecules involved in the Th17, Th2, and Treg pathways was significantly higher in PPP/PAO tonsils than in RT/SAS tonsils. A significant positive correlation between Streptococcus spp. and the expression of Th17 and Th2 pathway genes was revealed both in PPP/PAO and RT/SAS, however, different correlation patterns were observed between these groups for the other genera. PAO disease activity showed a negative correlation with the expression of CCR4, FOXP3, and CXCR3 genes.<br><br>CONCLUSION: PPP/PAO tonsils exhibit enhanced Th17, Th2, and Treg responses relative to RT/SAS, indicating a complex inflammatory condition. Streptococcus genus may be associated with inflammation, and interaction between microbiota and T cell immunity would be suggested in PPP/PAO tonsils. PAO disease activity inversely correlated with Treg response.}, }
@article {pmid41786183, year = {2026}, author = {Long, Z and Li, J and Zhu, F and Liu, X and Zhoua, J and Li, J and Xu, W}, title = {From intestinal messenger to next-generation therapeutics: A review on mechanisms and prospects of host metabolic regulation mediated by P9, a secreted protein from Akkermansia muciniphila.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {151199}, doi = {10.1016/j.ijbiomac.2026.151199}, pmid = {41786183}, issn = {1879-0003}, abstract = {P9, a protein secreted by Akkermansia muciniphila (A. muciniphila), serves as a key bioactive effector and exhibits promising therapeutic potential for metabolic disorders. This review systematically elucidates the molecular mechanisms by which P9 mediates microbe-host interactions through activation of the intercellular adhesion molecule-2 (ICAM-2) and interleukin-6 (IL-6) signaling pathways. It also summarizes recent advances in P9 biomanufacturing, summarizing advances in its heterologous expression in Escherichia coli (E. coli) and Lactobacillus lactis (L. lactis), and proposes innovative delivery strategies using engineered probiotics or nanocarriers to bypass gastrointestinal barriers. In addition, we explore the modular structure of P9 proteins predicted by AlphaFold, revealing potential domains amenable to functional optimization through protein engineering. By combining mechanistic insights with bioengineering approaches, this review positions engineered P9 as a multifunctional candidate for developing oral, targeted, and sustained-release therapies against obesity and type 2 diabetes mellitus (T2DM). This strategy offers new avenues for linking fundamental gut microbiome research with translational metabolic medicine applications.}, }
@article {pmid41786113, year = {2026}, author = {Huang, P and Gao, J and Cao, L and Li, J and Du, J and Xu, G}, title = {Effects of subchronic exposure to PFOA and nanoplastics on the gills of Eriocheir sinensis: Perspectives from the transcriptome, microbiome and physiology.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {}, number = {}, pages = {110502}, doi = {10.1016/j.cbpc.2026.110502}, pmid = {41786113}, issn = {1532-0456}, abstract = {PFOA and NPs are recognized as persistent organic pollutants with potential ecological risks in aquatic ecosystems, and they exhibit specific toxic effects on benthic invertebrates. As a vital respiratory organ of aquatic animals, the gill plays a key role in gas exchange and osmoregulation. However, studies on the potential adverse impacts of these two pollutants on the gill tissue remain scarce. In the present study, we conducted a 28-day stress experiment with the Eriocheir sinensis as a research model and systematically investigated the toxic effects of PFOA/NPs on gill organs by multi-omics sequencing. At the biochemical level, PFOA/NPs inhibited the activity and transcription of antioxidant enzymes (CAT, T-SOD, and GSH) or genes (gpx, gstd7), while triggering oxidative stress (MDA) and causing morphological damage. Moreover, PFOA/NPs induced inflammation (TNF-α, hil-6), apoptosis, autophagy (bnip3, stk17a, lc3a, epg5), suppression of immune responses (fcn, lyz), and disruption of glycolipid metabolism (fasn, acsl14, srebf1, acsly). In addition, the PFOA-NPs co-exposure disrupted the microbial flora structure in gill tissues, including reduced community evenness, increased dominance of specific species, and heightened abundances of both environmental organic pollutant-degrading microbes and opportunistic pathogens (Acidovorax, Sphaerotilus, Candidatus_Bacilloplasma). Furthermore, PFOA-NPs may disrupt microbial physiological homeostasis by suppressing the "LPS biosynthesis-antibiotic production-GAG degradation-lysosomal function" axis. These findings indicate that the gill organs of aquatic crustaceans are highly sensitive to organic pollutants such as PFOA and NPs, and long-term exposure disrupts their tissue physiology and microbial community homeostasis, thereby providing critical data to support the ecotoxicological assessment of PFOA/NPs in aquatic ecosystems.}, }
@article {pmid41785880, year = {2026}, author = {Petersen, A&#xd8; and Damholt, B and Grove, M and Hink, J and Marotte-Hurbon, T and Söderqvist, J and Troy, A and Zdravkovic, M and Bayer, L and Brunner, K and Bryde, T and Clube, J and Gencay, YE and Gram, A and Haaber, JK and Hallström, B and Jasinskytė, D and Pascal, R and Petersen, M and Semsey, S and Torio, AS and Turcu, IC and Smrekar, F and Taur, Y and Satlin, MJ and Sommer, MOA and van der Helm, E and Grøndahl, C}, title = {Safety, recovery, and pharmacodynamics of CRISPR-Cas therapeutic SNIPR001: a phase 1, randomised, double-blind, first-in-human, dose-escalation study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101257}, doi = {10.1016/j.lanmic.2025.101257}, pmid = {41785880}, issn = {2666-5247}, abstract = {BACKGROUND: Patients with haematological cancer who receive stem-cell transplantation are at risk of bloodstream infections, often caused by multidrug resistant gut pathogens such as Escherichia coli. SNIPR001 is a cocktail of four CRISPR-Cas-armed bacteriophages that reduce colonisation of E coli in the gastrointestinal tract in animal models and is designed to not affect other members of the commensal microbiota. We aimed to investigate the safety and tolerability of SNIPR001 in healthy participants.<br><br>METHODS: In this randomised, placebo-controlled, double-blind, first-in-human, dose-escalation trial conducted at a single centre (Medpace Clinical Pharmacology Unit; Cincinnati, OH, USA), we sequentially enrolled healthy participants (aged 18-65 years) with more than 10[7]E coli colony-forming units per gram of stool into cohorts 1, 2, and 3, pending a safety review of the previous enrolment group where applicable. Participants in each cohort were randomly assigned to treatment or placebo using a unique three-digit participant identification number. Participants were orally administered 10[8] plaque-forming units (PFU) per dose (cohort 1), 10[10] PFU per dose (cohort 2), and 10[12] PFU per dose (cohort 3) of SNIPR001 or placebo (phosphate-buffered saline buffer), twice daily for 7 days. All personnel, except for a pharmacy staff member who prepared both SNIPR001 and placebo vials, were masked to the administered dose and assignment; masking was ensured by fully covering the surface of each vial. Participants were followed up to day 187. The primary outcome was the incidence and severity of adverse events and medically attended adverse events from the first administration of the study drug until 4 weeks after the last dose administration on day 35 of the study. Recovery and biodistribution of SNIPR001 in faeces, blood, and urine; pharmacodynamics, including the ability of SNIPR001 to reduce E coli levels in stool (assessed using a linear mixed-effects model); and microbiome composition (using Bray-Curtis dissimilarity) were secondary outcomes. Primary safety analyses were assessed per-protocol (ie, all enrolled participants who received at least one administration of the study drug). This trial was conducted under an Investigational New Drug application from the US Food and Drug Administration, is registered with ClinicalTrials.gov (NCT05277350), and is closed to new participants.<br><br>FINDINGS: The trial was carried out between March 24, 2022, and Nov 30, 2022. 36 eligible participants were randomly assigned to receive SNIPR001 or placebo in cohorts 1 (six assigned to 10[8] PFU per dose and two assigned to placebo), 2 (six to 10[10] PFU per dose and two to placebo), and 3 (12 to 10[12] PFU per dose and eight to placebo). The mean age of participants was 42&#xb7;1 years (SD 13&#xb7;8), with 14 (39%) female participants and 22 (61%) male participants. During the trial and 4-week follow-up period, only mild and moderate adverse events were observed, with most adverse events occurring in the placebo group (13, six, one, and nine for participants receiving either placebo or SNIPR001 at 10[8], 10[10], and 10[12] PFU twice a day, respectively). The number of participants who had adverse events was not significantly higher in treatment groups than in the placebo group (p=0&#xb7;94, one-sided Fisher's exact test). The most frequently reported adverse events were headaches and diarrhoea. No grade 3-4 adverse events were reported and no serious adverse events were reported in the SNIPR001 dose groups. During and after the dosing period, the gut microbiota composition did not significantly differ between the treatment and placebo groups (p>0&#xb7;05, two-sided Mann-Whitney U test of Bray-Curtis distances, false discovery rate [FDR]-corrected). Functional SNIPR001 was recovered from stool samples in concentrations proportional to the administered dose but was not meaningfully detected in plasma (only one sample) or urine (only one sample). SNIPR001 was undetected in all samples 6 months after the last dosing, which is a favourable pharmacokinetic property and meets regulatory expectations. We observed the largest reduction in E coli levels compared with placebo 2 weeks after treatment initiation at day 14 (78%; -0&#xb7;65 log10 [SE 0&#xb7;64] for 10[12] PFU SNIPR001 twice-daily group), according to a linear mixed-effects model for the highest dose population; however, this change was not statistically significant (p=0&#xb7;811, linear mixed-effects model, FDR-corrected).<br><br>INTERPRETATION: This first-in-human study of SNIPR001 supported its safety, tolerability, and restriction to the gastrointestinal tract, while not systemically disrupting the gut microbiome. These results justify further clinical development of SNIPR001 in an ongoing phase 1b/2a trial.<br><br>FUNDING: Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator (CARB-X) and SNIPR Biome.}, }
@article {pmid41785672, year = {2026}, author = {Chen, Q and Feng, X and Wang, J and Zhu, H and Bo, Z and Wang, B and Zhao, Z}, title = {Impact of gut microbiota on hepatocellular carcinoma: Pathogenesis, diagnosis, prognosis, and therapeutic prospective.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {237}, number = {}, pages = {116581}, doi = {10.1016/j.ejca.2026.116581}, pmid = {41785672}, issn = {1879-0852}, abstract = {Advances in sequencing technology have elucidated the complex role of the gut microbiota in hepatocellular carcinoma (HCC). Communication between the gut and the liver occurs via the gut-liver axis, and dysbiosis of the gut microbiota has been implicated in both the promotion and suppression of HCC. Furthermore, through interactions with host metabolism and immune system, the gut microbiota significantly influences treatment responses and prognostic outcomes of HCC. Despite progress in therapeutic strategies, clinical efficacy remains suboptimal, underscoring the need for a deeper understanding of the gut microbiota's role. This review highlights the potential of gut microbiota as novel biomarkers for the diagnosis and prognostic prediction of HCC, and explores its therapeutic implications. We summarize current insights into the molecular mechanisms underlying the gut microbiota-HCC interplay, and emphasize the relationship between gut microbiota and the efficacy of various treatments, including surgery, chemotherapy, radiotherapy, immunotherapy, and targeted agents. Microbiome-targeting interventions like probiotics, fecal microbiota transplantation (FMT), and dietary changes as emerging adjuvant strategies are also discussed in detail to provide potential resources for advancing translational hepatology. Although challenges remain, this review aims to provide valuable perspectives for developing individualized therapeutic strategies in HCC management.}, }
@article {pmid41785480, year = {2026}, author = {Shekarriz, S and Vigod, SN and Bianco, T and Bala, A and Hao, C and Allard, JP and Hota, S and Poutanen, S and Surette, MG and Taylor, VH}, title = {The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.}, journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie}, volume = {}, number = {}, pages = {7067437261420877}, pmid = {41785480}, issn = {1497-0015}, abstract = {BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922.}, }
@article {pmid41770403, year = {2026}, author = {D'Souza, R and Pujare, K and Balu, SK and Kanojiya, D and Garg, Y and Ghag, SB}, title = {Differential Response of Banana Root Exudates and its Components on the Growth and Development of Banana Wilt Pathogen.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41770403}, issn = {1432-184X}, abstract = {UNLABELLED: Plant roots and rhizospheric microbes share an intricate relationship. Plants produce a complex mixture of root exudates that significantly affect the rhizospheric microbiome. Understanding the composition and functional significance of root exudates is essential for elucidating ecological mechanisms that can be leveraged to reduce disease severity. The significance of banana root exudates in Fusarium wilt disease caused by Fusarium oxysporum f. sp. cubense (Foc) remains poorly understood. This study investigates the differential effects of root exudates and their specific constituents derived from resistant and susceptible banana cultivars on the growth and development of Foc. Root exudates collected from four banana cultivars were evaluated for their effect on Foc mycelial growth, conidiospore germination and chemotropism. Exudates from susceptible cultivars (Rasthali, Red banana) significantly stimulated Foc conidiospore germination and chemotropism index as compared to those from resistant cultivars (Grand Naine, cv. Rose). Among the components, fumaric and salicylic acid showed dose-dependent increase in Foc conidia germination and chemotropism index. Conversely, oxalic and malic acid showed inhibition of Foc conidia germination at 0.5 µM, while phthalic acid showed inhibitory effects at 5 µM. Interestingly, oxalic, malic and phthalic acid treatment showed increased chemotropism index at 0.5 µM whereas, cinnamic acid showed a dose-dependent decrease. Mass spectrometric analysis revealed distinct profiles of organic acids among the four cultivars, while phenolic acids were detected in all four samples. This study enhances our understanding of the banana-Fusarium interaction and offer valuable insights into natural defense mechanisms and potential biocontrol strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-025-02693-z.}, }
@article {pmid41639642, year = {2026}, author = {Unrug-Bielawska, K and Dziełak, M and Sandowska-Markiewicz, Z and Piątkowska, M and Czarnowski, P and Goryca, K and Zeber-Lubecka, N and Dąbrowska, M and Bałabas, A and Statkiewicz, M and Rumieńczyk, I and Pyśniak, K and Wójcik-Trechcińska, U and Tyl-Bielicka, A and Ziemska-Legięcka, J and Mikula, M and Ostrowski, J}, title = {Sex- and mouse strain-related differences in body weight gain, composition of the gut microbiota, and levels of selected metabolites in response to a Western-style diet.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {}, pmid = {41639642}, issn = {1471-230X}, support = {2018/29/B/NZ7/00809//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Recent studies reveal an association between the mitochondrial Amidoxime Reducing Component (MTARC) 1 and 2 proteins and metabolism in Mtarc1/2-deficient mice that are resistant to diet-induced obesity; however, the impact of Mtarc1/2 knockout (KO) on the gut microbiota and metabolome has not been explored in the context of sex and diet.<br><br>AIM: To compare the effects of a Western diet (WD) or a Novel Gubra Amylin NASH (GAN) diet on body weight gain, and on the composition of the gut microbiome and metabolome, between the background mouse strain and male and female Mtarc1- or Mtarc2-KO mice.<br><br>METHODS: Seventy-two 8-week-old male and female mice from each strain were fed a WD or a corresponding control normal diet (ND/WD), or a GAN diet or a corresponding control normal diet (ND/GAN), for 16 weeks. Fecal samples were collected at the beginning and end of the experiments, and 16&#xa0;S rRNA-based microbiota profiling-based analysis was performed by sequencing the variable V3 and V4 regions of the bacterial 16&#xa0;S rRNA gene. Mass spectrometry was used to measure short-chain fatty acids (SCFAs) and amino acids (AAs).<br><br>RESULTS: Compared with a control ND, GAN feeding increased the body weight of all groups of mice, whereas the WD increased the body weight of all groups except Mtarc2-KO female mice. The most significant weight gain was observed for male and female C57BL6/NTac mice fed a WD or GAN. Differences in body weight were mirrored in the microbiota profiles. In each of the mouse strains tested, the number of differentially abundant taxa between the GAN- and ND/GAN-fed groups was greater than that between WD- and ND/WD-fed mice. Both the GAN and WD also altered the levels of SCFAs and AAs in feces in a manner dependent on the mouse strain and sex.<br><br>CONCLUSIONS: Significant differences in body weight gain and changes in the composition of the gut microbiome and metabolome between the background mouse strain and Mtarc1-KO or Mtarc2-KO mice were further modified by sex and diet. Therefore, preclinical studies using animal models of obesity should ensure the selection of the appropriate mouse strain and sex, and be mindful of diet composition.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12876-026-04647-2.}, }
@article {pmid41639630, year = {2026}, author = {Bansaghi, S and Gulyás, G and Járay, T and Tombácz, D and Boldogkői, Z and Klein, J}, title = {Effect of long-lasting antimicrobial surface sprays in real-life environment.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41639630}, issn = {1471-2334}, abstract = {Antimicrobial surfaces have the potential to continuously self-decontaminate, which can play a key role in infection control. Various surface treatment sprays are available on the market today, differing in their chemical compositions and active ingredients. This study aimed to evaluate the effectiveness of these surface treatment sprays in real-life settings. The effects of the sprays were examined both in vitro, using bacterial suspensions, and in real-life settings. Effectiveness was measured by the number of colony-forming units (CFU) and by ATP tests. Additionally, the microbiome of one door opener was sequenced to identify the predominant microbes on that surface. Sequencing revealed that the microbiome of the door openers is mainly composed of skin bacteria. Staphylococcus (49.2%) and Micrococcus (33.6%) were the dominant genera identified in the sample. In vitro experiments demonstrated that all spray treatments were effective when tested against bacteria in suspension. However, in real-life settings, none of our measurements detected a significant reduction in microbial presence following spray treatment. We hypothesize that this discrepancy is due to the presence of a fatty substance, likely from fingerprints, on surfaces. This oily layer may act as a barrier that physically separates microbes from the treated surfaces, thereby diminishing the efficacy of the antimicrobial sprays.}, }
@article {pmid41785450, year = {2026}, author = {Sun, QQ and Bao, MY and Gao, R and Wang, SK and Zhang, Y and Wang, LB and Zhang, Y and Li, X}, title = {Advances in Understanding Lipid Metabolism in Oligodendrocyte Development and Neurodegenerative Diseases.}, journal = {Clinical science (London, England : 1979)}, volume = {}, number = {}, pages = {}, doi = {10.1042/CS20258150}, pmid = {41785450}, issn = {1470-8736}, support = {82471421,82271199,82571568//National Natural Science Foundation of China/ ; 23JHQ057//Scientific Research Program Funded by Education Department of Shaanxi Provincial Government/ ; GK202501001, GK202505004//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Lipids are indispensable architectural and functional components of central nervous system (CNS) myelin, with cholesterol, sphingolipids, and phospholipids collectively constituting 70-80% of myelin membrane composition. Oligodendrocytes (OLs), the sole myelin-producing cells in the CNS, exhibit exquisite metabolic specialization to sustain lifelong myelination and remyelination. Mounting evidence implicates lipid metabolic dysregulation-spanning cholesterol efflux defects, sphingolipid imbalance, and peroxisomal dysfunction-as a convergent mechanism underlying OL differentiation failure and progressive demyelination in neurodegenerative diseases. This review explores the role of lipid metabolic rewiring in governing oligodendrocyte precursor cells (OPCs) fate determination, highlighting three crucial axes: the interplay between mitochondria and peroxisomes in lipid biosynthesis, the potential toxicity of accumulated myelin debris in the microenvironment, and the regulation of OPC differentiation through lactylation modification on lipid metabolism and the interaction between glycolipid metabolisms. We further synthesize emerging therapeutic strategies targeting these pathways, including immunometabolism modulators, precision lipid interventions; diet-microbiome synergies: ketogenic diets combined with butyrate-producing probiotics to amplify endogenous remyelination. By integrating lipidomics datasets and recent clinical trial evidence, we propose a shift from broad metabolic suppression to spatially resolved modulation of lipid flux. This synthesis not only clarifies the dual roles of lipids in OL development and degeneration but also highlights druggable targets for personalized treatment of neurodegenerative diseases.}, }
@article {pmid41785249, year = {2026}, author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR}, title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.}, journal = {PLoS computational biology}, volume = {22}, number = {3}, pages = {e1013185}, doi = {10.1371/journal.pcbi.1013185}, pmid = {41785249}, issn = {1553-7358}, abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.}, }
@article {pmid41785052, year = {2026}, author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S}, title = {MDPD reveals specific microbial signatures in human pulmonary diseases.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, doi = {10.1093/bib/bbag017}, pmid = {41785052}, issn = {1477-4054}, abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.}, }
@article {pmid41784969, year = {2026}, author = {Chen, Y and Xing, Z and Sheng, J and Liu, X and Ding, W and Chen, X}, title = {Trends in the Application of Multiomics Based on Machine Learning in the Development of Probiotics.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c15387}, pmid = {41784969}, issn = {1520-5118}, abstract = {With the rapid development of computational methods and high-throughput multiomics technologies, machine learning (ML) has emerged as an important analytical approach in probiotic research. This review summarizes recent ML-assisted applications across genomics, transcriptomics, metabolomics, microbiome profiling, and culturomics, and organizes current studies around four functional objectives: probiotic selection, functional prediction, metabolic activity prediction, and probiotic effectiveness optimization. We discuss how ML facilitates the integration of heterogeneous omics data to enable more systematic and quantitative probiotic development and highlight representative analytical tools and workflows. At the same time, key limitations remain, including cross-platform data heterogeneity, imbalanced functional labels, and limited robustness in capturing complex microbial and environmental interactions. Consequently, experimental validation remains essential for ensuring biological relevance. Future progress will rely on standardized multiomics integration and iterative computational-experimental frameworks to support rational probiotic optimization.}, }
@article {pmid41784899, year = {2026}, author = {Colaco, VS and Boleij, A}, title = {The gut microbiome as a biomarker and modifiable risk factor in Lynch Syndrome.}, journal = {Familial cancer}, volume = {25}, number = {1}, pages = {}, pmid = {41784899}, issn = {1573-7292}, support = {WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; KUN2015-7739//KWF Kankerbestrijding/ ; }, }
@article {pmid41784851, year = {2026}, author = {Yoshioka, H and Mary-Huard, T and Aubert, J and Toda, Y and Ohmori, Y and Yamasaki, Y and Tsujimoto, H and Takahashi, H and Nakazono, M and Takanashi, H and Fujiwara, T and Tsuda, M and Kaga, A and Inaba, J and Fuji, Y and Hirai, MY and Nose, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Ichihashi, Y and Iwata, H}, title = {Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {139}, number = {3}, pages = {}, pmid = {41784851}, issn = {1432-2242}, support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JP22K21352//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Corporation/ ; JPMJAN23D1//Japan Science and Technology Corporation/ ; }, abstract = {Intermediate omics traits, which mediate the effects of genetic variation on phenotypic traits, are increasingly recognized as valuable components of genetic evaluation. In particular, rhizosphere microbiota play a crucial role in plant health and productivity; however, their complex interactions with host genetics remain challenging to model. Although two-step modeling frameworks have been proposed to integrate intermediate omics traits into phenotype prediction, existing approaches do not incorporate nonlinear relationships between different omics layers. To address this, we have proposed a two-step phenotype prediction framework that integrates genomic, rhizosphere microbiome, and metabolome (meta-metabolome) data, while explicitly capturing omics-omics nonlinearities. The first step is to predict meta-metabolome traits from genetic and microbial features, thus effectively isolating them from the environmental noise. In this process, intermediate "proxy" omics traits are generated as general biological information to provide robust models. The second step utilizes this "proxy" to enhance the accuracy of the phenotype prediction. We compared a linear mixed model (Best Linear Unbiased Prediction, BLUP) and a nonlinear model (Random Forest, RF) at each step, as demonstrated through simulations and empirical analysis of a multi-omics soybean dataset in which nonlinear modeling captures intricate omics interactions. Notably, our approach enables phenotype prediction without requiring the original meta-metabolome data used in model training, thereby reducing reliance on costly omics measurements. This framework integrates intermediate omics traits into genomic prediction to improve prediction accuracy and provide solutions for deeper insights into plant-microbiome interactions.}, }
@article {pmid41784506, year = {2026}, author = {Ivanov, VA and Hartman, WH and Soheilypour, M}, title = {Decoding the Microbiome-Disease Axis with Interpretable Graph Neural Networks.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag063}, pmid = {41784506}, issn = {1365-2672}, abstract = {AIMS: The human gut microbiome is a complex ecosystem whose disruption is implicated in a wide spectrum of diseases, yet translating microbiome research into actionable therapeutics is hindered by a critical trade-off: existing models either prioritize predictive accuracy at the expense of interpretability or sacrifice performance for mechanistic insight, limiting their ability to pinpoint specific disease-driving microbial interactions and taxa.<br><br>METHODS AND RESULTS: To address this, we introduce Graph neural network for Interpretable Microbiome (GIM), a graph neural network framework that integrates minimally processed taxonomic metadata as sparse node embeddings within an unweighted complete graph, enabling direct modeling of high-order microbial interactions through message passing. GIM achieves state-of-the-art classification performance on microbiome-disease prediction tasks (e.g. healthy vs. allergic states) while generating finegrained, experimentally validated attributions at the level of taxonomic ranks, driver microbes, and putative microbe-to-microbe interactions.<br><br>CONCLUSIONS: By bridging the gap between predictive accuracy and biological interpretability, GIM overcomes a key limitation in current approaches, offering a unified framework to both predict dysbiosis-associated disease states and identify actionable microbial targets for therapeutic intervention. This dual capability represents a critical advance toward precision microbiome engineering and scalable hypothesis generation in translational microbiome research.}, }
@article {pmid41784373, year = {2026}, author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A}, title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0369125}, doi = {10.1128/spectrum.03691-25}, pmid = {41784373}, issn = {2165-0497}, abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.}, }
@article {pmid41784222, year = {2026}, author = {Barr, SA and Davis, LJ and Vidar, W and Williamson, RT and Strangman, WK}, title = {Assessing Digestive Transformations of Withania somnifera Extracts via LC-MS/MS Profiling with a Focus on Bioactive Compounds Withaferin A, Withanolide A, Withanoside IV, and Untargeted Metabolomics.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c09897}, pmid = {41784222}, issn = {1520-5118}, abstract = {Botanical extracts are widely employed as health care agents but lack the rigorous vetting required for FDA-approved pharmaceuticals. Research on phytochemical bioavailability and transformation has mainly focused on liver metabolism and plasma binding, while gastrointestinal and microbiome metabolism studies remain limited. This study combined digestive in vitro assays with mass spectrometry-based metabolomics and molecular networking to analyze metabolites in Withania somnifera leaf and root extracts, along with three known bioactive reference standards: withaferin A, withanolide A, and withanoside IV. Both withaferin A and withanoside IV underwent significant in vitro transformation, while withanolide A remained stable across conditions. Molecular networking revealed that withanolides in the root extract were largely stable, whereas many in the leaf extract were more labile under the assay conditions. Detailed network analysis also enabled the identification of specific metabolite transformations. These findings support the refinement of in vitro models to better predict in vivo behavior in complex botanical mixtures.}, }
@article {pmid41784027, year = {2026}, author = {Mekonnen, YT and Indio, V and Lucchi, A and Manfreda, G and Serraino, A and De Cesare, A}, title = {Detection of Chlamydia ibidis in the neck skin microbiome of broiler carcasses at the end of slaughter.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.14726}, pmid = {41784027}, issn = {2239-7132}, abstract = {Chlamydia is the etiological agent of chlamydiosis in wild and domestic birds, mammals, and humans. In this study, Chlamydia reads were detected in the microbiome of the neck skin of 76 broiler carcasses collected in the same slaughterhouse at the end of the chilling tunnel. The carcasses originated from four different flocks of female Ross 308, reared in two broiler houses located in Northern Italy. One flock from each poultry house was sampled in 2019 and one flock in 2023. The carcass neck skin microbiome was investigated by shotgun metagenomic sequencing. Chlamydia reads displayed a mean relative abundance of 7.38%, with significant differences between carcasses obtained from the two poultry houses, sampled at both sampling times. Chlamydia ibidis was the prevalent species among time points and poultry houses. The zoonotic potential of C. ibidis and foodborne transmission have never been demonstrated. However, it is known that the genus Chlamydia has "spore"-like extracellular forms able to survive for months outside the host. Therefore, the presence of C. ibidis reads on broiler carcasses at the end of the chilling tunnel deserves further investigation. The results of this study highlight the feasibility of microbiome investigations to detect unexpected biological hazards in foods.}, }
@article {pmid41783932, year = {2026}, author = {Gomez, R and Sun, W and Shyy, M and Ou, J and Sihota, A and Liu, B and Mesarwi, O and Malhotra, A}, title = {Mechanisms Linking Sleep-Disordered Breathing and Cardiometabolic Disease Risk.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.125.322874}, pmid = {41783932}, issn = {1524-4636}, abstract = {Sleep-disordered breathing (SDB) is a group of disorders defined by intermittent closure or narrowing of the upper airway, caused either by mechanical obstruction or dysregulation of the respiratory centers in the brainstem. The effects of SDB on cardiovascular and metabolic health and disease have been an area of growing interest. Many studies have shown mechanistic links between physiological changes seen in SDB and important cardiometabolic outcomes. In particular, SDB induces alterations in autonomic function, swings in intrathoracic pressure, systemic inflammation, sleep fragmentation, and oxidative stress, with diverse effectors including alterations in cellular gene expression, for example, through microRNA and hypoxia-inducible factor 1, changes in the gut microbiome, and many others. Ultimately, these mechanistic pathways have implications on vascular and myocardial dysfunction, hypertension, insulin sensitivity, lipid metabolism, and weight gain. Several treatment modalities exist for SDB, and are chosen based on the specific disease process and patient preference/tolerance. These therapies result in an improvement in symptoms related to SDB severity and varying levels of cardiometabolic disease risk mitigation. In this review, we will present some important mechanisms of SDB that increase the risk for cardiometabolic disease, and we will discuss therapies and their intended targets.}, }
@article {pmid41783924, year = {2026}, author = {Luo, S and Lou, F and Yang, P and Zhang, Y and Yan, L and Dong, Y and Yang, B and Wang, H and Liu, Y and Pu, J and Cannon, RD and Xie, P and Ji, P and Jin, X}, title = {Dysregulation of Oral Microbial Eicosapentaenoic Acid Induced by Chronic Restraint Stress Exacerbates Periodontitis via M1 Macrophage Polarization.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e21346}, doi = {10.1002/advs.202521346}, pmid = {41783924}, issn = {2198-3844}, support = {82370968//National Natural Science Foundation of China/ ; 2026MSXM055//Chongqing medical scientific research project (Joint project of the Chongqing Health Commission and the Science and Technology Bureau)/ ; CSTB2022NSCQ-MSX1148//Natural Science Foundation of Chongqing/ ; 2025JYJ099//Project of Luzhou Science and Technology Bureau/ ; }, abstract = {The intricate interplay between chronic psychological stress and periodontitis, mediated by oral microbiota and macrophage polarization, remains largely enigmatic. Here, we demonstrate that chronic restraint stress (CRS) exacerbates periodontitis by inducing oral microbial dysbiosis and a consequential shift in host metabolism. Clinical observations reveal a significant correlation between depressive symptoms and the severity of periodontitis, which is underpinned by a distinct oral microbiome. Crucially, fecal microbiota transplantation from CRS-exposed mice into germ-free mice was sufficient to transmit the heightened periodontitis phenotype, establishing a causal role for the stress-altered microbiota. Metabolomic profiling identified a depletion of eicosapentaenoic acid (EPA) in stressed, ligature-induced periodontitis mice. Mechanistically, supplementation with EPA ameliorates periodontitis by suppressing the NF-κB signaling pathway, thereby inhibiting the pro-inflammatory M1 polarization of macrophages. Our findings unveil a novel gut-oral axis mediated by microbiota and metabolites under stress, and position the omega-3 fatty acid EPA as a promising therapeutic agent for mitigating stress-aggravated inflammatory disorders.}, }
@article {pmid41783896, year = {2026}, author = {Zhang, Q and Wang, W and Yu, H and Wang, F and Chen, X and Liang, Z and Lu, Y}, title = {Research progress on immune tolerance mechanisms in liver metastatic tumors and the "Liver-metastasis-oriented shared-mechanism therapeutic strategy" approach.}, journal = {Medical review (2021)}, volume = {6}, number = {1}, pages = {57-74}, pmid = {41783896}, issn = {2749-9642}, abstract = {Liver metastases pose a serious challenge in the field of systemic cancer treatment, as this organ has a particular microenvironment that favours malignant cells disseminating to settle there. We outline major steps of liver immune tolerance in metastasis including pre-metastatic niche formation, immune evasion during circulation, establishment of an intrahepatic immune desert and metabolism, myeloid cell networks and gut microbiome-mediated coordinated tolerance. We then combine new combination and integrative therapies that are intended to break this tolerance; these include immunochemotherapy regimens, synergistic antiangiogenics and immunotherapies, dual immune checkpoint blockade and myeloid-cell reprogramming, combined locoregional and systemic therapies and new microenvironmental targeting. Each strategy is assessed with regard to its potential disruption of hepatic immune quiescence, improved clinical translation and durable antitumour activity. We suggest a proposed solution termed Liver-metastasis-oriented shared-mechanism therapeutic strategy, which may target multiple metastatic bottlenecks due to similarities. This framework provides a basis for personalizing combination therapies and designing future clinical trials for treating liver metastases, with organ-specific considerations and will be the subject of a commentary.}, }
@article {pmid41783828, year = {2026}, author = {Jurkovich, V and Fischer, L and Nagy, K and Ladányi, M and Hann, S and Dernovics, M}, title = {Targeting selenometabolites in the saliva of dairy cows: size-exclusion chromatography - inductively coupled plasma mass spectrometry-based characterization.}, journal = {Veterinary and animal science}, volume = {32}, number = {}, pages = {100600}, pmid = {41783828}, issn = {2451-943X}, abstract = {Selenium supply is an important input for milking cows, and the monitoring of selenium uptake has been carried out through total selenium determination in the blood serum samples or the concentration of selenoprotein P. While the optimum concentrations of these two parameters have already been established, the specific selenium requirement of cows' microbiomes has not been addressed. The oral cavity of cows contains basically the first, front-end microbiome of the animal. However, no information is available on its selenium-dependent/ independent strains, its distribution, and ratio. In any case, saliva would be the only readily accessible source of selenium for the microbiome of the oral cavity. Therefore, our study focused on the total selenium and selenium speciation analyses of saliva of Holstein cows, together with the determination of total selenium in whole blood and serum samples. A two-step feeding experiment was conducted with supplementing the selenite-containing daily ration with the hydroxy-analogue of selenomethionine (R,S-2-hydroxy-4-methylselenobutanoic acid, HMSeBA) at the highest authorized rate in the EU. Size-exclusion chromatography - inductively coupled plasma mass spectrometry was used for the speciation of saliva samples that revealed the presence of low molecular weight (LMW) selenometabolites in the 1.78-15.3 µg Se kg[-1] range. The supplementation of HMSeBA did not significantly increase the blood selenium concentrations, and no correlation was found between the LMW selenium concentration and blood selenium concentrations. While the identification of LMW selenometabolites with electrospray ionization high-resolution mass spectrometry could not be achieved, a dedicated sample preparation protocol has been suggested for future experiments.}, }
@article {pmid41783496, year = {2026}, author = {Qin, X and Song, S and Xiang, G and Luo, S and Wen, X}, title = {Microplastics: a potential threat to gut microbiota and antioxidant capacity of broiler chickens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1708036}, pmid = {41783496}, issn = {1664-302X}, abstract = {The detrimental effects of microplastics on environmental and biological health have been extensively documented, encompassing various aspects such as growth inhibition, metabolic disorders, and organ damage. However, current research predominantly focuses on model organisms, with limited studies investigating their effects on broiler chickens. Therefore, this study aims to examine the impact of microplastics exposure on the gut microbiota and antioxidant function in broiler chickens. The results indicated that microplastics significantly affect serum biochemical and antioxidant parameters, evidenced by marked increases in AST, ALT, and MDA levels, alongside decreases in SOD and GSH-Px levels. Microbiome analysis revealed a significant decrease in the alpha diversity of the gut microbiota, accompanied by significant alterations in microbial structure. Additionally, metastats analysis demonstrated a significant increase in the relative abundances of one phylum and 12 genera during microplastics exposure, contrasted with a significant decrease in the relative abundances of three phyla and 108 genera. Importantly, microplastics exposure also led to changes in gut microbial function, affecting energy metabolism, coenzyme transport and metabolism, and amino acid metabolism, etc. In summary, our study demonstrates that microplastics can adversely affect the health of broiler chickens by reducing their antioxidant capacity, and causing gut microbial dysbiosis. In light of the increasing pollution from microplastics, this study provides crucial information for assessing the risks posed by microplastics to livestock production. Furthermore, future research should prioritize monitoring the migration of microplastics within the food chain and examining their long-term effects on biological behavior and ecological functions.}, }
@article {pmid41783495, year = {2026}, author = {Xu, L and Wan, Q and Yang, Q and Shen, W and Dai, Y and Sun, H and Huang, L and Wang, M and Jiang, W and Hao, C}, title = {Microbial and metabolomic profiling of the upper respiratory tract in children with asthma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1672589}, pmid = {41783495}, issn = {1664-302X}, abstract = {BACKGROUND: This study aimed to investigate characteristic changes in the upper respiratory tract (URT) microbiome and metabolome in children with asthma and explore their associations with lung function.<br><br>METHODS: Children with asthma aged 6&#x202f;years and above admitted to the Children's Hospital of Soochow University from December 2022 to December 2023 comprised the study group. Age-matched healthy children undergoing physical examinations in the Department of Child Health were recruited as controls. Throat swabs were collected for microbiome detection using 16S rDNA sequencing and metabolomics analysis using liquid chromatography-mass spectrometry (LC-MS).<br><br>RESULTS: (1) Significant differences in alpha and beta diversity were observed among the control group (H), chronic persistent asthma group (CA), and acute exacerbation group (AA). In both CA and AA groups, FVC% predicted (FVC%/Pred) and FEV1% predicted (FEV1%/Pred) were negatively correlated with URT microbiota abundance. Actinobacillus abundance was positively correlated with FEV1%/Pred, FEV1/FVC, FEF25%/Pred, FEF50%/Pred, and FEF75%/Pred. (2) Metabolite differences between CA and AA groups were analyzed, and the top 5 differential metabolites were evaluated for their accuracy as asthma assessment biomarkers. L-carnitine showed an AUC&#x202f;>&#x202f;0.9, with a sensitivity of 85.7% and specificity of 85%. Other differential metabolites, including monoisobutyl phthalate, 4-hexyl-2,5-dimethyloxazole, and dibutyl phthalate, correlated with several lung function indices. The most relevant differential metabolic pathways included arginine biosynthesis, alanine-aspartate-glutamate metabolism, central carbon metabolism in cancer, and D-amino acid metabolism.<br><br>CONCLUSION: The URT microbiota in asthmatic children exhibits alterations in composition, structure, and diversity, with lower diversity in acute asthma compared to chronic persistent asthma. At the genus level, some microbiota (Actinobacillus, Fusobacterium) were correlated with FEV1%/Pred, FEV1/FVC, FEF25%/Pred, FEF50%/Pred, FEF75%/Pred. The differential metabolite L-carnitine may be a potential biomarker for asthma assessment.}, }
@article {pmid41783404, year = {2026}, author = {Liu, D and Ma, Y and Ma, Q and Huang, H and Li, T and Wang, J and Zhang, J and Cheng, X and Ge, X and Chen, Y and Zhang, Y}, title = {Clinical pathogen profiles and lung microbiome features in lung infection patients and concurrent cancer: insights from metagenomics next-generation sequencing.}, journal = {Open life sciences}, volume = {21}, number = {1}, pages = {20251220}, pmid = {41783404}, issn = {2391-5412}, abstract = {Pulmonary infections in immunocompromised cancer patients present significant diagnostic and therapeutic challenges. From Dec 2021 to Aug 2023, 85 patients with pulmonary infection were enrolled and categorized into a cancer group (CP, n = 20) and a non-cancer control group (NCP, n = 18). Pathogen detection was performed using both mNGS and culture and lung microbiome analysis was conducted. mNGS demonstrated a significantly higher pathogen detection rate than culture (P < 0.0001). The CP group exhibited older age (P < 0.001), elevated neutrophil counts (NE) and higher procalcitonin (PCT) levels compared to the NCP group. Furthermore, fungal pathogens were significantly more prevalent in the CP group (P = 0.046). Both cancer status and advanced age were independent influencing factors for the detection of pulmonary fungi. Pulmonary microbiome analysis revealed no significant differences in α-diversity or β-diversity between groups. These findings indicate that mNGS offers superior sensitivity over culture. Cancer-related pulmonary infections present a distinct pathogen profile characterized by a higher prevalence of fungal pathogens. This underscores the need for enhanced clinical vigilance, especially among elderly cancer patients.}, }
@article {pmid41783048, year = {2026}, author = {Wu, F and Zhu, B and Feng, S and Li, H and Zhou, J and Ning, Y and Huang, Y and Wu, K}, title = {The Brain-Gut Health Initiative (BIGHI): A Prospective Cohort on Psychiatric Disorders in China.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1142}, pmid = {41783048}, issn = {2639-5274}, abstract = {Major psychiatric disorders are characterized by substantial clinical heterogeneity and high comorbidity, yet their underlying biological mechanisms are not fully uncovered. The microbiota-gut-brain axis (MGBA) offers a cross-system perspective for elucidating the pathophysiology of major psychiatric disorders. The Brain-Gut Health Initiative (BIGHI) was established as the first prospective longitudinal cohort in China dedicated to investigating major psychiatric disorders guided by the framework of MGBA, enabling large-scale, transdiagnostic, and longitudinal analyses of brain-gut interactions. To date, the BIGHI has enrolled over 1,200 participants with schizophrenia, major depressive disorder, bipolar disorder, and healthy controls, with multidimensional data collected including clinical symptomatology, neurocognitive performance, electroencephalography, magnetic resonance imaging, peripheral blood biomarkers, and gut microbiome profiles. The studies within the BIGHI reveal (a) brain-gut physiological alterations in psychiatric disorders; (b) systematic relationships among brain function, peripheral physiological markers, and gut microbiome; and (c) brain-gut network patterns with marked interindividual heterogeneity. In future studies, we will expand the BIGHI into a collaborative network and promote data harmonization and interdisciplinary collaboration to advance computational psychiatry as well as its clinical translation.}, }
@article {pmid41782929, year = {2026}, author = {Gates, M and Schumacher, SM and Doyle, WJ and Sofaly, N and Roullet, JB and Ochoa-Repáraz, J}, title = {Farnesol, the farnesol pathway, and the immune-gut-brain axis.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1718322}, pmid = {41782929}, issn = {1663-9812}, abstract = {Experimental models and clinical evidence suggest that the gut and the central nervous system (CNS) interact in a multifactorial, bidirectional manner. A third player, the immune system, has recently been identified in these interactions, with research linking the gut microbiome to inflammatory conditions, including those affecting the CNS. The molecular signals involved in communication between the gut, brain, and immune system have been extensively studied. However, no unique signaling pathway has been identified for each component of the immune-gut-brain (IGB) axis to date. In this review, we argue that isoprenoids, and specifically farnesol, are key signaling molecules that link the gut and its microbiota, the immune system, and the CNS. The pharmacological properties of farnesol, an intermediate in the broadly conserved mevalonate pathway, are diverse and encompass quorum sensing and microbial biofilm inhibition, neuroinflammatory protection, and modulation of intracellular calcium (Ca[2+]) signaling pathways. Many of these signaling pathways are implicated in neuron-to-neuron communication and in the responses of immunocompetent cells to immunogenic stimuli. We will first address the biological relevance of the immune-gut-brain axis and the gut microbiome in regulating health and disease. Next, we will review the molecular and cellular mechanisms by which farnesol regulates both the gut microbiota and the host's innate and adaptive immune systems. Finally, we will provide a perspective on the immunoregulatory mechanisms underlying farnesol's protective properties in models of neuroinflammatory diseases. In summary, we propose a review of the most salient studies that establish farnesol as a significant modulator of the immune-gut-brain axis.}, }
@article {pmid41782866, year = {2026}, author = {Shen, S and Li, J and Zheng, S and Cui, X and Gou, X}, title = {Synergistic carcinogenesis of the nasopharyngeal microbiome and Epstein-Barr virus: mechanisms of metabolic reprogramming and immune evasion.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1771414}, pmid = {41782866}, issn = {1664-3224}, abstract = {Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection, but EBV alone is insufficient for tumorigenesis. Recent evidence suggests that the nasopharyngeal microbiome plays a critical, yet underexplored, role in NPC development. This review investigates the synergistic interaction between EBV and the nasopharyngeal microbiome, focusing on microbial dysbiosis and its role in NPC pathogenesis. We highlight significant microbial dysbiosis in NPC patients, characterized by an overgrowth of opportunistic pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis. These pathogens interact with EBV-infected epithelial cells, amplifying oncogenic signaling through the NF-κB and PI3K/AKT pathways. Crucially, we explore the "SCFA paradox," where microbial short-chain fatty acids (SCFAs), typically beneficial, act as HDAC inhibitors that paradoxically trigger EBV lytic reactivation in B-cells. Additionally, the microbiome facilitates immune evasion through interactions between F. nucleatum Fap2 and the TIGIT receptor, in synergy with EBV's LMP1 protein. These findings underscore the importance of the microbiome in NPC pathogenesis and highlight the potential for integrating microbial signatures into diagnostic tools. We conclude by discussing precision therapies, such as bacteriophage treatment, and emphasize the role of next-generation models-specifically Air-Liquid Interface organoids-as functional 'patient avatars.' These systems are essential for advancing personalized medicine, as they enable the functional validation of individualized microbial interventions that sequencing alone cannot predict.}, }
@article {pmid41782637, year = {2026}, author = {Ligezka, A and Lynch, BA and Saliba, M and Corral-Frias, MP and Johnson, S and Chen, J and Allen, SV and Frank, JM and Vande Voort, JL and Croarkin, PE and Romanowicz, M}, title = {Microbiome and Vocalization Biomarkers of Infant Distress, Maternal Depression and Parenting Styles.}, journal = {Chronic stress (Thousand Oaks, Calif.)}, volume = {10}, number = {}, pages = {24705470261425120}, pmid = {41782637}, issn = {2470-5470}, abstract = {INTRODUCTION: Psychiatric disorders have their genesis in early life. Standard screening approaches during well child visits for pathological infant distress, maternal depression, and dysfunctional parenting behaviors are likely inadequate. Microbiome measures and infant vocalizations have promise as scalable psychiatric biomarkers for infants. The purpose of this study was to examine associations among infant gut colonization based on microbiome measurements with maternal distress and maternal depressive symptoms in a sample of infants.<br><br>METHODS: This study sought to examine infant microbiome correlates of infant distress, parent-infant interactions, maternal distress, and maternal depressive symptoms. We collected (N&#x2009;=&#x2009;31) microbiome samples, infant vocalizations during vaccination, and behavioral measures during a 4 month well child visit (WCV) and did a battery of clinical assessments to assess for maternal depression, parent-child interactions, family characteristics and family stress. Whole-genome SHOTGUN sequencing was utilized to identify three types of associations: alpha-diversity using Shannon and Inverse-Simpson indexes, beta-diversity using Bray-Curtis and Jaccard distances, and differential abundance using LinDA. Spectral measures of infant cries were also modeled to assess potential relationships with clinical assessments and the microbiome.<br><br>RESULTS: There were 19 phyla, 417 genera, and 1246 species identified with taxonomic classification. Maternal distress as measured by PHQ-9 scores obtained when infants were 2 months old were associated with 4 bacterial species (Actinomyces johnsonii, Bilophila wadsworthia, Clostridium dakarense and Ruminococcus flavefaciens; FDR&#x2009;<&#x2009;0.1) and beta-diversity (p&#x2009;=&#x2009;0.006-BC; p&#x2009;=&#x2009;0.005-Jaccard). Infant cries with greater high frequency band power (p&#x2009;<&#x2009;0.03) and a greater high-to-mid frequency ratio-metrics (p&#x2009;<&#x2009;0.05) were associated with altered &#x3b1;-diversity of the microbiome. No correlations were present between maternal PHQ-9 at 4 months, PSI-IV and microbiome diversity.<br><br>CONCLUSION: The present findings suggest that an infant stress (assessed by quality of crying) is associated with lower microbiome diversity. Decreased diversity reflects an unhealthy microbiome. Parental depressive symptoms may also influence infant microbiome. Future interventional studies focused on the quality of the infant-caregiver relationship should examine related changes in intestinal microbiota.}, }
@article {pmid41782495, year = {2026}, author = {Loublier, C and Taminiau, B and Seidel, L and Moula, N and Tano, C and Cesarini, C and Costa, M and Lecoq, L and Daube, G and Amory, H}, title = {Survey on Faecal Microbiota Transplantation and Probiotic Use in Equine Practice in France and Belgium.}, journal = {Veterinary medicine and science}, volume = {12}, number = {2}, pages = {e70854}, pmid = {41782495}, issn = {2053-1095}, support = {40005849//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Belgium ; *Probiotics/therapeutic use ; Horses ; France ; Animals ; *Fecal Microbiota Transplantation/veterinary/statistics &amp; numerical data ; Cross-Sectional Studies ; *Horse Diseases/therapy ; *Veterinarians/statistics &amp; numerical data/psychology ; Female ; Male ; Surveys and Questionnaires ; Humans ; }, abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) and probiotics are used in equine practice. Understanding veterinarians' perceptions and practices is crucial for effective implementation.<br><br>OBJECTIVE: (1) Evaluate the prevalence, usage patterns and perceived effectiveness of probiotics and FMT among equine veterinarians in France and Belgium. (2) Assess their knowledge, practices and influencing factors across demographics and settings. (3) Explore links between FMT protocols and treatment satisfaction.<br><br>STUDY DESIGN: Cross-sectional survey.<br><br>METHODS: An online survey collected demographic data and responses on the use of probiotics and FMT. Analyses included descriptive statistics, chi-square tests and logistic regression models.<br><br>RESULTS: Ninety-six equine veterinarians participated, practicing in Belgium (52.1%), France (39.6%) or both (8.3%). Probiotic use was reported by 82.1%, more frequent in field than clinical practice (odds ratio [OR]&#xa0;=&#xa0;3.61, 95% CI [1.09, 12.02], p&#xa0;=&#xa0;0.036) and in France than Belgium (OR&#xa0;=&#xa0;5.08, 95% CI [1.44, 17.94], p&#xa0;=&#xa0;0.012). Probiotics were used for chronic diarrhoea (88.0%), acute diarrhoea (67.6%) and inflammatory bowel diseases (45.9%). Most veterinarians (83.3%) defined probiotics well, but 16.7% misidentified non-probiotic products. FMT was used by 76.0%, mainly occasionally and therapeutically, more in clinical than field practice (OR&#xa0;=&#xa0;4.79, 95% CI [1.03, 22.27], p&#xa0;=&#xa0;0.046). In theory, 58.3% prioritized infection-free donors, but only 22.5% tested donors before FMT, mostly using coprology (93.8%). Those who tested donors reported higher perceived efficacy (p&#xa0;=&#xa0;0.0029).<br><br>MAIN LIMITATIONS: Potential selection bias, as participation was voluntary. Generalizability might be limited by focus on France and Belgium. Sample size, while informative, should be expanded.<br><br>CONCLUSION: Probiotics and FMT were commonly used therapeutically by equine veterinarians in France and Belgium. Although probiotic use was widespread, some misunderstandings remained. FMT protocols varied, with donor faeces often untested. Treatment satisfaction was generally positive but estimated success rates varied. Standardized FMT protocols are needed to improve outcomes and consistency.}, }
@article {pmid41782409, year = {2026}, author = {Yang, J and Xiao, Y and Cui, J and Song, R and Ma, W and Liu, J and Miao, C and Sun, X and Kong, X and Zhang, ZS and Zhou, L and Yao, Z and Wang, Q}, title = {A 4-guanidinobutanoic acid-SLC36A1 axis drives a microbiota‒host feedback loop to regulate intestinal homeostasis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2639216}, doi = {10.1080/19490976.2026.2639216}, pmid = {41782409}, issn = {1949-0984}, abstract = {The role of gut microbiota‒derived metabolites in regulating the intestinal mucosal barrier remains poorly defined. Here, we identified 4-guanidinobutanoic acid (4-GBA), produced by Bacteroides stercorirosoris, as a critical regulator of intestinal homeostasis. Using untargeted metabolomics, organoid co-cultures, mouse models, and single-cell RNA sequencing, we demonstrated that 4-GBA enhances intestinal stem cells (ISCs) function and goblet cell differentiation. This promotes Akkermansia muciniphila enrichment through mucus-dependent niche expansion, establishing a microbiota‒host feedback loop. Mechanistically, 4-GBA upregulates the proton-coupled amino acid transporter SLC36A1 and activates the Hedgehog signaling pathway to drive epithelial reprogramming. Clinically, SLC36A1 expression inversely correlates with ulcerative colitis (UC) severity in human samples. Furthermore, the SLC36A1 agonist sarcosine enhances barrier homeostasis and attenuates colitis in mice, highlighting the diagnostic and therapeutic potential of this axis in UC. Our findings reveal a novel microbiome-host axis through which a microbial metabolite modulates epithelial function and microbial ecology, offering a potential therapeutic strategy targeting microbiota-epithelial crosstalk for UC management.}, }
@article {pmid41782343, year = {2026}, author = {Xu, Y and Xiao, J and Zhuang, Y and Gao, D and Jiang, W and Hou, G and Zhao, X and Li, S and Chen, T and Li, S and Zhang, S and Huang, Y and Liu, S and Yoon, I and Shi, W and Li, M and Wang, W and Li, S and Cao, Z}, title = {Performance, blood parameters, ruminal fermentation and microbial community of dairy cows supplemented with Saccharomyces cerevisiae fermentation product from dry-off to early lactation.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skag056}, pmid = {41782343}, issn = {1525-3163}, abstract = {Dairy cows experience oxidative stress, inflammation, and immune dysfunction during the transition from dry-off to early lactation. Postbiotics such as Saccharomyces cerevisiae fermentation product (SCFP), consisting of nonliving microorganisms with or without their components, have beneficial effects on the production efficiency and immune function of dairy cows. The objective of this study was to evaluate the effects of SCFP on milk production, milk composition, ruminal fermentation, blood metabolites, oxidative status, inflammatory responses, and the ruminal microbial community in Holstein dairy cows supplemented from the day of dry-off through early lactation. Two hundred cows were blocked on the basis of parity, BCS, milk yield and the time of dry-off, and were randomly allocated to specific treatment groups within each block. The treatments included the control group (CON, n = 100) receiving basal diets with no SCFP supplementation and the SCFP group (n = 100) receiving basal diets supplemented with 19 g/d of SCFP from d -60 to 60 relative to parturition. Milk yield-monitored for all 100 cows per treatment-was tracked until d 140 postpartum. In parallel, ruminal fluid, feces, milk, and blood samples were collected from a subset of cows (n = 20/treatment) during the treatment period for further analyses. Data were analyzed via the MIXED procedure in SAS (SAS Institute Inc.). The results revealed that the average milk yield of dairy cows in the SCFP group was greater than that in the CON group (43.93 vs. 42.08 kg/d, P = 0.04, n = 100) during the treatment period and remained greater (41.92 vs. 39.98 kg/d, P = 0.04, n = 100) throughout the 140 days postpartum recording period. Cows fed SCFP had significantly lower serum β-hydroxybutyrate and nonesterified fatty acid concentrations than did those in the CON group. Compared with the CON group, the SCFP group presented greater levels of superoxide dismutase and lower malonaldehyde concentrations. The SCFP group also presented a greater total antioxidant capacity prepartum and higher glutathione peroxidase levels postpartum. Additionally, the SCFP group had lower concentrations of proinflammatory factors, such as IL-1β, serum amyloid A, and haptoglobin, throughout the treatment period, indicating a stronger anti-inflammatory capability. Overall, SCFP supplementation improved the ruminal environment, reduced oxidative stress and the inflammatory status, and ultimately increased milk production.}, }
@article {pmid41782218, year = {2026}, author = {Li, L and Chen, M and Zhai, F and Li, Q}, title = {Foliar Silicon Nanoparticles Induce Coordinated Defense against Cadmium in Rice via Jasmonate-Mediated Metabolic Reprogramming.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c14175}, pmid = {41782218}, issn = {1520-5118}, abstract = {Foliar application of silicon nanoparticles (SiNPs) is a promising strategy for mitigating cadmium (Cd) contamination in rice; however, the systemic mechanisms remain poorly understood. Here, we reveal that foliar SiNPs activate a coordinated defense orchestrated by jasmonate (JA) signaling. 100 mg/L SiNPs reduced grain Cd by 66.58% and increased yield by 38.14%. Driven by this systemic regulation, the defense manifests in two dimensions: (1) internally, SiNP-activated JA signaling promoted Cd sequestration in leaf hemicellulose 2 fraction by 8.94% and regulated key transporter genes (upregulation of OsHMA3; downregulation of OsNramp1, OsZIP1, and OsZIP7); and (2) externally, this shoot-to-root signaling induced rhizosphere metabolic reprogramming (accumulation of secondary metabolites, lipids, and fatty acids) and recruited functional microbes (Desulfovibrio, Gallionellaceae, and Bacillus), resulting in a 17.02% reduction in bioavailable Cd via enriched oxygen-containing functional groups in soil. This work elucidates a novel biogeochemical framework for developing nanotechnology-based strategies for safe rice production in Cd-contaminated fields.}, }
@article {pmid41782168, year = {2026}, author = {Park, DE and Mohammadi, A and Nelson, SG and Salazar, JE and Bagherichimeh, S and Aziz, M and Onos, A and Villani, J and Fazel, A and Tevlin, E and Huibner, S and Tharao, W and Kaul, R and Liu, CM}, title = {Post-coital dynamics of the penile and cervico-vaginal genital microbiome.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02364-2}, pmid = {41782168}, issn = {2049-2618}, support = {PJT-156123 and TMI-138656/CAPMC/CIHR/Canada ; R01A123002-01A1/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The vaginal and penile coronal sulcus microbiome influence reproductive health outcomes and susceptibility to multiple sexually transmitted infections including HIV. There is evidence that genital bacteria are shared between heterosexual partners during sex, but the dynamics of this microbiota exchange remain poorly understood.<br><br>RESULTS: Using microbiome characterization from established heterosexual couples, we found that condomless penile-vaginal sex dramatically altered the coronal sulcus microbiome, with transient dominance by Lactobacillus spp. Conversely, condom-protected penile-vaginal sex did not result in significant shifts in overall composition (p&#x2009;=&#x2009;0.63). Significant changes were observed in the female partner's genital microbiome, including increased Corynebacterium spp. and increased abundance of Bacteria Associated with Seroconversion, Inflammation, and Cells (BASICs) (Prevotella bivia, Peptostreptococcus anaerobius, Dialister micraerophilus, Prevotella disiens, Dialister propionicifaciens, Dialister succinatiphilus) in individuals with a colonized male partner. By 72&#xa0;h post-coitus L. iners cell-normalized abundance remained elevated in the penile microbiome, but other taxa returned to baseline levels. Causal mediation analysis indicated a pH-mediated increase in vaginal Gardnerella at 72&#xa0;h.<br><br>CONCLUSIONS: Condom-protected penile-vaginal sex was associated with minimal genital microbiome changes, whereas condomless penile-vaginal sex among established couples led to extensive exchange of genital microbiota. Most disruptions to the microbiome resolved within 2-3&#xa0;days, although changes in vaginal pH were associated with longer-lasting increases in Gardnerella abundance. Video Abstract.}, }
@article {pmid41782027, year = {2026}, author = {Han, B and Li, X and Li, J and Liu, Y and Li, S and Tian, J and Lv, Z and Liu, D and Li, M and Ji, S and Lu, J and Zhang, Z}, title = {Spatial and cellular composition of lung fibrosis induced by multi-walled carbon nanotubes.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04135-5}, pmid = {41782027}, issn = {1477-3155}, support = {JJ2024ZL0127//Key Projects of the Joint Fund of Heilongjiang Provincial Natural Science Foundation/ ; 31972754//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The pulmonary immune system orchestrates lung homeostasis and protects against environmental insults through coordinated actions of immune and structural cells. Traditional Chinese medicine recognized the functional interaction between the lungs and the large intestine more than 2000 years ago, but direct evidence for this relationship in modern biomedical research remains limited. Although inhaled nanomaterials can induce lung fibrosis, the underlying immune mechanisms and their impact on large intestine remain poorly understood. Here, we integrated spatial transcriptomics, mRNA-seq, metabolomics, microbiome profiling, and validation in vitro to investigate how multi-walled carbon nanotubes (MWCNTs) exposure affects pulmonary immune responses and gut homeostasis in mice.<br><br>RESULTS: MWCNTs were administered to mice via oropharyngeal aspiration. We integrated spatial transcriptomics, bulk RNA sequencing, serum metabolomics, 16S rRNA microbiome profiling, and macrophage experiments in vitro. This multi-omics approach mapped pulmonary cellular alterations, identified key cell-cell signaling pathways, and examined downstream metabolic and intestinal changes provoked by MWCNTs. The results suggested that inhaled MWCNTs induced distinct spatial reorganization of pulmonary cellular architecture, characterized by macrophage- and fibroblast-enriched clusters associated with localized immune activation. Furthermore, cell-cell communication analysis identified Slamf7-Slamf7 interactions as key drivers of macrophage superactivation evidenced by excessive pro-inflammatory cytokine release. Notably, knockdown of Slamf7 in alveolar macrophages in vitro effectively attenuated the superactivation. The macrophage superactivation altered serum metabolic profiles, particularly in pathways related to energy metabolism and inflammation. Finally, lung injury extended to the distal intestine, where rectal epithelial barrier integrity was compromised, resulting in microbial and metabolic imbalance.<br><br>CONCLUSION: These findings highlight the hazardous potential of inhaled MWCNTs based on macrophage superactivation induced by Slamf7 in the lung, providing mechanistic evidence for the lung-gut link described in traditional Chinese medicine. Together, our results identify molecular targets to mitigate nanomaterial immunotoxicity and inform the design and using of safer, surface-engineered MWCNTs.}, }
@article {pmid41782023, year = {2026}, author = {Liu, J and Cao, J and Jia, L and Gan, Z and Zhao, X and Yang, A and Lai, S and Chen, F and Yang, YT and Zhao, XM}, title = {Impacts of host genetics on gut microbiome composition in Alzheimer's disease.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02342-8}, pmid = {41782023}, issn = {2049-2618}, support = {24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; 2023YFF1204800//National Key R&amp;D Program of China/ ; }, abstract = {BACKGROUND: Host-microbiome interactions play essential roles in the development of Alzheimer's disease (AD), yet the host genetic impacts on gut microbial alterations in AD remain poorly understood.<br><br>RESULTS: Here, we simultaneously profiled host genotype and gut microbiome in 252 Chinese individuals with varying degrees of cognitive disability. Using the latent Dirichlet allocation topic model, we identified the Anaerostipes-enriched enterosignature (ES-Ana) at the microbial subgroup level as significantly negatively associated with cognitive disability, which could be recapitulated in external cohorts. With the whole-genome sequencing data, we performed microbiome genome-wide association studies for the ES-Ana relative abundance. We prioritized 41 lead genetic variants and confirmed that the high ES-Ana relative abundance showed a negative correlation with the polygenic risk score of AD, indicating&#xa0;its protective effect against AD. Furthermore, we identified 174 ES-Ana-associated genes, which&#xa0;are&#xa0;enriched in AD-related biological functions and phenotypes, and exhibite pervasive underexpression in glial cells during brain aging.<br><br>CONCLUSIONS: In summary, our study reveals the complex genetic effects on the gut microbiota in AD, and provides novel evidence for the roles of the gut-brain axis in AD. Video Abstract.}, }
@article {pmid41782011, year = {2026}, author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J}, title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02368-y}, pmid = {41782011}, issn = {2049-2618}, support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.<br><br>RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.<br><br>CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.}, }
@article {pmid41781966, year = {2026}, author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X}, title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.}, journal = {Journal of nanobiotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12951-026-04231-6}, pmid = {41781966}, issn = {1477-3155}, support = {32272514//National Natural Science Foundation of China/ ; }, abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.}, }
@article {pmid41781883, year = {2026}, author = {Xie, Y and Wang, R and Liu, X and Du, Q and Mo, S and Liu, Q and Yang, G and Fan, Z and Li, J}, title = {Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04902-2}, pmid = {41781883}, issn = {1471-2180}, support = {32171607//National Natural Science Foundation of China/ ; }, }
@article {pmid41781872, year = {2026}, author = {Tian, N and Liu, M and Zhao, Y and Lian, Y and Jin, M and Yang, F}, title = {Gut microbiota dysbiosis and metabolic reprogramming in pediatric migraine: a multi-omics analysis revealing diagnostic biomarkers.}, journal = {The journal of headache and pain}, volume = {}, number = {}, pages = {}, doi = {10.1186/s10194-026-02315-0}, pmid = {41781872}, issn = {1129-2377}, support = {2022 Budget Approval No. 180 of Hebei Provincial Department of Finance//Provincial Medical Outstanding Talents Project funded by the Provincial Government in 2022/ ; Grant No. 20260868//Hebei Provincial Medical Science Research Project funded by the Health Commission of Hebei Province/ ; 2026 Hebei Provincial Introduction of Foreign Intelligence Project//Hebei Provincial Department of Science and Technology/ ; }, }
@article {pmid41781852, year = {2026}, author = {Eldridge, N and Spörri, L and Kreuzer, M and Haldimann, G and Zinkernagel, MS and Zysset-Burri, DC}, title = {Uncovering the relationship between the human ocular surface microbiome and gut microbiome.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04878-z}, pmid = {41781852}, issn = {1471-2180}, support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique F&#xe9;d&#xe9;rale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique F&#xe9;d&#xe9;rale de Lausanne), Lausanne, Switzerland/ ; }, }
@article {pmid41781851, year = {2026}, author = {Mougeot, JC and Beckman, MF and Henry, AA and Lalla, RV and Brennan, MT and Mougeot, FB}, title = {Oral dryness related symptoms in radiation-treated head and neck cancer patients: a pilot study of oral microbiome composition and function.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04885-0}, pmid = {41781851}, issn = {1471-2180}, }
@article {pmid41781692, year = {2026}, author = {Kim, H and Oh, S and Hong, JS and Kang, MS and Lee, HJ and Park, KU}, title = {Exploratory randomized trial of Weissella cibaria CMU and oral microbiome changes in peri implant mucositis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42961-7}, pmid = {41781692}, issn = {2045-2322}, support = {02-2022-0019//Seoul National University Bundang Hospital/ ; NRF-2023R1A2C2002783//National Research Foundation of Korea/ ; }, }
@article {pmid41781556, year = {2026}, author = {Le Bras, A}, title = {Breath as a marker of gut microbiome health.}, journal = {Lab animal}, volume = {55}, number = {3}, pages = {71}, doi = {10.1038/s41684-026-01705-w}, pmid = {41781556}, issn = {1548-4475}, }
@article {pmid41781471, year = {2026}, author = {Degraeve, AL and Cutignano, A and Piscitelli, F and Villano, R and De Simone, G and Verde, R and Thibaut, MM and Bindels, LB and Di Marzo, V}, title = {Changes in levels of endocannabinoidome mediators in mice with cancer cachexia: links with steatosis and gut microbial dysbiosis.}, journal = {BJC reports}, volume = {4}, number = {1}, pages = {}, pmid = {41781471}, issn = {2731-9377}, support = {F.R.S.-FNRS, MIS F.4512.20, 40009849//FNRS and the Walloon Region in the context of the funding of the strategic axis FRFS-WELBIO/ ; }, abstract = {BACKGROUND: Cachexia is a debilitating syndrome associated with involuntary weight loss, often occurring in cancer patients. In both humans and animal models, alterations in endocannabinoid (eCB) signaling occur in association with both metabolic disorders and several types of tumors. The wider signaling system, including the two eCBs, anandamide (AEA) and 2-arachidonoyl-glycerol (2-AG), their congeners and other long chain fatty acid amides, as well as their metabolic enzymes and receptors, is known as endocannabinoidome (eCBome). The eCBome is involved, among others, in the control of energy balance and cancer and interacts with the gut microbiome.<br><br>METHODS: Using mass spectrometry-based targeted lipidomics, we measured the hepatic and intestinal concentrations of eCBome mediators in mice injected with colon carcinoma 26 (C26) cells, a model of cancer cachexia characterized, among others, by weight loss, hepatic dyslipidemia, and gut microbiome dysbiosis.<br><br>RESULTS: We report that, 10 days after C26 cell injection, concomitant with >10% weight loss, eCBome lipids levels, namely 2-AG, AEA, and some of its N-acyl-ethanolamine congeners, as well as N-oleoyl-glycine, N-acyl-serotonins, and N-acyl-taurines (NATs), are altered in intestinal sections and the liver of C26 mice (e.g., hepatic 2-AG -30%, jejunal 2-AG&#x2009;+&#x2009;30%, jejunal AEA -55%, hepatic N-oleoyl-ethanolamine (OEA)&#x2009;+&#x2009;223%, hepatic NATs +144%, +141%, +216%). Gut dysbiosis was evident in these mice (PERMANOVA at the family level: R&#xb2;&#x2009;=&#x2009;69%, p&#x2009;<&#x2009;0.001), with altered levels in 3 phyla (mainly the Proteobacteria, +1484%), 12 families, and 12 genera (all with adjusted p&#x2009;<&#x2009;0.05). Additionally, 2-AG, AEA, OEA, N-arachidonoyl-serotonin, and NAT levels in the liver positively correlated with hepatic total lipids, triglycerides, and cholesterol, whereas N-docosahexaenoyl-ethanolamine and N-docosahexaenoyl-serotonin showed negative correlations. Jejunal AEA negatively, and hepatic OEA and NATs positively, correlated with weight loss. Intestinal eCBome mediators correlated with several cecal microbial taxa, including genera known to include strains beneficial in metabolic disorders, such as Bacteroides, Parabacteroides, Dysosmobacter, and Prevotella.<br><br>CONCLUSIONS: These observations pinpoint eCBome mediators as new multi-functional players in the hepatic complications and gut dysbiosis accompanying cancer cachexia.}, }
@article {pmid41781451, year = {2026}, author = {Martins, B and Martins, J and Castelo-Branco, M and Gonçalves, J}, title = {Sex-dependent dysregulation of the gut-brain NPYergic system in a mouse model of autism spectrum disorder.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-42601-0}, pmid = {41781451}, issn = {2045-2322}, support = {UI/BD/150837/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; FCT/UIDP&amp;B/04950/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.01066.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {The microbiome-gut-brain axis has been increasingly recognized for its role in the pathophysiology of autism spectrum disorder (ASD), yet the underlying molecular mechanisms remain poorly understood. Neuropeptide Y (NPY), a key modulator of gut-brain communication, may play a pivotal role in this axis. This study investigated the sex-specific molecular profile of the NPY system in gut-brain communication via a genetic mouse model of ASD, the Nf1[+/-] mice. Quantitative real-time PCR was performed to assess the expression of NPY and its receptor transcripts in the amygdala, hippocampus, prefrontal cortex and intestinal tissue of juvenile male and female Nf1[+/-] mice. Additionally, gut microbiota analysis focused on Lactobacillus species in stool samples. Special emphasis was placed on sex differences, an area underexplored in ASD research. Sex-specific differences in NPY and its receptor expression were observed in both the brain and intestinal tissues of Nf1[+/-] mice. In mutant females, estrous cycle fluctuations were partly associated with changes in the NPY system. Notably, distinct correlations between the brain and intestinal NPY systems were identified in both sexes of wild-type (WT) and Nf1[+/-] mice. Microbiota analysis revealed sex-dependent alterations in Lactobacillus abundance, which correlated with the intestinal NPY system. Importantly, the Y2 receptor exhibited sex-specific expression patterns in both the gut and brain of Nf1[+/-] mice. This study provides novel evidence that the NPY system may play a critical role in gut-brain communication in ASD, with sex-dependent alterations in both the brain and gut. The intestinal Y2 receptor has emerged as a potential molecular biomarker for ASD, underscoring the importance of incorporating sex as a biological variable in future ASD research.}, }
@article {pmid41781334, year = {2026}, author = {Duan, Y and Huang, M and Ye, L and Ma, L and Wu, Y and Du, Y and Liu, J and Song, F and Tian, L and Cai, W and Li, H and Zhou, X and Luo, S}, title = {Dynamic A-to-I RNA editing in response to gut microbiome in honey bees.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280291.124}, pmid = {41781334}, issn = {1549-5469}, abstract = {ADAR-mediated adenosine-to-inosine (A-to-I) mRNA editing contributes to the proteomic diversity and behavioral complexity of animals. While recent studies indicate that the gut microbiome influences various aspects of animal behavior, the potential involvement of RNA editing in gut-brain interactions remains unexplored. Comparative transcriptomic analyses were performed between heads of germ-free (GF) versus conventional (CV) honey bees. A total of 1,528 A-to-I editing sites are identified in honey bee heads, among which nonsynonymous editing sites are overrepresented compared to random expectation. Overall editing levels are significantly downregulated in GF compared with CV, but Adar gene is not differentially expressed. However, Adar p.482 Ile>Met auto-recoding site, which is speculated to modulate Adar activity, is identified as a high-confidence differential editing site (DES) with decreased editing level in GF. Quantification of gut microbiota across 12 CV individuals reveals a significant positive correlation between p.482 Ile>Met editing level and Lactobacillus and Bombilactobacillus abundance. Colonization of a single bacterium Lactobacillus or Bombilactobacillus instead of Gilliamella in GF bees successfully restores the Adar p.482 Ile>Met and the global editing level. Our work demonstrates the complex and dynamic transcriptomic diversity exerted by A-to-I RNA editing, and discovers the axis of gut-Lactobacillus/Bombilactobacillus-brain-Adar-global RNA editing, providing an exciting scenario that gut microbiomes could impact RNA editing which might further facilitate phenotypic plasticity of social insects.}, }
@article {pmid41781219, year = {2026}, author = {T Pallenberg, S and Zamarrón de Lucas, E and Párniczky, A and Lopes de Bragança, R}, title = {Cystic fibrosis year in review 2025.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.02.010}, pmid = {41781219}, issn = {1873-5010}, abstract = {Cystic fibrosis (CF) is being reshaped by CFTR modulators (CFTRm), yet infection, inflammation, and multisystem comorbidities persist. This review of the 2025 CF literature summarizes how CF is evolving into a chronic, heterogeneous condition in the modulator era. First, we discuss the consolidation of elexacaftor/tezacaftor/ivacaftor (ETI) and next-generation modulators, highlighting durable gains in lung function and survival alongside persistent gaps in eligibility, access, and long-term safety, particularly for individuals with advanced structural lung damage or class I variants. Second, emerging mutation-agnostic therapy strategies are outlined, including ENaC blockade, neutrophil-directed anti-inflammatories like brensocatib, and gene and nucleic acid-based therapeutic approaches . Third, we examine airway infection and inflammation: while ETI reduces pathogen detection and systemic inflammatory markers, chronic Pseudomonas aeruginosa and heterogeneous neutrophilic endotypes frequently persist, and mucosal immune defects remain incompletely corrected. In this context, bacteriophage therapy has emerged as a candidate for multidrug-resistant infections, while microbiome-focused interventions show limited clinical impact despite clear shifts in microbial communities. Finally, as survival improves, pregnancy, age-related malignancy, and cardiovascular disease are becoming increasingly relevant, necessitating new models of multidisciplinary, lifespan care. Collectively, these developments mark a shift towards equitable, lifelong, system-level management of health in an aging and increasingly diverse CF population.}, }
@article {pmid41781021, year = {2026}, author = {Hume-Nixon, M and Clark, S and Ratu, T and Nguyen, C and Neal, EFG and Bright, K and Strobel, AG and Watts, E and Hart, J and Fong, JJ and Rafai, E and Sakumeni, K and Steer, A and Vereti, I and Russell, F}, title = {The efficacy of a single dose of oral azithromycin in labour to prevent infections in infants and birthing parents in Fiji: secondary outcomes from a randomised controlled trial.}, journal = {BMJ global health}, volume = {11}, number = {3}, pages = {}, doi = {10.1136/bmjgh-2025-019851}, pmid = {41781021}, issn = {2059-7908}, mesh = {Humans ; *Azithromycin/administration &amp; dosage/therapeutic use ; Female ; Pregnancy ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Fiji/epidemiology ; Adult ; Administration, Oral ; Infant ; Infant, Newborn ; Labor, Obstetric ; *Soft Tissue Infections/prevention &amp; control/epidemiology ; Male ; Young Adult ; }, abstract = {INTRODUCTION: Our Bulabula MaPei trial of azithromycin administered during labour in Fiji found no evidence of a reduction in the primary endpoint of infant skin and soft tissue infections (SSTIs) at 3 months of age. Here, we determine the efficacy of this intervention on several secondary outcomes.<br><br>METHODS: This randomised controlled trial included healthy pregnant adults presenting to hospital in labour. Prior to delivery, participants were randomly assigned a single dose of 2&#x2009;g of oral azithromycin or placebo that were identical in appearance to mask treatment allocation, in a 1:1 ratio stratified by ethnicity. Cumulative incidence of infections and antibiotic prescription was compared using an intention-to-treat analysis of complete cases. Adverse events described as proportions by group at specified time points.<br><br>RESULTS: From June 2019 to January 2022, we enrolled 2110 pregnant people and their infants (n=2122; azithromycin n=1059; placebo n=1063). At 3&#x2009;months, the cumulative incidence of infant infections was 13.6% in the azithromycin group compared with 17.3% in the placebo group (risk ratio (RR) 0.79; 95%&#x2009;CI 0.63 to 0.99; p=0.038). Infections among birthing parents, including SSTIs, were reduced with the greatest effect 1&#x2009;week postdelivery (infections: RR 0.31; 95%&#x2009;CI 0.13 to 0.71; p=0.006, SSTIs: RR 0.25; 95%&#x2009;CI 0.08 to 0.75; p=0.013) but with a diminishing effect up to 6&#x2009;months postdelivery. There was no effect on the prescription of antibiotics at any time point.<br><br>CONCLUSIONS: Intrapartum azithromycin prevents a variety of infections for birthing parents and infants up to 12 months post partum in Fiji. However, further research is required to identify target populations and better characterise potential impacts on antimicrobial resistance and the infant microbiome and resistome.<br><br>TRIAL REGISTRATION NUMBER: NCT03925480.}, }
@article {pmid41780872, year = {2026}, author = {Vencek Enriquez, M and Waite-Cusic, J}, title = {Evaluation of bioprotective starter culture and aging temperature on gas formation by Paucilactobacillus wasatchensis in Gouda cheese using computed tomography imaging.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27847}, pmid = {41780872}, issn = {1525-3198}, abstract = {Late gas defects caused by nonstarter lactic acid bacteria (NSLAB) present significant economic and quality challenges in semi-hard aged cheeses. Finding practical mitigation strategies to defend against gas-producing NSLAB is important to reduce the economic impact of this defect. Paucilactobacillus wasatchensis is one species of NSLAB associated with late gas defects in Cheddar; however, little is known about its behavior in other semi-hard cheeses. This study investigated the behavior of Pa. wasatchensis in Gouda cheese and explored aging temperature and the use of bioprotective (nisin-producing) cultures to mitigate gas production. Gouda cheese was produced either using conventional or nisin-producing bioprotective starter culture with and without inoculation with Pa. wasatchensis SK0033 into the cheese milk (4 log cfu/mL). All treatment combinations of starter culture and inoculation status were replicated on 2 unique production days. Wheels (n = 4) from each production were randomized for aging at 4°C, 10°C, or 15°C for up to 40 wk. Computed tomography scanning was used as a novel, nondestructive method to observe gas formation and imaging analysis was used to quantify of gas volume within cheese wheels (n = 3/cheese make) throughout aging. Microbiome analysis was performed on selected cheese wheels at the end of aging. The fourth wheel for each treatment was used for intermittent sampling for destructive testing (i.e., pH, water activity, moisture, salt). The highest volume of gas was produced by Pa. wasatchensis in cheese made with the conventional starter at aged at 15°C. Gas volume in these wheels ranged from as low as 0.02% (0.5 wk) to as high as 2.54% (39 wk), which increased over the aging period. Considerable variability in gas volume between wheels from the same cheese make was observed which aligns with industry reports of defect variability at commercial scale. Reduced aging temperature (4°C) delayed but did not prevent gas production caused by Pa. wasatchensis during aging; growth of Pa. wasatchensis at all aging temperatures was confirmed by microbiome analysis. The replacement of the conventional starter with a nisin-producing bioprotective starter effectively prevented growth and gas formation caused by Pa. wasatchensis at all aging temperatures. The presence of nisin in the cheese made with bioprotective starter was confirmed to be active against Pa. wasatchensis using the soft agar overlay method. These findings illustrated the ability of Pa. wasatchensis to cause late gas defects in Gouda and demonstrated the efficacy of a bioprotective starter culture to mitigate this defect.}, }
@article {pmid41780827, year = {2026}, author = {Austin, RR and Fiszman, M and Guerra, E and Zhang, R and Kilicoglu, H}, title = {Advancing Whole-Person Health through Informatics: A Narrative Review of Knowledge Resources for Complementary and Integrative Health.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101461}, doi = {10.1016/j.tjnut.2026.101461}, pmid = {41780827}, issn = {1541-6100}, abstract = {OBJECTIVE: Complementary and integrative health (CIH) interventions, including nutritional strategies, are widely used to support whole-person health, yet evidence on their efficacy, safety, and mechanisms remains fragmented. This narrative review maps existing CIH knowledge resources, identifies critical gaps, and highlights challenges in interoperability and integration. We propose artificial intelligence-driven informatics strategies to standardize, connect, and leverage these resources, with the goal of advancing discovery, precision nutrition, and personalized approaches to health and well-being.<br><br>MATERIALS AND METHODS: We conducted a narrative review of publicly available knowledge resources on complementary health interventions, focusing on their effectiveness, safety, and biological mechanisms, including the microbiome. Interventions were categorized as nutritional, physical, or psychological. Resources were then classified as knowledge bases, datasets, databases, ontologies, knowledge graphs, platforms, or initiatives, with summaries of their scope, functionality, and contributions.<br><br>RESULTS: We identified 47 resources that can support complementary and integrative health informatics (15 knowledge bases, 13 databases, 7 datasets, 4 platforms, 3 initiatives, 3 ontologies, 2 knowledge graphs). Categories included nutritional interventions (32, with 13 on the microbiome), physical interventions (4), psychological interventions (3), and comprehensive or multi-modal resources (7). Most resources (39) were publicly available.<br><br>CONCLUSION: Advancing whole-person health requires greater standardization and integration of knowledge resources, which in turn enables more effective application of AI and informatics methods. When well-structured, interoperable resources are coupled with these computational methods, they can unify diverse knowledge domains, advance the science of complementary and integrative health, and accelerate discovery in personalized nutrition.}, }
@article {pmid41780804, year = {2026}, author = {Rotzetter, J and Spörri, L and Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC}, title = {A preliminary investigation on the influence of sample storage on the low-abundant ocular surface microbiome.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107437}, doi = {10.1016/j.mimet.2026.107437}, pmid = {41780804}, issn = {1872-8359}, abstract = {In this study, the impact of sample freezing prior to DNA extraction was investigated on a small sample set (n = 6) to determine whether this affects the composition of the ocular surface microbiome - a low biomass environment. Frozen samples exhibited a reduced detection of Gram-negative bacteria compared to directly processed samples.}, }
@article {pmid41780644, year = {2026}, author = {Basilicata, MG and Scisciola, L and Pesapane, A and Fontanella, RA and Balzano, N and Maddalena Palazzo, AM and Joshi, R and Zia, A and Tortorella, G and Ulfat, Z and Arshad, M and Aquino, G and Sommella, E and Malavolta, M and Giuliani, A and Campiglia, P and Barbieri, M and Paolisso, G}, title = {Volatilomics insights in older adults with diabetes: from metabolic mechanisms to precision geriatric medicine.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113194}, doi = {10.1016/j.diabres.2026.113194}, pmid = {41780644}, issn = {1872-8227}, abstract = {AIMS: This review aims to evaluate the hypothesis that Volatilomics-the comprehensive analysis of volatile organic compounds (VOCs) from breath, skin, urine, and other biological matrices-can serve as a non-invasive tool to characterize metabolic alterations associated with aging and diabetes mellitus in older adults, supporting precision geriatric medicine.<br><br>METHODS: We conducted a narrative review of experimental and clinical studies investigating VOC signatures in aging individuals with diabetes. The analysis focused on associations between VOC profiles and key biological mechanisms, including oxidative stress, lipid peroxidation, mitochondrial dysfunction, inflammaging, and host-microbiome interactions. We also examined analytical technologies and methodologies, such as advanced mass spectrometry platforms, sensor-based devices, and artificial intelligence-driven pattern recognition approaches.<br><br>RESULTS: The reviewed evidence suggests that diabetes is associated with distinctive VOC patterns; however, direct evidence specifically derived from geriatric cohorts remains limited. These VOC patterns are associated with glycemic imbalance and age-related metabolic dysfunction and show potential utility for early detection, clinical phenotyping, and individualized monitoring, particularly in frail or multimorbid patients. Technological advances are facilitating translation toward portable and home-based applications.<br><br>CONCLUSIONS: Volatilomics represents a promising, non-invasive approach to improve diabetes management in aging populations. Despite its potential, challenges remain, including methodological heterogeneity, limited reproducibility, confounding effects of comorbidities and polypharmacy, and the lack of large longitudinal geriatric cohorts.}, }
@article {pmid41780449, year = {2026}, author = {Wang, J and Zhang, Y and Ding, Y and Li, D and Zhang, Y}, title = {Hydrocarbon subsidy-stress and divergent reduced iron-manganese thresholds shape microbial resilience in anoxic aquifers.}, journal = {Water research}, volume = {296}, number = {}, pages = {125670}, doi = {10.1016/j.watres.2026.125670}, pmid = {41780449}, issn = {1879-2448}, abstract = {The co-occurrence of geogenic metal mobilization and anthropogenic hydrocarbon contamination represents a pervasive hydro-biogeochemical challenge, yet the non-linear mechanisms governing microbial resilience in these multi-stressor aquifers remain poorly constrained. Here, we decode these complex interactions by integrating high-resolution microbiome profiling with an interpretable machine learning framework (XGBoost-SHAP). We identify a "multi-threshold superposition" model for total petroleum hydrocarbons (TPHs) that delineates a tri-phasic ecological transition: a progression from carbon limitation to metabolic subsidization, culminating in a toxicity-driven regime shift beyond a mechanistically grounded tipping point (3.485 mg/L). Crucially, we unveil a "Fe(II)-Mn(II) Paradox" wherein geochemically similar metals exert divergent ecological controls. Deviating from the additive toxicity paradigm, elevated Fe(II) (>9.22 mg/L) serves as a redox-mediated buffer against hydrocarbon stress; in contrast, Mn(II) operates as a toxicological synergist, amplifying metabolic and structural impairments beyond predicted additive levels. Mechanistically, this resilience is underpinned by the rare taxa acting as a functional seed bank, which reconfigures network topology from competitive exclusion to cooperative syntrophy. These findings establish the stoichiometric Fe(II)/Mn(II) ratio (threshold: 1.935) as a master regulator of aquifer, providing a quantitative foundation for "precision zoned intervention" strategies-advocating for monitored natural attenuation in iron-buffered zones versus active engineering in manganese-aggravated hotspots.}, }
@article {pmid41780267, year = {2026}, author = {Zhou, Y and González, CA and Manquian, J and Vergara, K and Gajardo, G and Guzmán, L and Espinoza-González, O and Carbonell, P and Riquelme, C and Ueki, S and Nagai, S and Fujiyoshi, S and Maruyama, F and Yarimizu, K and Uhanie Perera, I and Acuña, JJ and Zhang, Q and Jorquera, MA}, title = {Microbial communities in coastal seawater during Heterosigma akashiwo and Alexandrium catenella blooms in Chilean Patagonian fjords.}, journal = {Marine environmental research}, volume = {217}, number = {}, pages = {107949}, doi = {10.1016/j.marenvres.2026.107949}, pmid = {41780267}, issn = {1879-0291}, abstract = {Harmful algal blooms (HABs) are recurring events in Chilean coasts where free-living and associated microbiota (also known as HAB holobiont) may play a crucial role for occurrence, monitoring and prediction of HAB. Here, we investigated the associated microbial communities with Heterosigma akashiwo and Alexandrium catenella blooms in the Chilean Patagonia fjords by microscopic observations and rRNA metabarcoding sequencing. By microscopic observations, H. akashiwo and A. catenella cells were accompanied by abundant diatoms (Skeletonema) and athecate dinoflagellates, and diatoms (Thalassiosira and Leptocylindrus) and dinoflagellates (Heterocapsa), respectively. By 16S rRNA- and 18S rRNA-based metabarcoding sequencing, our results not only revealed significant differences in richness, diversity, and taxonomic structure of microbial communities between blooms but also between the studied seawater fractions (1 and 0.2 μm). In 18S rRNA-based communities, H. akashiwo bloom was generally dominated by eukaryotic Stramenopiles, Raphidophyceae_X and Heterosigma, while A. catenella bloom was dominated by eukaryotic Alveolata and protists Syndiniales (Dino-Group-I) at the phylum, order, and genus level, respectively. Proteobacteria (Rhodobacteriales), Bacteroidota (Flavobacteriales) and Cyanobacteria (Synechococcales) were dominant taxa in the structure of 16S rRNA-based communities in both blooms and both seawater fractions. Our study also suggested a high and differentiated interaction between 16S rRNA- and 18S rRNA-based microbial communities in both blooms, with the bacteria Blastopirellula and the dinoflagellate Dino-Group-I-Clade-1 as keystone taxa in A. catenella bloom.}, }
@article {pmid41779349, year = {2026}, author = {González-González, A and Soria-Utrilla, V and Fontalba-Romero, MI and Núñez-Sánchez, M&#xc1; and Adarve-Castro, A and Queipo-Ortuño, MI and Ramos-Molina, B and Martínez-Montoro, JI and Fernández-García, JC}, title = {The Role of Butyrate in People with Metabolic Dysfunction-Associated Steatotic Liver Disease and Related Metabolic Comorbidities: A Systematic Review.}, journal = {Current obesity reports}, volume = {15}, number = {1}, pages = {}, pmid = {41779349}, issn = {2162-4968}, abstract = {BACKGROUND: Metabolic dysfunction–associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide and is strongly linked to obesity, type 2 diabetes, and cardiovascular disease. Growing evidence highlights the role of the gut–liver axis, particularly microbial metabolites such as the short-chain fatty acid (SCFA) butyrate, in MASLD pathophysiology. However, clinical data on butyrate levels and the abundance of butyrate-producing bacteria in MASLD patients remain inconsistent.<br><br>OBJECTIVES: To systematically synthesize human evidence evaluating the associations between butyrate levels and butyrate-producing gut bacteria with MASLD presence and severity, as well as related metabolic comorbidities.<br><br>METHODS: A systematic search was conducted in PubMed and Embase from inception to April 7, 2025, following PRISMA 2020 guidelines (PROSPERO registration CRD420251162439). Eligible studies included observational human research assessing fecal or plasma SCFA concentrations and/or the abundance of butyrate-producing taxa in adults with MASLD and related metabolic disorders. Study quality was appraised using the Newcastle&#x2013;Ottawa Scale, and results were narratively synthesized due to heterogeneity across methods and outcomes.<br><br>RESULTS: From 233 records, seven studies met inclusion criteria (2020&#x2013;2025; n&#x2009;=&#x2009;1,185). Most were cross-sectional or case&#x2013;control designs of moderate to high quality (NOS 6&#x2013;8/9). Individuals with MASLD generally exhibited lower fecal or serum butyrate concentrations and reduced abundance of Faecalibacterium prausnitzii, Eubacterium, and other butyrate-producing bacteria versus controls. These alterations were associated with hepatic steatosis, fibrosis, inflammation, and adverse metabolic profiles - higher BMI, insulin resistance, and dyslipidemia. Geographic and sex-related differences were also reported.<br><br>CONCLUSIONS: This systematic review suggests that reduced butyrate availability and alterations in butyrate-producing gut taxa are associated with MASLD presence and severity and with adverse metabolic traits. However, substantial methodological heterogeneity and the observational design of available studies preclude causal inference. Larger, well-phenotyped, multicentre studies using standardized SCFA quantification, dietary and medication ascertainment, and functional microbiome profiling are needed to validate these findings and clarify their diagnostic and therapeutic implications.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13679-026-00694-8.}, }
@article {pmid41779338, year = {2026}, author = {Ringold, SM and Cermak, SA and Labus, JS and Mayer, EA and Aziz-Zadeh, L}, title = {Sensory Over-Responsivity in Autism: A Bidirectional Brain-Gut-Microbiome Model.}, journal = {Journal of autism and developmental disorders}, volume = {}, number = {}, pages = {}, pmid = {41779338}, issn = {1573-3432}, }
@article {pmid41779301, year = {2026}, author = {Cheah, AS and Tan, JW and Jaafar, F and Yeo, WWY}, title = {Precision Microbiome Modulation: Exploring Lactobacillus spp. as A Targeted Strategy for Type 2 Diabetes Management.}, journal = {Current nutrition reports}, volume = {15}, number = {1}, pages = {}, pmid = {41779301}, issn = {2161-3311}, abstract = {PURPOSE OF REVIEW: The International Diabetes Federation projects a prevalence of 783.2 million cases of type 2 diabetes mellitus (T2DM) by 2045. The escalation in healthcare expenditure and adverse effects of current drugs necessitate a clinically effective and low-cost alternative therapeutic option with minimal health complications. Lactobacillus spp., a well-studied gut probiotic has shown promising antidiabetic effects against T2DM in several randomized controlled trials. However, the exact mechanisms of Lactobacillus spp. in regulating the glycaemic profile are not well elucidated, limiting the optimization of probiotic-based interventions. Therefore, this paper aims to explore the various antidiabetic mechanisms of Lactobacillus spp., with a focus on their integration into precision medicine approaches.<br><br>RECENT FINDINGS: Lactobacillus spp. supplementation alleviates insulin resistance in T2DM by modulating glucose metabolism and transport, exerting anti-inflammatory and anti-oxidative effects as well as restructuring gut microbiota. Lactobacillus spp. also enhance the functional properties of food by increasing the antioxidant capacity and improving glucose metabolism. Despite these promising effects, clinical translation is challenged by strain-specific survivability in the gastrointestinal tract and safety concerns. Thus, leveraging precision medicine via tailoring treatments based on individual microbiome profiles, genetic backgrounds and metabolic phenotype may unravel the full therapeutic potential of targeted Lactobacillus spp. for T2DM treatment. This approach can be reached by integrating multi-omics profiling and artificial intelligence technologies.<br><br>SUMMARY: Lactobacillus spp. may act as adjunctive support in the management T2DM rather than stand-alone therapies in T2DM management, as their efficacy is dependent on appropriate dietary interventions and metabolic context. Altogether, integrating Lactobacillus spp. into personalized treatment frameworks offers a promising avenue for developing more targeted, effective and safe interventions for T2DM.}, }
@article {pmid41779254, year = {2026}, author = {Stefanelli, LF and Cattarin, L and Martino, FK and Del Prete, D and Pierantonio, B and Nalesso, F and Mazzitelli, M}, title = {Microbiome alterations and their potential impact on infection risk in chronic kidney disease and end-stage kidney disease: a narrative review.}, journal = {International urology and nephrology}, volume = {}, number = {}, pages = {}, pmid = {41779254}, issn = {1573-2584}, abstract = {Chronic kidney disease [CKD] is associated with profound alterations of both gut microbiota composition and functions, commonly referred to as gut dysbiosis. These changes are driven by several factors such as dietary restrictions, medications, and uremia, which further contribute to patients with CKD to their pro-inflammatory and immunocompromised state. Recent evidence suggests that dysbiosis may also increase susceptibility to infections, which remain a leading cause of morbidity and mortality in CKD patients. In this review, we aimed at examining the features of the altered gut microbiome in patients with CKD, its potential role in promoting infection risk, and current therapeutic strategies targeting the gut microbiota to mitigate CKD-related complications.}, }
@article {pmid41778788, year = {2026}, author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N}, title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0097125}, doi = {10.1128/spectrum.00971-25}, pmid = {41778788}, issn = {2165-0497}, abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.}, }
@article {pmid41778780, year = {2026}, author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S}, title = {Beyond bacilli: integrating the microbiome into the TB research agenda.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638004}, pmid = {41778780}, issn = {1949-0984}, mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; }, abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.}, }
@article {pmid41778628, year = {2026}, author = {Wang, E and Yan, H and Kong, Z and Xu, X and Zhang, B}, title = {Gamma irradiation and heat exposure generate temperature-responsive microbiota shifts in predatory mite Phytoseiulus persimilis (Mesostigmata: Phytoseiidae).}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toag016}, pmid = {41778628}, issn = {1938-291X}, support = {6222052//Beijing Natural Science Foundation/ ; 32070402//National Natural Science Foundation of China/ ; BAIC01-2026//Beijing Innovation Consortium of Agriculture Research System/ ; }, abstract = {The growing urgency of climate change, particularly the rising frequency and severity of extreme heat events, has spotlighted the need for the thermal resilience of natural enemy in pest management. To understand the plasticity of predatory mite in response to thermal adaptation, 3 irradiated strains of Phytoseiulus persimilis Athias-Henriot were induced by Cobalt-60 gamma rays to evaluate the thermotolerance. We integrated both DNA- and RNA-based 16S rRNA gene sequencing to explore whether irradiation and heat stress could impact the microbiome of the predatory mites. Our findings revealed that irradiation enhanced the heat tolerance of predatory mites without compromising fecundity or predation efficiency. Unexpectedly, irradiation had minimal impacts on overall microbial diversity, whereas RNA-based 16S rRNA gene sequencing unveiled irradiation strain-specific enrichment of stress-responsive taxa (e.g., Bacillus sp.), while no such specific enrichment was observed at the DNA level. Furthermore, heat stress significantly restructured the microbiome of P. persimilis, particularly enriching Limnobacter thiooxidans. Methodologically, the DNA/RNA microbial profiles highlighted divergent functional partitioning: Gammaproteobacteria dominated at DNA level, while transcriptionally active Actinobacteria prevailed in RNA level. In conclusion, these results establish a "host-microbiota co-regulation" paradigm for resistance breeding, offering a sustainable pathway to reinforce biological control systems against global warming challenges.}, }
@article {pmid41778620, year = {2026}, author = {Wang, Y and OuYang, J and Zhang, H and Shen, Y and Guo, Z and Lv, W}, title = {The Efficacy of Gut Microbiome-Modulating Therapies on Liver Cirrhosis: A Systematic Review and Network Meta-Analysis.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000001010}, pmid = {41778620}, issn = {2155-384X}, abstract = {OBJECTIVE: Gut microbiome-modulating therapies are potential strategies for managing liver cirrhosis (LC), yet head-to-head comparisons to determine the optimal intervention are lacking. This study aimed to evaluate and rank the therapeutic efficacy of these therapies on liver function and disease progression in patients with LC.<br><br>METHODS: We searched major databases (PubMed, Web of Science, Embase, Cochrane Library) for randomized controlled trials (RCTs) published from January 1, 2000, to December 30, 2024. Interventions included probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) versus placebo or standard care. Primary outcomes were hepatic function indicators; secondary outcomes included inflammatory markers. Data were analyzed using random-effects frequentist network meta-analyses. The study was registered on PROSPERO (CRD420251000506).<br><br>RESULTS: Seventeen studies comprising 1051 individuals were included. Synbiotics demonstrated the most significant efficacy among all interventions, showing superior reduction in blood ammonia levels compared to placebo (Mean Difference (MD): -5.57), probiotics, and prebiotics. Prebiotics showed significant differences in lowering endotoxin levels compared to placebo (MD: -3.29) and probiotics. Furthermore, relative to placebo, prebiotics significantly reduced tumor necrosis factor-alpha (MD: -2.30) and interleukin-6 levels (MD: -4.60).<br><br>CONCLUSIONS: This network meta-analysis advances current knowledge by establishing an evidence-based hierarchy of efficacy. Synbiotics are most effective for reducing blood ammonia, whereas prebiotics demonstrate superior efficacy in lowering endotoxin and inflammatory markers. These results support a personalized therapeutic approach: prioritizing synbiotics for patients with hyperammonemia, and prebiotics for those characterized by systemic inflammation. Future high-quality RCTs are needed to standardize specific strain combinations.}, }
@article {pmid41778161, year = {2026}, author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z}, title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1755982}, pmid = {41778161}, issn = {1664-2392}, mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; }, abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.<br><br>METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.<br><br>RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial &#x3b2;-oxidation of long-chain saturated fatty acids, &#x3b1;-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).<br><br>DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.}, }
@article {pmid41778020, year = {2026}, author = {Zou, Q and Zhang, W and Xie, H and Ying, S and Zeng, X and Yao, Y and Zeng, D and Wang, J and Zhang, C and Meng, F}, title = {Inflammatory bowel disease through the lens of microbe-host interactions: immunomodulation, metabolic effects, and genetic susceptibility in microbiota dysbiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1745929}, pmid = {41778020}, issn = {2235-2988}, mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology/genetics/therapy ; *Gastrointestinal Microbiome/immunology ; *Genetic Predisposition to Disease ; *Immunomodulation ; *Host Microbial Interactions/immunology ; Animals ; *Host-Pathogen Interactions ; Probiotics/therapeutic use ; Prebiotics ; }, abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis, Crohn's disease, and inflammatory bowel disease-unclassified, is a complex intestinal disease influenced by microbial factors, genetic and environmental. IBD has become a global disease with an increasing prevalence, endangering human health worldwide. Through its interactions with host immunity, bacterial metabolites, and genetic components, the intestinal microbiome plays a crucial role in initiating and advancing IBD. Treatment for IBD includes not only corticosteroids, aminosalicylates, antibiotics, TNF-α, α4β7 integrins, IL-12/23 antibodies, and small molecule antibodies, but also complementary and alternative medical therapies such as probiotics and prebiotics. This review primarily explores the relationship between dysbiosis of the microbiota and IBD, including the immune system, metabolites, and genetics related to microorganisms, to provide a deeper and more systematic understanding of the mechanisms linking microbial imbalance to IBD.}, }
@article {pmid41777897, year = {2026}, author = {Tang, X and Man, C and Liu, Z and Gong, D and Fan, Y}, title = {Research on microbial communities in tumor microenvironments: cutting-edge dynamics and future trends from a bibliometric perspective.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745842}, pmid = {41777897}, issn = {1664-3224}, mesh = {*Tumor Microenvironment/immunology ; Humans ; *Neoplasms/microbiology/therapy/immunology ; Bibliometrics ; *Microbiota ; Animals ; Immunotherapy ; }, abstract = {BACKGROUND: In recent years, researchers have identified numerous potential biomarkers and therapeutic targets applicable to cancer immunotherapy, among which the role of tumor-internal microorganisms in the tumor microenvironment has been explored. However, this field is still in its early stages of development, facing limitations such as the unclear mechanisms of interaction between tumor-internal microorganisms and host immunity, as well as significant variations in microbial profiles among different tumor types and patients.<br><br>OBJECTIVE: This study aims to explore the research hotspots and development trends of tumor-internal microorganisms through bibliometric methods and to construct a systematic knowledge map.<br><br>METHODS: This study retrieved publications related to tumor-internal microorganisms from the Web of Science Core Collection (WOSCC) prior to December 22, 2025. Subsequently, the selected literature was analyzed using VOSviewer (v.1.6.20), CiteSpace (v.6.4.1R), and SCImago Graphica. In addition, we integrated PubMed data to assess status and trends in preclinical and clinical studies of intratumoral microbiota interventions for anti-tumor therapy efficacy.<br><br>RESULTS: From the Web of Science database, we retrieved 1,278 relevant articles. Since 2012, the number of papers published on the intratumoral microbiota has shown an overall upward trend. China and the United States are the two major countries in this field. Keyword analysis shows that "tumor microbiome," "gut microbiome," "cancer," and "Fusobacterium nucleatum" are frequent terms. 11 keyword groups have been identified, among which "tumor immunotherapy" and "immune microenvironment" form two important groups. A total of 69 preclinical and clinical studies has intervened in intratumoral microbiota and affected anti-tumor treatment outcomes. Among them, 25 studies involving Fusobacterium nucleatum account for a large proportion. However, most of these studies are still at the basic or preclinical stage, and clinical translation evidence is limited.}, }
@article {pmid41777702, year = {2026}, author = {Zhang, YW and Li, RY and Wu, Y and Wang, P and Zhou, QR and Su, JC}, title = {Gut microbiota and bone aging: Focusing on the gut-X axis modes.}, journal = {Journal of orthopaedic translation}, volume = {57}, number = {}, pages = {101064}, pmid = {41777702}, issn = {2214-031X}, abstract = {UNLABELLED: As studies have continuously advanced, cross-linking interplay between various organs in aging individuals have continuously emerged as research hotspots. The role of gut microbiota in bone aging-related diseases, including osteoporosis, osteoarthritis, and intervertebral disc degeneration, has been extensively probed. This review first summarized the inseparable association between gut microbiota and osteoporosis, osteoarthritis, and intervertebral disc degeneration, which then explored potential mechanisms of gut-X axis through neuromodulation (microbiota-gut-brain-bone axis), immunomodulation (Th17 and Treg balance), endocrine regulation (gut-derived hormones and 5-HT), metabolite-mediated regulation (SCFAs), bacterial extracellular vesicles, and changes in microbial niche and gut microbiome-associated biomarkers. Moreover, potential intervention strategies including diet, probiotics, fecal microbiota transplantation, and physical activity were summarized to enhance clinical translation applicability. This review creatively exhibited integrated concept of "gut-X axis" to explore common, patterned mechanisms underlying "gut-bone axis", "gut-joint axis", and "gut-disc axis". Furthermore, it delves into potential mechanisms by which this shared pattern regulates bone aging-related diseases and prospectively outlines therapeutic strategies for bone aging based on this axis.<br><br>This review presents crucial role and regulatory significance of gut-X axis modes in common bone-aging related diseases. By anchoring the gut-X axis as intervention targets, the thinking of gut microbiota and its related metabolites in basic studies and clinical prevention and treatment of bone aging-related diseases might be expanded, and its clinical application transformation and development could be innovated.}, }
@article {pmid41777631, year = {2026}, author = {Lin, F and Xu, Y and Lin, S and Zhao, Z and Zhao, J and Cheng, C and Luo, B}, title = {Unraveling volatile and microbial dynamics of Pukeng tea with different storage times using metabolomics, chemometrics, and microbiome analysis.}, journal = {Food chemistry: X}, volume = {34}, number = {}, pages = {103692}, pmid = {41777631}, issn = {2590-1575}, abstract = {Pukeng tea (PKT), a traditional Chinese dark tea, has been consumed for centuries, yet its volatile and microbial dynamics remain unclear. This study integrated metabolomics, chemometrics, and microbiome analysis to explore PKTs with 3-20 years of storage. HS-SPME-GC-MS identified 189 volatiles, mainly alcohols, aldehydes, and ketones. PCA and PLS-DA revealed distinct metabolite patterns, with 46 differential volatiles, such as 1-butanol and 1-penten-3-ol, characterized as potential discriminants among PKT samples. Microbiota analysis showed 11 dominant bacterial genera, shifting from Firmicutes in early storage to Actinobacteriota in later stages, while Aspergillus dominated fungal communities. Correlation analysis revealed significant associations between dominant microbes such as Staphylococcus and Saccharopolyspora and aroma-active volatiles, suggesting microbial contributions to PKT's evolving flavor. This study provides the first integrated characterization of volatile and microbial diversity in PKT, offering insights into quality control, product authentication, and functional microbe discovery for the sustainable development of traditional dark teas.}, }
@article {pmid41777547, year = {2026}, author = {Maisto, L and Telegrafo, C and Rubino, F and Santamaria, M and Traka, MH and Tullo, A and Bouwman, J and Sbisà, E and Balech, B}, title = {Multifaceted human gut microbiome data associated with health and nutrition.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1722500}, pmid = {41777547}, issn = {1664-302X}, abstract = {The microbiome, also considered the hidden organ, is a fundamental ecosystem directly associated with the disease and health status of the human body. With the availability of high-throughput DNA sequencing technologies, a growing number of studies from clinical and experimental (observation and intervention) samples are constantly revealing new findings on the relationship between human organs and their microbiomes. In such a context, diet and nutrition are among the key factors influencing microbiome composition, richness, and functional behavior. In this review, we illustrate how microbiome-related data and associated metadata are in recent times scattered across primary and specialized databases with different levels of curation, annotation, and standardization, limiting, to some extent, the possibility of deep data discovery, reuse, alignment, and harmonization. Therefore, we describe the way Findable, Accessible, Interoperable, and Reusable (FAIR) data principles would enhance the onset of novel scientific hypotheses and potential microbiome-targeted therapies by improving the standardization policies in data sources. Accordingly, using advanced semantic classification and data mining technologies based on suitable and comprehensive ontologies, annotations of studies present in source databases or in scientific literature would further improve the data and metadata enrichment, integration and alignment relevant to microbiome data associated with health, disease and nutrition.}, }
@article {pmid41777539, year = {2026}, author = {Wang, M and Li, X and Liu, X and Ye, Y and Zhou, P and Liu, Y and Zhu, L and Wei, W and Li, Z and Li, Z and Wu, R and Peng, Y and Liu, Z and Lu, X and Zhao, J and Kan, B}, title = {Restaurant occupational exposure affects the profiles of oral and gut pathobiomes and resistomes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771459}, pmid = {41777539}, issn = {1664-302X}, abstract = {INTRODUCTION: Restaurant occupational exposure refers to contact with food-processing environments, raw materials, and customers, which may influence the composition of the human microbiome. Differences and associations between human oral and gut pathobiome and their resistomes under restaurant occupational exposure remain unclear. We conducted a comprehensive metagenomic analysis of paired oral and fecal samples from Front-of-House (FOH) workers and Back-of-House (BOH) workers to elucidate the effects of occupational exposure in the restaurant environment on oral and gut pathobiome, antimicrobial resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs).<br><br>METHODS: We collected the oral and fecal samples from 35 FOH and 37 BOH workers across 24 Chinese restaurants in Zhengzhou, Henan, China. The diversity and relative abundances of microbial species, ARGs, VFs, and MGEs were compared. Clonal strains from paired oral and fecal samples were analyzed. The serovars of Salmonella were determined using the ucgMLST. Finally, we used the O2PLS method to explore relationships among ARG subtypes, bacterial communities (species-level), MGEs (subtype-level), and plasmids.<br><br>RESULTS: The gut microbiome acts as the primary reservoir, exhibiting greater alpha diversity and a higher burden of pathogens/resistomes (including high-risk Rank_I genes). In contrast, the oral microbiome was more sensitive to occupational differences. Significant beta diversity variations in microbiomes, antimicrobial resistance genes (ARGs), and virulence factors were observed exclusively in oral samples. Notably, Salmonella Typhimurium was significantly more prevalent in the oral cavity of BOH workers (R [2]&#x202f;=&#x202f;0.032, p&#x202f;=&#x202f;0.047), indicating their potential role as intermediaries in foodborne pathogen transmission. Strain-level analysis confirmed that clonal strains of the opportunistic pathogen and probiotics were shared between the oral cavity and the gut. O2PLS analysis identified plasmids as the main correlates of ARGs.<br><br>DISCUSSION: While the gut serves as the primary reservoir for pathogens/resistomes, restaurant occupational exposure distinctly shapes oral microbial/resistome profiles, underscoring the critical need for reinforced hygiene management, particularly for BOH workers, to mitigate pathogen and resistance transmission.}, }
@article {pmid41777533, year = {2026}, author = {Wang, S and Ding, Y and Cai, C and Ou, M and Niu, C}, title = {16S ribosomal ribonucleic acid sequencing reveals bile microbiome features in gallstone disease and their links to blood lipid subtypes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741489}, pmid = {41777533}, issn = {1664-302X}, abstract = {BACKGROUND: Gallstone disease (GSD) represents a major global health burden with complex pathophysiology involving bile microbiome dysbiosis and metabolic dysfunction. Although previous studies have examined bile microbial communities, the relationship between bile microbiome composition and specific lipid phenotypes remains incompletely understood.<br><br>METHODS: We conducted a cross-sectional study of 28 adults undergoing cholecystectomy for radiologically and pathologically confirmed gallstones. Bile samples were collected intraoperatively and subjected to 16S ribosomal ribonucleic acid V3-V4 region sequencing. Patients were stratified by lipid subtypes based on contemporary dyslipidaemia guidelines. Microbial diversity, community structure and differential abundance analyses were performed alongside machine learning classification.<br><br>RESULTS: The bile microbiome exhibited distinct compositional patterns between the hypertriglyceridaemia (HTG) and non-HTG (NTG) groups, with key phyla (Proteobacteria, Firmicutes) showing group-specific abundance trends and alpha diversity indices reflecting reduced evenness in HTG. Beta diversity analyses demonstrated mild-to-moderate separation between groups, and the linear discriminant analysis effect size technique identified discriminatory taxa with potential functional relevance. Random forest classification achieved moderate accuracy in predicting lipid subtypes based on microbial features.<br><br>CONCLUSIONS: This study revealed associations between bile microbiome composition and systemic lipid metabolism in GSD, suggesting potential mechanistic links through bile acid metabolism and farnesoid X receptor-fibroblast growth factor 19 signaling pathways.}, }
@article {pmid41777408, year = {2026}, author = {Qin, SD and Zhang, YW and Wang, JZ}, title = {Evaluating the association between oral microbiota and cardiovascular diseases: evidence from Mendelian randomization analysis.}, journal = {Journal of geriatric cardiology : JGC}, volume = {23}, number = {1}, pages = {36-44}, pmid = {41777408}, issn = {1671-5411}, abstract = {BACKGROUND: Recent studies have suggested a potential role of the oral microbiome in the development of cardiovascular diseases. This study aims to investigate the association between oral microbiota and cardiovascular disease risk, including atrial fibrillation, myocardial infarction, chronic heart failure, and hypertension.<br><br>METHODS: We analyzed GWAS data from East Asian populations' oral microbiome, involving 2,017 tongue and 1,915 saliva samples from 2,984 individuals with whole-genome sequencing. Additionally, we sourced cardiovascular disease GWAS data from NBDC, including atrial fibrillation (8,180 cases, 28,621 controls), myocardial infarction (14,992 cases, 146,214 controls), chronic heart failure (10,540 cases, 168,186 controls), and systolic blood pressure (145,505 individuals).<br><br>RESULTS: Several oral microbiota taxa were found to be significantly associated with cardiovascular disease outcomes. Specific microbiota, such as Centipeda, Corynebacterium, and Pseudomonas E, were negatively correlated with heart failure. In contrast, taxa like Neisseria D and Actinomyces were associated with an increased risk of atrial fibrillation and myocardial infarction. Additionally, certain oral microbiota showed correlations with changes in blood pressure, highlighting their potential role in hypertension.<br><br>CONCLUSION: Our findings suggest that the oral microbiota may influence the development and progression of cardiovascular diseases, providing new insights into the potential impact of oral health on cardiovascular risk.}, }
@article {pmid41715099, year = {2026}, author = {Fan, W and Tan, T and Yang, C and Cao, Y and Jin, C and Liu, X and Shang, K and Wang, J and Xu, J and Li, Y}, title = {Indole-acetaldehyde from Rothia mucilaginosa activates the PXR/NRF2 axis to enhance alveolar macrophage phagocytosis and protect against ARDS.}, journal = {Respiratory research}, volume = {27}, number = {1}, pages = {}, pmid = {41715099}, issn = {1465-993X}, support = {82102252//National Natural Science Foundation of China/ ; 82272245//National Natural Science Foundation of China/ ; 202440093, 2024ZZ1022//Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Despite advances in therapeutic strategies, acute respiratory distress syndrome (ARDS) mortality remains high. Growing evidence links respiratory microbiome composition to ARDS outcomes. This investigation sought to elucidate how colonizing bacteria and their metabolites influence ARDS pathogenesis.<br><br>METHODS: Bronchoalveolar lavage fluid (BALF) from patients with pulmonary infections was analyzed by metagenomic next-generation sequencing (mNGS) to identify characteristic bacteria. Bacterial culture supernatants were analyzed by untargeted metabolomics (LC-MS) to identify metabolites. A murine ARDS model was established through intratracheal LPS instillation. Single-cell sequencing datasets from the GEO database were analyzed to reveal differential cell populations and functional alterations in murine ARDS. Potential molecular mechanisms were explored through molecular docking, RNA-seq analysis, Western boltting, and targeted gene knockdown in murine and cellular model.<br><br>RESULTS: R. mucilaginosa demonstrated enrichment in patients without ARDS (nARDS). The bacterial culture supernatant conferred substantial protection in murine models, whereas viable bacteria showed minimal efficacy. LC-MS analysis identified indole-3-acetaldehyde (IAAld) as the predominant metabolite in the supernatant. Single-cell sequencing suggested that resident alveolar macrophages (RAMs) were pivotal cells in murine ARDS model. IAAld enhanced RAMs phagocytosis, facilitating neutrophil and LPS clearance. Mechanistic studies revealed that IAAld likely activated PXR signaling, promoted NRF2 nuclear translocation, and upregulated the phagocytosis-related gene CD36. Targeted PXR knockdown eliminated these protective effects.<br><br>CONCLUSION: The respiratory commensal R. mucilaginosa synthesizes IAAld, which&#x2014;independent of bacterial colonization per se&#x2014;ameliorates ARDS through PXR/NRF2/CD36 axis activation, thereby enhancing macrophage phagocytic function. These findings suggest that therapeutic targeting of microbial metabolites represents a novel ARDS treatment paradigm.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-026-03551-3.}, }
@article {pmid41634480, year = {2026}, author = {Ren, L and Wang, Z and Yang, Z and Tian, R and Du, J and Dang, Z and Li, J and Guo, X and Xia, Y and Cui, W and Wang, Y}, title = {Microbial succession and machine learning for postmortem interval estimation in bromadiolone-poisoned cadavers.}, journal = {AMB Express}, volume = {16}, number = {1}, pages = {}, pmid = {41634480}, issn = {2191-0855}, support = {tsqn202507262//Special Foundation of Taishan Scholars Program/ ; 2023JJ40797//Natural Science Foundation of Hunan Province/ ; KF202303//Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science/ ; cx2025078//Student's Platform for Innovation and Entrepreneurship Training Program/ ; }, abstract = {UNLABELLED: Accurate estimation of the postmortem interval (PMI) remains a major challenge in forensic investigations. Although microbial succession has emerged as a promising biological clock, the impact of xenobiotic exposure on internal microbial communities during decomposition remain poorly understood. Here, we established a bromadiolone-poisoned rat model and systematically sampled gut and anus swabs at 6 h intervals over 96 h postmortem period. Bromadiolone exposure produced dose-dependent effects on decomposition, with high-doses delaying the progression, potentially by altering tissue integrity or microbial activity. 16 S rRNA sequencing revealed that Firmicutes and Proteobacteria were the dominant phyla during decomposition, followed by Bacteroidota, Desulfobacterota, and Actinobacteriota. Notably, microbial community dynamics were driven more strongly by anatomical location than by toxicant exposure, highlighting the critical role of sampling site. Furthermore, five machine-learning algorithms were evaluated for PMI prediction. GB regression outperformed RF, RR, SV, and LR, achieving an R[2] of 0.954 and an RMSE of 5.6 h. Feature analysis identified Proteus mirabilis and Morganella morganii as dominant positive biomarkers, while gut-associated taxa (e.g., Lactobacillus and Ligilactobacillus) declined over time. Together, these results demonstrate that bromadiolone exposure induces site-specific perturbations in microbial community, the underlying successional dynamics remain sufficiently robust to support accurate PMI estimation. The GB model provides both predictive accuracy and biological interpretability, highlighting the importance of incorporating anatomical location and toxicological stress into microbiome-based PMI estimation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13568-026-02023-7.}, }
@article {pmid41777393, year = {2026}, author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D}, title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1685007}, pmid = {41777393}, issn = {1664-462X}, abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.}, }
@article {pmid41777263, year = {2026}, author = {Wang, X and He, J and Ding, G and Tang, Y and Wang, Q}, title = {Artificial Intelligence-Enabled Multi-Omics for Predicting Immune Checkpoint Inhibitor Response and Resistance.}, journal = {Journal of multidisciplinary healthcare}, volume = {19}, number = {}, pages = {572089}, pmid = {41777263}, issn = {1178-2390}, abstract = {Immune checkpoint inhibitors (ICIs) have reshaped oncology, yet overall response rates remain modest and resistance is common, driven by tumor heterogeneity and evolving tumor-immune crosstalk. Established biomarkers (PD-L1, tumor mutational burden, microsatellite instability) provide incomplete prediction. Multi-omics profiling across genomic, transcriptomic, proteomic, epigenomic, metabolomic and microbiomic layers offers a systems-level view of malignant and immune states, uncovering determinants of ICI efficacy such as lineage plasticity, stromal remodeling, immunometabolic reprogramming and microbiome-associated immune modulation. Artificial intelligence (AI) is uniquely positioned to fuse these heterogeneous data, learn non-linear cross-layer signatures, and enable interpretable predictions using approaches such as SHAP and Grad-CAM. Representative models link routine histology or imaging to molecular phenotypes, stratify patients beyond single biomarkers, and may nominate rational combinations that target oncogenic pathways, lactate-driven immune suppression, or the gut microbiome. In this narrative review, we synthesize recent AI-multi-omics advances for response modeling, immune-relevant tumor subtyping, and clinical translation, including radiomics/pathomics integration and liquid-biopsy-based monitoring, as well as emerging applications in toxicity risk prediction. We also discuss barriers to implementation-platform heterogeneity, limited prospective validation, bias, interpretability and cost-and outline future directions, including single-cell and spatial multi-omics integration, federated learning and generative modeling to improve robustness and equity of precision immunotherapy.}, }
@article {pmid41777157, year = {2026}, author = {Popova, PV and Loboda, AA and Liaudanski, A and Sitkin, SI and Anopova, AD and Vasukova, EA and O Isakov, A and Tkachuk, AS and Nemikina, IS and Akhmatova, M and Eriskovskaya, AI and Vasilieva, EY and Galyautdinov, IV and Babenko, A and Zgairy, S and Rubin, E and Even, C and Turjeman, S and Pervunina, TM and Kostareva, AA and Vatian, AS and Mohan, V and Grineva, EN and Koren, O and Shlyakhto, EV}, title = {Maternal Gut Microbiome as a Predictor of Insulin Therapy Requirement in Gestational Diabetes.}, journal = {Journal of diabetes science and technology}, volume = {}, number = {}, pages = {19322968261426025}, doi = {10.1177/19322968261426025}, pmid = {41777157}, issn = {1932-2968}, abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) often requires pharmacological intervention beyond lifestyle modification to achieve optimal glycemic control. This study aimed to develop machine learning models that integrate clinical and gut microbiome data to predict the need for insulin therapy (IT) in women with GDM.<br><br>METHODS: We characterized 205 pregnant women with GDM from the Genetic and Epigenetic Mechanisms of Developing Gestational Diabetes Mellitus and its Effects on the Fetus study, collecting clinical parameters, lifestyle questionnaires, self-monitored blood glucose records, and gut microbiome profiles based on 16S rRNA gene sequencing. Gradient-boosting models were trained to predict IT, basal insulin (BI), and prandial insulin (PI) requirements. Model discrimination was assessed using repeated stratified five-fold cross-validated area under the curve-receiver operating characteristic (AUC-ROC) (nested cross-validation). Feature importance and interpretability were evaluated with SHapley Additive exPlanations and permutation analyses. Differential microbial abundance was analyzed by ANCOM-BC2 (analysis of composition of microbiomes with bias correction, version 2), and metabolic pathways were predicted via PICRUSt2.<br><br>RESULTS: Women requiring insulin were older and had higher pre-pregnancy body mass index (BMI), fasting plasma glucose, 1-hour oral glucose tolerance test glucose, and glycated hemoglobin than diet-treated women (P < .05 for all). Adding microbiome data improved AUC-ROC for IT prediction from 0.63 (95% CI = 0.43, 0.83) to 0.70 (0.50, 0.89), BI from 0.77 (0.59, 0.95) to 0.82 (0.65, 0.99), and for PI from 0.69 (0.50, 0.88) to 0.70 (0.51, 0.89). Key influential features included glycemic markers, BMI, and microbial taxa, such as Phascolarctobacterium faecium, Alistipes ihumii, Cloacibacillus evryensis, Ruthenibacterium lactatiformans, and Methanosphaera stadtmanae, and the predicted microbial metabolic pathway PWY-5823.<br><br>CONCLUSION: Our findings demonstrate that integrating gut microbiome characteristics with clinical data improves the prediction of insulin treatment needs in GDM, particularly for BI initiation.}, }
@article {pmid41777065, year = {2025}, author = {Zhang, Y and Zhang, T and Wang, H}, title = {[Research Progress on the Regulatory Mechanism of Respiratory Microbiota in the Comorbidity of Chronic Obstructive Pulmonary Disease and Lung Cancer].}, journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer}, volume = {28}, number = {12}, pages = {939-947}, doi = {10.3779/j.issn.1009-3419.2025.106.33}, pmid = {41777065}, issn = {1999-6187}, abstract = {Both chronic obstructive pulmonary disease (COPD) and lung carcinoma (LC) are major public health challenges in China. With the continuous advancement of microbial detection methods, the role of the respiratory microbiome in the pathogenesis and progression of respiratory diseases has become increasingly prominent. This article systematically reviews the dynamic characteristics of the respiratory microbiome during the progression of COPD and LC, then explores its crucial bridging role in COPD-LC comorbidity through mechanisms such as persistently driving chronic inflammation, mediating genomic damage, and participating in immune regulation. The aim is to deepen the understanding of the respiratory microbiome, and to provide new perspectives for optimizing existing treatment strategies, exploring microbial biomarkers for early cancer screening, and improving the clinical management of chronic respiratory diseases. .}, }
@article {pmid41777057, year = {2026}, author = {Singh, A and Bhardwaj, A and Midha, V and Sood, A}, title = {Deciphering the diet-inflammatory bowel disease relationship: knowledge gaps and future perspectives.}, journal = {Intestinal research}, volume = {}, number = {}, pages = {}, doi = {10.5217/ir.2025.00278}, pmid = {41777057}, issn = {1598-9100}, abstract = {Diet is increasingly recognized not as a passive exposure but as a dynamic determinant of inflammatory bowel disease (IBD) pathogenesis, progression, and treatment response. This review article redefines diet as a multidimensional modifier acting through complex interactions with genetics, microbiota, intestinal barrier function, and environmental exposures. Beyond nutrient composition, we highlight how age, sex, habitual diet, cooking methods, contaminants, and lifestyle collectively shape disease trajectories. We also identify key research priorities: incorporation of long-term, mechanistically anchored trials; development of digital, biomarker-informed dietary assessment tools; and integration of polygenic, microbial, and metabolic data to inform individualized therapy. Emerging evidence also calls for culturally tailored and patient-centered frameworks that ensure real-world adherence and equity in dietary interventions. Reframing diet as a biological, behavioral, and environmental nexus shifts it from the periphery to the forefront of IBD care, transforming it from a confounder in research to a therapeutic frontier in clinical practice.}, }
@article {pmid41776947, year = {2026}, author = {Mitchell, A and Hayes, C and Hudson, CJ and Connell, SD and Harvey, BP and Agostini, S and Jolly, J and Ravasi, T and Booth, DJ and Nagelkerken, I}, title = {Marine Heatwaves, Ocean Warming and Acidification Reshape Reef Fish Gut Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {5}, pages = {e70275}, doi = {10.1111/mec.70275}, pmid = {41776947}, issn = {1365-294X}, support = {DP230101932//Australian Research Council/ ; JPJSCCA20210006//Japan Society for the Promotion of Science/ ; 23K26924//Japan Society for the Promotion of Science/ ; }, abstract = {Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host-associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (Abudefduf vaigiensis) and one subtropical (Microcanthus strigatus) reef fish species, across three temperate reefs representing natural analogues of climate change: a present-day baseline ('cool reef'), a chronically warmed reef ('warm reef') and a reef experiencing combined warming and extreme acidification ('extreme reef'). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre-heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus. We conclude that climate-driven microbiome reshuffling may alter host-microbiome relationships and functions in fishes in a future ocean.}, }
@article {pmid41776819, year = {2026}, author = {Holstein, T and Verschaffelt, P and Van Den Bossche, T and Van de Vyver, S and Martens, L and Mesuere, B and Muth, T}, title = {The Peptonizer2000: Bringing Confidence to Metaproteomics.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.5c00567}, pmid = {41776819}, issn = {1535-3907}, abstract = {Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available data sets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities.}, }
@article {pmid41776759, year = {2025}, author = {Fernhout, L and Lambrechts, H and van Zyl, JHC}, title = {Ovine balanoposthitis: observations on the microbiome and immunoglobulin response.}, journal = {Journal of the South African Veterinary Association}, volume = {96}, number = {2}, pages = {73}, doi = {10.36303/JSAVA.679}, pmid = {41776759}, issn = {2224-9435}, abstract = {The incidence of ulcerative balanoposthitis (UB) in rams contributes to significant economic losses in the national sheep population. Understanding the immune response in the reproductive tract can aid in developing preventive measures. This study aimed to characterise the immunoglobulin profiles and microbial diversity in the reproductive tract of rams affected by UB, providing insight into the immune responses to this disease. Serum and glans tissue samples from healthy and UB-affected rams were analysed using an ELISA approach to quantify IgG, IgA, and IgM levels. The microbial diversity in nasal, penile swabs, and smegma samples was assessed using an ARISA approach. Significant differences (p ≤ 0.001) were observed between the systemic and localised immune responses. UB-affected rams exhibited higher IgG and IgM levels but lower IgA levels in both serum and glans tissue compared to healthy rams. The study confirmed UB-induced shifts in the microbiome, with significant differences in microbial diversity indices in nasal, penile, and smegma samples. Specifically, there were changes in the nasal fungi Shannon (p = 0.047) and Simpson (p = 0.038) indices, the penile Shannon (p = 0.015) and Simpson (p = 0.006) bacterial indices, and the smegma bacterial species number index (p = 0.042). Correlations between microbial populations and immunoglobulin profiles indicated an interactive immune response in different health statuses. This study highlights the need to understand the immune system of the lower reproductive tract and its interaction with commensal organisms to develop therapeutic immunomodulators for preventing UB in sheep.}, }
@article {pmid41776699, year = {2026}, author = {Song, Y and Wen, S and Guan, LL}, title = {Unraveling the dynamic changes in the intestinal microbiome: impacts on pre-weaning calf health and productivity.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41776699}, issn = {1674-9782}, abstract = {The early life gut microbial colonization in pre-weaning calves plays a pivotal role in shaping their health, growth, and productivity. This review delves into the dynamic changes of intestinal microbiota during early life, emphasizing key factors such as colostrum management, feeding strategies, roughage supplementation, and microbial interventions including probiotics, prebiotics, and fecal microbiota transplantation (FMT), and non-nutritional stressors that can shape the early life microbial colonization. We highlight the microbiota's critical functions in nutrient metabolism, immune development, gut barrier integrity, and gut-brain axis regulation. Additionally, the consequences of microbial dysbiosis on calf health and its long-term effects on production performance in beef and dairy cattle are discussed. While current research has provided valuable insights, understanding causal mechanisms remains a challenge. This review aims to guide practical strategies for targeted microbial management, offering a pathway to optimize early-life interventions for improved calf health and productivity.}, }
@article {pmid41776621, year = {2026}, author = {Yadav, B and Banerjee, G and Srivastava, A and Madan, AK and Kumar, R and Banerjee, P}, title = {Host-microbiome interplay supports heat stress resilience in zebu calves.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00539-8}, pmid = {41776621}, issn = {2524-4671}, }
@article {pmid41776571, year = {2026}, author = {Ni, Z and Wang, G and Li, Q and Wu, X and Song, Z and Yu, H and Yu, P and Chen, Y and Li, L and Chen, H and Hou, H and Hu, Q}, title = {Sex-specific metabolic and microbial remodeling in a rotenone-induced rat model of Parkinson's disease following nicotine administration.}, journal = {Biology of sex differences}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13293-026-00865-1}, pmid = {41776571}, issn = {2042-6410}, support = {2023100CC0190//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0090//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0100//the Science and Technology Project of Beijing Life Science Academy/ ; }, abstract = {BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder with established sex differences in incidence and progression. Epidemiological evidence suggests nicotine may confer protection against PD, but its mechanisms, particularly regarding sex-specific effects, remain unclear. This study investigated the neuroprotective mechanisms of nicotine in a rotenone-induced PD rat model, with a specific focus on evaluating sex-dependent modulation across behavioral, pathological, and gut-related outcomes.<br><br>METHODS: Male and female Sprague-Dawley rats were administered rotenone (2&#xa0;mg/kg/day, s.c.) for four weeks to induce PD. Nicotine (0.5&#xa0;mg/kg/day, s.c.) was administered 30&#xa0;min after rotenone. Motor function was assessed using rotarod and CatWalk XT gait analysis. Neuropathology in the substantia nigra was evaluated via immunofluorescence for &#x3b1;-synuclein and tyrosine hydroxylase (TH). Gut pathology was analyzed through colon histopathology (H&amp;E staining) and ELISA for IL-6 and &#x3b1;-synuclein. Gut microbiota composition was assessed by 16&#xa0;S rDNA sequencing, and serum metabolomics was performed using UPLC-MS/MS. Data were analyzed by two-way ANOVA with Tukey's post-hoc test.<br><br>RESULTS: Nicotine significantly attenuated rotenone-induced motor impairments: males showed a superior response in balance-related parameters, while females exhibited enhanced efficacy in dynamic gait metrics. Pathologically, nicotine reduced nigral &#x3b1;-synuclein accumulation and TH depletion in both sexes, with males showing greater &#x3b1;-synuclein accumulation following rotenone exposure. Crucially, nicotine exclusively ameliorated colon histopathology, reduced plasma &#x3b1;-synuclein, and suppressed colon IL-6 in females, while attenuating intestinal &#x3b1;-synuclein accumulation in both sexes. Microbiota analysis revealed sex-divergent taxonomic shifts with nicotine treatment. Metabolomics showed significantly more extensive metabolic reprogramming in females, particularly affecting indole derivatives. Pearson correlations revealed significant sex-specific associations between altered serum indole derivatives and gut microbiota genera.<br><br>CONCLUSIONS: Nicotine exerts neuroprotection in PD through sex-dependent modulation of multiple pathological pathways, primarily involving the gut-microbiota-metabolite axis. Females benefit from enhanced gastrointestinal protection and metabolic reprogramming, while males show preferential motor balance restoration. These findings underscore the critical importance of sex-stratified therapeutic strategies for PD.}, }
@article {pmid41776310, year = {2026}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {41776310}, issn = {2662-8465}, support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; }, abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.}, }
@article {pmid41776177, year = {2026}, author = {Liu, J and Li, J and Li, Y and Gao, Z and Wang, L and Song, Q and Ye, Y and Liang, J}, title = {Mechanism of Morchella polysaccharide in anti-fatigue: the role of the gut microbiota-metabolite axis in mice.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00763-1}, pmid = {41776177}, issn = {2396-8370}, support = {2023-ZJ-904T//Science and Technology Plan Project of Qinghai Province/ ; }, abstract = {This study aims to investigate the anti-fatigue effects of crude Morchella polysaccharide (MP) extracted from the Qinghai-Tibet Plateau region in mice, and to preliminarily explore its potential mechanisms based on the gut microbiota-metabolite axis. Chemical analysis indicates that MP exhibits typical characteristics of crude polysaccharides: it consists of multiple monosaccharides (primarily glucose at 72.33%, along with mannose, galactose, etc) and possesses a broad molecular weight distribution (dispersion index (Mw/Mn) of 30.97). To investigate its material basis, we further isolated and purified the primary water-soluble neutral fraction MP1-1. Structural characterization confirmed MP1-1 as a homogeneous glucan composed solely of glucose units, with a backbone linked via →4)-α-D-Glcp-(1 → 4)-type bonds. A negative control group (NC), a positive control group (PC, Rhodiola glycoside,100 mg/kg), and low-, medium-, and high-dose MP groups (50, 100, 200 mg/kg) were established, with continuous gavage for four weeks. Following the final gavage, a weight-bearing swimming test was conducted to record the time to exhaustion and establish a fatigue model. Subsequently, fatigue-related biochemical indicators, gut microbiota composition, and metabolite changes were assessed. The results indicate that MP intervention is significantly associated with an anti-fatigue phenotype. This may occur through regulating the gut microbiota by enriching beneficial bacteria (such as Lactobacillus and Bifidobacterium) and suppressing harmful bacteria (such as Desulfovibrio and Helicobacter), thereby reshaping the intestinal microbiome. These alterations were associated with changes in the host's metabolic profile, particularly the upregulation of energy metabolism pathways (e.g., β-alanine metabolism, pentose phosphate pathway, glycerolipid metabolism) and the disruption of inflammation- and oxidative stress-related metabolic pathways. Ultimately, the MP intervention group exhibited increased glycogen reserves, enhanced antioxidant capacity (elevated SOD and GSH-Px; reduced MDA), and reduced systemic inflammation (decreased IL-6 and TNF-α; increased IL-10). Collectively, these effects delayed fatigue onset, promoted recovery, and significantly prolonged swimming duration. In summary, this study suggests that the polysaccharide extract from Morchella elata, native to the Qinghai-Tibet Plateau, may exert anti-fatigue effects by regulating the "gut microbiota-metabolite-host physiological phenotype" network, providing preliminary experimental evidence for its application in the functional food sector.}, }
@article {pmid41776098, year = {2026}, author = {Xiang, X and Zhu, J and Jiang, J and Ding, P and Zhu, Y and Cheng, K and Ming, Y}, title = {Unique gut microbiota and metabolomic profiling as biomarker of post-transplant recovery in acute-on-chronic liver failure after liver transplantation.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41776098}, issn = {1432-0614}, support = {81771722 and 82570782//National Natural Science Foundation of China/ ; }, abstract = {Acute-on-chronic liver failure (ACLF) is a severe condition arising from chronic liver disease, characterized by acute decompensation, organ failure, and high short-term mortality. Poor outcomes have also been observed in patients with ACLF after liver transplantation (LT). Emerging evidence, including a study from our center, suggests that gut microbiota plays an important role in ACLF. Patients who underwent LT at our center between October 2022 and June 2024 were included. Fecal samples were collected within 1 month post-LT for 16S rRNA and untargeted metabolomic sequencing. In this study, 144 samples from 69 patients with ACLF, cirrhosis, or hepatocellular carcinoma (HCC) were analyzed. Distinct microbiota and metabolic profiles were observed among the groups. ACLF patients exhibited significantly altered beta diversity, with notable depletion of g__Anaerostipes. Metabolomic analysis revealed substantial differences, including enrichment of tangeritin and depletion of candesartan in the ACLF group. Network analysis identified g__Anaerostipes as a key node linking differential taxa and metabolites. A random forest model based on these features effectively distinguished patient groups, with the highest classification accuracy observed in HCC. Multi-omic signatures were also associated with early allograft dysfunction (EAD), particularly g__Lachnoclostridium. Several microbial and metabolic features, including g__Lachnoclostridium, showed significant correlations with clinical indicators. The gut microbiome after LT is closely associated with ACLF. This study offers valuable insights for further investigation into the pathogenesis and post-LT prognosis. KEY POINTS: • ACLF patients have a unique gut microbiota and metabolic profile after LT • g__Anaerostipes is the prominent biomarker of ACLF's multi-omics signature • g__Lachnoclostridium is a promising indicator of recovery after LT.}, }
@article {pmid41776009, year = {2026}, author = {Kumar, Y and Xu, B}, title = {A critical review on the roles of natural products in shaping oral microbiota and preventing chronic diseases.}, journal = {Natural products and bioprospecting}, volume = {16}, number = {1}, pages = {}, pmid = {41776009}, issn = {2192-2195}, support = {UICR0400015-24B//Beijing Normal-Hong Kong Baptist University/ ; UICR0400016-24B//Beijing Normal-Hong Kong Baptist University/ ; }, abstract = {The oral microbiome plays a central role in maintaining both oral and systemic health, and disruptions in its balance can contribute to a wide range of diseases. This review brings together current evidence on how natural products modulate oral microbial communities, promote microbial equilibrium, and help prevent conditions such as dental caries, periodontitis, and chronic systemic disorders linked to oral dysbiosis. Recent studies highlight that phytochemicals particularly polyphenols, terpenoids, saponins, and alkaloids exert antimicrobial, anti-inflammatory, and antioxidant effects that influence bacterial adhesion, biofilm development, gene expression, and acid production. These compounds not only inhibit key oral pathogens but also support beneficial species, helping to sustain a stable and resilient microbiome. Evidence was gathered from PubMed, Scopus, ScienceDirect, and Google Scholar using relevant keywords and focusing on literature from 2015 to 2025. Insights into microbial diversity, environmental influences, host genetics, and advanced sequencing tools further strengthen understanding of oral microbial dynamics. While natural products show strong potential, challenges related to safety, bioavailability, regulatory clarity, and clinical translation remain to explore. This review outlines current progress and future directions needed to transform natural compounds into effective, evidence-based strategies for improving oral and systemic health through microbiome modulation.}, }
@article {pmid41776008, year = {2026}, author = {Ticinesi, A and Maggi, S and Nouvenne, A and Zuliani, G and Franceschi, C}, title = {The gut microbiome and ageing trajectories: mechanisms and clinical implications.}, journal = {Nature reviews. Endocrinology}, volume = {}, number = {}, pages = {}, pmid = {41776008}, issn = {1759-5037}, abstract = {This Review discusses the current state of knowledge on the contribution of the gut microbiome as a potential key actor in defining how we age. The gut microbiome is a complex ecosystem that establishes lifelong dynamic interactions with the host at multiple levels (several gut-organ axes), differently influencing ageing patterns and age-related disease onset and progression across populations. Accordingly, the definition of a 'normative' gut microbiome remains elusive, depending largely on the interaction with the external environment. In this complex scenario, the causal role of the gut microbiome in defining the ageing trajectory and its precise contribution to various organ-specific age-related diseases is still uncertain in clinical terms and could be context specific. Multiparametric and uniqueness indexes within a given population have shown a certain capacity for predicting disability and mortality. However, the gut microbiome is shaped over time by exposure to different intrinsic and environmental factors, resulting in a high degree of inter-individual variability, a key phenomenon that should be considered to develop novel personalized strategies to counteract age-related disease and frailty.}, }
@article {pmid41775773, year = {2026}, author = {Chowdhury, SF and Sarkar, MMH and Al Sium, SM and Naser, SR and Hossain, MS and Habib, MA and Akter, S and Banu, TA and Goswami, B and Jahan, I and Chakrovarty, T and Molla, MMA and Nafisa, T and Yeasmin, M and Ghosh, AK and Khan, MS}, title = {Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40563-x}, pmid = {41775773}, issn = {2045-2322}, support = {GOB 224125200//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; }, }
@article {pmid41775715, year = {2026}, author = {Zhu, B and Wang, J and Zhang, X and Zhang, B and Li, Z and Hao, L}, title = {A bacteria community sequencing data set from pothos (Epipremnum aureum).}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06677-7}, pmid = {41775715}, issn = {2052-4463}, abstract = {Pothos, with the scientific name of Epipremnum aureum, is a popular ornamental plant widely utilized for indoor greening, which is adaptable to both soil-based and hydroponic cultivation. Plant-associated microorganisms significantly influence plant health and productivity by facilitating nutrient acquisition and enhancing stress tolerance. Pothos, which is tolerant to low-nutrient conditions, is thus a suitable model plant to study plant-microorganisms interaction. However, knowledge about the microbiome of pothos is lacking, especially under hydroponic cultivation conditions. In this study, we recorded the dynamic changes of the bacterial communities associated with pothos during a transition from soil-based to hydroponic growth conditions in a 86-day cultivation. Bacterial communities from root tissues, hydroponic solutions, leaves, and soils were characterized through 16S rRNA gene amplicon sequencing, generating 98 community composition profiles. Significant shifts in microbial diversity and composition were observed during the transition, highlighting specific bacterial taxa associated with hydroponic adaptation. Across sample types, Proteobacteria dominated, with Actinobacteriota as the second most abundant group, while Bacteroidota and Firmicutes were present at lower relative abundances. This is the first high resolution and comprehensive data set of the pothos microbiome, offering a foundational resource for studying plant-microbe interactions in aquatic systems.}, }
@article {pmid41775278, year = {2026}, author = {Kim, YS and Woo, SY and Ha, E and Ahn, SH and Kim, E and Kim, SI and Lim, WJ and Kim, SY}, title = {Role of Gut Microbiota in Psychiatric Disorders: From Mechanistic Insights to Therapeutic Strategies.}, journal = {Journal of Korean medical science}, volume = {41}, number = {8}, pages = {e78}, pmid = {41775278}, issn = {1598-6357}, support = {/NRF/National Research Foundation of Korea/Korea ; }, abstract = {Mental health disorders are a global health challenge, and the underlying biological mechanisms remain unclear. Recent evidence has linked gut microbiota to psychiatric symptoms through complex bidirectional interactions along the gut-brain axis, which involve neural, endocrine, and immune pathways. This narrative review aims to synthesize current findings on how gut microbiota contributes to the pathophysiology of major psychiatric disorders, and explore microbiota-based therapeutic interventions, and discusses emerging strategies for personalized treatment. Relevant literature up to July 2025 was reviewed using targeted keywords in major databases, including PubMed and Google Scholar. Rather than applying formal systematic review criteria, we focused on selecting influential and high-impact studies, and the findings were synthesized thematically to provide a comprehensive overview. Consistent findings across psychiatric conditions include a decreased abundance of short-chain fatty acid-producing bacteria and an increased presence of pro-inflammatory taxa. These shifts correlate with heightened systemic inflammation, disrupted neurotransmitter synthesis, and dysregulation of the hypothalamic-pituitary-adrenal axis. Thus, the gut microbiota is increasingly recognized as playing a potential role in the pathophysiology of psychiatric disorders through multifaceted mechanisms involving the gut-brain axis. Probiotics, prebiotics, and dietary modifications show promise in modulating gut microbiota and alleviating psychiatric symptoms, although clinical outcomes remain heterogeneous. Emerging precision medicine strategies indicate promising potential for personalized microbiota-based treatments. Although microbiota-targeted therapies offer promising adjunctive strategies, large-scale, mechanistically informed clinical trials remain warranted. Future research should leverage artificial intelligence and multi-omics tools to develop personalized interventions tailored to individual microbiome profiles.}, }
@article {pmid41775266, year = {2026}, author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J}, title = {Competition and compromise between exogenous probiotics and native microbiota.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101516}, doi = {10.1016/j.cels.2025.101516}, pmid = {41775266}, issn = {2405-4720}, abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.}, }
@article {pmid41775198, year = {2026}, author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z}, title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141645}, doi = {10.1016/j.jhazmat.2026.141645}, pmid = {41775198}, issn = {1873-3336}, abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.}, }
@article {pmid41634593, year = {2026}, author = {Narem, RSR and Mathakala, V and Sallabathula, ST and Peddiboyina, VL and Palempalli, UMD}, title = {Probiotics as emerging adjuncts in metabolic associated fatty liver disease therapy-a systemic review.}, journal = {BMC gastroenterology}, volume = {26}, number = {1}, pages = {}, pmid = {41634593}, issn = {1471-230X}, abstract = {Metabolic associated fatty liver disease (MAFLD), a leading cause of chronic liver disorders globally, is closely linked with the dysbiosis of the gut. These microbial imbalances contribute to pathogenesis of MAFLD through intestinal barrier dysfunction, systemic inflammation, and hepatic fat accumulation. This review aims to provide an in-depth analysis of the complex interaction between the gut microbiome and MAFLD, through literature search of articles published in open access journals of two electronic data bases PubMed, Medline from January 2015 to May 2025. Among 602 publications identified initially, 54 studies were considered based on inclusion and exclusion criteria as per the PRISMA guidelines. The results assimilate the findings from both preclinical models and human clinical trials, highlighting the influence of probiotic strains on key metabolic pathways. Lactobacillus and Bifidobacterium species were shown to regulate lipid metabolism, normalize liver enzyme activity, reduce insulin resistance, and attenuate hepatic inflammation. These effects are mediated through multiple mechanisms, including enhancement of gut barrier integrity, modulation of bile acid metabolismsuppression of endotoxemia and modulation of gut–liver axis. By summarizing emerging insights, this review offers an updated perspective on the role of probiotic interventions as a promising adjunct strategy in the prevention and management of MAFLD.}, }
@article {pmid41775960, year = {2024}, author = {Liu, Y and Du, Z and Lu, Y and Ma, Y and Yang, Y and Osmanaj, F and Zhang, Y and Guo, X and Qin, Y and Yang, X and Hua, K}, title = {Gut microbiota metabolism disturbance is associated with postoperative atrial fibrillation after coronary artery bypass grafting.}, journal = {NPJ cardiovascular health}, volume = {1}, number = {1}, pages = {}, pmid = {41775960}, issn = {2948-2836}, support = {82100295//National Natural Science Foundation of China/ ; CI2021A04110//China Academy of Chinese Medical Sciences/ ; 7222049//Beijing Natural Science Foundation of China/ ; }, abstract = {Postoperative atrial fibrillation (POAF) is a common complication after coronary artery bypass grafting (CABG) surgery. Gut microbiota and its metabolites have been implicated in the development of AF. However, whether the gut-host metabolic interaction contributes to POAF is still unknown. This study aimed to investigate the POAF-associated gut microbiota metabolism biomarkers and related risk model. The POAF (N = 30) patients and non-POAF (N = 60) patients from the discovery cohort exhibited significantly different microbiome and metabolome profiles. The differentiated features were mainly implicated in the bile acids (BAs) and short-chain fatty acids metabolism, inflammation, and oxidative stress. Random forest analysis identified the combination of five secondary BAs showed a powerful performance on predicting POAF in the discovery cohort, highlighting significant values of area under the curve (AUC = 0.954) and correct classification rate (CCR, 93.3%). In addition, the five secondary BAs-based risk model also exhibited good performance in differentiating the POAF (N = 114) and non-POAF individuals (N = 253) in an independent validation cohort (AUC = 0.872; CCR = 90.4%). This work revealed perturbed microbial and metabolic traits in POAF, providing potential avenues for the prediction and prevention of POAF after CABG.}, }
@article {pmid41774605, year = {2026}, author = {Wang, T and Lu, S and Sun, L and Cheng, Y}, title = {Skin Barrier Compromise: A Central Early Event in Ultraviolet Radiation-Induced Skin Pathogenesis.}, journal = {Dermatology (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-11}, doi = {10.1159/000551027}, pmid = {41774605}, issn = {1421-9832}, abstract = {Ultraviolet radiation (UVR) is a major environmental stressor to the epidermal barrier, extending beyond erythema or photoaging. Emerging evidence reframes barrier impairment as an early and central event, integrating DNA and oxidative injury with inflammatory, immune, and microbial disturbances in a self-reinforcing cycle of fragility. This perspective challenges the traditional view of UVR damage as isolated mechanisms and highlights the need for barrier-focused research. Sunscreens remain essential, and recent formulations now extend beyond optical filtering by incorporating biologically active components such as antioxidants and photolyase that enhance photostability and support DNA lesion clearance. Emerging research also suggests that microbiome-preserving compositions may help maintain commensal balance during UVR exposure. Together, these developments point to a shift toward multifunctional photoprotection, although evidence is still accumulating. This review synthesizes recent advances alongside remaining gaps in the field. By integrating mechanistic evidence on UVR-induced barrier injury, it identifies directions that can support the design of more biologically grounded photoprotective strategies and delineates priority topics for future research.}, }
@article {pmid41774204, year = {2026}, author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M}, title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.}, journal = {Current microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {41774204}, issn = {1432-0991}, abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.}, }
@article {pmid41774188, year = {2026}, author = {Yadav, A and Melkani, GC}, title = {Microbes, mood, and metabolism/obesity: Pharmacological insights into the gut-obesity-depression triad.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-025-06022-y}, pmid = {41774188}, issn = {1420-9071}, support = {AG065992//National Institute of Aging/ ; }, }
@article {pmid41773937, year = {2026}, author = {Wang, A and Dao, LQ and Ramos-Gomez, F and Wang, Y}, title = {Maternal influences on oral microbiome development and implications for early childhood health: a systematic review.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0058525}, doi = {10.1128/iai.00585-25}, pmid = {41773937}, issn = {1098-5522}, abstract = {A deeper understanding of how maternal-infant interactions shape the establishment and diversification of the oral microbiome could have significant clinical applications; however, relatively few studies emphasize early maternal-infant microbial connections. This systematic review provides a longitudinal analysis of oral microbiome development from birth to five years, focusing on the relationship between maternal and infant microbiomes. We conducted a systematic search (June 2025) using keywords "mother," "children," "oral microbiome," and "longitudinal" across PubMed, Cochrane Library, and Embase. Twelve studies fulfilled the inclusion criteria: longitudinal design, healthy mother-child dyads, saliva sample collection, and relevant age range. We excluded review articles, non-English publications, and studies with overlapping data. Results were synthesized by developmental stage and topic. Overall, current literature agrees that the mother is an important source of exposure for initial colonization of the newborn's oral microbiome. Several studies indicated that the oral microbiome at birth is diverse and unspecialized, composed mostly of maternally derived strains. Rapid selection occurs over the first few weeks, as the relative abundances of typical oral bacterial species increase. Throughout the first year, increases in diversity strengthen the resemblance between infant and maternal microbiomes. The microbiome appears to stabilize around 3-5 years. In conclusion, maternal-infant connections play a significant role in influencing oral microbiome development during the first 5 years of life. This review highlights the need for future studies to incorporate larger, longitudinal designs with metadata and advanced tools to clarify the roles of delivery mode, tooth eruption, and parental lifestyle habits in shaping early oral microbiome development.}, }
@article {pmid41773902, year = {2026}, author = {Vidal, VM and Montes-Cobos, E and Canto, FB and Bozza, MT}, title = {The different meanings of tolerating the gut microbiome.}, journal = {mBio}, volume = {}, number = {}, pages = {e0173624}, doi = {10.1128/mbio.01736-24}, pmid = {41773902}, issn = {2150-7511}, abstract = {Multicellular life arose in a world dominated by microorganisms, a reality that has imposed a constant and pervasive selective pressure on all subsequent complex organisms. The immune system has been historically defined by its role in pathogen clearance through resistance mechanisms. However, a complementary and equally critical strategy is to enable the peaceful and inevitable coexistence with microorganisms, allowing each host species to shelter a unique associated microbiome. The term tolerance holds multiple meanings in immunology, yet all underlie a balanced and cooperative host-microorganism relationship. Each represents a different aspect of how the immune system limits tissue damage while maintaining functionality in the presence of microbial or inflammatory stimuli. Using the intestinal mucosa as a paradigm, we explore how epithelial barrier integrity, toxin neutralization, tissue repair, and stress response underpin disease tolerance; how microbial exposure calibrates innate immunity via epigenetic and metabolic reprogramming (LPS tolerance); and how the gut microenvironment fosters the generation of tolerogenic antigen-presenting cells and microbe-specific regulatory T cells to enforce immunological tolerance. We further explore how the microbiota itself is a potent inducer of these tolerogenic pathways and highlight IL-10 as a major hub, connecting different tolerogenic circuits. Finally, we examine the hygiene hypothesis, arguing that lifestyle changes during the Anthropocene disrupt these finely tuned tolerance mechanisms, thereby contributing to the rising incidence of immune-mediated diseases. We posit that these tolerance programs are fundamental prerequisites for engendering host-microbiota symbiosis, a relationship forged over millennia of co-evolution and endangered in the contemporary world.}, }
@article {pmid41773862, year = {2026}, author = {Makori, TO and Gicheru, ET and Mburu, MW and Sada, MS and Nyawa, O and Mutunga, M and Lewa, C and Cheruiyot, R and Kiguli, S and Olupot-Olupot, P and Muhindo, R and Mogaka, C and Williams, TN and Agoti, CN and Maitland, K and Sande, CJ}, title = {Nasopharyngeal Microbiome Composition and its Clinical Correlates in Children Hospitalized with Severe Pneumonia in East Africa.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag093}, pmid = {41773862}, issn = {1537-6613}, support = {P46493//Imperial College London/ ; //Medical Research Council Department for International Development/ ; MR/L004364/1/WT_/Wellcome Trust/United Kingdom ; 102231/WT_/Wellcome Trust/United Kingdom ; }, abstract = {BACKGROUND: Pneumonia remains the leading cause of infectious mortality in children under 5, with the highest burden in sub-Saharan Africa. Dysbiosis in nasopharyngeal (NP) microbiota may influence pneumonia susceptibility and progression, but little is known about its composition or clinical relevance in low- and middle-income countries. We characterized the NP microbiota of children hospitalized with severe pneumonia in East Africa and investigated associations with clinical outcomes.<br><br>METHODS: We performed 16S rRNA partial gene sequencing of NP swabs collected at hospital admission from 876 children enrolled in the COAST trial across 5 sites in Kenya and Uganda. Clinical, demographic, and virological data were prospectively collected. Microbial profiles were analyzed using hierarchical clustering, nonmetric multidimensional scaling, and multivariable regression to assess associations with respiratory viral infections, sepsis, cyanosis, bacteremia, coma, HIV status, malnutrition, sickle cell disease, malaria, and mortality.<br><br>RESULTS: The NP microbiome was structured in 6 distinct clusters, each dominated by different genera, including Staphylococcus, Streptococcus, Haemophilus, Dolosigranulum, Corynebacterium, and Moraxella. Multivariable models adjusting for study site and age showed a positive association between Corynebacterium and early mortality. Temporal analysis showed elevated Corynebacterium abundance in children who died within 48&#x2005;hours of admission, then declined over longer 56 survival intervals, approaching levels observed in survivors. However, time-continuous models did not support this persistent association, suggesting a subgroup effect.<br><br>CONCLUSIONS: We provide one of the largest high-resolution surveys of the pediatric upper airway microbiome in Africa, identifying microbial patterns associated with viral infection, HIV status, early death, and bacteremia.}, }
@article {pmid41773858, year = {2026}, author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M}, title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0222025}, doi = {10.1128/spectrum.02220-25}, pmid = {41773858}, issn = {2165-0497}, abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.<br><br>IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.}, }
@article {pmid41773303, year = {2026}, author = {Ma, H and Hu, K and Wang, Y}, title = {Dynamic changes of cervical microbiome during pregnancy for preterm birth risk prediction: A prospective cohort study.}, journal = {African journal of reproductive health}, volume = {30}, number = {4}, pages = {50-63}, doi = {10.29063/ajrh2026/v30i4.5}, pmid = {41773303}, issn = {1118-4841}, abstract = {This prospective cohort study investigated the dynamic changes in the cervical microbiome during pregnancy and developed a predictive model for preterm birth risk. Ninety-three singleton pregnant women were enrolled, including 41 with preterm birth and 52 with term delivery. Cervical secretions were collected at four gestational stages and analyzed using 16S rRNA sequencing, alongside ELISA testing for inflammatory markers. The preterm group exhibited significantly lower microbial diversity and a progressively increasing ratio of Lactobacillus iners to Lactobacillus crispatus throughout pregnancy. Early pregnancy IL-6 levels were also significantly elevated in this group. Logistic regression identified the L. iners/L. crispatus ratio, IL-6, history of preterm birth, and short cervical length as independent risk factors. The integrated prediction model demonstrated high accuracy (AUC 0.847), with even stronger performance in predicting births before 34 weeks (AUC 0.892). These findings suggest that microbiome patterns and inflammatory markers can effectively predict preterm birth risk, supporting early clinical intervention.}, }
@article {pmid41773092, year = {2026}, author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS}, title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.}, journal = {Research and reports in urology}, volume = {18}, number = {}, pages = {580953}, pmid = {41773092}, issn = {2253-2447}, abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).<br><br>METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.<br><br>RESULTS: Baseline &#x3b2; diversity did not differ between groups. Post-instillation, &#x3b2; diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.<br><br>CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.}, }
@article {pmid41772961, year = {2026}, author = {Li, M and Zong, H and Yang, X and Liu, Q and Wang, J and Wang, M and Wu, D and Zheng, S and Wang, H and Long, Q}, title = {A flavonoid-rich medicinal herb extract ameliorates high-fat diet-induced obesity and insulin resistance in mice.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2026007}, pmid = {41772961}, issn = {1745-7270}, abstract = {Obesity has emerged as a critical global health challenge, contributing to severe metabolic and neoplastic complications. However, most existing anti-obesity drugs exhibit significant adverse effects, necessitating the development of safer therapeutic alternatives. In this study, we evaluate the efficacy and safety of a flavonoid-rich medicinal herb extract (MHE) in a high-fat diet (HFD)-induced murine obesity model. Daily oral administration of MHE does not alter food intake or induce hepatic injury but significantly attenuates HFD-induced weight gain (P < 0.05) and adiposity accumulation. Furthermore, MHE treatment improves systemic insulin sensitivity and glycemic control. Notably, MHE enhances whole-body energy expenditure, as evidenced by elevated oxygen consumption (VO 2), carbon dioxide production (VCO 2), and heat generation (P < 0.01). Mechanistically, MHE selectively promotes the proliferation of beneficial gut microbiota, including Lactobacillus, Akkermansia, and Bifidobacterium species, resulting in increased production of the short-chain fatty acid propionate (PA). Elevated circulating PA levels subsequently stimulate the browning/beiging of inguinal white adipose tissue (iWAT) and upregulate thermogenic pathways. Collectively, our findings demonstrate that MHE exerts anti-obesity effects through gut microbiota modulation and adipose tissue remodeling, offering a promising natural alternative for obesity management.}, }
@article {pmid41772824, year = {2026}, author = {Ndhlovu, A and von der Heyden, S}, title = {Spatial Patterns and Overlap of Sedimentary and Rhizosphere Microbiomes of the Seagrass Zostera capensis.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70313}, pmid = {41772824}, issn = {1758-2229}, support = {//African Research Universities Alliance/ ; //National Research Foundation/ ; }, abstract = {Seagrasses are important nature-based solutions for climate change mitigation and adaptation due to their carbon stocks and ecosystem service co-benefits. Characterising microbial communities in seagrass sediments and rhizospheres is essential for understanding their roles in biogeochemical cycling, seagrass health, and potential contributions to ecosystem functioning. However, the extent to which seagrass microbiomes are shared at different spatial scales is not well understood. We utilised 16S rRNA metabarcoding to characterise prokaryotic communities in the sediments of the seagrass Zostera capensis at three estuaries spanning the environmental gradient of South Africa. In addition, we characterised the rhizosphere microbiome (rhizobiome) to better understand rhizosphere and sediment community dynamics. Overall, after accounting for community in adjacent seawater, we found that Z. capensis sediment and rhizosphere microbiomes largely overlap, sharing 34 genera but also harbour core genera. The sediment microbiome and rhizobiome showed significant spatial variability, suggesting that both local-scale and broader estuary-specific factors shape site-level microbial signatures. Further, predictive functional analysis showed that the rhizobiome was enriched for nutrient cycling pathways potentially beneficial to Z. capensis. Our findings support the exploration of sediment and rhizosphere microbial communities for monitoring ecosystem health and assessing impacts from threats such as pollution and climate change.}, }
@article {pmid41772743, year = {2026}, author = {He, J and Wang, MN and Chen, HJ and Zuo, GY and Li, JL and Yin, WF and Pan, XG and Cheng, YC and Xia, CY and Xu, JK and Zhang, WK}, title = {Muribaculum intestinale alleviates depressive-like behaviors by inhibiting Th17 cell differentiation and M1 microglia polarization.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02354-4}, pmid = {41772743}, issn = {2049-2618}, support = {ZRZC2025-KCC03//National High Level &amp; Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 2025-NHLHCRF-JBGS-A-WZ-10; ZRJY2024-BJ01//National High Level &amp; Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 82474100//National Natural Science Foundation of China/ ; 82474100, 82273815, 82273809, 82073731//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in the pathogenesis of depression. Our previous studies identified loganin as a potential antidepressant agent; however, its oral bioavailability is low. Whether loganin alleviates depression via modulation of the gut microbiota remains unclear.<br><br>METHODS: Chronic unpredictable stress mice model was used to evaluate the antidepressant-like effects of loganin. To determine the role of gut microbiota, mice were treated with an antibiotic cocktail (ABX) to deplete microbiota. Fecal microbiota transplantation (FMT) from loganin-treated donors and Muribaculum intestinale (M. intestinale) were performed to assess microbial contributions.<br><br>RESULTS: Loganin exerted antidepressant-like effects by modulating gut microbiota, as evidenced by reduced efficacy in ABX-treated mice and behavioral improvements in recipients of FMT from loganin-treated donors. Loganin modulated gut microbiota composition particularly increasing the abundance of Muribaculum, and increased short-chain fatty acids (SCFAs). M. intestinale alleviated depressive-like behaviors, prompted the butyrylation of ROR&#x3b3;t, inhibited Th17 cells differentiation, and suppressed M1 microglia polarization. Importantly, overexpression of ROR&#x3b3;t attenuated the behavioral benefits of M. intestinale.<br><br>CONCLUSION: Loganin exerts antidepressant-like effects by enriching Muribaculum and SCFAs, thereby inhibiting Th17 cell differentiation and M1 microglia polarization. M. intestinale may represent a promising microbial-based therapeutic strategy for depression.}, }
@article {pmid41772715, year = {2026}, author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD}, title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02362-4}, pmid = {41772715}, issn = {2049-2618}, support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.<br><br>RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.<br><br>CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.}, }
@article {pmid41772405, year = {2026}, author = {Luo, H and Kamer, AR and Xu, Z and Qi, X and Liu, R and Wu, B}, title = {Moderating Effects of Oral Bacteria and Tooth Loss on Cognitive Performance.}, journal = {JDR clinical and translational research}, volume = {}, number = {}, pages = {23800844261423487}, doi = {10.1177/23800844261423487}, pmid = {41772405}, issn = {2380-0852}, abstract = {INTRODUCTION: The oral microbiome may influence brain health and contribute to cognitive decline. However, little evidence exists on the potential modifying role of the oral microbiome in the relationship between tooth loss and cognitive performance. This study aimed to investigate the interaction effects between tooth loss and oral dysbiotic status on cognitive performance.<br><br>METHODS: Data were from the 2011-2012 National Health and Nutrition Examination Survey. The sample included 677 adults aged 60 to 69 y. Cognitive performance was assessed by the Consortium to Establish a Registry for Alzheimer's Disease, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test. Significant tooth loss was defined as a loss of &#x2265;10 permanent teeth out of 28. A high dysbiotic index was defined as being in the upper tertile of the ratio of periodontal disease-associated bacteria (Treponema, Porphyromonas, and Tannerella) to healthy bacteria (Rothia and Corynebacterium).<br><br>RESULTS: A multivariable linear regression model showed a significant interaction effect between tooth loss and dysbiotic index on the AFT (b = -1.87, P = 0.03), indicating that participants with a higher dysbiosis index and fewer missing teeth scored lower on the AFT.<br><br>CONCLUSIONS: The effect of tooth loss on verbal fluency depends on oral bacterial imbalances: if there is significant tooth loss, bacterial imbalances may not be important. However, when fewer teeth are lost, high bacterial imbalances may account for lower verbal fluency. These findings suggest that maintaining periodontal health aimed at decreasing oral dysbiosis should be promoted among older adults in the community.Knowledge Transfer Statement:Our findings highlight the importance of preserving the health of the teeth and not just retaining the teeth. Oral health awareness and good oral hygiene practice should be further promoted among older adults in the community.}, }
@article {pmid41771971, year = {2026}, author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J}, title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40137-x}, pmid = {41771971}, issn = {2045-2322}, support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; }, }
@article {pmid41771954, year = {2026}, author = {Nicotra, D and Mosca, A and Dimaria, G and Tessitori, M and Vetukuri, RR and Catara, V}, title = {Temporal dynamics of the tomato rhizosphere microbiome in response to synthetic communities of plant growth-promoting rhizobacteria.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41771954}, issn = {2045-2322}, abstract = {UNLABELLED: The rhizosphere microbiome plays a crucial role in plant health and productivity, yet intensive agriculture has diminished soil microbial diversity, increasing reliance on chemical inputs. Plant growth-promoting rhizobacteria offer a sustainable alternative, enhancing nutrient uptake, stress tolerance, and pathogen resistance. While single-strain inoculants have shown promise, microbial consortia may improve resilience through functional diversity. However, their impact on resident microbial communities remains understudied. In this study, three SynComs (four, six, and ten strains) were assembled from taxonomically diverse native PGPR strains identified as part of the tomato core microbiome, including Bacillus, Pseudomonas, Glutamicibacter, Paenarthrobacter, Chryseobacterium and Leclercia. All consortia significantly enhanced tomato growth, with the six- and ten-strain SynComs (containing Pseudomonas) exhibiting the most pronounced effects, increasing plant height by up to 94% in the indeterminate-growth variety ‘Proxy’. High-throughput sequencing revealed that while temporal factors were the primary drivers of community assembly, SynCom application triggered dynamic, time-dependent shifts specifically targeting the bacterial “rare biosphere”. Early-stage (T1) responses were characterized by the enrichment of rare bacterial taxa involved in key biogeochemical processes, such as the sulphur (Sulfurovum, Desulfosporosinus) and nitrogen (Azospirillum) cycles. By four weeks post-inoculation, community responses converged, primarily through the depletion of rare taxa and a predicted functional redirection toward xenobiotic degradation pathways. While SynCom strains showed a decline in absolute abundance over time, the persistence of growth-promoting effects suggests that these consortia act through early-stage indirect microbiome modulation rather than long-term high-density colonization. Furthermore, the consortia exerted a subtle cross-kingdom influence, modulating fungal succession by sustaining Basidiomycota and Mucoromycota populations. These findings demonstrate that small, host-derived, taxonomically diverse SynComs can enhance tomato growth and restructure rhizosphere microbial communities, especially impacting rare bacterial taxa and metabolic potential of the communities, with Pseudomonas-containing consortia exerting the most pronounced effects. These insights support the use of tailored, core-based microbial communities to improve crop productivity and soil health, though further research is needed to optimize SynCom design for agricultural applications.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41114-0.}, }
@article {pmid41771940, year = {2026}, author = {Li, Y and Azman, EA and Ismail, R and Deng, X and Dhar, S and Noviardi, R and Citraresmini, A and Zi, T and Yang, L}, title = {Effect of root promoter on tobacco (Nicotiana tabacum L.) growth and nutrient accumulation at Hunan Province, China.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40215-0}, pmid = {41771940}, issn = {2045-2322}, }
@article {pmid41771883, year = {2026}, author = {Mao, C and Jin, W and Dou, L and Guo, T and Huang, J and Wang, Y and Liu, X and Wu, S and Qiao, W and Xiang, Y and Zhu, Y and Wu, J and Yeung, KWK}, title = {Bioengineered ROS-tolerant probiotic reshapes gut microbiota-host axis to ameliorate type 2 diabetes in male mice.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70138-3}, pmid = {41771883}, issn = {2041-1723}, support = {2023YFB3810200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 21200592//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 22210832//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 23220952//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; }, abstract = {The pandemic-scale progression of type 2 diabetes mellitus (T2DM) necessitates innovative interventions targeting the pathogenic triad of insulin resistance, dysregulation of lipid metabolism, and gut microbiome dysbiosis. Here, we report a synthetically bioengineered probiotic consortium (REcN-F/Ca) developed through directed metabolic adaptations of Escherichia coli Nissle 1917 (EcN) under iterative hydrogen peroxide selection, subsequently functionalized with fructooligosaccharide-calcium carbonate composites. REcN-F/Ca exhibits enhanced reactive oxygen species tolerance through upregulated antioxidant enzymes and hydrogen sulfide-mediated redox balancing, alongside improved gastrointestinal survivability. In high-fat diet-induced obese male mice, REcN-F/Ca restores gut microbiota diversity, enriches butyrogenic taxa (Lachnospiraceae and Blautia), and rescues short-chain fatty acids depletion. Transcriptomic profiling reveals PPAR signaling activation, driving lipid metabolism and suppressing adipose inflammation. These effects translate to systemic metabolic improvements with attenuated weight gain (-25.4%), restored glucose homeostasis, and reduced insulin resistance (HOMA-IR: -73.2%) in the obesity and T2DM murine model. Our findings establish REcN-F/Ca as a synthetically engineered probiotic that simultaneously corrects intestinal ecological perturbations and reverses host metabolic dysfunction, proposing a paradigm for metabolic syndrome management.}, }
@article {pmid41771597, year = {2026}, author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R}, title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e100158}, doi = {10.1136/bmjopen-2025-100158}, pmid = {41771597}, issn = {2044-6055}, abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.<br><br>METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged &#x2265;40 years; n=50) and Group B (patients aged &#x2265;40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged &#x2265;65 years (or &#x2265;55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150&#x2009;bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.<br><br>ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.}, }
@article {pmid41771438, year = {2026}, author = {Lynch, SV and Nagler, CR and Rachid, R}, title = {Microbial Therapeutics for the Prevention and Treatment of Food Allergy.}, journal = {The journal of allergy and clinical immunology. In practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaip.2026.02.024}, pmid = {41771438}, issn = {2213-2201}, abstract = {Food allergy affects approximately 8% of children and 11% of adults in the United States. Available treatment including oral immunotherapy and anti-IgE are not known to lead to remission. There is now increasing evidence implicating the gut microbiome as a key regulator of allergic inflammation. Distinct microbial and metabolomic alterations characterize food-allergic individuals, and gnotobiotic mouse models show that fecal microbiota from food-allergic donors transfers allergic sensitization, whereas microbiota from healthy donors protects from anaphylaxis through induction of tolerogenic Foxp3[+]RORγt[+] regulatory T cells. Goblet cell-derived resistin-like molecule beta (RELM β) induces food allergy through modulation of the gut microbiome and depletion of indole-producing species. These findings have inspired the development of five microbial therapeutics approaches: probiotics, rationally defined bacterial consortia, fecal microbiota transplantation, metabolite-based approaches, and biologics targeting dysbiosis-associated pathways. Early-phase clinical studies support feasibility, yet long-term safety, durability, and reproducibility remain uncertain. Major challenges include inter-individual variability, ecological complexity, and regulatory standardization. Microbiome-directed therapeutics hold promise to transform food allergy management from temporary desensitization toward remission and durable immune tolerance. The application of systems biology approaches integrating metabolomics, transcriptomics, and immune phenotyping will be essential to unravel the complex host-microbial interactions that underlie the efficacy of these approaches.}, }
@article {pmid41771260, year = {2026}, author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR}, title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70309}, pmid = {41771260}, issn = {1758-2229}, support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; }, abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.}, }
@article {pmid41771225, year = {2026}, author = {Maria-Alexia, P and Cristina, R and Andreea-Ramona, T and Octavian, A and Viorica, R}, title = {Familial colorectal cancer: risk factors, screening strategies and personalized medicine.}, journal = {Cancer genetics}, volume = {302-303}, number = {}, pages = {166-175}, doi = {10.1016/j.cancergen.2026.02.008}, pmid = {41771225}, issn = {2210-7762}, abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with approximately 25-30 % of cases exhibiting a familial component driven by germline mutations in DNA mismatch repair genes (Lynch syndrome) or the APC gene (familial adenomatous polyposis). Despite advances in screening and early detection, significant challenges persist in identifying at-risk individuals, optimizing surveillance strategies and addressing disparities in access to genetic testing and preventive care. This narrative review synthesizes current evidence on the genetic underpinnings, modifiable risk factors and personalized screening approaches for familial CRC. We highlight the critical interplay between hereditary predisposition and environmental exposures including diet, obesity, smoking and gut microbiome alterations, which cumulatively influence disease penetrance and clinical outcomes. Emerging predictive models integrating family history, polygenic risk scores and proteomic biomarkers offer unprecedented opportunities for risk stratification, enabling tailored screening initiation and intervals that balance clinical efficacy with cost-effectiveness. Novel non-invasive biomarkers, such as circulating tumor DNA and stool RNA tests, demonstrate promising sensitivity and specificity, potentially enhancing patient adherence while complementing gold-standard colonoscopy. Furthermore, artificial intelligence-assisted endoscopy and comprehensive genetic panels are reshaping precision oncology by improving adenoma detection rates and guiding targeted therapies. Addressing social determinants of health and implementing structured genetic counseling remain essential to achieving equitable CRC prevention. By transitioning from age-based to individualized, risk-adapted screening paradigms, healthcare systems can significantly reduce CRC incidence and mortality, particularly among genetically predisposed populations.}, }
@article {pmid41771203, year = {2026}, author = {Khan, SM and Hussain, JM and Khan, B and Saad, A and Mehboob, J and Rukh, G and Manzoor, M and Mughal, AW and Kayani, A and Baig, MA and Khan, SRM and Saleem, Z and Hashim, R}, title = {Dark side of nocturnal eating: Unraveling the emerging axis between meal timing, gut microbiota, and early-onset cancer risk.}, journal = {Nutrition research (New York, N.Y.)}, volume = {148}, number = {}, pages = {1-14}, doi = {10.1016/j.nutres.2026.01.007}, pmid = {41771203}, issn = {1879-0739}, abstract = {The worldwide increase in early-onset metabolic disorders and digestive system cancers has elicited serious concern about lifestyle and diet as contributors to chronic disease risk. Disruption of circadian rhythms, particularly through nocturnal eating, is implicated in the development of various malignancies. This narrative review explored the emerging interplay between nocturnal eating, gut microbiota disruption, and early-onset cancer risk. Literature was sourced from PubMed, Scopus, Google Scholar, and Elsevier databases, emphasizing mechanistic studies and key findings in chrononutrition, microbiome research, and oncology. Nocturnal eating desynchronizes central and peripheral clocks, alters clock-gene expression, and provokes gut dysbiosis and inflammatory signaling that promote tumorigenic pathways. In contrast, daytime-aligned time-restricted eating (TRE) has shown potential to restore circadian synchrony, enhance metabolic resilience, and improve gut health even in the absence of caloric restriction. While TRE's role in cancer prevention remains hypothetical, its circadian benefits warrant further investigation. Overall, meal timing represents a modifiable factor influencing metabolic health and possibly early carcinogenesis. Aligning eating behavior with intrinsic circadian rhythms may help mitigate cancer risk and improve long-term well-being.}, }
@article {pmid41771182, year = {2026}, author = {Carrillo, MP and Berrojalbiz, N and Sánz, C and Iriarte, J and Trilla-Prieto, N and Calbet, A and Saiz, E and Barata, C and Dachs, J and Vila-Costa, M}, title = {Copepod-associated microbiome responses to organophosphate ester plasticizers and other bioaccumulative organic pollutants in the ocean.}, journal = {Water research}, volume = {296}, number = {}, pages = {125640}, doi = {10.1016/j.watres.2026.125640}, pmid = {41771182}, issn = {1879-2448}, abstract = {Organic pollutants pose a growing threat to ocean ecosystems, largely due to their persistence, bioaccumulation potential, and toxicity. Yet, directly measuring the full spectrum of pollutants in situ remains unfeasible, and thus there is a dearth of alternative indicators of exposure. Host-associated microbiomes offer a promising but underexplored approach to fill this gap. Along a latitudinal transect of the Atlantic Ocean (40°N - 52°S), we observed significant correlations between the relative abundance of Enterobacterales in copepod-associated bacterial communities and seawater concentrations of organophosphate esters (OPEs), polycyclic aromatic hydrocarbons (PAHs) and with some perfluoroalkyl acids (PFAAs). All these chemicals bioaccumulate in marine zooplankton. Laboratory exposures of the copepod Paracartia grani to environmentally relevant OPE concentrations revealed similar microbiome composition shifts and decreased fecundity, revealing active depuration processes, including microbial degradation and fecal pellet production. These findings establish the basis for exploring host-associated microbiomes as sensitive indicators of bioaccumulative contaminant exposure in marine ecosystems, offering a novel avenue for large-scale pollution monitoring.}, }
@article {pmid41770930, year = {2026}, author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G}, title = {High bacterial diversity drives the suppression of a soilborne plant disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {10}, pages = {e2509303123}, doi = {10.1073/pnas.2509303123}, pmid = {41770930}, issn = {1091-6490}, abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.}, }
@article {pmid41770903, year = {2026}, author = {Wang, X and Sun, H and Tan, Y and Xu, S and Liu, Z and Ji, K and Qiu, D and Deng, J and Feng, B and Wu, X and Iwakura, Y and Chen, M and Feng, R and Huang, C and Tang, C}, title = {Colonic Engyodontium fungus triggers neutrophil antimicrobial activity to suppress Lactobacillus johnsonii-derived glutamic acid-maintained Tregs.}, journal = {The Journal of clinical investigation}, volume = {}, number = {}, pages = {}, doi = {10.1172/JCI196788}, pmid = {41770903}, issn = {1558-8238}, abstract = {Isolating commensal fungi from mouse intestines has been challenging, limiting our understanding of their role in intestinal immune homeostasis and diseases. Using an Fc fusion protein of the C-type lectin Dectin-2, we successfully purified the commensal Ascomycota fungus Engyodontium sp. from mouse feces. Engyodontium enhances the antimicrobial activity of colonic neutrophils via CARD9 pathway, and exacerbates colitis by impairing the colonization of intestinal Lactobacillus johnsonii (L. johnsonii) WXY strain. L. johnsonii produces high levels of L-glutamic acid by expressing the glutaminase-encoding gene glsA to facilitate Treg expansion via enhancing IL-2 receptor signaling. Patients with Crohn's disease (CD) and ulcerative colitis harbored increased Engyodontium and decreased L. johnsonii abundance. Engyodontium directly induced calprotectin in human colonic neutrophils, and CD patients exhibited lower levels of L-glutamic acid which also promoted human Treg expansion. These findings highlight the Engyodontium-calprotectin axis against the Lactobacillus-glutamate-Treg cascade to aggravate colitis, suggesting commensal Engyodontium-triggered signaling as a therapeutic target for mucosal inflammatory diseases.}, }
@article {pmid41770693, year = {2026}, author = {Lin, A and Bik, EM and Costello, EK and Dethlefsen, L and Haque, R and Relman, DA and Singh, U}, title = {Correction: Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States.}, journal = {PloS one}, volume = {21}, number = {3}, pages = {e0343568}, pmid = {41770693}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0053838.].}, }
@article {pmid41770447, year = {2026}, author = {Sosanya, ME and Temple, JL}, title = {Two Sides of a Coin: Molecular, metabolic, and Phenotypic Convergence in Pediatric Undernutrition and Obesity.}, journal = {Current obesity reports}, volume = {15}, number = {1}, pages = {}, pmid = {41770447}, issn = {2162-4968}, abstract = {PURPOSE OF REVIEW: This narrative review juxtaposes the metabolic and molecular consequences of pediatric under- and overnutrition, highlighting the similarities and differences between these two nutritional states occurring simultaneously in different parts of the world.<br><br>RECENT FINDINGS: Numerous biological changes in pediatric acute undernutrition and obesity have been linked to elevated risks of chronic metabolic disorders. We summarize recent evidence on pathophysiological pathways and outcomes common to both conditions. Despite etiological divergence, early-life nutritional imbalances converge on shared mechanisms and consequences with intergenerational implications.<br><br>SUMMARY: Both acute undernutrition and obesity in childhood have intersecting long-term outcomes including insulin resistance, type 2 diabetes, cardiovascular diseases, hepatic steatosis, cancers, and others, mediated through endocrine, immunological, epigenetic, and gut microbiome pathways, albeit via diverse specific mechanisms. Robust, longitudinal studies in varied geopolitical settings are needed to further elucidate the complex mechanisms, long-term phenotypic consequences, and therapeutic effects in these twin conditions.}, }
@article {pmid41770016, year = {2026}, author = {Martins, I and Silva, JM and Almeida, JR}, title = {HYMET: A Hybrid Metagenomic Pipeline for Accurate and Efficient Taxonomic Classification.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag024}, pmid = {41770016}, issn = {2047-217X}, abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a two-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor (LCA) classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.<br><br>RESULTS: Across seven CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93&#xa0;s runtime and a mean peak memory of 6.24&#xa0;GB. Performance remained stable under mutation rates up to 30% for most domains (F1 &#x2265; 0.8), with viral sequences showing the expected decline (F1 &#x2248; 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson r = 0.998, Bray-Curtis =0.04) across bacteria, fungi, and archaea.<br><br>CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.}, }
@article {pmid41769660, year = {2026}, author = {He, X and Chen, C and Shen, L and Su, X and Xie, H and Yang, M and Jiang, W}, title = {Retrospective insights into probiotic and prebiotic interventions: associations with gut microbiota profiles and nutritional outcomes.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1729480}, pmid = {41769660}, issn = {2296-861X}, abstract = {BACKGROUND: Probiotics and prebiotics are known to regulate the gut microbiota, however, their relations with the metabolic and nutritional outcomes in adults are under-investigated in practical environments.<br><br>OBJECTIVE: To provide light on microbiome-targeted metabolic health initiatives, this retrospective study investigates relationships among probiotic and prebiotic therapies, gut microbiota profiles, and nutritional outcomes.<br><br>METHODS: Clinical and nutritional history (n&#x202f;=&#x202f;350 adults) in probiotic (n&#x202f;=&#x202f;140), prebiotic (n&#x202f;=&#x202f;120), and control (n&#x202f;=&#x202f;90) were compared. The microbiota data were obtained with the help of 16S rRNA sequencing in the stool samples at baseline and 4-12&#x202f;weeks of the intervention. Alpha (Shannon, Simpson) and beta diversity (Bray-Curtis) was evaluated by means of PERMANOVA, and the relative abundance of the main taxa (Lactobacillus spp., Bifidobacterium spp., Faecalibacterium prausnitzii) was determined. The adjusted ANCOVA and multivariate regression models adjusted to the difference between baseline were used to analyze the anthropometric and biochemical outcomes, including body mass index (BMI) and lipid profiles.<br><br>RESULTS: Alpha diversity (Shannon index: probiotics 3.4-4.2, p&#x202f;<&#x202f;0.01; prebiotics 3.3-4.0, p&#x202f;<&#x202f;0.01) and beta diversity clustering (PERMANOVA R2&#x202f;=&#x202f;0.12, p&#x202f;<&#x202f;0.001 in probiotics) were significantly increased by the use of probiotics and prebiotics, respectively. Lactobacillus (2.1-4.8%, p&#x202f;<&#x202f;0.01) and Bifidobacterium (3.5-7.9%, p&#x202f;<&#x202f;0.001) were increased due to probiotic supplementation, whereas Bifidobacterium (3.7-6.8%, p&#x202f;<&#x202f;0.001) and F. prausnitzii (6.1-8.3%, p&#x202f;=&#x202f;0.04) were increased due to prebiotics supplementation. The two interventions were better than controls in terms of BMI and lipid levels (reduction of BMI: probiotics -1.6&#x202f;+&#x202f;- 0.4&#x202f;kg/m2, prebiotics -2.0&#x202f;+&#x202f;- 0.5&#x202f;kg/m2; total cholesterol: probiotics -18&#x202f;+&#x202f;-5&#x202f;mg/dL, prebiotics -17&#x202f;+&#x202f;-6&#x202f;mg/dL; all p&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: The use of probiotic and prebiotic supplementation was found to be related to an augmented gut microbial and better metabolic results in grown-ups. Such results point to possible advantages of the dietary microbiota modulation, but due to the retrospective design, it is not possible to make causal conclusions.}, }
@article {pmid41769659, year = {2026}, author = {Alhodieb, FS}, title = {Microbial biofortification of fermented foods: a review of probiotic-mediated nutrient enhancement.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1754233}, pmid = {41769659}, issn = {2296-861X}, abstract = {Microbial biofortification via probiotic fermentation is a unique solution to reducing micronutrient deficiencies worldwide and it is a sustainable approach to prevention and German fermentation is widely applicable for plant-based diets as these micronutrients, such as B12 and K, are hardly present. Fermentative microbes such as Lactobacillus, Bifidobacterium, Propionibacterium synthesis of the vitamins like folate, riboflavin, vitamin K. They also facilitate the accessibility of minerals and increase the quality of proteins in many foods. This process not only enhances vitamins and minerals as a result of antinutrient such as phytate breakdown, but also bioactive peptides and short-chain fatty acids are produced. These are beneficial compounds for gut health and are helpful to the health of the immune system. Studies in labs, animals, and humans indicate that consumption of biofortified fermented foods increases micronutrient levels, promotes gut microbial balance, and increases immunity. In order to exploit this approach to its fullest potential, there are hurdles to overcome, ensuring that the strain remains viable, enhancing product taste, and overcoming regulatory hurdles. Future advances will require engineering strains of probiotics to produce even greater amounts of vitamins and implementing personalized microbiome information, as well as their public health interventions, in resource-limited situations.}, }
@article {pmid41769655, year = {2026}, author = {Ray, S and Shankaran, P}, title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1761992}, pmid = {41769655}, issn = {2296-861X}, abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.}, }
@article {pmid41769611, year = {2026}, author = {Li, X and Xu, S and Li, Y and Wang, R and Qin, C and Wang, X}, title = {Research Progress on the Mechanisms of Gut Microbiota Dysbiosis Associated With Idiopathic Pulmonary Fibrosis: A Review.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e102429}, pmid = {41769611}, issn = {2168-8184}, abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic interstitial lung disease with an incompletely understood pathogenesis. In recent years, growing evidence has highlighted the critical role of gut microbiota dysbiosis in the onset and progression of IPF. This review comprehensively summarizes the characteristics of gut microbiota alterations associated with IPF, explores the underlying mechanisms driving these changes, and examines their impact on disease development. Particular emphasis is placed on the emerging concept of the "gut-lung axis," which elucidates the bidirectional communication between the intestinal microbiome and pulmonary health. The review further discusses microbial metabolites and immune modulation as key mediators linking gut dysbiosis to pulmonary fibrosis. Additionally, current advances in microbiota-targeted therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation, are analyzed for their potential in IPF management. By systematically integrating recent findings, this article aims to deepen the understanding of IPF pathophysiology and provide a theoretical foundation for novel treatment targets centered on gut microbiota regulation.}, }
@article {pmid41769608, year = {2026}, author = {Beniwal, P and Singla, M and Kar, DP and Bhargava, V and Chandra, N and Sinha, DK and Ruhela, V and Jha, R and Joseph, R and Rs, V and Bhosle, N and Mehta, K and Bajpai, S}, title = {Multispecies Probiotic Supplementation in Chronic Kidney Disease (CKD): Insights From Indian Nephrology Experts.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e102520}, pmid = {41769608}, issn = {2168-8184}, abstract = {Chronic kidney disease (CKD) is a progressive condition leading to the accumulation of uremic toxins and systemic complications, eventually resulting in loss of kidney function. One of the major mechanisms behind the CKD complications is gut dysbiosis, a commotion in the gut micro-ecology that aggravates systemic inflammation and worsens the CKD management. Probiotics, through their ability to restore gut micro-ecology, strengthen the intestinal barrier integrity, modulate the immune system, and mitigate systemic inflammation, offer a promising add-on therapy to traditional CKD therapies. Specific probiotic strains, including Streptococcus thermophilus, Lactobacillus acidophilus, Bifidobacterium longum, and Bacillus coagulans, have demonstrated antimicrobial effects by promoting commensal bacterial growth and inhibiting pathogenic bacterial growth. Studies indicate that these probiotics reduce uremic toxin levels, such as indoxyl sulfate and p-cresyl sulfate, blood urea nitrogen, urea, and creatinine levels, enhance gut integrity, alleviate inflammation, and are beneficial for patients with CKD stages 3 to 5. While the evidence for probiotic supplementation is promising, further studies are required to establish their long-term benefits, especially in patients with immune deficiency or kidney transplants. Overall, this consensus article provides insights from Indian nephrology experts on the potential benefits of multispecies probiotic supplementation in CKD patients, focusing on improving their quality of life, delaying disease progression, and ultimately augmenting survival outcomes.}, }
@article {pmid41769348, year = {2026}, author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J}, title = {Epistemic compression in large language model explanations of the gut-liver axis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1773593}, pmid = {41769348}, issn = {2235-2988}, abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.<br><br>METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.<br><br>RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.<br><br>CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.}, }
@article {pmid41769343, year = {2026}, author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y}, title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1688580}, pmid = {41769343}, issn = {2235-2988}, abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.<br><br>METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).<br><br>RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in &#x3b1;-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.<br><br>CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.}, }
@article {pmid41769336, year = {2026}, author = {Wu, Y and Han, B and Zhang, B and Li, J and Ren, B and Su, Z}, title = {Metabolic crosstalk between oral microbiota and the host in OSCC: emerging roles of microbial metabolites in tumor initiation and progression.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1778329}, pmid = {41769336}, issn = {2235-2988}, abstract = {Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by profound metabolic reprogramming and a persistently poor clinical outcome. Beyond genetic and environmental risk factors, growing evidence indicates that dysbiosis of the oral microbiome is associated with metabolic perturbations observed in OSCC and may contribute to tumor initiation and progression. Microbiome-derived metabolites represent a previously underappreciated layer of cancer metabolism, linking microbial activity to host metabolic states, epigenetic regulation, and immune dysfunction within the tumor microenvironment. In this review, we provide a comprehensive synthesis of current evidence highlighting how microbial metabolites shape metabolic vulnerabilities in OSCC through the microbiome-metabolite-host axis. We focus on key metabolite classes, including short-chain fatty acids, tryptophan-derived metabolites, sulfur-containing compounds, and other emerging metabolic intermediates, and discuss their roles in modulating cellular energy metabolism, epigenetic remodeling, oxidative stress responses, and immune evasion. Particular emphasis is placed on the context-dependent and often dualistic functions of metabolites such as butyrate, which can exert tumor-suppressive or tumor-promoting effects depending on microbial source, concentration, and local inflammatory conditions. By integrating insights from metabolomics, microbial functional profiling, and mechanistic studies, this review underscores microbial metabolism as an integral component of OSCC pathobiology. Recognizing microbial metabolites as active metabolic regulators rather than passive byproducts provides a conceptual framework for identifying novel biomarkers and metabolic intervention strategies in OSCC.}, }
@article {pmid41769334, year = {2026}, author = {Zhong, L and Zhou, X and Su, J and Zhang, Y and Zhang, D and Wan, H}, title = {Microbiome dysbiosis and therapeutic restoration in atopic dermatitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1693905}, pmid = {41769334}, issn = {2235-2988}, abstract = {Atopic dermatitis (AD) is increasingly recognized as a chronic inflammatory skin disease driven by a self-reinforcing vicious cycle involving skin barrier dysfunction, immune dysregulation, and cutaneous microbiome dysbiosis. A hallmark of this dysbiosis is the overrepresentation of pathogens like Staphylococcus aureus and Malassezia species, alongside a marked loss of microbial diversity, particularly during disease flares. This review systematically dissects the host-derived factors-such as altered lipid profiles, reduced antimicrobial peptides, and elevated skin pH-that facilitate S. aureus colonization. We further examine how bacterial virulence factors amplify type 2 inflammation and impair barrier integrity, thereby sustaining the pathological loop. We also explore the emerging roles of the skin virome, particularly the phageome, and discuss how microbiome-targeted interventions, including bacteriotherapy with commensal bacteria and precision phage therapy, offer promising avenues for ecological restoration. Finally, we argue that future research must leverage multi-omics to understand strain-specific functions, ultimately guiding the development of personalized microbiome interventions for AD.}, }
@article {pmid41768933, year = {2025}, author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S}, title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.}, journal = {Frontiers in systems biology}, volume = {5}, number = {}, pages = {1659648}, pmid = {41768933}, issn = {2674-0702}, abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.}, }
@article {pmid41768524, year = {2026}, author = {Hirano, T and Wagatsuma, K and Shimomori, Y and Akita, K and Nakamura, T and Yamakawa, T and Yokoyama, Y and Kurumi, H and Ishigami, K and Nagaishi, K and Nakase, H}, title = {Loss of Nonhematopoietic Osteopontin Weakens the Intestinal Barrier and Alters the Microbiome and Metabolome in Mice.}, journal = {Gastro hep advances}, volume = {5}, number = {4}, pages = {100883}, pmid = {41768524}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) is characterized by intestinal barrier disruption and dysregulated interactions between host immunity and gut microbiota. Osteopontin (OPN) is considered a proinflammatory mediator in IBD, but nonhematopoietic cell-derived OPN may exert barrier-protective functions. This study aimed to determine the effects of OPN in a murine model of acute colitis.<br><br>METHODS: We examined wild-type and OPN knockout mice under steady-state conditions and in dextran sulfate sodium-induced colitis, including bone marrow chimeras to distinguish the effects of hematopoietic and nonhematopoietic OPN.<br><br>RESULTS: Overt colitis did not occur under steady-state conditions. Compared with wild-type mice, OPN knockout mice exhibited crypt elongation, goblet cell hyperplasia, and increased epithelial proliferation. Gene expression analysis revealed reduced interleukin (IL)-22, IL-23, and IL-13 levels alongside increased interferon-&#x3b3;, IL-1&#x3b2;, and IL-17A levels. 16S rRNA sequencing revealed increased alpha diversity, expansion of Akkermansia and Prevotellaceae, and reduced Lactobacillus abundance. Functional prediction identified enrichment of microbial sulfur metabolism pathways, and metabolomic analysis demonstrated increased L-proline and L-(-)-fucose levels and reduced &#x3b2;-sitosterol levels. These shifts indicate enhanced mucinolytic activity and altered energy metabolism, consistent with a latent "preinflammatory state." Bone marrow chimera experiments demonstrated that OPN deficiency in the recipients reproduced changes in the microbiota composition and lipocalin-2 expression at the steady state and conferred heightened susceptibility to dextran sulfate sodium-induced acute colitis, irrespective of donor genotype.<br><br>CONCLUSION: These findings indicate that nonhematopoietic cell-derived "guardian-type" OPN preserves barrier integrity, sustains IL-22/IL-23 production, and maintains microbiota-metabolome balance, whereas its loss induces a preinflammatory state that predisposes to acute mucosal injury. These findings provide a conceptual basis for stage- and source-specific therapeutic strategies in IBD.}, }
@article {pmid41768503, year = {2025}, author = {Lundberg, HE and Kafel, J and Holo, H and Larsen, SE}, title = {Daily cheese intake positively affects serum osteocalcin levels, vitamin K status and bone turnover markers in elderly men and women.}, journal = {BMJ nutrition, prevention &amp; health}, volume = {8}, number = {2}, pages = {e000933}, pmid = {41768503}, issn = {2516-5542}, abstract = {INTRODUCTION: Daily intake of vitamin K2-rich Jarlsberg cheese is shown to positively affect bone turnover markers (BTMs) in fertile women. How do postmenopausal women and adult men respond to a cheese intervention?<br><br>PURPOSE: To estimate the optimal daily efficacy dose (OED) of Jarlsberg cheese to increase serum osteocalcin level in postmenopausal females and males past 55 years of age and estimate the effect on BTMs.<br><br>METHODS: Ten expected healthy postmenopausal females and 10 healthy males past 55 years voluntarily participated in a two-dimensional response surface pathway designed dose-response study with three design levels. The duration of each design level was 4&#x2009;weeks. Blood samples were taken at baseline and the end of each design level for measurements of osteocalcin (OC), vitamin K2, the BTMs procollagen type 1 N-terminal propeptide (P1NP) and serum cross-linked C-telopeptide type I collagen (CTX-1) and other biochemical parameters.<br><br>RESULTS: In the female group, the OC level increased significantly (p<0.01) during the first design level but decreased slightly during the second and third design levels. Among males, the OC level increased monotonously during the study and significantly in the second and third design levels (p<0.01). There was no significant change in P1NP, but CTX decreased significantly (p&#x2264;0.05) in both sex groups. The ratio P1NP/CTX increased significantly (p&#x2264;0.05) in the female group. S-phosphate and s-urea increased significantly (p&#x2264;0.02) while s-calcium and s-magnesium were unchanged. After the study, four of the participating women received a diagnosis of osteoporosis.<br><br>CONCLUSION: Estimated OED of Jarlsberg cheese was 47 and 67&#x2009;g/day for postmenopausal females and adult males, respectively. The development in OC and BTMs suggests an anabolic effect of Jarlsberg cheese on bone tissue.}, }
@article {pmid41768492, year = {2025}, author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P}, title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).}, journal = {BMJ nutrition, prevention &amp; health}, volume = {8}, number = {2}, pages = {e001112}, pmid = {41768492}, issn = {2516-5542}, abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.<br><br>DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.<br><br>RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.<br><br>CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.}, }
@article {pmid41768489, year = {2025}, author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.}, journal = {BMJ nutrition, prevention &amp; health}, volume = {8}, number = {2}, pages = {e000776}, pmid = {41768489}, issn = {2516-5542}, abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.<br><br>DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.<br><br>RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.<br><br>CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.<br><br>TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.}, }
@article {pmid41768415, year = {2026}, author = {Panda, A and Adhikari, M and Nasker, SS and Nayak, AK and Das, D and Nayak, SK and Dash, SK and Nayak, S}, title = {Enhanced formulation of precision probiotics through active machine learning.}, journal = {Biology methods &amp; protocols}, volume = {11}, number = {1}, pages = {bpag007}, pmid = {41768415}, issn = {2396-8923}, abstract = {The human gut microbiome is crucial to health, with dysbiosis increasingly linked to disease. Precision probiotics offer a promising approach to restoring microbial balance, but ensuring probiotic viability through gastrointestinal transit remains a challenge. This study applies an advanced active machine learning (ML) approach to predict how excipients affect the growth of Lactobacillus plantarum, a commonly used probiotic. State-of-the-art experiments were carried out to complement the ML study. Starting with five known excipient-probiotic interactions, we apply active ML over three rounds to predict the effects of 116 excipients, iteratively refining model certainty and accuracy. Five ML models-neural networks, gradient boosting, logistic regression, random forest, and support vector machines-were trained and evaluated, with the final model achieving certainty levels close to 90%. Unlike previous methods, which retrained new models per iteration, our approach continuously optimized a single model, enhancing prediction stability and reducing uncertainty spread. These results highlight the potential of active ML to support accurate excipient selection in probiotic formulations.}, }
@article {pmid41768127, year = {2026}, author = {Alsaid, F and Davila, B and He, B}, title = {Plant-derived extracellular vesicles and nanoparticles: origins, functions, and applications.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1758558}, pmid = {41768127}, issn = {2296-4185}, abstract = {Plant-derived extracellular vesicles (PDEVs) and plant-derived nanoparticles (PDNPs) are emerging plant-based nanomaterials with growing relevance in biotechnology, agriculture, and health. Although often grouped together, they arise from distinct origins: PDEVs are actively secreted vesicles with selective cargo loading, whereas PDNPs form during tissue disruption and reflect the lipid-metabolite composition of plant biomass. This review summarizes recent progress in distinguishing these systems, including advances in biogenesis, isolation, biomarkers, and functional characterization. We highlight mechanistic insights into PDEV-mediated cross-kingdom RNA communication in plant immunity and the strong translational potential of PDNPs in oral drug delivery, immunomodulation, and microbiome regulation. Remaining challenges include standardization, scalable purification, and deeper mechanistic clarity. By clarifying their differences and complementary strengths, this review outlines a foundation for developing reliable plant-derived nanovesicle technologies.}, }
@article {pmid41768053, year = {2026}, author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W}, title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1753229}, pmid = {41768053}, issn = {1664-462X}, abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.<br><br>METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.<br><br>RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial &#x3b2;-diversity differed among treatments, while &#x3b1;-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.<br><br>DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.}, }
@article {pmid41767851, year = {2026}, author = {Khanehzar, E and Shams, F and Jafari, A and Poustforoosh, A}, title = {Next-generation AI-assisted drug design against cancer: large language models meet conventional in silico methods.}, journal = {In silico pharmacology}, volume = {14}, number = {1}, pages = {76}, pmid = {41767851}, issn = {2193-9616}, abstract = {UNLABELLED: Cancer remains a leading cause of death, with limited effective therapies. The AXL-GAS6 pathway promotes tumor growth, invasion, metastasis, and resistance to apoptosis. Large Language Models (LLMs) can predict drug-target interactions, generate novel molecular scaffolds, and optimize lead compounds. This study aims to design novel small molecules through a computational pipeline integrating commercial LLMs, molecular docking, molecular dynamics (MD), and ADMET evaluation. We combined DeepSeek LLM with conventional computational methods to design AXL inhibitors via three strategies: natural product-based, microbiome-derived, and FDA-approved drug-inspired scaffolds. Structured prompt engineering generated novel candidates, filtered for drug-likeness, synthetic feasibility, and docking score (Glide, Schrödinger). Top hits underwent 100 ns MD simulations and ADMET evaluation (SwissADME, ADMETLab3). AIC1 showed the highest binding affinity (- 10.079 kcal/mol), surpassing clinical-stage bemcentinib (- 8.234 kcal/mol). MD confirmed stable complexes (RMSD < 3 Å), with AIC1 and AIC4 forming extensive hydrogen bonds. ADMET profiling indicated favorable pharmacokinetics for all, with AIC2 exhibiting the lowest toxicity (hERG inhibition: 34.2%, hematotoxicity: 36.8%) and optimal drug-like properties. This work pioneers LLM-driven in silico design of AXL inhibitors, offering a scalable blueprint for accelerated anticancer drug development.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-026-00582-y.}, }
@article {pmid41767845, year = {2026}, author = {Ortutu, BF and Okin, AO and Darkwah, KO and Onuorah, UM and Maigoro, AY and Iheme, GO}, title = {Gut microbiota and brain aging: a comparative review of African and western populations.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1740408}, pmid = {41767845}, issn = {1663-4365}, abstract = {As the population ages, cognitive decline and neurodegenerative diseases have become major public health concerns. The human gut microbiota plays a major role in regulating neurodevelopment, neuroinflammation, and cognitive decline through the gut-brain axis. Emerging evidence reveals a possible association between alterations in gut microbial diversity and age-related neurological disorders, including Alzheimer's disease and neurodegeneration. Regional and dietary differences shape the gut microbiome. These variations may, in turn, be associated with differences in brain aging across populations. Several cross-sectional studies indicate that rural African communities consuming predominantly fiber-rich diets exhibit distinct gut microbiota profiles characterized by increased abundance of genera, including Prevotella, Faecalibacterium, and Ruminococcus. These microbial configurations have been associated with improved gut barrier integrity, reduced systemic inflammation, and enhanced production of short-chain fatty acids in some preclinical and human studies. All these factors have been studied as potential mechanisms linked to delayed brain aging. Furthermore, epidemiological reports suggest lower prevalence rates of dementia and other neurodegenerative disorders in these populations, although such comparisons may be influenced by differences in study design, diagnosis, and case ascertainment across regions. This narrative review synthesized current understanding of the gut microbiota's role in brain aging, summarized available data on gut microbiota composition in African versus Western populations, and explored the pathways by which traditional African diets may contribute to neuroprotection. By critically examining this evidence and highlighting major research gaps, the review advocates for region-specific investigations and future longitudinal studies to validate causal links.}, }
@article {pmid41767840, year = {2026}, author = {Kost, E and Kundel, D and Barthel, M and Conz, RF and Werner, RA and Ghiasi, S and Bublitz, TA and Mäder, P and Krause, HM and Six, J and Hartmann, M and Mayer, J}, title = {Drought increases root and rhizodeposition carbon inputs into soils.}, journal = {Plant and soil}, volume = {519}, number = {1}, pages = {103-127}, pmid = {41767840}, issn = {0032-079X}, abstract = {AIMS: Increasing droughts affect crop yield and health. Plants can respond to drought by adapting their root biomass, root morphology, and quality and quantity of rhizodeposition to improve water and nutrient uptake. Besides droughts, agricultural management influences roots and rhizodeposition; however, it is not well studied how agricultural management can affect the response of roots and rhizodeposition to drought.<br><br>METHODS: A semi-continuous [13]CO2 isotope labelling experiment was performed in a long-term field experiment comparing biodynamic, mixed conventional, and mineral conventional cropping systems. Rainout shelters were installed to induce drought. Root, net rhizodeposition, and the rhizosphere microbiome were determined at ripening of wheat.<br><br>RESULTS: Drought enhanced the total root carbon mainly through the increase of fine roots. Fine root carbon under drought was primarily enhanced in the mixed conventional and biodynamic cropping system, both receiving farmyard manure, whereas no increase was measured in the mineral fertilized conventional system. Net rhizodeposition carbon was enhanced in all cropping systems under drought, particularly in the first 0.25&#xa0;m. While some plant-growth-promoting genera such as Streptomyces and Rhizophagus showed relative increases under drought, other plant growth-promoting genera often involved in nitrogen fixation such as Rhodoferax and Mesorhizobium were decreased.<br><br>CONCLUSION: This field trial suggests that drought increases total belowground carbon input via fine root and net rhizodeposition carbon inputs. Since fine root carbon increased under drought in cropping systems with farmyard manure, adding manure under future drought periods could be advantageous to increase soil carbon inputs and improve nutrient foraging.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-08021-1.}, }
@article {pmid41767763, year = {2026}, author = {Samara, P and Athanasopoulos, M and Athanasopoulos, I}, title = {Benign, persistent, and invasive: mechanistic and translational approaches to middle‑ear cholesteatoma.}, journal = {Exploration of targeted anti-tumor therapy}, volume = {7}, number = {}, pages = {1002359}, pmid = {41767763}, issn = {2692-3114}, abstract = {Acquired middle-ear cholesteatoma is a histologically benign keratinizing squamous epithelial lesion that paradoxically exhibits locally destructive, recurrent, and invasive behavior, often resulting in ossicular erosion, hearing loss, labyrinthine fistula, and, rarely, intracranial complications. Surgical excision remains the primary management strategy; however, recurrence is common due to persistent microenvironmental drivers. Recent mechanistic studies-including single-cell transcriptomics, spatial proteomics, and epigenetic profiling-reveal a multifactorial pathogenesis orchestrated by chronic inflammation, proteolytic extracellular-matrix remodeling, osteoclast activation via RANKL and activin A, epithelial plasticity with partial epithelial-to-mesenchymal transition (EMT), and a dysbiotic, biofilm-forming microbiome. Emerging evidence further implicates oxidative stress, RNA and epigenetic modifications, miRNA dysregulation, and immune cell infiltration as central modulators of lesion chronicity and bone resorption. Collectively, these processes establish a self-sustaining pro-osteolytic microenvironment that drives bone erosion and postoperative recurrence. Cholesteatoma recapitulates several features of malignant lesions-hyperproliferation, local invasion, and stromal/immune cell recruitment-yet remains fundamentally benign, lacking metastatic potential and genomic instability. Its aggression is ecological rather than genetic, highlighting the potential for microenvironment-directed, precision-based strategies. Adjunctive approaches may include local delivery of modulatory agents, targeted interference with inflammatory, proteolytic, osteoclastogenic, and microbial axes, and biomarker-guided patient stratification. Preclinical and early-phase experimental studies assessing target engagement, radiologic stabilization, and molecular surrogates of efficacy could inform safer, mechanism-driven interventions that complement surgery, reduce recurrence, and preserve hearing. Integrating molecular pathobiology with clinical strategy positions cholesteatoma as a model for benign yet locally aggressive, microenvironment-driven disease, providing a roadmap for translational therapies with direct relevance to surgical practice.}, }
@article {pmid41767584, year = {2025}, author = {Dang, Y and Xu, S and Huang, J and Peng, X and Yang, Y and Wang, Y and Yan, Y and Jiang, F and Wang, J and Liu, J}, title = {Comprehensive identification of microbial and metabolomic factors impacting ICC recurrence.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1703182}, pmid = {41767584}, issn = {2234-943X}, abstract = {INTRODUCTION: Intrahepatic cholangiocarcinoma (ICC) originates from intrahepatic bile duct epithelial cells and its global incidence is rising. Surgery remains the primary treatment, but postoperative recurrence rates remain high.<br><br>METHODS: We analyzed ICC patients' gut microbiota at four stages (preoperative, 7 days postoperative, 1 month postoperative, and during recurrence) using 16S rRNA sequencing and their serum metabolome via LC-MS/MS. Correlations among gut microbiota, metabolome, and clinical indicators were investigated, and candidate microorganisms and metabolites were integrated for multiomics clustering and staging.<br><br>RESULTS: This revealed significant increases in Bacteroides, Veillonella, and Enterococcus in ICC patients compared to healthy controls across all stages, suggesting these bacteria as potential markers of ICC progression. Microbial and metabolite changes were observed, with gut microbes influencing ICC development through kynurenic acid, linoleic acid, creatine, cholic acid, L-arginine, and the tumor microenvironment. Multiomics analysis showed that cholangiocarcinoma staging improves patient prognosis, particularly highlighting bile acids' role in type II hepatic phenotypes related to cholesterol metabolism.<br><br>DISCUSSION: Our study provides insights into ICC microbiome and metabolome associations with clinical features and survival.}, }
@article {pmid41767576, year = {2026}, author = {Luppi, S and Topouzova, GA and Campisciano, G and Giolo, E and Bulfone, T and Rossi, F and Zito, G and Ricci, G and Comar, M and Andreuzzi, E}, title = {Impact of hormonal treatments for endometriosis on the reproductive microbiome: a systematic review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755725}, pmid = {41767576}, issn = {1664-302X}, abstract = {INTRODUCTION: The reproductive microbiome plays a key role in disease progression and fertility in women with endometriosis. Vaginal and endometrial dysbiosis has been increasingly linked to inflammation, impaired reproductive outcomes, and symptom severity. Although estro-progestins, progestins, and GnRH agonists are widely used, their impact on microbial communities remains poorly understood, highlighting the need to clarify microbiome-therapy interactions. This systematic review aims to comprehensively synthesize current evidence on how hormonal therapies influence the reproductive microbial environment and to offer insights for optimizing clinical management of endometriosis.<br><br>METHODS: Literature screening and data extraction followed PRISMA guidelines using PubMed, Scopus, and Google Scholar. The search combined terms on endometriosis, hormonal therapy, and reproductive microbiome. Non-English studies, reviews, and those without original data were excluded. Risk of bias was assessed with ROBINS-I-V2, and microbial composition and diversity were analyzed and synthesized qualitatively.<br><br>RESULTS: The literature search retrieved 577 publications, of which 6 met eligibility criteria and were analyzed. The evidence collected through sequencing or culture-based methods suggested that the use of hormonal therapies to treat endometriosis may impact both vaginal and endometrial microbiome, favoring the colonization of bacterial species associated with infertility. GnRHa resulted to foster the dominance of potentially pathogenic bacteria, as Gardnerella and Streptococcaceae, in the endometrium, and supporting bacterial vaginosis by increasing intermediate flora (Nugent score 4-6). A similar effect on the vaginal environment has been reported upon the use of oral contraceptive pills, which was shown to prompt the increase of Prevotella, Ureaplasma, Streptococcus anginosus and Streptococcus agalactiae, among other pathogenic microbes, and to enhance the Bacillota/Bacteroidota ratio.<br><br>DISCUSSION: Despite affected by several limitations and heterogeneity of included studies, this review provides a preliminary overview of the possible pejorative effect of hormonal therapy on the reproductive microbiome of endometriosis patients. While further investigations are required to consolidate these findings, the observations raised offer a valuable basis for opening a discussion about improving management strategies for affected women. By highlighting confounding factors overlooked in the selected papers, the present work will also be functional to optimize the design of future studies.<br><br>https://www.crd.york.ac.uk/PROSPERO/view/CRD420251042858, identifier PROSPERO (CRD420251042858).}, }
@article {pmid41767572, year = {2026}, author = {Pattapulavar, V and S, SK and Ramanujam, S and Subburaj, S and John, GC}, title = {Probiotic-based therapeutics for a One Health future: redefining antibiotic dependency to combat antimicrobial resistance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736436}, pmid = {41767572}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) has become a major One Health concern, affecting the interconnected microbial systems shared by humans, animals, and the environment. Decades of antibiotic-driven control have disturbed ecological stability and contributed to the expansion of the global resistome. This Perspective approaches AMR mitigation through an ecological restoration lens, outlining a three-part strategy that brings together probiotic therapeutics, microbiome-focused public awareness, and integrated surveillance. Probiotics are presented as biologically compatible tools that promote microbial stability through competitive niche occupation, immune support, and environmental biodegradation, thereby reducing selective pressures that favor resistance. In parallel, strengthening microbiome literacy can guide behavioral choices that support stewardship and reduce unnecessary antimicrobial use. The proposed One Health Microbiome Intelligence Framework (OH-MIF) adds a data-driven layer by linking genomic, clinical, agricultural, and environmental information through AI-enabled analytics. Together, these components form an adaptable system that shifts AMR management from reactive dependence on antibiotics toward a more resilient, coexistence-based approach. By aligning ecological interventions with education and policy intelligence, this Perspective positions microbial balance as a practical foundation for sustainable AMR control within broader planetary health goals.}, }
@article {pmid41767565, year = {2026}, author = {Doku, TE and Belford, JDE and Sylverken, AA}, title = {Rhizosphere microbiome assembly drives metal sequestration in Leucaena leucocephala during tailing phytoremediation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1745018}, pmid = {41767565}, issn = {1664-302X}, abstract = {INTRODUCTION: Ghana's water and soil resources face severe challenges due to heavy metal contamination from gold mining operations. Although Leucaena leucocephala exhibits potential for phytoremediation, little is known about the contribution of its rhizosphere microbiomes to metal uptake and tolerance in multiple-metal contaminated tailings in field conditions.<br><br>METHODS: We investigated the rhizosphere bacterial community dynamics in L. leucocephala across three soil treatments (garden soil, 1:1 soil-tailings mixture, and pure tailings) using 16S rRNA amplicon sequencing and atomic absorption spectrophotometry. Briefly, transplanted seedlings of L. leucocephala were harvested at three-month intervals for three consecutive harvests to assess metal accumulation and changes in the microbiome.<br><br>RESULTS AND DISCUSSION: Leucaena leucocephala demonstrated notable tolerance to elevated metal concentrations (>10,000 mg/kg Fe and Mn) under acidic conditions (pH 4.57-5.97). Maximum metal uptake occurred at final harvest, with Fe reaching 14,605&#x202f;&#xb1;&#x202f;1.40&#x202f;mg/kg in shoots and Mn reaching 12,279&#x202f;&#xb1;&#x202f;1.13&#x202f;mg/kg in roots. The elevated concentrations of metals reduced overall bacterial diversity, except for selected metal-tolerant Actinobacteria, Proteobacteria, and Acidobacteria, which dominated bacterial communities across all treatments. The initial proliferation of Nocardioides and Streptomyces corroborated nutrient and metal-induced stress, while key genera such as Arthrobacter, Gaiella, Skermanella, and Chelatococcus showed strong positive associations with metal accumulation and maintained essential ecological functions.<br><br>CONCLUSION: Rhizosphere bacterial communities undergo stress-specific assembly processes, with specific taxa facilitating L. leucocephala's exceptional phytoremediation capacity. These findings provide insights into microbiome-enhanced strategies for mine site rehabilitation.}, }
@article {pmid41767558, year = {2026}, author = {Song, L and Yu, QY}, title = {Stratified management of residual gastric cancer risk after Helicobacter pylori eradication.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1779490}, pmid = {41767558}, issn = {1664-302X}, abstract = {Despite the established efficacy of Helicobacter pylori eradication in reducing gastric cancer (GC) incidence, a significant residual risk persists in successfully treated individuals, driven by lasting pathological alterations termed "oncogenic memory," including irreversible mucosal damage (e.g., intestinal metaplasia), residual pro-inflammatory and epigenetic "molecular scars," and gastric microbiome dysbiosis. This perspective synthesizes current evidence to advocate for a paradigm shift from a singular focus on pathogen clearance towards a comprehensive, risk-adapted management strategy. We propose a novel, dual-dimensional framework centered on a multidimensional risk assessment that integrates OLGA/OLGIM staging, demographic, lifestyle, and genetic factors to stratify post-eradication individuals into distinct risk categories. The framework subsequently outlines tailored surveillance protocols-specifying endoscopy frequency and advanced biomarker application-leverages technological support from AI-assisted endoscopy and molecular testing, and details differentiated resource allocation models based on regional GC incidence and economic development. This integrated approach provides a practical roadmap for implementing precision prevention, aiming to mitigate the lingering GC risk and ultimately reduce the global disease burden through a dynamic, lifelong management system beyond eradication. To facilitate implementation, we provide a user-ready risk calculator that operationalizes the multidimensional score for cohort-level application.}, }
@article {pmid41767542, year = {2026}, author = {Effendi, RMRA and Witkam, WCAM and Dwiyana, RF and Suwarsa, O and Kraaij, R and Murad, C and Thio, HB and Nijsten, T and Pardo, LM}, title = {Profiling skin microbiota in an underrepresented population: Indonesian children with atopic dermatitis and controls.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1697420}, pmid = {41767542}, issn = {2296-858X}, abstract = {INTRODUCTION: The skin microbiome plays a central role in the pathogenesis of atopic dermatitis (AD), but most studies have focused on high-income populations of European ancestry. Microbiome data from tropical and developing regions remains limited. In Asia, microbiome research has similarly centered around developed countries, leaving populous developing countries like Indonesia underrepresented. The aim was to profile the cutaneous bacterial microbiota of children with AD from Indonesia and compare it with controls.<br><br>METHODS: Skin swabs were collected from lesional sites of 111 children aged 4-18 years with AD and from the forearms of 107 controls, all attending Pediatric Dermatology Clinic of Dr. Hasan Sadikin General Hospital, an urban tertiary-care referral center in Bandung, West Java, Indonesia. AD was diagnosed using Hanifin-Rajka criteria, while controls had non-atopic, non-inflammatory dermatological conditions. Cutaneous bacterial microbiota was profiled using 16S rRNA sequencing with amplicon sequence variant (ASV) level analysis using DADA2 pipeline. Data was analyzed after quality control to estimate alpha and beta diversities, the later using, permutational multivariate analysis of variance (PERMANOVA) to assess contribution of individual variables to the variation in microbiota composition. Univariable differential abundance was done to analysis the composition of specific bacteria in cases versus controls. Analysis of core microbiota compositions and phylogenetic relationships were explored to identify key taxa associated with AD.<br><br>RESULTS: Most children came from families with higher household incomes, and children with AD were younger than controls (mean age 8.35 &#xb1; 3.51 vs. 9.91 &#xb1; 3.79 years, P = 0.002). Lesional AD skin showed a significantly reduced alpha diversity and a marked overrepresentation of Staphylococcus aureus and Staphylococcus epidermidis. Less commonly reported genera, including Acetobacter and Gluconobacter, were enriched in cases, potentially reflecting environmental exposure in this cohort. PERMANOVA revealed that case-control status, family income, maternal atopy, maternal education and DNA concentration significantly influenced microbial composition. Phylogenetic analysis showed a clear lineage-level distinction between Staphylococcus ASVs.<br><br>CONCLUSION: Our findings reveal distinct microbial profiles in children with AD from a tropical, underrepresented population with predominantly higher household incomes, and underscore the role of environmental and sociodemographic factors associated with skin microbiota. While generalizability to lower-income or rural populations may be limited, the value of ASV-level analysis lies in its ability to capture both known and less characterized microbial signals.}, }
@article {pmid41767378, year = {2026}, author = {Xu, Y and Cao, Y and Zou, L and Wulanna,  and Liu, X and Yan, S and Liu, C and Gao, M and Zhan, J and Wang, Q and Wu, C}, title = {Protective role of aqueous Coriandrum sativum seed extract in diet-induced glucolipid metabolic disorder through gut-liver axis regulation.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1744741}, pmid = {41767378}, issn = {1664-2392}, abstract = {OBJECTIVE: To elucidate the protective effects of aqueous Coriandrum sativum seed extract against high-fat, high-sugar diet (HSFD)-induced glucolipid metabolic disorder in mice, with particular focus on gut-liver axis regulation involving hepatic metabolism, oxidative stress, inflammation, and gut microbiota composition.<br><br>METHODS: Male mice were fed an HSFD and orally treated with Coriandrum sativum seed extract (1.0 or 2.0 g/kg/day) for eight weeks. Biochemical parameters, histopathology, hepatic gene expression, oxidative stress markers, and gut microbial profiles were assessed via standard assays, RT-qPCR, Western blot, histological staining, and full-length 16S rRNA gene sequencing with functional prediction.<br><br>RESULTS: The extract significantly ameliorated HSFD-induced metabolic impairments, including hyperglycemia, hyperlipidemia, insulin resistance, and hepatic steatosis. Histological improvements were observed in the liver, pancreas, and colon. Hepatic expression of FAS, NF-&#x3ba;B, and IL-6 was suppressed, while PPAR&#x3b1; and LDLR expression was restored. Antioxidant defenses were enhanced by reducing malondialdehyde and increasing superoxide dismutase activity. Microbiota analysis revealed partial restoration of beneficial taxa such as Lactobacillus murinus and Lachnospiraceae_UCG-006, alongside enrichment of microbial pathways related to energy and carbohydrate metabolism.<br><br>CONCLUSION: Aqueous Coriandrum sativum seed extract exerts systemic metabolic benefits in diet-induced glucolipid dysregulation by targeting the gut-liver axis. Its multi-targeted actions on hepatic metabolism, inflammatory signaling, oxidative balance, and gut microbiota composition support its potential as a natural therapeutic agent for metabolic disorders.}, }
@article {pmid41767368, year = {2026}, author = {De Pasquale, C and Harrison, LC}, title = {Early-life antibiotic exposure and type 1 diabetes risk: a systematic review and meta-analysis.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1764522}, pmid = {41767368}, issn = {1664-2392}, abstract = {OBJECTIVE: Antibiotic exposure impacts the gut microbiome and potentially, in an infant, the developing immune system, with implications for the emergence of immune disorders such as type 1 diabetes (T1D). Reports of early-life antibiotic exposure on risk for T1D are inconsistent. We aimed to perform a systematic review and meta-analysis of the association between antibiotic exposure in early life and the development of T1D.<br><br>METHODS: Observational studies were assembled that reported an association between early-life antibiotic exposure and the development of T1D. Four early-life periods were covered: 12 months preconception, prenatal (in pregnancy), neonatal and up to 24 months postnatal. Medline, Embase, Web of Science Core Collection, and Scopus were searched from inception to August 28, 2024. All records were imported into Covidence for automated deduplication, abstract screening and full-text screening by two independent reviewers. Data from 20 studies and 10, 960 T1D cases were extracted and analysed using a random effects meta-analysis. Pooled odds ratios (ORs) and hazard ratios (HRs) with associated 95% confidence intervals (CIs) were calculated.<br><br>RESULTS: In the preconception period, maternal exposure to macrolide (OR = 1.23 [95% CI: 1.02-1.48]), sulfonamide/trimethoprim (OR = 1.34 [95% CI: 1.07-1.69]) or tetracycline (OR = 1.26 [95% CI: 1.11-1.44]) antibiotics was associated with an increased odds of T1D. Prenatal, neonatal and postnatal antibiotic exposure was not significantly associated with T1D.<br><br>CONCLUSION: Preconception exposure to specific antibiotic classes may represent a modifiable maternal risk factor for T1D in the offspring. This would have implications for antibiotic prescribing guidelines but requires validation by the further study of defined antibiotic classes and their exact timing of preconception exposure.<br><br>The protocol was pre-registered on PROSPERO (CRD42024589374) and followed PRISMA guidelines.}, }
@article {pmid41767236, year = {2026}, author = {Tavassol, ZH and Farsi, F and Ettehad-Marvasti, F and Ejtahed, HS and Hasani-Ranjbar, S}, title = {Gut Microbiota Alterations in Hypothyroidism: A Pilot Study Revealing Increased Abundance of Specific Bacterial Genera.}, journal = {Journal of nutrition and metabolism}, volume = {2026}, number = {}, pages = {9988966}, pmid = {41767236}, issn = {2090-0724}, abstract = {BACKGROUND: Hypothyroidism (HT) is a prevalent thyroid disorder characterized by insufficient thyroid hormone production, leading to metabolic complications. Emerging research suggests a link between gut microbiota and thyroid regulation, positing that alterations in gut bacterial populations may contribute to HT's development and progression. This study aimed to investigate these associations by comparing gut microbiota compositions between individuals with HT and healthy adults, potentially refining diagnostic tools and therapeutic strategies.<br><br>METHODS: In this pilot study conducted between 2019 and 2023, 15 hypothyroid patients and 15 age- and gender-matched healthy controls participated in the study. Exclusion criteria were applied to eliminate confounding factors. Anthropometric data were collected, and stool samples underwent microbial analysis. Total bacterial DNA was extracted, and quantitative real-time PCR targeting 16S rRNA genes across eight bacterial genera was performed. The Mann-Whitney U test was used for statistical analyses.<br><br>RESULTS: No significant differences were observed in baseline demographic and anthropometric characteristics between groups. However, hypothyroid patients exhibited significantly elevated levels of Bacteroides, Bifidobacterium, Escherichia, Fecalibacterium, and Prevotella (p values <&#x2009;0.001-0.030). No significant differences were found in levels of Akkermansia, Lactobacillus, or in the Bacteroides/Prevotella ratio.<br><br>CONCLUSION: This pilot study provides preliminary indications of a possible role of gut microbiota in the pathophysiology of HT. Variations in bacterial composition suggest a significant influence of gut health on thyroid regulation. Future studies with larger cohorts are needed to explore the biological pathways linking the gut microbiome to thyroid function, which may lead to novel microbiota-targeted therapeutic approaches.}, }
@article {pmid41767117, year = {2026}, author = {Hu, T and Chen, Z and Yin, Z and Zhou, L and Chen, Q and Han, Y and Li, K}, title = {New concept in wound infection management: From bacterial eradication to microbiome modulation.}, journal = {APL bioengineering}, volume = {10}, number = {1}, pages = {010901}, pmid = {41767117}, issn = {2473-2877}, abstract = {Wound infection represents a significant challenge in clinical practice. Traditional wound management, targeting sterility and relying on strategies of broad-spectrum bactericidal activity and antibiotic dependence, achieves partial infection control but induces severe complications, including exacerbated bacterial resistance and skin microbiota dysbiosis. With the continuous advancement of microbiome research, a novel consensus has emerged: the key to wound healing lies not in the complete eradication of all microorganisms but in maintaining the dynamic balance of the microbial ecosystem. This review aims to elaborate on the paradigm shift from "bactericidal eradication" to "microbial modulation" in wound care, analyze the inherent limitations of conventional antibacterial strategies, and systematically summarize the critical roles of skin commensal microbiota in promoting wound healing through core mechanisms such as competitive inhibition, metabolic regulation, and immune modulation. Furthermore, it proposes that the core strategy of future wound care should focus on precision microbial modulation and discusses the application prospects of cutting-edge technologies, including probiotics, postbiotics, and individualized precision interventions. The innovative significance of this paradigm in wound dressing design is envisaged, emphasizing the development of novel materials integrating microbiota-specific regulatory capabilities and smart responsive functions. This work provides theoretical support for the precision prevention and control of wound infections, the improvement of healing quality, and technological innovation in the field of wound care.}, }
@article {pmid41767020, year = {2026}, author = {Alachraf, K and Trouten, P and Thayer, J}, title = {Zoonotic Streptococcus canis Bacteremia Following a Dog Scratch in an Elderly Patient With a Nonconditional Pacemaker.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {2485747}, pmid = {41767020}, issn = {2090-6625}, abstract = {Streptococcus canis is a β-hemolytic Group G streptococcus commonly found in the microbiome of dogs and cats and is an uncommon cause of invasive human infection. Although typically regarded as a veterinary pathogen, S. canis has been reported to cause bacteremia, endocarditis, and other severe infections in humans, particularly in older adults with significant comorbidities or implanted medical devices. We describe a case of Streptococcus canis bacteremia in an 89-year-old woman with multiple comorbidities and a nonconditional permanent pacemaker who presented with fever, dyspnea, and severe lower back pain. Blood cultures grew S. canis, identified using standard microbiologic techniques. The clinical course raised concern for metastatic infection and pacemaker involvement. Imaging of the thoracic and lumbar spine demonstrated no evidence of discitis or osteomyelitis, and both transthoracic and transesophageal echocardiography showed no valvular or pacemaker lead vegetations. Further history revealed a dog scratch several weeks prior to presentation that resulted in skin disruption, representing a plausible portal of entry. The patient was treated with intravenous ceftriaxone with rapid clinical improvement, resolution of hypoxia, clearance of bacteremia, and declining inflammatory markers. She was discharged to inpatient rehabilitation to complete a 2-week course of antimicrobial therapy and recovered without evidence of recurrent infection. This case underscores Streptococcus canis as an uncommon but clinically relevant zoonotic pathogen and highlights the importance of detailed exposure history, appropriate microbiologic identification, and careful evaluation for device-related infection in high-risk patients.}, }
@article {pmid41766754, year = {2026}, author = {Devinsky, O and Leitner, DF and Kamondi, A and Wisniewski, T}, title = {Epilepsy and Alzheimer Disease: Epidemiologic, Clinical, Molecular, and Neuropathologic Convergences and Divergences.}, journal = {Neurology. Clinical practice}, volume = {16}, number = {2}, pages = {e200589}, pmid = {41766754}, issn = {2163-0402}, abstract = {PURPOSE OF REVIEW: Alzheimer disease (AD) and epilepsy are major causes of neurologic disability and are reciprocally related: epileptiform discharges, subclinical seizures, and epilepsy are more prevalent in patients with AD compared with controls; progressive cognitive impairment commonly afflicts epilepsy patients; and late-onset epilepsy patients have higher rates of new-onset dementia.<br><br>RECENT FINDINGS: Epidemiologic studies support shared risk factors (e.g., genetic variants, vascular disease, sleep disorders, microbiome) with notable divergences. AD and epilepsy have some overlapping anatomic (e.g., hippocampus, entorhinal, and association cortex), clinical (e.g., memory, attentional, and executive) impairments, and neuropathologic (e.g., amyloid, tau, neurofibrillary tangles) features. Shared clinical and translational challenges include underlying mechanisms (e.g., genetic variants, neuroinflammation, metabolic and mitochondrial dysfunction, excitatory/inhibitory imbalance, microbiome, and sociodemographic factors) and identifying valid and reliable biomarkers (e.g., total tau and phosphorylated tau (p-tau), amyloid deposition, A&#x3b2;42/A&#x3b2;40 ratio) to assess disease progression, predict outcomes, and assess potentially disease-modifying interventions.<br><br>SUMMARY: Identifying convergences and divergences between epilepsy and AD may inform our understanding. The clinical, neurophysiologic, neuropathologic, and molecular pathologic changes in AD and epilepsy may reveal pathophysiologic insights and therapeutic opportunities.}, }
@article {pmid41766731, year = {2026}, author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF}, title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73172}, pmid = {41766731}, issn = {2045-7758}, abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.}, }
@article {pmid41766653, year = {2026}, author = {Jiang, Z and Zhai, C and He, C and Shen, L and Tang, G and Xu, L and Yang, H and Hu, H and Han, J}, title = {Effects and mechanisms of probiotics supplement on hypertension.}, journal = {Journal of hypertension}, volume = {}, number = {}, pages = {}, doi = {10.1097/HJH.0000000000004258}, pmid = {41766653}, issn = {1473-5598}, abstract = {The global population of individuals suffering from hypertension is estimated to surpass 1.28 billion. Uncontrolled hypertension makes contributions to the development of cardiovascular and cerebrovascular diseases. Emerging evidence indicates a significant correlation between hypertension and gut microbiota. As an intestinal regulator, which could confer health benefits to the host in adequate amounts, probiotics may become a novel approach to regulating blood pressure without side effects. Therefore, we overview the antihypertensive effects and the potential mechanisms of probiotics supplement on hypertension.}, }
@article {pmid41766520, year = {2026}, author = {Wallander, K and Beijer, G and Eliasson, E and Giske, CG and Ponzer, S and Söderquist, B and Eriksen, J}, title = {Is current guidance for cloxacillin prophylaxis dosages in hip and knee arthroplasty adequate? Evidence from a prospective Swedish cohort.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {3}, pages = {}, doi = {10.1093/jac/dkag067}, pmid = {41766520}, issn = {1460-2091}, support = {//Region/ ; FoUI-954900//Stockholm/ ; FoUI-973467//Stockholm/ ; FoUI-974859//Stockholm/ ; 2021-02699//Stockholm/ ; OLL-983304//Region &#xd6;rebro County/ ; }, abstract = {OBJECTIVES: Perioperative antibiotic prophylaxis is crucial for preventing detrimental postoperative prosthetic joint infections (PJIs). Guidelines aim to prevent infection with methicillin-susceptible staphylococci-in Sweden through administering cloxacillin, at fixed doses with minimal consideration to kidney function or patient weight. Over- and under-dosing could have adverse effects, negative effects on the microbiome, or increase the risk of PJI. We aimed primarily to evaluate whether the current uniform prophylactic regimen of cloxacillin in hip and knee arthroplasty is adequate.<br><br>PATIENTS AND METHODS: Patients subjected to elective prosthetic joint surgery (N&#x200a;=&#x200a;204) were included in a prospective study. Free plasma concentrations of cloxacillin were measured on three occasions throughout arthroplasty surgery. Samples were analysed using a validated HPLC-MS/MS method. A free concentration of <2&#x2005;mg/L was deemed a theoretically appropriate concentration to suppress growth of methicillin-susceptible staphylococci in bone. A sensitivity analysis with values of 1 and 4&#x2005;mg/L was included.<br><br>RESULTS: Potentially subtherapeutic concentrations (&#x2264;2&#x2005;mg/L) at the end of surgery were found in 31 cases (15%). The corresponding numbers for 1 and 4&#x2005;mg/L were 3 and 88 (1% and 43%). In multivariable logistic regression analysis, an ASA (American Association of Anesthesiologists physical status) score of I (relatively healthy patients), estimated glomerular filtration rate >90&#x2005;mL/min/1.73&#x2005;m2, body weight >100&#x2005;kg and long duration of surgery significantly predicted suboptimal concentrations.<br><br>CONCLUSIONS: Current cloxacillin dosing in hip and knee arthroplasty surgery results in a risk for subtherapeutic levels in patients with high body weight and preserved renal function. Therefore, dosing guidelines for cloxacillin prophylaxis in arthroplasty should be reviewed.}, }
@article {pmid41766340, year = {2026}, author = {Kovner, A and Kapushchak, Y and Pakharukova, M}, title = {Liver flukes and kidney injury: systematic review of human and animal data (from 1950 to 2025).}, journal = {Journal of helminthology}, volume = {100}, number = {}, pages = {e24}, doi = {10.1017/S0022149X26101187}, pmid = {41766340}, issn = {1475-2697}, support = {grant number 24-44-00048//Russian Science Foundation/ ; }, abstract = {Foodborne trematodes, particularly from families Opisthorchiidae and Fasciolidae, significantly impact human health. Research on trematode-related diseases has primarily focused on the hepatobiliary system and carcinogenic potential of these flukes. Nonetheless, chronic infection by these parasites likely affects other organ systems. This review emphasises the need to expand studies beyond the hepatobiliary system to fully understand the pathogenesis of liver fluke infections and advocates for a systematic approach to the management of affected humans. This review analyses scientific data from 1950 to 2025, including studies on laboratory animals, wild animals, and humans. Databases such as PubMed, Google Scholar, WHO, IARC, Rospotrebnadzor, and eLibrary were utilised. Common kidney injuries from trematode infections include glomerular and tubular damage, interstitial inflammation, and fibrosis. These injuries are influenced by liver damage and gut microbiome imbalances. Interspecies differences highlight the complexity of host-parasite interactions. Research indicates that foodborne-trematode-associated nephropathy exists in both humans and animals and involves immune complexes, oxidative stress, and biomarkers like KIM1. The documented renal damage underscores the need for further investigation into the mechanisms of the trematode-associated renal pathologies.}, }
@article {pmid41766326, year = {2026}, author = {Troielli, P and Moreno, J and Cortes, A and Cardenas, P and Kerob, D and Gamarra, A and Dreno, B}, title = {Integrating Dermocosmetics Into Acne Care in Latin America.}, journal = {Journal of cosmetic dermatology}, volume = {25}, number = {3}, pages = {e70776}, pmid = {41766326}, issn = {1473-2165}, support = {//La Roche-Posay Laboratoire Dermatologique, L'Oreal Dermatological Beauty Division/ ; }, abstract = {BACKGROUND: Prescription acne products have proven efficacy and safety, yet management can pose a challenge. This review discusses the benefits of adding dermocosmetics to acne management.<br><br>METHODS: We add expert consensus with review of the literature to provide guidance for clinicians managing patients with acne in Latin America.<br><br>RESULTS: There is increasing evidence that dermocosmetics (over-the-counter cleansers, moisturizers, and sunscreens that contain acne-targeting ingredients) can be a good alternative to prescription acne treatments as well as adjuncts. Milder forms of acne may be present in any age patient, but prepubertal acne and acne cosmetica may be particularly well suited to a dermocosmetic approach. More severe acne may need a dermocosmetic added if there is sensitive skin or poor tolerance to prescription medications, and when the patient or family does not wish to use antibiotics or other acne prescription treatments. Dermocosmetics may be used as adjuncts to any type of prescription therapy, but may be most effective when used with products associated with skin irritation such as topical retinoids or benzoyl peroxide. Appropriate dermocosmetics can also fortify the skin barrier and help to protect the skin microbiome.<br><br>CONCLUSIONS: Acne management is complex and there can be adherence, tolerability, and efficacy problems. Dermocosmetics alone can be used in milder forms of acne or in maintenance post treatment, as a good compromise between efficacy and tolerability. As adjuncts, dermocosmetics can also decrease skin irritation and thereby increase adherence, can enhance the efficacy of prescription therapies, and can normalize dysbiosis in acne.}, }
@article {pmid41766111, year = {2026}, author = {Zhao, C and Ye, S and Chen, M and Qian, J and Xu, J}, title = {First-line immunotherapy for advanced HER2-negative gastric cancer: differences between Asian and non-Asian patients.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2025.0398}, pmid = {41766111}, issn = {2095-3941}, support = {2024ZD0520600//Non-communicable Chronic Diseases-National Science and Technology Major Project/ ; }, abstract = {Emerging evidence suggests that the efficacy of immunotherapy in patients with advanced HER2-negative gastric cancer differs between Asian and non-Asian populations. This review examines potential factors contributing to these disparities, including differences in demographic and clinicopathologic characteristics, somatic mutations, molecular subtypes, tumor immunity, Helicobacter pylori (H. pylori) infection, dietary habits, and gut microbiome composition. These factors may serve as predictors of immunotherapy response in gastric cancer patients. For example, the prevalence of molecular subtypes and somatic mutations have been linked to variations in immunotherapy efficacy between Asian and non-Asian populations. In addition, differences in H. pylori infection rates, dietary habits, and gut microbiota composition may influence systemic immune responses, and consequently, immunotherapy outcomes. Understanding the factors contributing to these disparities in immunotherapy response is crucial for optimizing treatment strategies and improving outcomes for patients with gastric cancer. Further research into the mechanisms underlying racial and ethnic disparities in immunotherapy response is needed to identify potential biomarkers predictive of immunotherapy response in diverse patient populations.}, }
@article {pmid41766018, year = {2026}, author = {You, Y and Peng, H and Gu, A and Liu, Y}, title = {High-throughput sequencing-based profiling of endophytic bacterial community composition and diversity in seeds of Yunnan cytoplasmic male-sterile rice.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {3}, pages = {}, pmid = {41766018}, issn = {1572-9699}, support = {Y20240210, QN2021105002L//the National Foreign Expert Program of China/ ; 20250484961, 20220484220//the Beijing Nova Program/ ; FM2025-09//the Opening Project of Food Microbiology Key Laboratory of Sichuan Province/ ; }, abstract = {As an important food crop in China, hybrid rice is of significant importance for national food security and supply. Cytoplasmic male-sterile (CMS) rice is a key component of hybrid rice technology, while plant endophytes, especially seed endophytes, play a crucial role in promoting plant growth and reproduction. Therefore, understanding the diversity and community structure of seed endophytes in CMS rice is essential for hybrid rice technology. However, relevant research in this area remains scarce. This study systematically analyzed the diversity and community structure characteristics of seed endophytic bacteria in 14 Yunnan CMS rice varieties (totaling 42 samples) based on Illumina NovaSeq 6000 high-throughput sequencing technology, aiming to elucidate the core microbial community structure and diversity. A total of 503 operational taxonomic units (OTUs) were identified. At the phylum level, the dominant microbial groups in all samples were Proteobacteria (relative abundance 91.53-99.95%). At the genus level, the core microbial community consisted of Pantoea (64.29-93.11%), Xanthomonas (1.08-16.97%), and Kosakonia (0.46-12.66%). Both α- and β-diversity analyses revealed no significant inter-line differentiation, indicating a highly stable and conserved endophytic bacterial community across the Yunnan CMS rice germplasm. This study provides the first comprehensive characterization of the seed-associated core microbiome of Yunnan CMS rice lines.}, }
@article {pmid41765557, year = {2026}, author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W}, title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.}, journal = {Journal of environmental sciences (China)}, volume = {162}, number = {}, pages = {573-583}, doi = {10.1016/j.jes.2025.05.044}, pmid = {41765557}, issn = {1001-0742}, abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.}, }
@article {pmid41765175, year = {2026}, author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C}, title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.}, journal = {Journal of endodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joen.2026.02.016}, pmid = {41765175}, issn = {1878-3554}, abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.<br><br>METHODS: Samples from 25 teeth with large (>8mm) and 20 with small periapical lesions (<2mm) were analyzed. Quantitative PCR, 16S next-generation and whole genome sequencing (WGS) were used to assess microbial load, diversity, and composition. Functional predictions were performed using the KEGG and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.<br><br>RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (p = 0.011), but comparable alpha diversity and number of species per group in 16S and Whole genome analysis (P > 0.05). Lesion size showed significance by ANOSIM (p = 0.04) but not in PERMANOVA (p = 0.36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, p = 0.012; PERMANOVA R[2] = 0.063, p = 0.046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.<br><br>CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.}, }
@article {pmid41765047, year = {2026}, author = {Himmerich, H and Keeler, JL and King, JA and Ehrlich, S and Kaufmann, LK and Bulik, CM and Cohen-Woods, S and Wade, T and Steiger, H and Booij, L and Monteleone, P and Cascino, G and Monteleone, AM and Cuntz, U and Voderholzer, U and Tessema, SA and Lewis, YD and Sjögren, M and Hebebrand, J and Seitz, J and Tyszkiewicz-Nwafor, M and Karpenko, O and Mutwalli, H and Fetissov, SO and Mack, I and Dhopatkar, N and Mörkl, S and Kan, C and Uribe, MM and Yoshiuchi, K and Abuobeid, N and Kapogiannis, D and Stein, D and Bektas, S and Müller, DJ and Gorwood, P and Duriez, P and Montcel, CTD and Paszyńska, E and McElroy, SL and Wranik, WD and Fernandez-Aranda, F and Mehler, PS and Papežová, H and Roubalová, R and Procházková, P and Morris, R and Lewczuk, P and Hiemke, C and Berk, M and Karwautz, A and Treasure, J and Kasper, S and ,  and , }, title = {World Federation of Societies of Biological Psychiatry (WFSBP) consensus statement on candidate biomarkers for anorexia nervosa.}, journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry}, volume = {}, number = {}, pages = {1-92}, doi = {10.1080/15622975.2026.2626934}, pmid = {41765047}, issn = {1814-1412}, abstract = {OBJECTIVES: This World Federation of Societies of Biological Psychiatry (WFSBP) consensus paper aims to summarise and evaluate the published study results on objectively measurable biological markers associated with anorexia nervosa (AN).<br><br>METHODS: The relevant literature was reviewed by the WFSBP Task Forces on Eating Disorders and on Biological Markers, and a consensus regarding the significance of the published evidence was reached.<br><br>RESULTS: Candidate biological markers that have been associated with AN include clinical (e.g. body weight), molecular (e.g. genetic, epigenetic, hormonal, immunological, metabolomic), cellular (e.g. leukocytes), neuroimaging (e.g. structure, function, connectivity), digital, cardiac and neurophysiological parameters. Some clinical and laboratory parameters are risk markers in clinical practice. Biological markers have pathophysiological relevance in understanding the biological and metabolic pathophysiology of AN and its physical health consequences. Few studies have examined pharmacogenetics or therapeutic drug monitoring as tools to monitor and guide the treatment of AN.<br><br>CONCLUSIONS: Biological markers will hopefully soon enable clinicians to intervene earlier in a more targeted manner to mitigate treatment resistance. However, the current scientific basis for most biological markers are group comparisons only. Studies on sensitivity, specificity and the prognostic value of these markers are lacking.}, }
@article {pmid41764962, year = {2026}, author = {Kong, J and Han, C and Shao, G and Feng, K and Song, C and Xie, Q}, title = {Virulence attenuation of intestinal pathogenicity via combined gene deletion in duck enteritis vaccine strain restores gut microbiota balance and enhances safety.}, journal = {Poultry science}, volume = {105}, number = {5}, pages = {106633}, doi = {10.1016/j.psj.2026.106633}, pmid = {41764962}, issn = {1525-3171}, abstract = {There is an increasing need for a new generation of effective and safe vaccines, in the context of large-scale poultry farming and the prevalence of infectious diseases. With this in mind, we developed, for the first time, a duck enteritis virus (DEV) mutant, ΔTK-ΔgI/gE-ΔgG/gJ, through the deletion of multiple virulence genes. The resulting gene-deletion strain exhibited replication kinetics similar to those of the parent strain and was found to be safe in various animal models, offering a strategy for rapidly generating attenuated DEV strains. Previously, our team reported that DEV infection leads to intestinal dysbiosis; however, the impact of DEV vaccines on the gut microbiota remains unclear. This study aimed to characterize the gut microbiota of ducks, chicks, and mice immunized with DEV strains using microbiome analysis, assess the effects on microbial composition, and compare the outcomes. Both two strains caused significant shifts in gut microbiota diversity. Both strains restored the diversity of the microbiota, whereas the parental vaccine caused the enrichment of potential pathogens in chicks. Moreover, the conventional DEV vaccine disrupted gut microbiota and morphology, but the gene-deleted strain largely reversed these changes. These findings may improve the safety of vaccine through gene editing, thereby enhancing the protection of target animals.}, }
@article {pmid41764831, year = {2026}, author = {Peng, X and Zhang, L}, title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {2}, pages = {117321}, doi = {10.1016/j.diagmicrobio.2026.117321}, pmid = {41764831}, issn = {1879-0070}, abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.}, }
@article {pmid41764596, year = {2026}, author = {Yao, W and Du, H and Kulyar, MF and Pan, H and Ren, H and Luo, Q and Bhutta, ZA and Liu, S and Fang, R and Li, J}, title = {Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02328-y}, pmid = {41764596}, issn = {2049-2618}, abstract = {BACKGROUND: Metabolic syndrome disrupts metabolic resilience in periparturient sows and compromises piglet growth. As intestinal microbes govern host energy homeostasis, microbiome-directed feed additives represent a practical solution. We therefore evaluated the Tibetan‑pig isolate Bacillus amyloliquefaciens TL106, previously validated in weanlings for its capacity to alleviate sow-associated metabolic syndrome.<br><br>RESULTS: In a 43&#x2011;day trial (20 sows per group), dietary TL106 (5&#x2009;&#xd7;&#x2009;10[9]&#xa0;CFU&#xa0;kg[-1]) increased digestibility of crude fiber (+&#x2009;12.5%, p&#x2009;<&#x2009;0.05) and crude fat (+&#x2009;9.3%, p&#x2009;<&#x2009;0.01), lowered serum IL&#x2011;1&#x3b2; (-&#x2009;34%) and TNF&#x2011;&#x3b1; (-&#x2009;28%), and boosted antioxidant enzymes and immunoglobulins (all p&#x2009;<&#x2009;0.05). Litter performance improved, with a two&#x2011;thirds reduction in diarrhea and heavier piglets at 21&#xa0;days (+&#x2009;15%, aggregate n&#x2009;=&#x2009;300). Multi&#x2011;omics profiling revealed higher cecal &#x3b1;&#x2011;diversity, enrichment of butyrate&#x2011;producing Ruminococcus and Butyricicoccus (log2C 2.1 and 1.8; FDR&#x2009;<&#x2009;0.05), and activation of histidine&#x2011;metabolism and ABC&#x2011;transporter pathways (q&#x2009;&#x2264;&#x2009;0.03) in piglets, while pathways for amino&#x2011;acid biosynthesis, lipid utilization, and steroidogenesis were favored in sows.<br><br>CONCLUSIONS: Bacillus amyloliquefaciens TL106 simultaneously enhanced maternal metabolic health and neonatal development by reshaping gut microbiota and host metabolism, positioning it as a micro&#x2011;ecological tool for managing metabolic syndrome in Landrace&#x2009;&#xd7;&#x2009;Yorkshire sows and Duroc&#x2009;&#xd7;&#x2009;Landrace&#x2009;&#xd7;&#x2009;Yorkshire suckling piglets. Video Abstract.}, }
@article {pmid41764594, year = {2026}, author = {Geng, M and Zheng, Y and Tang, S and Fang, Z and Wang, T and Li, K and Chen, H and Zhang, J and Zhou, N and Wei, X and Yang, J}, title = {Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02370-4}, pmid = {41764594}, issn = {2049-2618}, support = {2025T180854//China Postdoctoral Science Foundation/ ; 24ZR1419700//Natural Science Foundation of Shanghai Municipality/ ; 32373165//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: T cells cooperate with the intestinal microbiota to coordinate antimicrobial defense, but whether this crosstalk arose as an independent innovation in mammals or represents an evolutionarily conserved feature of vertebrate immunity remains unknown.<br><br>RESULTS: Using the teleost Nile tilapia as a model, we demonstrate that both systemic and localized infection with Edwardsiella piscicida induce enteritis, correlated with robust intestinal T cell responses. Selective T cell depletion triggered excessive expression of proinflammatory cytokines, impaired mucosal architecture, and diminished host resistance to infection, underscoring the essential role of T cells in gut immunity. Strikingly, T cell depletion also caused profound alterations in gut microbial composition, characterized by a sharp decline in beneficial taxa such as Cetobacterium and the expansion of opportunistic pathogens including Klebsiella and Acinetobacter, indicating that T cells are required to maintain microbiome homeostasis. Conversely, broad-spectrum antibiotic eradication of the microbiota provoked hyperproliferation of intestinal T cells and barrier disruption, revealing reciprocal regulation between T cells and commensals. From the gut content, we isolated a C. somerae strain SH518, whose dietary supplementation for 6-8&#xa0;weeks enhanced the activation, proliferation, and effector function of intestinal T cells, preserved mucosal homeostasis during E. piscicida challenge, and even boosted systemic T cell immunity in the spleen.<br><br>CONCLUSIONS: Collectively, these findings demonstrate that teleost T cells engage in bidirectional interactions with gut microbiota to orchestrate both antimicrobial defense and mucosal homeostasis. We therefore propose that T cell-microbiota cooperation represents an evolutionarily ancient strategy predates terrestrial adaptation, offering new insights into the coevolution of mucosal T cell immunity and microbiome. Video Abstract.}, }
@article {pmid41764576, year = {2026}, author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S}, title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41764576}, issn = {1674-9782}, support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; }, abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.<br><br>RESULTS: Twenty first-lambing East Friesian&#x2009;&#xd7;&#x2009;Hu sheep hybrids weighing 54.49&#x2009;&#xb1;&#x2009;7.94&#xa0;kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet&#x2009;+&#x2009;50&#xa0;g/d CMR) feeding at 4&#xa0;h after approximately 300&#xa0;km of short-distance transport. Results indicated that 4&#xa0;h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, &#x3b1;-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.<br><br>CONCLUSION: This study confirmed that 4&#xa0;h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.}, }
@article {pmid41764274, year = {2026}, author = {ElNaggar, S and Chen, WC and Prodehl, LM and Marumo, TK and Khan, MU and Mathew, CG and Ruff, P and Jin, Z and Neugut, AI and Rustgi, AK and Uhlemann, AC and Korem, T and Abrams, JA}, title = {A generalizable cross-continent prediction of esophageal squamous cell carcinoma using the oral microbiome.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01468-y}, pmid = {41764274}, issn = {2730-664X}, abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) has a poor prognosis and limited tools for early detection. Saliva is easily accessible and its microbiome composition can serve as a marker for upper gastrointestinal tract disease. This study aims to evaluate the potential of an oral microbiome signature for classifying ESCC.<br><br>METHODS: In a cross-sectional study of 48 ESCC patients and 110 controls from South Africa, a region with high ESCC incidence, we studied the potential utility of an oral microbiome signature for the disease. We built models using nested cross-validation to evaluate whether this signature is generalizable to held-out samples and further evaluated generalizability in studies from China, a distinct geographic region.<br><br>RESULTS: We find significant alterations in the oral microbiome in patients with ESCC including significantly reduced &#x3b1; diversity and increased abundance of Fusobacterium nucleatum. We also find that logistic regression models based on microbiome data can better classify ESCC in held-out samples (auROC=0.96) compared to clinical and demographic data (auROC&#x2009;=&#x2009;0.69; DeLong p&#x2009;<&#x2009;1&#x2009;x&#x2009;10[-8]). Lastly, we find that microbiome-based models trained across multiple studies can generalize well to geographically distinct studies.<br><br>CONCLUSIONS: Our results show that the oral microbiome in individuals with ESCC is distinct from controls and that this signal can generalize across unseen samples, suggesting the potential of saliva to serve as a non-invasive screening tool for ESCC.}, }
@article {pmid41764142, year = {2026}, author = {Brayley, ODM and McCready, K and Liu, S and Convey, P and Chen, Y and Ullah, S and Teets, N and Hayward, SAL}, title = {The Microbiome of an Invasive Antarctic insect, Eretmoptera Murphyi (Diptera: Chironomidae), and its Potential Role in Nutrient Cycling.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02706-5}, pmid = {41764142}, issn = {1432-184X}, support = {NE/S007350/1//NERC CENTA2/ ; NE/S007350/1//NERC CENTA2/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; NE/T009446/1//NSFGEO-NERC/ ; OPP-1850988//National Science Foundation/ ; 700545//USDA National Institute of Food and Agriculture Hatch Project/ ; RF-2024-396/2//Leverhulme Research Fellowship/ ; }, }
@article {pmid41764137, year = {2026}, author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J}, title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.}, journal = {Obesity surgery}, volume = {}, number = {}, pages = {}, pmid = {41764137}, issn = {1708-0428}, }
@article {pmid41764092, year = {2026}, author = {Kurbanova, DI and Gurov, AV and Romanenko, SG and Pavlikhin, OG and Lesogorova, EV and Krasilnikova, EN and Zemlyanov, VA and Eliseev, OV and Teplykh, EA and Safyannikova, EA}, title = {[Features of the laryngeal mucosa microbiota in patients with chronic hyperplastic laryngitis (literature review)].}, journal = {Vestnik otorinolaringologii}, volume = {91}, number = {1}, pages = {64-69}, doi = {10.17116/otorino20269101164}, pmid = {41764092}, issn = {0042-4668}, abstract = {The literature review analyzed the data concerning studies of the microbiome of the laryngeal mucosa in patients with chronic hyperplastic laryngitis. It remains a matter of discussion whether the inflammatory process in the larynx is primary with subsequent dysbiosis and excessive growth of pathogenic microorganisms, or whether changes in the structure of the normal microbial landscape become an inducer of the disease. The article reflects the results of basic research on the role of bacterial, fungal, and viral pathogens detected on the mucous membrane of the larynx in patients with chronic hyperplastic laryngitis, conducted by Russian and foreign scientists using various technological approaches.}, }
@article {pmid41764036, year = {2026}, author = {Salaün, C and Huré, M and Guérin, C and Bôle-Feysot, C and Valentin, A and Léon, F and Lenoir, S and do-Rego, JL and do-Rego, JC and Langlois, L and Ribet, D and Achamrah, N and Coëffier, M}, title = {Intestinal epithelial TLR4 knock out induces sex-specific effects on gut barrier and microbiome in an activity-based anorexia model.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2637316}, doi = {10.1080/19490976.2026.2637316}, pmid = {41764036}, issn = {1949-0984}, abstract = {The role of the microbiota‒gut‒brain axis in the pathophysiology of anorexia nervosa has emerged in recent decades. Increased expression of Toll-like receptor 4 (TLR4) has been reported in the intestinal epithelial cells (IEC) of activity-based anorexia (ABA) mice. The inducible TLR4 knockout in IEC (TLR4[IEC][-/-]) was subsequently associated with behavioral and energy balance changes in ABA mice. Our study aimed to assess the intestinal response to TLR4[IEC][-/-] in both male and female ABA mice by focusing on three components: inflammation, the gut barrier, and the gut microbiota composition. After 12 d of undernutrition with free wheel access, the colonic expression of 43 markers was measured by RT-qPCR. The gut microbiota composition was analyzed by Illumina sequencing of the 16S rRNA gene. First, TLR4[IEC][-/-] was associated with more marked alterations in male control mice compared to females. Indeed, a reduction in the mRNA expression of eight inflammatory factors, seven tight junction proteins and fecal calprotectin levels was observed in males. Control TLR4[IEC][-/-] females showed increased expression of four inflammatory markers and one target involved in the gut barrier. The levels of the Bacillota phylum and the Deltaproteobacteria class and their subdivisions, up to the Desulfovibrio genus, increased in the control TLR4[IEC][-/-] males compared to wt. In females, only an increase in the Alcaligenaceae genus, which ranks from the Betaproteobacteria phylum, was observed. Interestingly, in both males and females, these alterations were not observed in response to ABA model in TLR4[IEC][-/-] mice. Similarly, ABA increased Tjp1 expression and Lactobacillus abundance, both of which were decreased by TLR4[IEC][-/-]. Our study shows for the first time the impact of inducible TLR4[IEC][-/-] on the intestinal response. TLR4[IEC][-/-] induced sex-specific colonic alterations and changes in the gut microbiota, which disappeared after the ABA model. Further studies are warranted to decipher the underlying mechanisms.}, }
@article {pmid41763984, year = {2026}, author = {Amirsultan, S and Odunayo, A}, title = {From Diagnosis to Resolution: A Practical Guide to Acute Diarrhea in Veterinary Patients.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cvsm.2025.12.003}, pmid = {41763984}, issn = {1878-1306}, abstract = {This review emphasizes that most cases of acute diarrhea (AD) in dogs and cats are self-limiting and primarily managed with supportive care, including hydration and nutrition. Diagnostic testing should be tailored to individual cases, focusing on ruling out systemic illness or infectious causes. Recent evidence advocates against routine antibiotic use in uncomplicated AD to prevent antimicrobial resistance and microbiome disruption. Instead, targeted therapy is reserved for systemic or bacterial infections. Additional treatments such as antiemetics and careful hygiene are discussed. Clinicians should prioritize supportive care and judicious diagnostics, adhering to antimicrobial stewardship principles to optimize patient outcomes and combat resistance.}, }
@article {pmid41763967, year = {2026}, author = {Boix-Amorós, A and Bu, K and Blank, RB and Cantor, A and Gutiérrez-Casbas, A and Rodríguez-Lago, I and Marin-Jimenez, I and Sanz, J and Masmitja, JG and Trujillo, E and Muñoz, MC and Vivar, MLG and Carrillo, M and Hernández, MVH and Calvet, X and Salaet, MA and Romero, MI and García, AB and Pérez, S and Llorente, JFG and Gonzalez-Lama, Y and Argumánez, CM and Plaza, Z and Domínguez, M and Cañete, JD and Diaz-Gonzalez, JF and Scher, JU and Clemente, JC}, title = {Microbial signatures in psoriatic arthritis distinguish disease phenotypes and newly diagnosed inflammatory bowel disease independent of faecal calprotectin.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ard.2026.01.018}, pmid = {41763967}, issn = {1468-2060}, abstract = {OBJECTIVES: There is growing evidence of microbial involvement in immune-mediated inflammatory diseases, including psoriatic arthritis (PsA) and inflammatory bowel disease (IBD). However, it remains unclear whether different PsA phenotypes exhibit distinct microbial profiles. Furthermore, up to 4% of patients with PsA have comorbid IBD, which often remains undiagnosed. We hypothesised that the gut microbiome distinguishes PsA subphenotypes and serves as a biomarker of IBD in patients with PsA independent of faecal calprotectin (fCAL).<br><br>METHODS: We obtained samples from 192 patients with axial or peripheral PsA and no prior diagnosis of IBD enrolled in the EISER study. Patients with elevated fCAL and subclinical IBD symptoms underwent colonoscopy with intestinal biopsy. Stool samples were used to measure fCAL, and gut microbiome was characterised using shotgun metagenomics. Serum samples were used for cytokine profiling.<br><br>RESULTS: Axial PsA had lower alpha diversity and loss of several commensals compared with peripheral PsA, as well as a depletion of microbial biotin and arginine metabolism and higher levels of IL-23, IL-17F, and IL-8. Five subjects had newly diagnosed IBD which was characterised by a depletion of tryptophan and vitamin B6 metabolism. They also showed significant enrichment of several taxa compared to non-IBD and with a larger effect size than fCAL.<br><br>CONCLUSIONS: Our results identify a distinct microbiome and immune profile in axial PsA, with lower microbiome diversity, a depletion of commensals and protective microbial mechanisms, and higher levels of some proinflammatory cytokines. In patients with newly diagnosed IBD, we identified microbial taxa associated with the condition yet independent of fCAL, the current clinical standard.}, }
@article {pmid41763775, year = {2026}, author = {Li, S and Liu, S and Yu, Y and Huang, X and Yang, M and Tian, L and Zhang, T and Liu, J and Li, Y and Du, Z}, title = {Bifunctional nanoparticles based on esterified hydroxypropyl β-cyclodextrin/quaternary ammonium chitosan for ulcerative colitis intervention.}, journal = {Food research international (Ottawa, Ont.)}, volume = {229}, number = {}, pages = {118450}, doi = {10.1016/j.foodres.2026.118450}, pmid = {41763775}, issn = {1873-7145}, abstract = {Developing oral nanoparticles (NPs) that combine anti-inflammatory effects with gut microbiome modulation enables an effective strategy for integrated ulcerative colitis (UC) therapy. Yet, the complex and dynamically evolving nature of the gastrointestinal milieu presents formidable challenges to the consistency and specificity of NP interventions. To address this challenge, this study designed and developed gastrointestinal microenvironment-adaptive NP via self-assembly, utilizing curcumin (Cur) for anti-inflammatory effects and anthocyanin (Cy) for microbiome regulation to achieve dual functional therapeutic outcomes. Employing the esterification strategy, hydroxypropyl-β-cyclodextrin (HPCD) was modified using citric acid (CA) and sulfonic acid (SA) to synthesize CACD (CA-modified HPCD) and SACD (SA-modified HPCD), respectively, which self-assembled in the presence of quaternary ammonium chitosan (HTCC), Cur, and Cy to yield NPs. NPs demonstrated high Cur encapsulation efficiency (EE) and encapsulation capacity (EC) across pH 2.0-7.0, highlighting their high gastrointestinal adaptability. In vivo experiments showed clear amelioration of colitis symptoms, including downregulation of pro-inflammatory cytokines and attenuation of tissue damage. HTCC-Cy-CACD-Cur NPs enriched Eubacterium siraeum_group and Prevotellaceae, HTCC-Cy-SACD-Cur NPs favored Peptococcus expansion, potentially contributing to improved immune regulation and attenuation of UC. These bifunctional NPs offer innovative UC therapy and precision nutrition interventions.}, }
@article {pmid41763459, year = {2026}, author = {Xu, X and Wei, X and Yang, X and Lin, S}, title = {Inflammaging in Geriatric Liver Disease: Mechanistic Insights and Therapeutic Frontiers.}, journal = {Mechanisms of ageing and development}, volume = {}, number = {}, pages = {112165}, doi = {10.1016/j.mad.2026.112165}, pmid = {41763459}, issn = {1872-6216}, abstract = {The rising prevalence of chronic liver disease in older adults necessitates a deeper understanding of the mechanisms driving hepatic vulnerability to aging. This review proposes a mechanistic framework positioning hepatic "inflammaging"-a chronic, low-grade inflammatory state-as a key driver of geriatric liver pathology. This review synthesizes evidence linking three interconnected processes: hepatocellular senescence, innate immune dysregulation, and gut-liver axis impairment. Senescent hepatocytes secrete senescence-associated secretory phenotype (SASP) factors that activate Kupffer and stellate cells, forming self-sustaining inflammatory loops. The NLRP3 inflammasome functions as a central integrator of stress and metabolic dysfunction, while age-related intestinal barrier decline continuously supplies inflammatory stimuli such as lipopolysaccharides. These converging pathways perpetuate a pathological hepatic microenvironment characterized by oxidative stress, fibrogenesis, and impaired regeneration. Emerging therapeutics-validated primarily in preclinical murine models-include senolytic CAR-T cells, inflammasome inhibitors, and microbiome-targeted interventions, illustrating the translational potential of this paradigm. However, clinical validation in human cohorts remains a critical next step. This mechanistic framework redefines geriatric liver disease as an active, targetable pathology rather than a passive consequence of chronological aging, highlighting new avenues for precision therapies.}, }
@article {pmid41763351, year = {2026}, author = {Murillo-Saich, JD and Mannochio-Russo, H and Sala-Climent, M and Argel, N and Quan, A and Hose, MK and Paz-Gonzalez, R and Akkati, M and Chang, E and Cutuk, A and Gentry, E and Coras, R and Lane, NE and Dorrestein, PC and Guma, M}, title = {Potential Role of Bile Acids as a Microbiome-Derived Mechanism in Synovitis of Knee Osteoarthritis Synovitis.}, journal = {Osteoarthritis and cartilage}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.joca.2026.02.011}, pmid = {41763351}, issn = {1522-9653}, abstract = {OBJECTIVE: To evaluate the relationship between bile acids (BAs) and synovitis in knee osteoarthritis (KOA).<br><br>METHODS: Radiographic KOA patients with complete datasets were included. WOMAC total and subscores were calculated. Synovitis was assessed by ultrasound or Krenn score. BAs were profiled in plasma (N=28) or synovial fluid (SF, N=29) using liquid chromatography-tandem mass spectrometry. OA synovial explants, OA fibroblast-like synoviocytes (FLS), and bone marrow-derived macrophages (BMDM) were used for in vitro experiments. Data analysis was performed using R and MetaboAnalyst.<br><br>RESULTS: Sixteen KOA participants had low-grade (0-1) and twelve had high-grade synovitis (2-3). Glycohyodeoxycholic acid (1.198 &#xb1; 0.983 vs. 1.954 &#xb1; 0.686, 0.76[95% CI: 0.04 to 1.89]) and lithocholic acid (0.19 &#xb1; 0.53 vs. 0.825 &#xb1; 0.866, 0.63[95% CI: 0.00 to 1.58]) were elevated in subjects with high-grade synovitis. LPS-binding protein (LBP) (rho = 0.58, p = 0.037, [95% CI: -0.807 to 0.46]) correlated with synovitis but only in obese participants (BMI &#x2265; 30). LBP, lithocholic acid, and glycohyodeoxycholic acid predicted high synovitis (92% sensitivity, 75% specificity, AUC = 0.875[95% CI: 0.99 to 1.05], p < 0.001). In SF, taurodeoxycholic and glycohyodeoxycholic acids correlated positively with WOMAC pain and stiffness subscores and the total WOMAC score. The BA receptors, TGR5 and LXR, were present in synovial tissue. In vitro, BAs reduced cytokine secretion in FLS and BMDM.<br><br>CONCLUSION: Detection of BAs and their receptors in synovial tissue, together with their modulatory effects on synovial cells, supports a potential biological role for BAs in KOA.}, }
@article {pmid41763194, year = {2026}, author = {Chi, F and Han, S and Yilmaz, &#xd6;H}, title = {Purified diets enable experimental rigor through compositional control in animal research.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2026.01.010}, pmid = {41763194}, issn = {1932-7420}, abstract = {Purified diets offer compositionally defined platforms that improve causal inference in nutrition studies. When aligned with the biological question, they enable targeted nutrient loss- and gain-of-function experiments, systematic lipid-source swaps, and the discovery of diet-microbiome-drug interactions. We recommend complementary validation in grain-based chow or human-relevant diets to maximize translational relevance.}, }
@article {pmid41762976, year = {2026}, author = {Hao, D and Han, H and Li, D and Sun, Y and Wang, Y and Yan, H and Li, G and Liu, H and Li, B and Li, F and Liu, W}, title = {Lactobacillus salivarius SNK-6 improves egg quality, yolk nutrient composition, and yolk flavor profile in laying hens via modulation of tissue metabolites and Cecal microbiomes.}, journal = {Poultry science}, volume = {105}, number = {5}, pages = {106649}, doi = {10.1016/j.psj.2026.106649}, pmid = {41762976}, issn = {1525-3171}, abstract = {This study aimed to investigate the effects of Lactobacillus salivarius SNK-6 (L.a-SNK-6) supplementation on the laying performance, egg quality and yolk nutrition composition, including amino acid (AAs), fatty acids, and flavor profile, of Wenshang Barred hens. A total of 432 healthy 40-week-old hens were randomly assigned to three groups with 6 replicates each: control group (CON), a group supplemented with 2.0 × 10[8] CFU/kg L.a-SNK-6 (T1), and a group supplemented with 2.0 × 10[9] CFU/kg L.a-SNK-6 (T2). Compared with the CON group, both the T1 and T2 groups showed a reduction in the broken egg rate and increases in serum alkaline phosphatase, calcium (Ca) and calcitonin levels (P < 0.05). These groups also exhibited higher Haugh unit, eggshell strength and eggshell Ca content (P < 0.05). Furthermore, egg yolks from the T1 and T2 groups contained higher levels of α-linolenic acid, and oleic acid than those of the CON group. Total AAs content in the egg yolks was markedly elevated in both T1 and T2 groups, particularly the glutamic acid and aspartic acid (P < 0.05). Twenty volatile compounds that differed significantly among the three groups were identified, including d-limonene and β-pinene. Metabolomic analyses revealed 326, 237, and 108 differential metabolites in plasma, liver, and cecal content, respectively, between the T1 and CON group. These metabolites were significantly enriched in the tryptophan metabolism (map00380) pathway in both plasma and cecal content. 16S rRNA sequencing indicated that cecal microbiome diversity and abundance were higher in T1 group compared with the CON group, although the differences were not statistically significant. Combined analysis showed seventy-five host metabolite-microbiota pairs were significantly correlated (P-adjust < 0.05). Collectively, L.a-SNK-6 supplementation modulated metabolites across multiple host tissues and the cecal microbiome, leading to improved egg quality, enhanced yolk nutrient composition, and alterations in yolk volatile compounds.}, }
@article {pmid41762973, year = {2026}, author = {Vanderghinste, P and Bautil, A and Simmonds, SJ and Apajalahti, J and Bedford, MR and González-Ortiz, G and Courtin, CM}, title = {Extensive particle size reduction of wheat bran increases the broiler's caecal fermentative capacity, but not bran fermentability ex vivo.}, journal = {Poultry science}, volume = {105}, number = {5}, pages = {106695}, doi = {10.1016/j.psj.2026.106695}, pmid = {41762973}, issn = {1525-3171}, abstract = {The inclusion of fibre-rich fractions such as wheat bran in broiler feed can increase the production of short-chain fatty acids (SCFA) in the broiler's gut, improving performance, gut health and immunity. Benefits of fine fibre additions (< 300 µm) on caecal fibre fermentation in broilers have been reported, but it is unclear if further reduction in bran particle size continues to stimulate caecal fermentation, and if the ideal particle size for such fermentation is driven by its effects in the gastrointestinal tract or by microbial size preference. To separate these effects, the caecal inocula of 198 Ross 308 male broilers (d 21 and d 35) which received a 0.5% dietary inclusion of 452 µm bran (WB452), 27 µm bran (WB27) or no bran (control) were combined with the same bran fractions in a 3 × 3 ex vivo fermentation simulation design (n = 8). Gas production, pH, SCFA, branched-chain fatty acid (BCFA) content and total bacteria count were measured to assess the effect of bran particle size on the fermentation of the added bran, the fermentative capacity of the bran-fed caecal inocula and their interaction. Both sizes of added bran increased SCFA content (P < 0.05) and lowered the pH (P < 0.05) and tended to increase SCFA-to-BCFA ratio (P < 0.10) and gas production (P < 0.10), while bran particle size had little effect on these parameters during the ex vivo fermentation. The size of the in vivo-fed bran altered the fermentative capacity of the caecal inocula, based on decreased total gas production (P = 0.010) and increased acetic acid content (P = 0.005) for the WB452-fed inoculum, in contrast to tendencies towards a higher total bacteria count (P = 0.075) and SCFA-to-BCFA ratio (P = 0.059) for the WB27-fed inoculum. This shows that bran size does not directly control microbial fermentation but mainly affects the fibre-fermenting capacity of the caecal inocula through its presence in vivo. The lack of an interaction effect between the bran additions and the bran-fed inocula indicates that bran size does not play a major role in priming the fibre-fermenting microbiome. These results highlight the importance of selecting fibre size in feed additions to stimulate broilers' caecal fibre-fermenting capacity.}, }
@article {pmid41762911, year = {2026}, author = {Abdel Jaleel, GA and Ammar, NM and Shabaan, A and El Hotaby, W and Elshamy, AI and El-Gendy, ZA}, title = {Metabolite-rich Saccharomyces cerevisiae cell wall extract counter diabetic tissue damage via AMPK activation and microbiome modulation in rats.}, journal = {Tissue &amp; cell}, volume = {101}, number = {}, pages = {103414}, doi = {10.1016/j.tice.2026.103414}, pmid = {41762911}, issn = {1532-3072}, abstract = {Saccharomyces cerevisiae cell wall extract (SCCWE) contains a variety of bioactive compounds, yet its antidiabetic action mechanisms remain unclear. The current work aimed to characterize the chemical components using GC-MS of SCCWE along with its antidiabetic, hepatoprotective, antioxidant, and microbiome-modulating properties in streptozotocin (STZ)-induced diabetic rats. The rats were treated with glibenclamide, SCCWE (25, 50, or 100 mg/kg), or non-diabetic normal rats as a control. Key regulators (P-AMPK, HMGR, SREBP-1c, and LXRα) as well as metabolic parameters, oxidative and inflammatory indicators, and histopathology and FTIR analysis were evaluated. Trehalose (16.03%), turanose (15.05%), glycerol (12.24%), and mannobiose (7.38%) were found to be the primary constituents by GC-MS profiling. STZ elevated fasting glucose 1.5-fold and reduced lactic acid bacteria 6.6-fold. SCCWE lowered glucose by 27.4-30.4% and restored lactic acid bacteria by 266.7-711.6%. Serum ALT, increased 2.1-fold in diabetic rats, decreased by 35.3-55.6% with SCCWE. Dyslipidemia improved markedly, with total lipids, cholesterol, and triglycerides reduced by up to 45.6%, 63.9%, and 46%. SCCWE decreased hepatic MDA by 56.5% and increased GSH up to 607.2%. It elevated P-AMPK while suppressing HMGR (18.9-154.6%), SREBP-1c (29.7-92.6%), and LXRα mRNA (21.3-87.6%). Histopathology and FTIR confirmed tissue and membrane restoration. SCCWE demonstrates potent antidiabetic and hepatoprotective activities, supporting its potential as a natural therapeutic for diabetes.}, }
@article {pmid41762838, year = {2026}, author = {Li, D and Diao, Z and Shu, A and Gan, S and Zhang, W and Zhang, Y and Xiong, L and Wei, D and He, L and Shi, W and Sun, G and Yuan, F and Liu, Z and Gao, Z}, title = {Deinococcus sp. NH1 enhances cadmium tolerance in rice by modulating rhizosphere microbiome and plant metabolism.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141623}, doi = {10.1016/j.jhazmat.2026.141623}, pmid = {41762838}, issn = {1873-3336}, abstract = {Cadmium stress threatens rice safety and farmland management. To investigate the role of high‑cadmium‑tolerant Deinococcus in alleviating plant cadmium stress, this study identified a strain, Deinococcus sp. NH1, with highly cadmium-tolerant and growth-promoting potential, via 16S rRNA gene sequencing and whole-genome average nucleotide identity analysis. Under cadmium stress conditions, inoculation with NH1 significantly alleviated growth inhibition in rice, resulting in notable increases in plant height, fresh weight, and root density. In soil containing 10 mg/kg cadmium, NH1 inoculation downregulated originally elevated genes related to cadmium detoxification and stress response, while upregulating biosynthesis and energy metabolism genes. Cadmium reduced rhizobacterial diversity, but NH1 restored diversity and induced community restructuring, significantly enriching beneficial microorganisms, such as Massilia and Haliangium. At the metabolic level, NH1 treatment altered the rhizosphere metabolome, in which terpenoids, and shikimates and phenylpropanoids such as 5-O-methylembelin and linoleate that showed significant positive correlations with the enriched microorganisms may play key roles. In summary, NH1 enhances rice tolerance to cadmium stress by regulating host gene expression, restoring and reshaping the rhizosphere microbial community structure, and driving beneficial microbe‑metabolite interactions. This study offers new insights into plant-microbe interactions in heavy metal stress mitigation.}, }
@article {pmid41762502, year = {2026}, author = {Lei, J and Wu, Z and Liu, Z and Yang, R and Cheng, L and Wang, J and Liu, Y and Chen, R}, title = {Predicting aerobic granular sludge structural instability: An intelligent early-warning framework integrating convolutional neural network and fluorescence fingerprint features.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129115}, doi = {10.1016/j.jenvman.2026.129115}, pmid = {41762502}, issn = {1095-8630}, abstract = {Aerobic granular sludge (AGS) was recognized as an innovative alternative superior to activated sludge processes, yet its development has been constrained by structural instability and the lack of early-warning methods for critical states. To address this limitation, an intelligent early-warning model (EPS-ResNet) based on multi-view convolutional neural networks was developed. This model achieved a 6±1-day advance prediction of AGS structural destabilization (accuracy:97.6%) by analyzing fluorescence characteristics in Excitation-Emission-Matrix Spectra (EEMs) of loosely/tightly bound extracellular polymeric substances (LB-EPS/TB-EPS). Through occlusion sensitivity analysis and fluorescence region segmentation, Region I (tyrosine-like proteins) of TB-EPS, Region IV (soluble microbial metabolites) of TB-EPS, and Region IV of LB-EPS were identified as the top three contributors to early-warning efficacy. Integrated microbiome analysis revealed that the superior early-warning performance of the model was primarily attributed to the capacity of key EEMs regions (I, IV, and V) of EPS to sensitively capture dynamic succession of dominant phyla and functional genera in AGS following shocks. Correlation analysis conducted through the Mantel test demonstrated that key dominant phyla responding to the model included Bacteroidota and Patescibacteria, while critical functional genera comprised Flavobacterium, Pseudazoarcus, Thauera, and Candidatus_Competibacter. An early-warning framework for abnormal states of AGS integrating scalability and mechanistic interpretation was developed in this study. This framework was demonstrated to be applicable not only for the early warning of AGS structural destabilization, but also extensible to the early detection of anomalies in biological treatment systems, thereby promoting the transformation of water treatment process operation and maintenance toward digitalization and intelligentization.}, }
@article {pmid41762333, year = {2026}, author = {Pavan, JS and Deeksha, PM and Rajarushi, CN and Paschapur, AU and Rishika, KS and Ramakrishnan, B and Subramanian, S}, title = {Gut microbiota-mediated nitrogen recycling in the white Grub Holotrichia longipennis: A model for microbiome-targeted pest control.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41762333}, issn = {1573-0972}, }
@article {pmid41762294, year = {2026}, author = {Joda, JF and Raji, RO and Nmadu, ME and Oyewole, OA}, title = {The Interactions of Emergent Contaminants (ECs) with Soil Microbiome.}, journal = {Ecotoxicology (London, England)}, volume = {35}, number = {4}, pages = {}, pmid = {41762294}, issn = {1573-3017}, }
@article {pmid41762172, year = {2026}, author = {Ghahari, AA and Nourizadeh, M and SalekShahabi, M and Davari, S and Mohammadzadeh Mounesyar, S}, title = {Psychobiotics and the microbiota-gut-brain axis: Emerging paradigms in mental health modulation.}, journal = {Experimental physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/EP093301}, pmid = {41762172}, issn = {1469-445X}, abstract = {The global rise in mental health conditions has prompted interest in interventions that act beyond conventional psychopharmacology. Psychobiotics, broadly understood as live microorganisms or microbe-derived products that interact with the microbiota-gut-brain axis, have been suggested to exert neuroactive effects through neural, immune, endocrine and metabolic routes. This narrative review synthesizes recent preclinical, mechanistic and early clinical observations. Experimental studies show that selected strains can modulate cytokine signalling, influence stress-responsive systems such as the hypothalamic-pituitary-adrenal axis, and support synaptic plasticity via factors such as brain-derived neurotrophic factor. A limited number of human trials using well-characterized Lactobacillus and Bifidobacterium strains have reported improvements in affective and stress-related outcomes, but these effects are generally small to moderate, more apparent in adjunctive than stand-alone use, and dependent on strain, dose, population and intervention length (typically 4-12 weeks). Evidence on neurodevelopmental conditions (e.g., autism spectrum disorder, attention-deficit/hyperactivity disorder) remains preliminary, based on small and heterogeneous samples. Across studies, key constraints include methodological heterogeneity, incomplete strain-level reporting, and gaps in mechanistic resolution that make it difficult to link microbial shifts to psychiatric benefit. Emerging microbiome- and metabolomics-informed approaches may help identify likely responders and improve translational precision, but they are not yet ready for routine clinical application. Overall, psychobiotics should currently be viewed as a promising adjunct within integrative mental health care, warranting larger, standardized trials with clearly defined strains, doses and mechanistic endpoints.}, }
@article {pmid41762163, year = {2026}, author = {Lu, Y and Nguyen, KN and Xia, J}, title = {Interpreting Microbiome Signatures with MicrobiomeNet.}, journal = {Current protocols}, volume = {6}, number = {3}, pages = {e70338}, pmid = {41762163}, issn = {2691-1299}, abstract = {MicrobiomeNet (https://microbiomenet.com) is a web-based platform developed to provide functional insights into microbiome signatures using genome-scale metabolic models (GEMs). It currently hosts 12,400 GEMs and around 6 million microbial signatures. Users can start by searching microbes, metabolites, genes, or enzymes, and perform common tasks such as to characterize the metabolic capacity for a given microbe, to explore known microbial associations, as well as to understand potential metabolic interactions. This book chapter provides practical, step-by-step instructions for navigating MicrobiomeNet to obtain functional insights into individual microbes or microbial association networks. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterizing the Metabolic Profile of a Microbe of Interest Basic Protocol 2: Elucidating Metabolic Interactions from Microbial Associations Basic Protocol 3: Analyzing Carbohydrate-Utilization Pathways to Explain Co-Responsive Taxa Basic Protocol 4: Identifying Novel Deoxycholic Acid-Producing Gut Microbes Basic Protocol 5: Assessing the Faecalibacterium prausnitzii-Coprococcus Relationship.}, }
@article {pmid41762159, year = {2026}, author = {Zhang, Y and Liu, Q and Jing, L and Li, D}, title = {Suppressive microbiome protects against mulberry wilt by safeguarding host glycosylphosphatidylinositol-anchor biosynthesis.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag060}, pmid = {41762159}, issn = {1365-2672}, abstract = {AIMS: Soil-borne pathogens pose a significant threat to global agriculture. While certain soils naturally suppress disease, the complex interplay between different microbial kingdoms and their metabolic functions in orchestrating this suppression remains poorly understood.<br><br>METHODS AND RESULTS: We integrated 16S/ITS/18S rRNA amplicon sequencing with non-targeted LC-MS/MS metabolomics to elucidate the multi-kingdom microbial drivers and metabolic profiles of rhizosphere soils from healthy (HS) and diseased (DS) mulberry (Morus alba L.) orchards. The HS orchard, under long-term organic fertilization, exhibited strong disease suppression (12% incidence), whereas the DS orchard, under chemical fertilization, was highly susceptible (85% incidence) to wilt disease. The HS soils harbored a more complex and stable microbial co-occurrence network. This community was significantly enriched in putative beneficial taxa, including the bacteria Stenotrophomonas and Pseudomonas, the fungus Mortierella, and the predatory protist Colpoda. In contrast, the pathogen Fusarium was enriched in DS soils. Functional profiling predicted that the HS microbiome possessed a higher potential for antibiotic biosynthesis and stress tolerance. Metabolomic analysis revealed a striking divergence in metabolic pathways. Diseased plants mounted a massive but ineffective defense, characterized by the accumulation of phytoalexins. We identified a significant downregulation of the glycosylphosphatidylinositol-anchor biosynthesis pathway in DS soils, a fundamental process for anchoring functional proteins to the plant cell surface.<br><br>CONCLUSIONS: Our findings reveal a novel pathogenic strategy of targeting host cell-surface architecture and the corresponding community-level defense mechanism.}, }
@article {pmid41761982, year = {2026}, author = {Yan, L and Hu, J and Feng, Q and Sun, J and Huang, X and Xu, C}, title = {A Unique Perspective on Auto-reactive Antibody Production in Autoimmune Disease Induced by Microbiome.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {2}, pages = {45424}, doi = {10.31083/FBL45424}, pmid = {41761982}, issn = {2768-6698}, support = {2023-JC-QN-0855//Natural Science Basic Research Program of Shaanxi/ ; 2021JY-17//Shaanxi Provincial People's Hospital Science and Technology Talent Support Program Project/ ; }, abstract = {Activation of autoreactive lymphocytes leads to cellular and tissue damage, which results in the development of autoimmune diseases. External environmental changes, such as chronic microbial infections, can alter the immune homeostasis and disrupt the balance of autoreactive T and B cells. In this review, we first summarize immune tolerance mechanisms of T and B cells, and then describe the breakthroughs of immune tolerance in T and B cells, followed by related autoimmune diseases. Furthermore, we explore how microbial infections can induce the production of autoreactive antibodies via carrier effects when the balance of autoreactive T and B cells is disrupted. These kinds of antibodies can lead to autoimmune diseases through molecular mimicry mechanisms. Our perspective provides a theoretical framework and novel insights into the mechanism of autoreactive antibodies in the pathogenesis of autoimmune diseases associated with microbial infections. This analysis may offer novel directions for drug discovery of autoimmune diseases.}, }
@article {pmid41761881, year = {2026}, author = {Jin, X and Luo, X and Shen, W and Lv, G and Jiang, X and Jin, C and Feng, B and Che, L and Xu, S and Lin, Y and Zhuo, Y and Wu, D and Hua, L}, title = {Nicotinamide Riboside Alleviates Heat Stress-Induced Intestinal Dysfunction by Enhancing Antioxidant Capacity, Restoring Immune Homeostasis, and Modulating Gut Microbiota in a Boar Model.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {5}, pages = {e70418}, doi = {10.1002/mnfr.70418}, pmid = {41761881}, issn = {1613-4133}, support = {2023YFD1300804/5//National Key R&amp;D Program of China/ ; NCTIP XD/B04//Strategic Priority Research Program of the National Center of Technology Innovation for Pigs/ ; 32472948//National Natural Science Foundation of China/ ; U21A20255//National Natural Science Foundation of China/ ; 2023NSFSC1139//Sichuan Science and Technology Program/ ; CARS-35//earmarked fund for China Agriculture Research System/ ; }, abstract = {Heat stress (HS) induces adverse intestinal effects, including morphological damage, immune dysfunction, and microbial dysbiosis. Nicotinamide riboside (NR) supplementation has shown promise in protecting against intestinal injury. This study aimed to investigate the efficacy of NR in alleviating HS-induced intestinal damage in a porcine model. Eighteen boars were randomized into three groups (n = 6): control (CON, thermoneutral), heat stress (HS), and HS with NR supplementation (HS-NR). After an initial feeding phase, the HS and HS-NR groups were exposed to an HS environment (35 ± 1°C) for 2 weeks, while the CON group remained thermoneutral. Intestinal injury was assessed via histomorphology, biochemical parameters, transcriptomics, and microbiome sequencing. We found that NR supplementation significantly restored intestinal morphology and attenuated colonic oxidative stress compared to the HS group. Moreover, NR ameliorated HS-induced immune dysfunction and corrected gut microbial dysbiosis. These results suggest the therapeutic potential of NR as a nutritional intervention to mitigate HS-induced intestinal damage.}, }
@article {pmid41761700, year = {2026}, author = {Pepke, ML and Hansen, SB and Limborg, MT}, title = {The ageing holobiont: crosstalk between telomere dynamics, oxidative stress and the gut microbiome.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1002/brv.70152}, pmid = {41761700}, issn = {1469-185X}, support = {DNRF143//Danmarks Grundforskningsfond/ ; CF21-0356//Carlsbergfondet/ ; }, abstract = {The gut tissue is at the frontline of early onset of ageing. It exhibits high cell turnover rates and rapid telomere shortening, which can have systemic effects on the developing or senescing organism. We conducted a literature review of studies on the crosstalk between telomere length dynamics, telomerase activity, oxidative stress, and gut microbiota composition and activity in animals. Studies mainly on humans and animal models include correlations between telomere dynamics and gut microbiome components, particularly under pathogenic conditions, but also manipulations of either the gut microbiome through faecal microbiota transplantations or of telomere dynamics using telomerase knockout models. This synthesis reveals that components of the gut microbiome including microbial metabolites and pathogenic bacteria can affect telomere dynamics through oxidative-stress-inducing processes, and that telomere maintenance is critical in maintaining gut barrier and tissue integrity, which link inflammation and gut dysbiosis. Some of the interactions between the gut microbiome and host telomere dynamics are bidirectional and important in maintaining intestinal homeostasis. However, many of the causal molecular or cellular mechanisms - and how they translate into organismal senescence - remain to be identified. Furthermore, we highlight how recent advances in whole genome sequencing capacities and bioinformatic tools represent an often-unexploited resource for measuring telomere lengths and may be particularly valuable tools within the hologenomic framework outlined here. Investigating the role of telomere dynamics in mediating gut microbiota-host interactions in different species will improve our understanding of how crosstalk between these hallmarks of ageing shape holobiont physiology in general and the ageing phenotype in particular.}, }
@article {pmid41761590, year = {2026}, author = {Matera, MG and Calzetta, L and De Biase, A and Parente, V and Cazzola, M}, title = {Emerging pharmacotherapies in chronic rhinosinusitis with nasal polyps.}, journal = {Expert opinion on pharmacotherapy}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/14656566.2026.2638480}, pmid = {41761590}, issn = {1744-7666}, abstract = {INTRODUCTION: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic, heterogeneous inflammatory disorder of the sinonasal mucosa that substantially impairs quality of life. It is characterized by T2 or non-T2 inflammatory endotypes and often coexists with asthma or aspirin-exacerbated respiratory disease, complicating management due to high recurrence rates and limited disease-modifying options.<br><br>AREAS COVERED: This review evaluates emerging pharmacotherapies for CRSwNP, emphasizing targeted biologics developed from mechanistic understanding of inflammatory pathways. Approved monoclonal antibodies, dupilumab, omalizumab, and mepolizumab, are discussed regarding their effects on nasal polyp size, symptom relief, and patient-reported outcomes, with reference to comparative efficacy and safety. Evidence is drawn from RCTs, meta-analyses, and real-world studies, highlighting both clinical benefits and current limitations. Emerging therapies targeting upstream epithelial cytokines (TSLP, IL-33) and complementary strategies, including small-molecule inhibitors, microbiome modulation, and advanced topical delivery systems, are also addressed.<br><br>EXPERT OPINION: Biologics have transformed CRSwNP treatment, but challenges remain in cost, treatment duration, and patient selection. Integrating endotype characterization, biomarkers, and comparative effectiveness data is crucial for personalized management. Future advances are expected from upstream immune modulation, restoration of epithelial barrier integrity, and optimized local drug delivery, enabling mechanism-based, adaptive approaches that maximize efficacy while minimizing systemic exposure.}, }
@article {pmid41761576, year = {2026}, author = {Amancio, BR and Magnani, E and T Nunes, A and Silva, TH and Cortinhas, C and Carvalho, VV and Tamassia, LFM and Zihlmann, R and Berndt, A and Marcatto, JOS and Consolo, NRB and Benedeti, PDB and Branco, RH and Paula, EM}, title = {Effect of two-doses of 3-Nitrooxypropanol (3-NOP) on methane emissions, performance, rumen microbiome, and metabolomics in Nellore cattle.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skag068}, pmid = {41761576}, issn = {1525-3163}, abstract = {This study evaluated the effects of two doses of 3-nitrooxypropanol (3-NOP) on methane (CH4) emissions, performance, dry matter (DM) intake, apparent digestibility, rumen microbiome and metabolomic profile of Nellore cattle fed a high concentrate finishing finishing diet. Seventy-five 20-month-old Nellore bulls, 361.6 ± 30.08 kg body weight (BW) were individually housed with ad libitum access to feed and water. Animals were distributed in a completely randomized study design, with three treatments and 25 animals per treatment, which were: 1) CON, control (basal diet + mineral premix without 3-NOP), 2) 3-NOP65 (Basal diet + mineral premix + 65 mg 3-NOP/kg of DM), 3) 3-NOP85 (Basal diet + mineral premix + 85 mg 3-NOP/kg of DM). The 115-day trial included a 3-week adaptation period with increasing dietary concentrate levels from 50% to 88%. Enteric CH4 emissions were measured using the sulfur hexafluoride (SF6) tracer gas technique. Supplementation with 3-NOP had no detrimental effect on final BW (P = 0.89) and average daily gain (ADG; P = 0.94), but DM intake increased linearly with 3-NOP inclusion (P = 0.05). Methane emissions (g/d) were reduced by 13.2% and 26.7% in the 3-NOP65 and 3-NOP85 groups, respectively (P < 0.05), without adverse effects on animal health. Rumen microbiome analysis revealed a quadratic response in the relative abundance of the phylum Euryarchaeota (P = 0.01). Metabolomic analysis indicated significant changes in amino acid and energy metabolism, with proline, arginine, and threonine identified as key discriminant metabolites (VIP > 1) in the 3-NOP85 group. These findings demonstrate that 3-NOP supplementation effectively reduces CH4 emissions in a dose-dependent manner, while maintaining animal performance and health.}, }
@article {pmid41761296, year = {2026}, author = {Ye, H and Yang, X and Zheng, M and Dong, W and Chen, X and Chen, J and Hu, M and Zhou, M and Zheng, P and Shen, L and Wu, Y and Zheng, K and Huang, XF and Yu, Y}, title = {Early risperidone exposure impairs cognitive function by perturbation of the gut microbiome and bile acids/tyrosine-PTP1B axis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02358-0}, pmid = {41761296}, issn = {2049-2618}, abstract = {BACKGROUND: Second-generation antipsychotics (SGAs) are increasingly being utilized in children and adolescents. Risperidone, one of the most commonly prescribed SGAs in this population, has been found to adversely affect cognitive function; however, limited knowledge exists regarding the impact of risperidone on the gut microbiome-brain axis. We hypothesized that the cognitive impairment induced by risperidone is mediated by alterations in the gut microbiome and its metabolites.<br><br>RESULTS: In this study, we found that early-life risperidone exposure impaired cognition in mice, including deficits in behavior tests and hippocampal dendritic architecture. The risperidone-exposed mice also exhibited gut microbiota dysbiosis along with damage to the intestinal barrier. Fecal microbiota transplantation (FMT) from treated donors to recipients demonstrated the causal role of the gut microbiome in risperidone-induced cognitive deficits. Of note, risperidone increased the abundance of species Escherichia coli, Eggerthella lenta, Ruminococcus gnavus, Clostridium perfringens, Clostridium difficile, and Blautia hydrogenotrophica. These altered species are identified to encode 7&#x3b1;-HSDH, 3&#x3b2;/&#x3b1;-HSDH, TyrB, and porA, the key enzymes in secondary bile acid metabolism and tyrosine metabolism. Furthermore, a significant reduction in tauroursodeoxycholic acid (TUDCA, the metabolite of bile acid metabolism) and accumulation of p-cresol (the metabolite of tyrosine metabolism) were observed in the brains of mice exposed to risperidone. Mechanically, TUDCA prevented cognitive impairment and endoplasmic reticulum (ER) stress in the hippocampus induced by risperidone, while p-cresol induced neuronal ER stress. Knockout of protein tyrosine phosphatase 1B (PTP1B, ER stress-associated protein) in neurons ameliorated cognitive impairment and neurological damage induced by risperidone.<br><br>CONCLUSIONS: This study, for the first time, reveals that early risperidone exposure induces gut microbiome dysbiosis and disturbs the bile acids/tyrosine-PTP1B axis to impair cognitive function. These findings alert the risk of gut and neurological side effects of SGAs treatment and highlight that it is crucial to maintain gut homeostasis during the brain developmental phases of children and adolescents with SGAs exposure. Video Abstract.}, }
@article {pmid41761226, year = {2026}, author = {Zhao, X and Weng, Y and Huang, R and Hu, Y}, title = {From mouth to muscle: mechanistic and interventional perspectives on the tongue-coating microbiome in sarcopenia.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07874-z}, pmid = {41761226}, issn = {1479-5876}, support = {U22A20287; 82571011//National Natural Science Foundation of China/ ; 202140058//Shanghai Municipal Health Commission/ ; 202240042//Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Sarcopenia, the progressive loss of skeletal muscle mass and function, needs upstream, low-burden tools for early detection and high-frequency monitoring, especially in older adults. Conventional assessments such as handgrip strength and gait speed mainly capture downstream impairment and may miss early physiological change. The tongue-coating microbiome is an emerging, measurable niche on the oral-gut-muscle axis that may provide proximal signals of metabolic, inflammatory, and circadian status.<br><br>METHODS: We performed a narrative summary of recent evidence on tongue-gut coupling, mapped plausible mechanisms to muscle regulation, and evaluated the feasibility of tongue-based measurement. We propose a minimal methods set (fixed pre-breakfast sampling, strict low-biomass quality control, AI-assisted standardized tongue imaging, saliva assays integrated with multi-omics) and a three-tier metric structure aligned to the minimal clinically important difference (MCID) for functional endpoints.<br><br>RESULTS: Evidence supports links across three axes: metabolic (microbial metabolites such as short-chain fatty acids and niacin that modulate mitochondrial energetics and anabolism), inflammatory (oral dysbiosis and barrier disruption amplifying systemic inflammation via lipopolysaccharide, Toll-like receptor 4, and NF-&#x3ba;B signaling), and circadian (microbiome rhythms coupled to eating and sleep timing). The tongue coating forms a stable niche suitable for frequent follow-up. An upstream-midstream-downstream metric stack enables MCID-anchored interpretation. Current data are limited and heterogeneous, so tongue-derived metrics should complement stool testing and functional standards.<br><br>CONCLUSIONS: Tongue-based monitoring is a practical adjunct for earlier risk signaling and community-level follow-up. Priorities are multicenter validation, interpretable and device agnostic models, and axis-stratified trials to define when and for whom tongue-derived signals add MCID-level clinical value. Because direct longitudinal human evidence linking tongue-coating signals to clinically meaningful sarcopenia outcomes remains limited, we frame the tongue-coating microbiome primarily as a hypothesis-driven, upstream monitoring niche and outline testable priorities for validation and translation.}, }
@article {pmid41761093, year = {2026}, author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA}, title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06400-8}, pmid = {41761093}, issn = {1471-2105}, }
@article {pmid41760891, year = {2026}, author = {Song, B and Zeb, J and Sparagano, OA}, title = {Reactive oxygen species-producing genes regulate mosquito midgut bacteria colonization, transcriptomic changes and cell repair.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41760891}, issn = {2399-3642}, abstract = {The mosquito midgut uses ROS (Reactive Oxygen Species)-producing pathway to control midgut bacteria and maintain cell regeneration. However, it is not clear what are the functional and mechanistic differences between the two components, NOX (NADPH oxidase) and DUOX (Dual Oxidase) enzymes. In this study, we characterize the different roles of Nox and Duox gene in eliminating ECC15 (Erwinia carotovora 15) after oral infection and controlling the microbiome by counting CFU (Colony-forming unit) and 16S rRNA sequencing after RNA interference-mediated knockdown. We also determined the different transcriptomic changes by RNA-sequencing and cell regeneration by immunostaining after knocking down the genes upon ECC15 infection. Here, we report that Nox but not Duox was necessary for eliminating ECC15 and suppressed more rare species in the microbiome. Transcriptionally, we found that Nox controls more gene responses than Duox upon ECC15 infection; the heat shock protein pathway may be the main stress pathway induced by ECC15 that discriminates Nox (highly-related) and Duox. The MAPK pathway was robustly induced in control (LacZ) and Duox-knockdown mosquitoes, but not in Nox-knockdown mosquitoes. AMP gene induction was also suppressed only in Nox-knockdown mosquitoes. We also found that ECC15 infection induced strong cell regeneration, while Nox RNAi suppressed it strongly. Although, Duox was highly related to metalloexopeptidase activity genes comparing to Nox.}, }
@article {pmid41760847, year = {2026}, author = {Eilers, T and Delanghe, L and De Boeck, I and Van Rillaer, T and Van Malderen, J and Bakelants, S and Van Beeck, W and Wittouck, S and Lebeer, S}, title = {Pangenome-based design of strain-specific primers enables precise monitoring of bacteria in human microbiome intervention trials.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-41449-8}, pmid = {41760847}, issn = {2045-2322}, support = {HBC.2022.1000//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 1224923N//Fonds Wetenschappelijk Onderzoek/ ; 12AZ624N//Fonds Wetenschappelijk Onderzoek/ ; 852600//Horizon 2020 Framework Programme/ ; }, }
@article {pmid41760690, year = {2026}, author = {Sammons, SL and Kuntz, TM and DiLullo, M and Morgan, XC and Martin, A and Hughes, ME and Rahman, T and Barroso-Sousa, R and Ogayo, ER and Giordano, J and Ryan, S and Waks, AG and Schlam, I and Ligibel, J and Lin, NU and Garrido-Castro, AC and Mittendorf, EA and Tolaney, SM}, title = {The landscape of the intestinal microbiome among patients with newly diagnosed invasive breast cancer and ductal carcinoma in situ (DCIS).}, journal = {NPJ breast cancer}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41523-026-00922-3}, pmid = {41760690}, issn = {2374-4677}, support = {P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; P50CA168504 to DF/HCC//National Cancer Institute (NCI) Breast Cancer SPORE/ ; Dana-Farber Cancer Institute project number 6395601//Massachusetts Life Sciences Center/ ; }, abstract = {The intestinal microbiome shapes immune responses and is associated with patient outcomes in cancer following immunotherapy. We evaluated differences between the intestinal microbiome profiles of patients with early-stage invasive breast cancer (BC) and ductal carcinoma in situ (DCIS) by subtype using whole genome metagenomic sequencing. There were no significant differences in microbiome composition between DCIS and invasive BC as measured by alpha diversity (p = 0.20, ANOVA) or beta diversity (p = 0.52, PERMANOVA). Within invasive BC, patients with hormone receptor-positive (HR +)/HER2 + BC differed significantly in beta diversity relative to other subtypes (p < 0.05), with differences in six species (q < 0.25). Bacteroides ovatus was significantly more abundant in patients with stage III BC vs. stage I (p = 0.0003). Functional pathway analysis using HUMAnN3 revealed stage-specific enrichment of amino acid biosynthesis and nucleotide-related pathways. Altogether, these findings highlight potential microbial signatures associated with BC subtype and stage.}, }
@article {pmid41760491, year = {2026}, author = {Fu, X and Jang, YF and Dang, D and Hu, X and Wu, H}, title = {Decrease in intestinal microbiome diversity at birth is related to moderate and severe bronchopulmonary dysplasia in premature infants.}, journal = {Pediatrics and neonatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pedneo.2025.03.012}, pmid = {41760491}, issn = {2212-1692}, abstract = {BACKGROUND: Bronchopulmonary dysplasia (BPD) is a prevalent respiratory disorder in premature infants. Recent studies have revealed an association between the intestinal microbiome and respiratory diseases. This study aims to explore the characteristics of the gut microbiome of premature infants with moderate and severe BPD.<br><br>METHODS: The study population consisted of preterm infants with a gestational age of &#x2264;34 weeks. Infants with moderate and severe BPD were selected as the case group. Stool samples were collected at birth and 28 days after delivery. The obtained samples were processed using 16sRNA technology for diversity analysis, taxonomic composition, and LEfSe analysis.<br><br>RESULTS: In this study, 15 infants were enrolled in the BPD group, while 15 infants were included as controls. At birth, the alpha diversity of the BPD group was significantly lower compared to the control group. Infants with severe BPD had even lower diversity. The relative abundance of Staphylococcus in the BPD group was higher, whereas Sphingomonas and Veillonella were the predominant species in the control group. Additionally, the severe BPD group exhibited a higher abundance of Bacillales and Oscillospiraceae compared to the moderate BPD group. At 28 days after birth, there was an increase in the abundance of Escherichia, Klebsiella, and Bifidobacterium compared with previous levels, and a decrease in the abundance of Herbaspirillum.<br><br>CONCLUSIONS: The diversity of intestinal microbiota in infants with moderate and severe BPD appears to be relatively lower, and specific microbial species such as Staphylococcus and Bacillales may contribute to the pathogenesis and progression of BPD. The intestinal microbiota in infants with BPD interacts with the oxygen environment in the gut, and its early formation is influenced by maternal factors. These findings regarding the diversity and specific flora of gut microbiota could potentially offer insights into the pathogenesis of BPD.}, }
@article {pmid41759957, year = {2026}, author = {Pinar, I and Nielsen, TSS and Brach, T and Moll, JM and Nielsen, BH and Hvistendahl, MK and Berner-Hansen, M and Jeppesen, PB}, title = {Investigation of the stool microbiome of Short Bowel Syndrome patients before and after a 24-week treatment with the Glucagon-like Peptide 2 analog glepaglutide.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {102989}, doi = {10.1016/j.clnesp.2026.102989}, pmid = {41759957}, issn = {2405-4577}, abstract = {BACKGROUND AND AIMS: Glepaglutide is a long-acting glucagon-like peptide 2 (GLP-2) analog under development for the treatment of short bowel syndrome (SBS). Glepaglutide enhances intestinal absorption, which may hypothetically lead to changes in the intestinal microbiota, mainly by slowing gastrointestinal transit time. This study evaluated whether glepaglutide affects bacterial load and composition of the intestinal microbiota in SBS patients enrolled in a phase 3b trial assessing its 24-week efficacy on intestinal wet weight and energy absorption.<br><br>METHODS: In this single-center, open-label, EASE SBS-4 phase 3b study, 10 patients with SBS (8 of the 10 with intestinal failure and 8 of the 10 without colon-in-continuity) were treated with glepaglutide 10 mg by subcutaneous injection once weekly for 24 weeks. While the primary trial findings demonstrated increased intestinal wet weight and energy absorption assessed by metabolic balance studies, this study investigated whether these adaptations were associated with changes in bacterial load and composition of the intestinal microbiota. Samples were obtained from either stool or ostomy effluent at baseline and after 24 weeks of treatment with glepaglutide. Bacterial load was quantified using a spike-in approach, and microbiota composition was assessed by V3V4 16S rRNA gene sequencing.<br><br>RESULTS: No major changes in bacterial load or microbiota composition were observed following glepaglutide treatment. Bacterial load showed distinct differences between patients with and without a colon-in-continuity; in patients without a colon, most samples had values below 10[9] cells per gram, whereas those with a colon-in-continuity had bacterial loads within the physiological range observed in healthy individuals, ranging from 10[10] to 10[11] cells per gram feces. Microbiota composition also differed markedly by intestinal anatomy: patients without a colon-in-continuity had higher abundances of genera mainly associated with the upper gastrointestinal tract, such as Streptococcus, while those with a colon-in-continuity exhibited greater abundance of genera more commonly found in the lower gastrointestinal tract, including Bifidobacterium.<br><br>CONCLUSIONS: Treatment with the GLP-2 analog glepaglutide increased intestinal wet weight and energy absorption without altering the intestinal bacterial microbiota in the majority of the SBS patients participating in this study. Differences in bacterial load and composition were influenced by intestinal anatomy.<br><br>CLINICALTRIALS: gov no: NCT04991311; ClincalTrialsRegister.eu EudraCT no: 2020-005194-27.}, }
@article {pmid41759953, year = {2026}, author = {Liu, X and Huang, Z and Liu, L and Wang, S and Huang, Y and Liu, X}, title = {Gut unclassified Ruminococcaceae reweights cortical functional gradients and small-world topology with links to mood and diet.}, journal = {NeuroImage}, volume = {329}, number = {}, pages = {121830}, doi = {10.1016/j.neuroimage.2026.121830}, pmid = {41759953}, issn = {1095-9572}, abstract = {The microbiota-gut-brain axis is a key conduit linking metabolism, mood, and cognition; however, its position within the continuous functional hierarchy of the cortex and the underlying mechanisms are unclear. In this study, a cross-modal brain-gut dataset from 88 healthy male participants was utilized. By integrating functional magnetic resonance imaging (fMRI) gradient analysis, microbiome sequencing, and dietary behavioral information, this study systematically evaluated the relationships between the abundance of unclassified Ruminococcaceae (Ruminococcaceae_unc), cerebral functional hierarchy, network topology, and emotional symptoms. The results demonstrated that increased abundance of this bacterial group was associated with a functional shift in the brain from unimodal to transmodal hubs, accompanied by a drift of the small-world network toward randomization. Functional gradient values were significantly negatively correlated with depression and anxiety scores and were tightly coupled with latent components in the dietary behavioral dimension, including education, physical activity, and nutrient intake. Transcriptomic analysis further revealed that the GPCR-Rho/integrin-vesicular trafficking pathway may serve as the key molecular mechanism. In conclusion, this study proposes a multiscale coupling framework encompassing the gut microbiota, functional gradients, and emotional health, thereby providing a theoretical basis for the development of microbiota-targeted intervention strategies for modulating transmodal emotions and cognition.}, }
@article {pmid41759950, year = {2026}, author = {Yang, J and Shi, L and Jin, X and Shi, D and Cui, J and Wang, K and Xing, X and Qin, X and Dong, C}, title = {Multi-dimensional dynamic monitoring of gut microbiota-emotion axis and precision exercise intervention in compulsory drug rehabilitation: A 24-week randomized controlled trial.}, journal = {Psychology of sport and exercise}, volume = {}, number = {}, pages = {103095}, doi = {10.1016/j.psychsport.2026.103095}, pmid = {41759950}, issn = {1878-5476}, abstract = {BACKGROUND/OBJECTIVES: Substance use disorders (SUDs) present a global health challenge with high relapse rates. Emerging evidence implicates gut microbiota dysbiosis in SUD pathophysiology via the gut-brain axis. This 24-week randomized controlled trial investigated whether precision exercise interventions could modulate the gut microbiota-emotion axis to improve psychological outcomes in individuals undergoing compulsory drug rehabilitation.<br><br>METHODS: Thirty male participants were randomized to a precision exercise group (n=15; individualized aerobic + resistance training, 4-5 sessions/week) or control group (n=15; standard rehabilitation activities). Multi-dimensional assessments included weekly fecal (16S rRNA sequencing), urine (SCFAs via GC-MS), and saliva samples (cortisol, serotonin, BDNF via ELISA), alongside psychological evaluations (SCL-90-R, POMS) and physiological measures.<br><br>RESULTS: The exercise group exhibited significant increases in gut microbial diversity (Shannon index: +18.2%, p<0.001; Cohen's d = 2.14) and enrichment of beneficial taxa (e.g., Faecalibacterium, Bifidobacterium; LDA >3.5). Urinary SCFAs increased markedly (butyrate: 3.12-fold, p<0.001), correlating with elevated salivary BDNF (+82%, p<0.001) and reduced cortisol (-41.1%, p<0.001). Psychological outcomes improved substantially: SCL-90-R Global Severity Index decreased by 43.3% (p<0.001), and 78.6% of exercise participants achieved clinically meaningful improvement. Machine learning models predicted treatment response (AUC = 0.91) using baseline microbiome features.<br><br>CONCLUSIONS: Precision exercise restores gut microbiota homeostasis, enhances neuroactive metabolite production, and improves emotional regulation in SUD recovery. The gut microbiota-emotion axis represents a viable target for non-pharmacological interventions, with microbiome profiles enabling personalized treatment strategies.}, }
@article {pmid41759875, year = {2026}, author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F}, title = {Metatranscriptomic Analysis of Anopheles Species from Menoreh Hills Endemic Area in Central Java, Indonesia.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108033}, doi = {10.1016/j.actatropica.2026.108033}, pmid = {41759875}, issn = {1873-6254}, abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.<br><br>METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.<br><br>RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.<br><br>CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.}, }
@article {pmid41759844, year = {2026}, author = {Leghari, A and Khand, FM and Laghari, S and Lakho, SA}, title = {Engineering bioavailability: Polysaccharide-protein-lipid delivery platforms for postbiotic therapeutics in gastrointestinal and systemic disorders.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {151123}, doi = {10.1016/j.ijbiomac.2026.151123}, pmid = {41759844}, issn = {1879-0003}, abstract = {Postbiotics, inanimate microorganisms and their components that confer health benefits, represent a promising therapeutic class with superior stability and safety profiles compared to live probiotics. However, their clinical translation is hindered by a critical bioavailability paradox such as physiological barriers, compound-specific instability, and the need for precise spatiotemporal release limit their efficacy at target sites. This review provides the first systematic analysis of how advanced pharmaceutical and food-grade delivery platforms can be engineered to overcome these challenges and unlock the clinical potential of postbiotics across gastrointestinal, metabolic, autoimmune, and neurological disorders. We critically evaluate a spectrum of technologies including micro/nanoencapsulation, smart hydrogels, lipid-based nanocarriers, and fermented food matrices and establish a rational framework for matching these platforms to disease-specific pathophysiology and delivery goals. Our analysis demonstrates that targeted strategies, such as pH-sensitive nanoparticles for colonic delivery in inflammatory bowel disease or brain-targeted carriers for gut-brain axis disorders, are essential for effective intervention. Furthermore, we identify and discuss key translational hurdles, including scalable manufacturing, regulatory ambiguity, and economic viability, while forecasting future trends toward personalized, microbiome-responsive smart systems. We conclude that the therapeutic success of postbiotics is intrinsically tied to the efficiency of their delivery. Bridging the gap between their documented biological activity and the engineered platforms designed to ensure targeted, sustained release is the decisive next step in transforming postbiotics from compelling concepts into cornerstone therapeutics of precision medicine.}, }
@article {pmid41759744, year = {2026}, author = {Waghmare, PV and Kolekar, KA and Bashir, B and Kumbhar, PS and Patil, KS and Gupta, G and Prasher, P and Jha, SK and Disouza, J and Gurav, SS and Dua, K and Singh, SK}, title = {Advocating gut-retina connection and microbiota mediated pathways in management of age-related macular degeneration: Preclinical to clinical perspective.}, journal = {Ageing research reviews}, volume = {117}, number = {}, pages = {103071}, doi = {10.1016/j.arr.2026.103071}, pmid = {41759744}, issn = {1872-9649}, abstract = {Age-related macular degeneration (ARMD) is the primary manifestation of permanent vision loss internationally. Different factors that contribute to ARMD involve ageing, genetic predisposition, oxidative stress, immunological imbalances, aberrations in the breakdown of lipids, and persistent inflammation. Gut microbiota has emerged as the significant cause of ARMD by disrupting systemic immune and inflammatory responses and metabolic homeostasis. Age-related changes in gut microbiota (dysbiosis) cause lowered microbial diversity, enhanced gut permeability, and pro-inflammatory species, leading to macular damage. The healthy gut microbiota containing Lactobacillus casei, Lactobacillus plantarum, Lactobacillus rhamnosus, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, and Faecalibacterium prausnitzii, are responsible for maintaining gut homeostasis, protecting the retina, and preventing ARMD progression. In contrast, the elevated population of pathogenic species such as Escherichia coli, Prevotella, Desulfovibrio, Enterococcus faecalis, and Streptococcus salivarius in gut dysbiosis is involved in ARMD progression. This review explores gut microbiota and their dynamics in ageing. The age-dependent gut microbiota variations and potential biological implications for the progression of ARMD are discussed. The review also discusses observations from experimental animals and explores potential microbiome-centered treatment avenues, covering probiotics, synbiotics, dietary remedies, metabolite-based treatment, and fecal microbiota transplantation for managing ARMD. Furthermore, various challenges in the management of gut microbiota-driven ARMD are also briefed with future directions. Thus, a gut microbiota-focused paradigm can offer novel choices for ARMD prevention and treatment.}, }
@article {pmid41759737, year = {2026}, author = {Ju, T and Wang, Y and Nishio, H and Kudelka, MR and Sun, X and Wang, J and Zeng, J and Song, L and Akkas, G and Adsay, V and Parkos, CA and Cummings, RD}, title = {Deletion of Core 1 β3GalT-specific Molecular Chaperone (Cosmc) in murine intestinal epithelia leads to major alterations in glycocalyx and tumorigenesis.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {111319}, doi = {10.1016/j.jbc.2026.111319}, pmid = {41759737}, issn = {1083-351X}, abstract = {Intestinal mucins have extended O-glycans comprised primarily of the common Core 1 O-glycan (Galβ1-3GalNAcα1-Ser/Thr/Tyr) and its modifications. Expression of such glycans is under control of Cosmc (C1GalT1C1) that encodes a key ER molecular chaperone required for formation of active T-synthase, a Golgi enzyme that modifies the Tn antigen (GalNAcα1-Ser/Thr/Tyr - CD175) to generate a Core 1 O-glycan. We previously observed that targeted deletion of Cosmc in murine intestinal epithelial cells (IEC-Cosmc-KO mice) resulted in dysbiosis and alteration of the microbiome. Here we report a detailed description of these mutant mice and find that IEC-Cosmc-KO mice, but not WT mice, express CD175 throughout the intestinal epithelia. CD175 expression is accompanied by loss of glycocalyx, shortening of microvilli, compromised MUC2, thickening of the epithelial layer, as well as generation of high levels of reactive oxygen species. The majority of IEC-Cosmc[-/y] mice beginning at ∼3-9 months spontaneously developed colorectal adenocarcinomas, some with invasive features evidenced by mesenteric metastases, which were potentially associated with activation of TGFβ signaling. Thus, deletion of Cosmc results in expression of CD175 and loss of extended O-glycans in IEC, which is associated with dysregulation of epithelial cell surfaces, leading to spontaneous tumor development. SIGNIFICANCE: Extended O-glycans from the Tn antigen GalNAcα1-Ser/Thr/Tyr (CD175) have many biological functions but roles are poorly understood. Here we show that targeted deletion of Cosmc (C1GalT1C1) in murine intestinal epithelial cells leads to CD175 expression and a loss of extended O-glycans, dysregulation of multiple pathways, and spontaneous colorectal tumors.}, }
@article {pmid41759557, year = {2026}, author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C}, title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0327625}, doi = {10.1128/spectrum.03276-25}, pmid = {41759557}, issn = {2165-0497}, abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.}, }
@article {pmid41759554, year = {2026}, author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J}, title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0240725}, doi = {10.1128/spectrum.02407-25}, pmid = {41759554}, issn = {2165-0497}, abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.}, }
@article {pmid41759472, year = {2026}, author = {Wang, Q and Zhai, Y and Zhang, Y and Li, Z and Wang, Q and Liu, S}, title = {Assessing links between dental fluorosis and oral/systemic health via salivary microbiome in Chinese young adults.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109461}, doi = {10.1016/j.identj.2026.109461}, pmid = {41759472}, issn = {1875-595X}, abstract = {OBJECTIVES: This study utilized dual control groups, caries patients (a representative bacterial infectious disease) and healthy individuals, to identify the core microbiome specific to dental fluorosis and elucidate the potential associations with systemic health and diseases from the perspective of the oral-gut-lung axis.<br><br>METHODS: Initially, 1001 volunteers were recruited, among whom 959 provided complete questionnaire data. In subsequent omics analyses, saliva samples from 387 participants (HC: n = 117; DC: n = 138; DF: n = 132) were included, and background confounders were controlled via partial correlation analysis. Multidimensional analyses based on 16S rRNA sequencing revealed significant intergroup separation of microbial communities.<br><br>RESULTS: By comparing differentially abundant taxa across pairwise comparisons (HC vs DC, HC vs DF, DC vs DF), 24 key DF-associated microorganisms were identified. These microbial markers exhibited high diagnostic accuracy, with area under the receiver operating characteristic curve values of 92.6% and 89.3% for distinguishing DF from HC and DF from DC, respectively. t-SNE dimensionality reduction further confirmed that the microbial signature clearly separated the DF group from both HC and DC groups. Microbial co-occurrence network analysis revealed significant positive correlations between Enhydrobacter and Caulobacter, Mycobacterium and Enhydrobacter, and Mycobacterium and Caulobacter.<br><br>CONCLUSIONS: This study provides evidence at the transmissible microecological level that dental fluorosis possesses a distinct microbiome profile compared to dental caries. In addition, the long-term periodontal status of patients with dental fluorosis and its potential link to periodontitis, intestinal and respiratory system diseases merit further investigation.}, }
@article {pmid41759374, year = {2026}, author = {Zhou, H and Huang, Y and Chen, C and Song, M and Hylemon, PB}, title = {Gut microbiome and bile acid metabolism in liver disease: Mechanisms, clinical implications, and therapeutic opportunities.}, journal = {Pharmacological reviews}, volume = {78}, number = {2}, pages = {100120}, doi = {10.1016/j.pharmr.2026.100120}, pmid = {41759374}, issn = {1521-0081}, abstract = {The intricate interplay between the gut microbiome and bile acid metabolism via the gut-liver axis is fundamental to hepatic homeostasis. Perturbations in this axis are increasingly implicated in the pathogenesis of diverse liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and hepatocellular carcinoma. This review integrates current understanding of hepatic bile acid synthesis, enterohepatic circulation, and gut microbial bile acid transformations, detailing how bile acids function as signaling molecules through nuclear receptors including farnesoid X receptor, pregnane X receptor, vitamin D receptor, constitutive androstane receptor, and G-protein-coupled receptors; G protein-coupled bile acid receptor 1 (also known as Takeda G protein-coupled receptor 5), and sphingosine-1-phosphate receptor 2. We explore disease-specific alterations in gut microbiota composition and bile acid profiles in metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and liver cancers, focusing on mechanisms linking gut dysbiosis, impaired intestinal barrier function, altered bile acid signaling, inflammation, and immune modulation to liver injury and progression. Furthermore, we discuss the clinical implications, highlighting the potential of microbiome signatures and bile acid profiles as diagnostic and prognostic biomarkers. Therapeutic strategies targeting the gut-liver axis, including probiotics, fecal microbiota transplantation, farnesoid X receptor agonists, and fibroblast growth factor 19 analogs, are reviewed. Finally, we address current challenges and future directions, emphasizing the need for multiomics integration, functional studies, and personalized medicine approaches to leverage the gut-liver axis for improved liver disease management. SIGNIFICANCE STATEMENT: Disruption of the gut microbiome-bile acid-liver axis is now recognized as a unifying mechanism driving multiple liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cholestatic liver diseases, and hepatocellular carcinoma. Unraveling the molecular and microbial interactions within this axis offers fundamental insights into disease pathogenesis and reveals novel therapeutic opportunities. Integrating multiomics technologies with artificial intelligence-based analytics will accelerate the discovery of predictive biomarkers and personalized interventions, advancing the field toward precision-based liver disease treatment protocols.}, }
@article {pmid41759241, year = {2026}, author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S}, title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106602}, doi = {10.1016/j.clnu.2026.106602}, pmid = {41759241}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.<br><br>METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.<br><br>RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.<br><br>CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.}, }
@article {pmid41759031, year = {2026}, author = {Gudi, CR and Neilson, WJ and Mansell, TJ}, title = {An Engineered Variant of E. coli Nissle 1917 with Enhanced Transformation Efficiency and Robustness.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00852}, pmid = {41759031}, issn = {2161-5063}, abstract = {The gut microbiome and its effects on human health have generated considerable scientific, veterinary, and medical interest in recent years. Several gut bacterial species have emerged as potential chassis organisms for the delivery of therapeutics in this milieu. Among these, E. coli Nissle 1917 (EcN), a nonpathogenic gut isolate bacterium, is quickly gaining popularity. However, a bottleneck in harnessing EcN's potential has been its poor transformation efficiency relative to other bacterial strains. In this study, we present the use of adaptive laboratory evolution to increase EcN's transformation efficiency by subjecting the strain to repeated cycles of electroporation and recovery. This new strain has been comprehensively characterized in comparison to the wild-type EcN, including assessments of growth under gut-mimicking duress conditions, permeability, motility, hydrophobicity, and plasmid replication. Since EcN is known to compete with pathogenic strains in the gut for iron, the competition dynamics and iron consumption of the strain were also significant factors to consider. Furthermore, we conducted genome sequencing and gene ontology enrichment analysis to identify affected genes and pathways to probe the potential mechanisms of the improved phenotype. Overall, the strain shows improved transformation efficiency and robustness while preserving its key biological functionality.}, }
@article {pmid41758920, year = {2026}, author = {Sakaguchi, N and Kusamoto, A and Harada, M and Shashni, B and Komura, A and Teshima, A and Tanaka, T and Koike, H and Xu, Z and Kawahara, Y and Tsuchida, C and Kunitomi, C and Takahashi, N and Urata, Y and Wada-Hiraike, O and Hirota, Y and Nagasaki, Y and Osuga, Y}, title = {Butyric acid-based self-assembling nanoparticles: a potential strategy to prevent development of polycystic ovary syndrome.}, journal = {Molecular human reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/molehr/gaag013}, pmid = {41758920}, issn = {1460-2407}, abstract = {Polycystic ovary syndrome (PCOS) is the most common endocrine disorder affecting women of reproductive age and cannot currently be cured or prevented fundamentally. Prenatal androgen exposure is a key factor in PCOS development, and both PCOS patients and animal models exhibit gut microbiota alterations. We previously demonstrated that prenatally androgenized (PNA) model mice display changes of gut microbiota before the manifestation of PCOS phenotypes, suggesting that an intervention targeting gut microbiota from the early stage of life can prevent development of PCOS. Butyric acid, a short-chain fatty acid produced by bacteria in the intestines, has various physiological effects. We investigated whether butyric acid could prevent PCOS phenotypes in PNA mice when administered from the early stage of life as a nanoparticle-based donor. We have developed butyric acid-based self-assembling nanoparticles (BNP), which release butyric acid in a sustained manner when exposed to digestive enzymes so that butyrate is delivered to the intestines. Control and PNA offspring were administered water containing or lacking BNP from just after weaning until 20 weeks of age. Reproductive and metabolic phenotypes were compared among these offspring (n = 10-14 for each group). Administration of BNP normalized irregular estrus cyclicity and improved the polycystic ovarian morphology, as evidenced by smaller numbers of atretic follicles in PNA offspring. Regarding metabolic phenotypes, administration of BNP improved hypertrophy of adipocytes and insulin resistance. Furthermore, analysis of the gut microbiota suggested that these primary effects were caused by butyrate itself, with an increase in certain butyrate-producing bacteria supporting this mechanism. The present findings indicate that administration of butyric acid to PNA offspring, which are at high risk of developing PCOS, from the early stage of life effectively prevents development of PCOS phenotypes at reproductive ages. Further exploration is necessary to clarify the mechanism by which butyric acid prevents development of PCOS.}, }
@article {pmid41758783, year = {2026}, author = {Dimmers, F and Reichert, D and Nguyen, T and Lück, N and Ramachandran, H and Bremges, A and Schild, J and Humbek, M and Grether-Beck, S and Rossi, A and Staerk, C and Esser, C and Krutmann, J}, title = {Monocentric, vehicle-controlled, double-blind study to assess the short- and long-term effects of a Ceramide NP C15-containing emollient on the skin microbiome and the skin barrier function in sensitive skin.}, journal = {Skin pharmacology and physiology}, volume = {}, number = {}, pages = {1-30}, doi = {10.1159/000551043}, pmid = {41758783}, issn = {1660-5535}, abstract = {INTRODUCTION: Sensitive skin is a common skin condition that impairs quality of life and is characterised by unpleasant sensations to normally non-irritating stimuli. Restoration of skin barrier integrity can relieve symptoms, and accumulating evidence indicates a contributory role of the skin microbiome not only in barrier function but also as a potential modulator in sensitive skin. Ceramide-containing emollients improve barrier function and may modulate microbial communities via restoration of stratum corneum lipids, hydration, and immune regulation.<br><br>METHODS: In this randomized, double-blind, vehicle-controlled trial, an emollient containing Ceramide NP C15 was evaluated for its effects on sensitive skin symptoms and skin barrier function. Fifty participants applied the study products in a split-body design for six weeks. Primary assessments included skin physiology and symptom burden. Furthermore, skin microbiota changes were explored using flow cytometry (FC)-based bacterial profiling and 16s rRNA gene sequencing.<br><br>RESULTS: Both the Ceramide NP C15 formulation and the vehicle were associated with improvements in subjective symptoms. In participants with impaired skin barrier, treatment with the ceramide formulation was associated with a significant reduction in transepidermal water loss. FC- and 16S-based analyses indicated modest, treatment-associated changes in skin microbiota composition including an early and sustained increase in microbial evenness and a significant enrichment of Bifidobacterium.<br><br>CONCLUSION: In this exploratory, randomized controlled study, a Ceramide NP C15-containing emollient was associated with improvements in skin barrier function. Exploratory microbiome analyses suggested treatment-associated changes in microbial community characteristics, which should prompt further investigations in their clinical relevance for sensitive skin.}, }
@article {pmid41758690, year = {2026}, author = {Yin, S and Cheng, L and Hu, E and Li, J and Wu, G and An, J and Nunez, L and Kawachi, N and Zhu, J and Rosenblatt, G and Segall, JE and Ostrer, H and Augustine, S and Song, EZ and Ow, TJ and Smith, RV and Prystowsky, MB and Verma, A and Deng, W}, title = {Association of Intratumoral Microbiota with Prognosis in Head and Neck Squamous Cell Carcinoma.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {}, number = {}, pages = {}, doi = {10.1158/1078-0432.CCR-25-4420}, pmid = {41758690}, issn = {1557-3265}, abstract = {PURPOSE: To evaluate whether intratumoral bacterial load and diversity are associated with survival outcomes in HNSCC and to examine their relationship with HPV status.<br><br>EXPERIMENTAL DESIGN: This retrospective cohort study included 312 adults with surgically treated, primary HNSCC at Montefiore Einstein Cancer Center (2000-2023). Intratumoral bacterial load was quantified by qPCR, and microbial diversity was assessed by 16S rRNA sequencing in 312 tumor and 34 paired normal tissues. HPV status was determined by p16 immunohistochemistry and qPCR. Overall survival was the primary outcome.<br><br>RESULTS: HNSCC tumors showed higher bacterial load and lower bacterial diversity compared to adjacent normal tissues. High bacterial load (HR, 1.85; 95% CI, 1.31-2.61; P<0.001) and low bacterial diversity (HR, 1.65; 95% CI, 1.19-2.28; P=0.003) were independently associated with reduced OS, with the greatest risk in patients carrying both features (HR, 3.00; 95% CI, 1.76-5.09; P<0.001). The high-risk bacterial features were less frequent in HPV-positive than in HPV-negative tumors (high load: OR, 0.46; 95% CI, 0.29-0.73; P=0.001; low diversity: OR, 0.51; 95% CI, 0.32-0.81; P=0.004), and their prognostic significance was more pronounced in HPV-negative cases. Taxonomic profiling revealed marked depletion of predominant bacterial taxa in HNSCC, especially in HPV-negative tumors. Notably, loss of the class TM7-3 and the orders Actinomycetales and Burkholderiales was specifically associated with poor HNSCC survival, including early mortality.<br><br>CONCLUSIONS: High intratumoral bacterial load and low diversity are prognostic factors associated with survival in HNSCC, particularly in HPV-negative patients. Incorporating microbiome assessment into risk stratification may enhance prognostic precision and inform microbiota-directed therapeutic approaches.}, }
@article {pmid41758194, year = {2026}, author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L}, title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2638009}, doi = {10.1080/19490976.2026.2638009}, pmid = {41758194}, issn = {1949-0984}, abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.}, }
@article {pmid41758122, year = {2026}, author = {Madushani, GRDS and Wu, X and Jayasinghe, WH and Wang, Q and Vinit, K and Hao, GF}, title = {Harnessing eCISs for precision phytomicrobiome engineering and biocontrol.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuag006}, pmid = {41758122}, issn = {1574-6976}, abstract = {Plant microbiome disruption often increases vulnerability to crop diseases, endangering worldwide food production, while chemical pesticides become increasingly less viable and continue to damage ecosystems. To safeguard plant microbiome health, several biological control strategies offer alternatives, yet many operate through broader or weakly defined target mechanisms. In recent years, bacterial contractile injection systems (BCISs) have emerged as a promising class of naturally evolved nanomachines that translocate molecular payloads directly into target cells. Subsets of these systems, extracellular contractile injection systems (eCISs), are distinguished by their specific narrow host range and receptor-dependent specificity. Recent studies have demonstrated that eCISs provide a transformative approach for targeted microbial manipulation, enabling the delivery of specialized molecules into particular microbes with higher precision. However, despite their potential, the integration of these engineered injection systems with microbial modulation for phytomicrobiome remains largely underexplored. Here, we explore the capabilities of eCISs as an advanced approach for the biocontrol, leveraging their tailored mechanisms for targeted payload delivery in plant-associated microbial communities with enhanced host specificity. This study aims to address the potential of engineered injection systems in facilitating sustainable phytomicrobiome engineering strategies that enhance biocontrol, aiming to reduce environmental harm while improving agricultural productivity.}, }
@article {pmid41757979, year = {2026}, author = {Zhang, X and Luo, Q and Gong, Z and Yang, H and Chen, X and Wang, B and Yuan, M and Chen, Y and Jia, Y and Guo, S}, title = {Nano-selenium mitigates antibiotic resistance in paddy ecosystems via microbiome remodeling and environmental filtering shifts.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0223125}, doi = {10.1128/aem.02231-25}, pmid = {41757979}, issn = {1098-5336}, abstract = {UNLABELLED: The dissemination of antibiotic resistance genes (ARGs) in paddy ecosystems poses a serious threat to environmental health. A pot experiment was conducted to assess the efficacy of alkyl glycoside-stabilized selenium nanoparticles (AG-SeNPs) in mitigating ARG abundance within the soil, phyllosphere, and rice grains. Functional prediction, null model analysis, variance partitioning, and structural equation modeling were employed to identify ARG hosts, key metabolic pathways, and environmental drivers of ARG dynamics. Results showed that foliar application of AG-SeNPs (30 g ha[-1]) reduced ARGs by 5.13 × 10[6] copies g[-1], 2.28 × 10[7] copies g[-1], and 1.25 × 10[6] copies g[-1] in the rhizosphere soil, phyllosphere, and grains, respectively. TetPA and tetGF were dominant ARGs, predominantly associated with Mariniphaga anaerophila, Sediminibacter magnilacihabitans, and Limnospira fusiformis. ARG attenuation was linked to enhanced ABC transporter activity and suppressed purine metabolism and ribosome function, thereby reducing intracellular antibiotic pressure and limiting ARG expression in soil microbes. In the phyllosphere, activation of two-component systems modulated stress responses and antimicrobial resistance pathways, constraining horizontal gene transfer. Nano-selenium increased heterogeneous selection in the phyllosphere, enhancing deterministic filtering of ARG hosts and restructuring microbial communities. Environmental factors explained 42.81% of ARG variation, wherein selenium accumulation in leaves directly reduced ARG abundance, and soil pH, electrical conductivity, and organic matter indirectly influenced ARG dynamics through microbial community restructuring. These findings highlight that AG-SeNPs mitigate ARGs through an environmentally mediated, microbially driven cascade, offering a promising strategy for antibiotic resistance control in agricultural systems.<br><br>IMPORTANCE: The dissemination of antibiotic resistance genes within agricultural soil-plant systems poses a severe threat to food safety and public health. This study demonstrates that foliar application of nano-selenium fertilizer effectively reduces ARG abundance in the soil, phyllosphere, and rice grains. We found that nano-selenium functions not by direct bactericidal action but by beneficially reshaping the microbial communities in both the leaves and soil, thereby suppressing the pathways for ARG transmission. Our findings provide a novel and sustainable strategy to mitigate antibiotic resistance in agricultural ecosystems, potentially reducing the risk of these genes entering the human food chain via rice.}, }
@article {pmid41757954, year = {2026}, author = {Ke, Y and Sun, Y and Wu, J and Ye, L and Zhu, Z}, title = {Association of vaginal microbiome, cytokines, and spontaneous preterm birth among Chinese women: a nested case-control study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0260725}, doi = {10.1128/spectrum.02607-25}, pmid = {41757954}, issn = {2165-0497}, abstract = {An imbalance of the vaginal microbiome and dysregulation of cytokines are associated with spontaneous preterm birth (sPTB). To date, the relationship between the vaginal microbiome, cytokines, and sPTB remains unclear in the Chinese population. Herein, we conducted a nested case-control study using data from a prospective cohort of 749 Chinese women with a singleton pregnancy who were enrolled between 16 and 28 weeks of pregnancy. Cases consisted of individuals experiencing sPTB (n = 38), while controls were selected randomly at a 4:1 ratio to cases (n = 152). Compared to the term group, the sPTB group exhibited significantly increased abundance of vaginal Aerococcus christensenii, Gardnerella swidsinskii, and Lactobacillus iners, along with elevated levels of interleukin (IL)-1β, IL-6, and IL-12p70 in vaginal fluid (P < 0.05). Least absolute shrinkage and selection operator (LASSO) regression identified L. iners, G. swidsinskii, and IL-6 as significant risk factors for sPTB, with adjusted odds ratios (ORs) (95% CI) of 1.57 (1.06-2.34), 1.45 (1.03-2.05), and 2.05 (1.43-2.93), respectively. Finally, a logistic regression model for sPTB was established incorporating L. iners, G. swidsinskii, and IL-6, which yielded an area under the receiver operating characteristic curve (AUC) of 0.73. These findings suggest that alterations in the vaginal microbiome and cytokine levels may contribute to sPTB in the Chinese population.IMPORTANCEPreterm birth (PTB) is the leading cause of death in children under 5 years of age, of which about 70% were spontaneous ones (sPTB); while genitourinary infections are implicated in 25-40% of sPTB cases. Previous studies have revealed some features of vaginal microbiome and cytokines related to sPTB: increased richness and diversity, increased levels of Lactobacillus iners, BV-associated bacteria, low abundance of L. crispatus, and high levels of pro-inflammatory cytokines. However, there were also some inconsistent findings, and little is known in the Chinese population. This study confirmed the correlations between vaginal microbiome, cytokines, and sPTB in Chinese pregnant women. Specifically, elevated vaginal L. iners, G. swidsinskii, and IL-6 levels were significantly associated factors, which may help to identify women at high risk of sPTB.}, }
@article {pmid41757945, year = {2026}, author = {Surve, SV and Valls, RA and Barrack, KE and Gwilt, LL and Gardner, TB and O'Toole, GA}, title = {The regional landscape of the human colon culturome in health and cystic fibrosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0312625}, doi = {10.1128/spectrum.03126-25}, pmid = {41757945}, issn = {2165-0497}, abstract = {UNLABELLED: Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in a small cohort of 32 individuals (22 non-CF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than non-CF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status within this cohort. Whole-genome sequencing of Bacteroides fragilis (n = 21) and Escherichia coli (n = 15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study, after future validation, may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.<br><br>IMPORTANCE: This pilot study of a small cohort represents the first culturome analysis of the cystic fibrosis colon. Our preliminary findings demonstrate that cystic fibrosis (CF)-associated gut dysbiosis is spatially specific, with mucosal bacterial communities showing pronounced alterations while luminal communities show comparatively subtle phylum-specific shifts. This spatial specificity suggests the mucosal microenvironment as a potential therapeutic target and indicates that interventions focused solely on luminal bacteria may be insufficient. The promising predictive accuracy of culturome-based machine learning models in this small cohort suggests these viable bacterial signatures could serve as biomarkers for CF management pending larger validation studies. Additionally, our initial observations of CFTR modulator effects on gut microbial communities provide insight for future studies optimizing combination therapies.}, }
@article {pmid41757889, year = {2026}, author = {El Hafi, B and Jean-Pierre, F and Taub, L and Hampton, TH and O'Toole, GA}, title = {Streptococcus sanguinis antagonizes Prevotella melaninogenica in the context of the cystic fibrosis respiratory microbiome.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0000526}, doi = {10.1128/jb.00005-26}, pmid = {41757889}, issn = {1098-5530}, abstract = {The latest generation of cystic fibrosis transmembrane conductance regulator-targeted modulator therapy, Elexacaftor/Tezacaftor/Ivacaftor (ETI), has significantly improved the clinical outcomes of persons with cystic fibrosis (pwCF) but does not appear to completely eliminate CF respiratory microbial colonization. Here, we analyzed over 4,200 publicly available respiratory microbiomes spanning pre- and post-ETI treatment periods and further stratified by age and type of sample. Our analyses reveal that despite reshaping of community composition by ETI, classical CF pathogens such as Pseudomonas and Staphylococcus spp. persist in sputum and sinonasal samples, while Streptococcus spp. drastically increase in prevalence and relative abundance post-ETI treatment. Obligate anaerobes such as Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Veillonella spp. were readily detected post-ETI. We observed changes in the sputum samples from pwCF post-ETI, with an increase in the relative abundance of Streptococcus spp. and prevalence of Prevotella and a decline in Pseudomonas spp. Analysis of co-occurrence networks revealed mostly positive correlations between the different genera pre- and post-ETI; however, these correlations were reduced in number following ETI treatment, suggesting a disruption of community connectivity. To test one of the hypotheses raised by the computational analyses, we experimentally investigated the relationship between Streptococcus sanguinis and Prevotella melaninogenica in a CF sputum-like medium. Our data suggest that S. sanguinis uses reactive nitrogen species, and likely other factors, to antagonize P. melaninogenica, while Pseudomonas aeruginosa protects P. melaninogenica in CF-like culture conditions. Our findings implicate polymicrobial interactions, rather than individual species abundance, in determining microbial persistence and adaptation within the CF airway post-ETI.IMPORTANCEThe introduction of the latest cystic fibrosis transmembrane conductance regulator (CFTR)-targeted Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy represents a major therapeutic advance for persons with cystic fibrosis (pwCF); however, this therapy does not completely negate respiratory infections and colonization. We leverage large-scale publicly available microbiome data to demonstrate that while ETI therapy alters the respiratory microbial landscape, canonically prevalent and abundant CF pathogens persist in many pwCF and likely maintain ecological relevance through adaptive interactions with other taxa. Our in vitro findings also reveal that Streptococcus sanguinis can antagonize Prevotella melaninogenica, and that Pseudomonas aeruginosa can provide selective protection to quell this antagonism. These insights highlight the need to consider microbial interactions and community dynamics when evaluating long-term responses to CFTR modulators.}, }
@article {pmid41757865, year = {2026}, author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y}, title = {Characterization of the dynamic microbiome evolution across thrips species.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70265}, pmid = {41757865}, issn = {1744-7917}, support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; }, abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.}, }
@article {pmid41757862, year = {2026}, author = {Zhang, Y and Zhang, R and Wang, G and Liu, Y}, title = {Antibiotic-Mediated Microbiota Depletion Suggests an Association Between Gastric Juice Dysbacteriosis and Abnormal Bile Acid Metabolism in Chronic Atrophic Gastritis Rats.}, journal = {Biomedical chromatography : BMC}, volume = {40}, number = {4}, pages = {e70404}, doi = {10.1002/bmc.70404}, pmid = {41757862}, issn = {1099-0801}, support = {82374025//National Natural Science Foundation of China/ ; 82073988//National Natural Science Foundation of China/ ; 202403021221327//Fundamental Research Program of Shanxi Province/ ; zyytd2024020//Traditional Chinese Medicine Innovation Team of Shanxi Province/ ; }, abstract = {Current research on chronic atrophic gastritis (CAG) has primarily focused on intestinal flora, while the role of gastric juice microecology remains poorly understood. This study investigated whether alterations in gastric juice microbiota and bile acid (BA) profiles are associated with CAG under microbiota perturbation. A CAG rat model was designed by a multifactor modeling method, and an antibiotic cocktail (Abx) was administered to deplete gastrointestinal microbiota. Full-length 16S rRNA gene sequencing and LC-MS technology were conducted to characterize microbial composition and metabolite profiles in gastric juice. An integrated strategy combining microbiome and metabolome data was employed to validate associations between microbiota and metabolites. CAG rats exhibited elevated proinflammatory cytokines and lipopolysaccharide (LPS) levels in gastric juice, accompanied by dysbacteriosis and aberrant BA profiles. After antibiotic treatment, LPS level and bile salt hydrolase (BSH) activity were reduced, along with the lower abundances of LPS-producing bacteria and multiple BA levels. Correlation analysis demonstrated a positive association between deoxycholic acid (DCA) and LPS-producing bacteria (Escherichia coli). These findings revealed that gastric juice dysbacteriosis and abnormal BA metabolism were relevant to the inflammatory status of CAG. This study provided multi-omics evidence supporting a potential involvement of gastric juice microecological imbalance in CAG progression.}, }
@article {pmid41757733, year = {2026}, author = {Rau, SR and Kalkuhl, A and van Esch, E and Hahn, C and Nolte, T and Hempel, K}, title = {NPY2R Agonist-Induced Gastric Effects Leading to Intestinal Dysbiosis and Secondary Intestinal Pathology in CD1 Mice.}, journal = {Toxicologic pathology}, volume = {54}, number = {2}, pages = {167-180}, doi = {10.1177/01926233251392878}, pmid = {41757733}, issn = {1533-1601}, abstract = {Obesity research has identified several drug targets, including the neuropeptide Y receptor 2 (NPY2R), which causes anorexigenic effects and delays gastric emptying. Test Peptide, an NPY2R agonist, was tested for toxicity in CD1 mice. Following unexpected mortality in a 4-week study, a 4-day study was conducted to determine the cause. The examination included clinical observations, pathology, and microbiome analysis of jejunal samples. Histopathologic lesions were primarily observed in animals showing clinical signs of toxicity ("responders"), including vacuolation of gastric parietal cells, inflammation, ulcers, and bacterial overgrowth in the small intestine. Occasionally, vacuolation of parietal cells was noted in clinically asymptomatic animals ("non-responders") terminated after 4 days, but not in nonresponders treated for 4 weeks. Microbiome analysis revealed in responders a significantly increased abundance of pathogenic bacteria like Shigella and a significant decrease in probiotic bacteria like Lactobacillus. The altered intestinal microflora resulted in overt dysbiosis, leading to intestinal inflammation, sepsis, and death. The intestinal microbiome appears to be an important factor determining differences in the interindividual susceptibility of mice to Test Peptide treatment. The human relevance of these murine findings is considered low, owing to substantial anatomical and physiological gastrointestinal differences, and the absence of comparable observations in nonhuman primates.}, }
@article {pmid41757159, year = {2026}, author = {Zhang, L and Ding, Z and Yi, N}, title = {BCGLMs: Bayesian modeling for disease prediction using compositional microbiome features.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag041}, pmid = {41757159}, issn = {2635-0041}, abstract = {MOTIVATION: BCGLMs is a freely available R package that provides functions for setting up and fitting Bayesian compositional models for continuous, binary, ordinal and survival responses. It also includes models with random effects to capture sample-related accumulated small effects, improving prediction accuracy. The package includes tools for summarizing results from fitted models both numerically and graphically. Built on top of the widely used brms package, BCGLMs enable users to incorporate phylogenetic relationships between microbiome taxa into the modeling framework. Overall, BCGLMs package offers a flexible and powerful set of tools for analyzing compositional microbiome data.<br><br>The package is publicly available via GitHub https://github.com/Li-Zhang28/BCGLMs.}, }
@article {pmid41757098, year = {2026}, author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA}, title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.18.706612}, pmid = {41757098}, issn = {2692-8205}, abstract = {UNLABELLED: Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.<br><br>IMPORTANCE: Widespread fungicide use contaminates ecosystems worldwide, but the biological pathways underlying their effects on humans and other animals are not well understood. Using zebrafish (Danio rerio), we found that short-term exposure to the fungicide azoxystrobin was associated with changes in the gut microbiome, liver gene activity, and liver changes. Exposure produced dose- and sex-dependent shifts in microbial communities, including changes in predicted microbial functions involved in chemical metabolism, bacterial motility and defense. Compositional changes in the microbiome correlated with gene-expression changes consistent with stress and altered metabolism in exposed fish, suggesting that exposure induced disruption may contribute to exposure impact to the host. These results highlight a potential role for the microbiome in mediation of the impacts of azoxystrobin on host physiology. As such microbial based interventions could be a viable strategy to mitigate exposure impacts on health.}, }
@article {pmid41757095, year = {2026}, author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ}, title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.13.705642}, pmid = {41757095}, issn = {2692-8205}, abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus , reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.}, }
@article {pmid41757041, year = {2026}, author = {Tschang, MA and Vuong, RD and Eilers, B and Chac, D and Waalkes, A and Penewit, K and Easton, A and Schuessler, B and Daniels, R and Weil, AA and Salipante, SJ and Gibbons, SM and Schindler, AG}, title = {If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.16.705192}, pmid = {41757041}, issn = {2692-8205}, abstract = {The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures. We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into pellets ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the pellets, and blood was collected to compare corticosterone levels relative to traditional gavage FMT. Plasma corticosterone levels were found to be significantly lower in mice receiving FMT via pellets compared to oral gavage. Furthermore, relative to gavage FMT, microbial signatures of mice receiving FMT via pellets were more similar to those of the donor pellets at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta-diversity distances. Together, these results establish effective antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.}, }
@article {pmid41757006, year = {2026}, author = {Tran, HN and Kirven, KJ and Davenport, ER}, title = {SCiMS: Sex Calling in Metagenomic Sequences.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.17.705110}, pmid = {41757006}, issn = {2692-8205}, abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.<br><br>RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.<br><br>CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS .}, }
@article {pmid41756980, year = {2026}, author = {Park, H and Shen, X and Perelman, D and Berry, P and Lu, Y and Battersby, R and Rose, SMS and Celli, A and Bejikian, C and Snyder, M}, title = {Insulin resistance modifies longitudinal multi-omics responses to habitual diet.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.17.706440}, pmid = {41756980}, issn = {2692-8205}, abstract = {How habitual diet influences the gut microbiome and plasma metabolome across insulin resistance states remains unclear. We conducted year-long multi-omics profiling of 71 deeply phenotyped adults, integrating repeated assessments of diet, metabolome, gut microbiome, clinical laboratory measures, and inflammatory markers. Using gold-standard insulin suppression tests and machine learning-derived dietary patterns, we examined how dietary patterns relate to metabolic and microbial landscapes by insulin resistance status. Insulin-sensitive individuals exhibited stronger and more numerous diet-omics associations than insulin-resistant individuals, identifying metabolic flexibility as a central determinant of dietary responsiveness. Parabacteroides emerged as a candidate microbial mediator between refined carbohydrate-rich dietary patterns and host metabolic signatures. Integrated into a cardiovascular risk prediction model, diet, metabolites, microbial taxa, and immune markers each contributed to 10-year atherosclerotic cardiovascular disease risk. These findings show that inter-individual variation in cardiometabolic risk partly reflects differences in molecular responsiveness to habitual diet, informing precision nutrition and cardiovascular prevention.}, }
@article {pmid41756930, year = {2026}, author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L}, title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.21.707213}, pmid = {41756930}, issn = {2692-8205}, abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.}, }
@article {pmid41748722, year = {2026}, author = {Hanz, U and Mueller, B and Bart, MC and Busch, K and Reichart, GJ and Rapp, HT and de Goeij, JM and Mienis, F}, title = {Unveiling in situ oxygen, carbon and nutrient cycling of a sponge-driven biological hotspot in the arctic.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41748722}, issn = {2045-2322}, abstract = {UNLABELLED: Deep-sea sponge grounds are habitat-forming benthic communities characterized by high biomass and structural complexity. Despite their ecological significance, their role for the deep-sea environment remains poorly understood and their functioning is often inferred from ex situ studies. We hypothesized that deep-sea sponge grounds exhibit substantially higher respiration and nutrient turnover than surrounding soft sediments, making them hotspots of carbon and nutrient cycling in the deep sea. Integrated respiration and nutrient cycling were quantified in a sponge ground on the summit of an Arctic seamount (Schulz Bank, ~ 580 m depth). We used in-situ incubation chambers measuring oxygen consumption, prokaryotic cell removal, and inorganic nutrient fluxes. Respiration rates ranged from 0.13 to 0.93 mmol O2 m[-2] h[-1], which is comparable to cold-water coral reefs and up to 7–21 times higher than reported for soft sediments of the Arctic deep sea. This indicates a high organic carbon demand exceeding surface-derived supply, suggesting the uptake of additional food resources. All incubations showed net release of ammonium, phosphate, nitrite and nitrate, with fluxes correlating with sponge biomass. Our results demonstrate that deep-sea sponge grounds function as hotspots of carbon and nutrient cycling and suggest distinct functional contributions of sponge groups and their microbiome.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41798-4.}, }
@article {pmid41756883, year = {2026}, author = {Wirbel, J and Saber, W and Martens, MJ and Peled, JU and Andermann, TM and Fei, T and Brooks, EF and Doyle, B and Pincus, NB and Jenq, RR and Bar, M and Bolaños-Meade, J and Bratrude, B and Chhabra, S and Choi, SW and Clark, W and Das, S and Elmariah, H and Gooptu, M and Holtan, SG and Jones, RJ and Levine, JE and Logan, BR and Al Malki, MM and Murthy, HS and Rashidi, A and Rezvani, AR and Riches, ML and Runaas, L and Sandhu, K and Spahn, A and Sung, AD and van den Brink, MRM and Horowitz, MM and Hamadani, M and Kean, LS and Perales, MA and Bhatt, AS}, title = {Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.19.706769}, pmid = {41756883}, issn = {2692-8205}, abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment for many hematological malignancies, but graft-versus-host disease (GVHD) is a common complication. Low gut microbiome diversity is associated with higher GVHD risk and shorter survival in multiple studies. Recently, the BMT CTN 1703 clinical trial demonstrated superiority of a GVHD-prophylaxis regimen including post-transplant cyclophosphamide (PTCy) compared to the standard prophylaxis (tacrolimus and methotrexate, Tac/MTX) in terms of GVHD-free, relapse-free survival at one year among reduced intensity conditioning allo-HCT recipients. However, the effect of PTCy on the gut microbiome and its association with clinical outcome have not been described. Here, we report on a companion randomized clinical controlled trial (BMT CTN 1801), which collected 2575 longitudinal stool samples from 304 study participants. Samples were obtained up to weekly up to day 84 post allo-HCT and at less frequent intervals thereafter, up to 2 years. Microbiome diversity and absolute microbial load were lower in the PTCy group compared to the Tac/MTX group on days 14-28 post-HCT. However, diversity at the timepoint closest to neutrophil engraftment was not significantly associated with non-relapse mortality after one year or other clinical outcomes, contrary to expectations from previous studies. Microbial domination events, when a single species exceeds 30% relative abundance, were comparable across treatment arms and reflected both pathogen blooms as well as less severe disruptions of the microbial community. Clostridium scindens and secondary bile acid metabolism pathways were less prevalent in the PTCy arm than in the Tac/MTX arm post-HCT, yet presence of secondary bile acid metabolism pathways was associated with a lower risk of chronic GVHD. Given that PTCy was associated with a greater disruption of the microbiome as measured by diversity, absolute microbial abundance, and bile acid metabolism capability, but better clinical outcomes overall, these data suggest that the importance of the microbiome in modulating the host immune systems after allo-HCT is specific to different types of GVHD prophylaxis.}, }
@article {pmid41756881, year = {2026}, author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL}, title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.20.706901}, pmid = {41756881}, issn = {2692-8205}, abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.<br><br>METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.<br><br>RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.<br><br>CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.}, }
@article {pmid41756820, year = {2026}, author = {Trang, KT and Gulick, DA and Truell, J and Tian, J and Bodkhe, R and Hiseni, P and Gravdal, K and Kirubakaran, TG and Casén, C and Singh, R and Ziegler, TR and Reimer, RA and Kraft, CS}, title = {Diet-Microbiome Analysis in a Healthy Cohort Reveals Potential Role of Intestinal Microbiota in Metabolism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.17.706416}, pmid = {41756820}, issn = {2692-8205}, abstract = {UNLABELLED: Both preclinical and clinical studies have revealed the indisputable importance of intestinal bacterial community composition in pathogenesis of various disease states, from obesity to neurodegeneration. Diet remains one of the most important factors shaping human intestinal microbiota composition. In this study, we investigated diet-microbiome interactions in a healthy cohort of 88 participants from Atlanta and Calgary. We examine microbial composition (16S rRNA sequencing) with dietary records using Spearman Correlation tests with Benjamini-Hochberg multiple hypothesis correction to make community-level comparisons between dietary scores and microbial diversity index scores. Predictive models were used for molecular-level comparisons between microbial gene pathways and molecules. Among generalized dietary and microbial indices, we identified a negative association between dietary whole grain consumption and a microbial dysbiosis score. Comparisons between dietary food groups and bacterial family abundance reveal significant associations between dairy consumption and Lactobacillaceae abundance, dietary unsaturated to saturated fatty acid ratio and Clostridia Cluster Family XIII, salt intake and Lachnospiraceae , and consumption of 'greens and beans' and Veillonellaceae . Predictive models of microbial gene pathways and molecules reveal significant positive associations between several dietary fatty acids and microbial short-chain fatty acid fermentation pathways, and between dietary lignans and archaeal methanogenesis pathways. Overall, these associations may inform future explorations on specific dietary interventions to impact the gut microbiome.<br><br>IMPORTANCE: In this study, we compare dietary records and composition of intestinal microbes in a cohort of 88 participants. We identified associations between dietary consumption of dairy and the presence of dairy-consuming bacteria called Lactobacteriaceae and between consumption of dietary fats and the presence of fat-consuming bacteria called Clostridia . Using predictive analysis, we identify specific fatty acids associated with specific biochemical pathways found in Clostridia that might underlie these associations, in addition to an association between archaeal microbes and dietary consumption of estrogen-binding molecules called lignans, which are commonly found in whole grains and vegetables. Overall, our study generates useful associations between diet and intestinal microbes that can be tested in experiments that may help scientists use diet to control intestinal microbes in order to improve human health.}, }
@article {pmid41756623, year = {2026}, author = {Szilagyi, A and Galiatsatos, P and Margolese, N}, title = {There may be a differential mechanistic impact on colorectal cancer of lactose-containing foods between lactase persistent and lactase non-persistent populations.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1671166}, pmid = {41756623}, issn = {2296-861X}, abstract = {It is generally suggested that milk and milk products reduce the risk of colorectal cancer (CRC). While there is some controversy over specific sites affected throughout the colon and the benefits of specific dairy foods (DFs), there is a general consensus that calcium intake is the main mechanism of the cancer-reducing effects. This opinion may be sidelined by several other mechanisms. There is also a potentially important compensatory mechanism in populations with adult genetic lactase deficiency. The microbiome changes occur through a process of adaptation to continued lactose consumption. The bacterial blooms consist largely of Bifidobacterial species. These bacteria may exert anti-neoplastic effects and also increase the capacity of persons with adapted lactase insufficiency to consume dairy products. Bacterial metabolism thus provides a second pathway for lactose digestion. Since the use of Mendelian randomization (MR) accuracy disallow two different pathways for the genetic variable, this process constitutes a horizontal pleiotropy. This narrative review using articles from PubMed and Google Scholar will discuss different nutrients and mechanisms in milk and milk products that are involved in anti-neoplastic effects. The impact of adult lactase deficiency and continued dairy consumption on the microbiome, and its contribution to colorectal cancer reduction, is highlighted. The conclusions from this review are that calcium has multifaceted mechanisms of anti-carcinogenesis, but other nutrients, such as conjugated linoleic acid (CLA), lactoferrin, and folate in the dairy matrix, could also contribute. In lactase non-persistent (LNP) populations adapted to dairy foods, a bifidogenic bloom in the microbiome may add additional anti-neoplastic effects and /or increase dairy food consumption. We argue that predictions of colon cancer effects from dairy foods may be inaccurate, and that evaluating both populations together may confound outcomes.}, }
@article {pmid41756428, year = {2026}, author = {Li, J and Bu, E and Lian, A and Li, Y and Tao, C}, title = {Polarity-Aware Knowledge Graph Reveals Diet-Microbiome-Health Mechanisms with Relevance to Muscle, Immune and Metabolic Aging.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-8771108/v1}, pmid = {41756428}, issn = {2693-5015}, abstract = {Diet profoundly influences gut microbial composition and metabolism, yet mechanistic pathways linking dietary exposures to human health remain fragmented across the literature. To systematically organize and integrate this evidence, we constructed an evidence-weighted Diet-Microbiome-Health Knowledge Graph (DMH-KG) from 1,309 curated PubMed abstracts (2023-2025), using a standardized schema spanning 11 entity categories and 12 relationship types with explicit polarity labels. Entities and relationships were identified through manual annotation, yielding 10,270 entity mentions and 4,866 relationships. Expert-guided consolidation of synonymous and lexically variant terms, along with pruning of disconnected concepts, resulted in 4,766 unique entities connected by 4,772 polarity-weighted edges. To prioritize robust biological signals, a composite edge-weighting function was applied, integrating both relationship frequency and polarity. Network analysis revealed a modular small-world structure centered on microbial and inflammatory mediators. High-confidence pathways emerged, including the probiotic-SCFA-immunity axis (34 supporting documents) and the high-fat diet-LPS-endotoxemia cascade (8 documents), both of which are central to age-related immune modulation and metabolic health. Quantitative validation against five KEGG and Reactome pathways demonstrated high biological fidelity: the DMH-KG recovered all reference diet-microbiome-outcome edges for Butanoate metabolism and Secondary Bile Acid biosynthesis (100% coverage) and achieved a mean pathway-level entity coverage of 92.0%, measured as the proportion of predefined pathway components represented in the graph. A comparative pilot study further demonstrated that DMH-KG augmentation improves mechanistic specificity inference across Diet-Microbiome-Health interactions. These features position the DMH-KG as a scalable platform for mechanistic inference across Diet-Microbiome-Health interactions, with direct relevance to immune regulation, muscle health, metabolic aging, and chronic disease prevention. The framework preserves evidence provenance, relationship polarity, and biological direction, supporting both discovery science and AI-driven nutritional reasoning.}, }
@article {pmid41756197, year = {2026}, author = {Li, F and Anyaso-Samuel, S and Yano, Y and Chang, VC and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Liao, LM and Huang, WY and Freedman, ND and Beane Freeman, LE and Sandler, DP and Abnet, CC and Sinha, R and Shi, J and Loftfield, E and Vogtmann, E}, title = {Association between diet quality and the oral microbiome in three US cohort studies.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2635238}, pmid = {41756197}, issn = {2000-2297}, abstract = {BACKGROUND: The oral microbiome has been associated with overall health, but the contribution of dietary habits to oral microbial composition is not well understood.<br><br>OBJECTIVE: We evaluated the association between diet quality (Healthy Eating Index [HEI] 2015) and the oral microbiome in the Agricultural Health Study, NIH-AARP Diet and Health Study, and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial within 5,546 participants.<br><br>METHODS: Individual HEI components were scored from FFQ data and summed. Alpha and beta diversity and genus-level presence and relative abundance were estimated. The proportion of variability in the beta diversity matrices explained by diet quality and other covariates were calculated. Linear, logistic, and zero-inflated negative binomial regression models with adjustment for confounders were used and cohort-specific estimates were meta-analyzed.<br><br>RESULTS: Age explained the largest variability in beta diversity (Bray-Curtis), followed by smoking, education, and the HEI component for added sugar. Although overall diet quality was not associated with alpha diversity overall, the added sugar component was consistently inversely associated with alpha diversity. At the genus-level, most of the identified associations were with added sugar.<br><br>CONCLUSIONS: Consumption of added sugars was consistently associated with oral microbial diversity and specific genera.}, }
@article {pmid41756132, year = {2026}, author = {Bamrung, V and Sitthicharoenchai, P}, title = {The evolving story of Streptococcus gallolyticus: classification, pathogenesis, role in human and animal disease, and laboratory diagnostics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1765252}, pmid = {41756132}, issn = {1664-302X}, abstract = {Streptococcus gallolyticus, formerly known as S. bovis, belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Besides being a part of the gut microbiome, this organism has gained interest due to its association with infective endocarditis and its strong correlation with colorectal cancer in humans. In veterinary medicine, systemic infection caused by S. gallolyticus has been reported in various animal populations, including porcine, ruminant, and avian species. Despite its clinical importance in humans and animals, two key challenges persist: the limited understanding of the pathogenesis due to its ubiquitous nature and inconsistencies in diagnostic laboratory reporting of the bacteria in SBSEC. This review summarizes the taxonomic characterization of the SBSEC, its clinical manifestations across species, current understanding of the bacterial pathogenesis, and the laboratory diagnostic assays used for its detection. We will further discuss the importance of SBSEC speciation and subspeciation, highlighting their distinct clinical implications and potential impact on human and animal health.}, }
@article {pmid41756131, year = {2026}, author = {Liu, Z and Deng, W and Xu, W and Ye, L and Rao, Z}, title = {Probiotic supplementation modulates the gut microbiome and improves clinical outcomes in pediatric refractory asthma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1756436}, pmid = {41756131}, issn = {1664-302X}, abstract = {BACKGROUND: Refractory asthma in children remains a clinical challenge despite conventional therapies, with emerging evidence linking gut microbiome dysbiosis to persistent inflammation via the gut-lung axis. This study investigated whether multi-strain probiotic supplementation could improve asthma control and restore microbial balance when added to standard treatment.<br><br>METHODS: This prospective randomized controlled trial enrolled 88 children aged 4-8&#x202f;years with refractory asthma. Participants were allocated into two groups (n&#x202f;=&#x202f;44 each): a conventional treatment group (bronchodilators and glucocorticoids) and a combination treatment group, which received conventional therapy plus a multi-strain probiotic (Bifidobacterium, Lactobacillus acidophilus, Streptococcus thermophilus) for 4&#x202f;months. Primary outcomes were asthma control level, Asthma Control Test (ACT) scores, and pulmonary function (FEV&#x2081;, FVC, PEF). Secondary outcomes included gut microbiota changes, assessed by 16S rRNA gene sequencing.<br><br>RESULTS: Combination therapy achieved complete asthma control in 68.18% of patients versus 36.36% with conventional therapy (Z&#x202f;=&#x202f;2.415, p&#x202f;<&#x202f;0.05). Post-treatment ACT scores were higher in the combination group (22.45&#x202f;&#xb1;&#x202f;1.20 vs. 19.78&#x202f;&#xb1;&#x202f;1.45; p&#x202f;<&#x202f;0.05), with superior improvements in FEV1 (2.65&#x202f;&#xb1;&#x202f;0.10&#x202f;L vs. 2.30&#x202f;&#xb1;&#x202f;0.08&#x202f;L; p&#x202f;<&#x202f;0.001), FVC (3.10&#x202f;&#xb1;&#x202f;0.18&#x202f;L vs. 2.80&#x202f;&#xb1;&#x202f;0.15&#x202f;L; p&#x202f;<&#x202f;0.001), and PEF (4.00&#x202f;&#xb1;&#x202f;0.25&#x202f;L/s vs. 3.50&#x202f;&#xb1;&#x202f;0.20&#x202f;L/s; p&#x202f;<&#x202f;0.001). Symptoms resolved faster with combination therapy (e.g., cough: 5.60&#x202f;&#xb1;&#x202f;1.50 vs. 10.45&#x202f;&#xb1;&#x202f;2.30&#x202f;days; p&#x202f;<&#x202f;0.05). Microbiome analysis showed increased alpha diversity (e.g., Shannon index: p&#x202f;<&#x202f;0.05) and beneficial shifts in the combination group, including higher Bifidobacterium (25.00&#x202f;&#xb1;&#x202f;15.31% vs. 0.98&#x202f;&#xb1;&#x202f;1.92%; p&#x202f;<&#x202f;0.001) and reduced Bacteroides, with distinct beta diversity clustering (PERMANOVA p&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: Adjunctive multi-strain probiotics enhance clinical outcomes and gut microbiome health in pediatric refractory asthma, supporting microbiome-targeted therapies via the gut-lung axis. Larger, double-blind randomized controlled trials are warranted to confirm long-term benefits.}, }
@article {pmid41756119, year = {2026}, author = {Cai, L and Sun, J and Li, H and Wang, C and Zhang, M and Shao, Q and Wang, Z}, title = {A novel internal reference microorganism-based method reveals wild-enriched Penicillium for enhancing growth and disease resistance in Fritillaria thunbergii.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1746815}, pmid = {41756119}, issn = {1664-302X}, abstract = {INTRODUCTION: Fritillaria thunbergii Miq. is an important traditional Chinese medicinal herb, but bulb rot disease causes severe losses during its cultivation. Screening and reintroducing beneficial microorganisms from the wild rhizosphere is an effective strategy to increase disease resistance in cultivated plants. However, the absolute quantitative characteristics of microorganisms cannot be reflected by traditional methods based on relative abundance analysis due to compositional bias.<br><br>METHODS: In this study, we identified Clavatospora as a host-specific internal reference microorganism (IRM) and established an IRM-based relative abundance differential microorganism analysis (IRMRADMA) method.<br><br>RESULTS: Application of this method revealed that wild F. thunbergii possesses greater potential than cultivated plants for mining beneficial rhizosphere microorganisms. Specifically, Penicillium was identified as a key wild-enriched genus. Subsequently, two strains, Penicillium korosum and Penicillium aculeatum, were isolated from the rhizosphere of wild F. thunbergii. Functional tests confirmed that these strains demonstrated dual functions in disease suppression and plant growth promotion by solubilizing phosphate, producing siderophores, antagonizing pathogens, and upregulating defenserelated genes.<br><br>CONCLUSION: This study established the IRM-RADMA method and identified key Penicillium strains from the wild Fritillaria thunbergii rhizosphere. Their confirmed dual functions in growth promotion and disease suppression validate the 'plant microbiome rewilding' strategy, offering a new paradigm for the biological control of F. thunbergii diseases.}, }
@article {pmid41755783, year = {2026}, author = {Kim, KS and Cho, JY and Park, YC and Hong, JH and Jung, JG and Sunwoo, J}, title = {Exploring LEPR-Linked Metabolic Diversity through Gut Microbiome-Metabolome Network Analysis in Non-Obese Adults.}, journal = {Biomolecules &amp; therapeutics}, volume = {34}, number = {2}, pages = {448-460}, doi = {10.4062/biomolther.2025.161}, pmid = {41755783}, issn = {1976-9148}, abstract = {Genetic variation in the leptin receptor (LEPR) gene has been implicated in metabolic regulation, while the gut microbiome and circulating metabolites are increasingly recognized as mediators of host metabolic phenotype. However, the systems-level interactions among LEPR genotypes, gut microbial composition, and serum metabolomic profiles remain poorly understood, particularly in healthy individuals. We conducted a cross-sectional study involving 37 healthy Korean adults. Three LEPR single nucleotide polymorphisms (rs1137101, rs1173100, rs790419) were genotyped. Untargeted metabolomics of fasting serum was performed using gas chromatography-time-of-flight mass spectrometry, and gut microbiome composition was profiled by 16S rRNA gene sequencing. Statistical analysis included principal component analysis, Mann-Whitney U tests, and Spearman correlations. Network analysis integrating microbiome, metabolomic, and clinical phenotype data was conducted using Cytoscape. A total of 54 serum metabolites were identified. LEPR genotypes, particularly rs1137101 and rs1173100, were associated with differences in metabolites such as pimelic acid, malonic acid, and 2,4-dihydroxybutyric acid. Firmicutes negatively correlated with saturated fatty acids and organic acids, whereas Actinobacteria positively correlated with cholesterol and amino acids. Network analysis revealed indole-3-acetate and cholesterol as central nodes linking microbial taxa with body mass index and leptin levels. However, no direct molecular pathways connecting leptin or its receptor were identified. LEPR genetic variation is associated with distinct serum metabolomic patterns and microbiome-host networks in healthy adults. Although no direct leptin signaling links were found, network-level associations suggest indirect genetic influences on metabolic states through microbiome-metabolome interactions. These findings advance understanding of personalized metabolic regulation and gene-microbiome interplay.}, }
@article {pmid41755580, year = {2026}, author = {Mendoza, ADG and Nuncio-Mora, L and Sánchez, V and Gonzalez, V and Nicolini, H}, title = {Dysbiosis in the Family nucleus of Children Diagnosed With Autism Spectrumin Mexico City.}, journal = {Actas espanolas de psiquiatria}, volume = {54}, number = {1}, pages = {121-127}, pmid = {41755580}, issn = {1578-2735}, abstract = {BACKGROUND: The relationship between the gut microbiome and Autism Spectrum Disorder (ASD) has been the subject of growing interest in scientific research. Research into the relationship between the gut microbiome and ASD has gained relevance in recent years as recent studies have identified significant differences in the gut microbiome abundance and composition in ASD children compared to neurotypical ones. However, little is known about the microbiome interplay, changes and relationship in parents and children with ASD, considering that they share a consistent environment. Charactering the microbiota of trio-type families with a child diagnosed with autism.<br><br>METHODS: The hypervariable region of the 16s ribosomal gene was sequenced from stool samples from adolescents with ASD and their parents. The analysis was performed using various software programs, including QIIME2 and DADA2.<br><br>RESULTS: In this paper, we discuss this relationship in three families, and observed that the gut microbiome of the offspring with ASD is more similar to the mother's than the father's microbiome.<br><br>CONCLUSIONS: These observations could lead to the understanding of the potential heritability of the disorder through parental connectedness of the gut microbiome and eventually to the development of interventions aimed at modulating the gut microbiota to improve symptoms associated with ASD.}, }
@article {pmid41755545, year = {2026}, author = {Song, Z and Song, C and Yi, X and Shao, Y and Zhang, Y}, title = {Targeting the transferrin receptor in breast cancer: nanotechnology-based drug delivery strategies.}, journal = {Nanomedicine (London, England)}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/17435889.2026.2628237}, pmid = {41755545}, issn = {1748-6963}, abstract = {Breast cancer remains a leading cause of cancer-related morbidity and mortality worldwide, with treatment efficacy often limited by systemic toxicity, poor tumor selectivity, and multidrug resistance. Nanotechnology-based drug delivery systems offer a promising strategy to enhance therapeutic precision, particularly through active targeting of tumor-associated receptors. The transferrin receptor (TfR), which is frequently overexpressed in breast cancer cells, has emerged as an attractive target due to its role in receptor-mediated endocytosis. This review critically summarizes recent advances in transferrin-functionalized nanocarriers for breast cancer therapy, including liposomal, polymeric, dendrimeric, metallic, and hybrid platforms. Key design parameters influencing cellular uptake, biodistribution, and therapeutic efficacy - such as particle size, surface charge, ligand density, and release behavior - are discussed. We highlight progress in multifunctional and stimuli-responsive systems designed to overcome tumor microenvironment barriers and multidrug resistance. In addition, emerging evidence on the role of the gut microbiota in modulating breast cancer progression and treatment response is examined, with a focus on its potential impact on targeted nanomedicine efficacy. Finally, current translational challenges and future directions, including personalized and microbiome-informed nanotherapeutic strategies, are outlined. Literature was identified through systematic searches of PubMed, Web of Science, Scopus, and Google Scholar from January 2005 to March 2025.}, }
@article {pmid41755503, year = {2026}, author = {Li, J and Will, I and Silva, LM and Travers-Cook, TJ and Blackwood, PE and King, KC}, title = {Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals.}, journal = {Molecular ecology}, volume = {35}, number = {5}, pages = {e70281}, pmid = {41755503}, issn = {1365-294X}, support = {//Canada Excellence Research Chairs, Government of Canada/ ; }, abstract = {Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essential for host development, physiology and immunity. We synthesise current understanding of the ecological interactions between host microbiomes and parasites, ranging from competitive to facilitative, and explore their potential evolutionary consequences for parasite virulence and transmission in the wild. We highlight recent mechanistic insights that support integrating a microbiome perspective into wildlife parasitology, with examples across diverse animal taxa including amphibians, bats, insects and corals, particularly within the context of climate change. Adopting such a holistic approach can open new avenues whereby host microbial shifts can be used to predict and mitigate infectious diseases in wild populations. Finally, we propose a conceptual framework to guide future research on microbiome-parasite-host interactions, aiming to better reflect natural ecological complexities and advance both fundamental understanding and conservation applications.}, }
@article {pmid41755380, year = {2026}, author = {Lee, Y and Mustakim, KR and Eo, MY and Cho, YJ and Kim, SM}, title = {Peri-implantitis as a potential risk factor for peri-implant oral malignancy.}, journal = {Journal of the Korean Association of Oral and Maxillofacial Surgeons}, volume = {52}, number = {1}, pages = {27-33}, doi = {10.5125/jkaoms.2026.52.1.27}, pmid = {41755380}, issn = {2234-7550}, abstract = {Peri-implant oral malignancy (PIOM) refers to malignant tumors arising around dental implants and is an increasingly reported complication of implant therapy. PIOM may follow distinct pathophysiological mechanisms, including chronic peri-implant inflammation and implant-related factors that contribute to carcinogenesis. This current review aims to explore the potential role of peri-implantitis (PI) as a risk factor for PIOM, discussing the proposed pathogenic mechanisms, histological findings, and clinical implications. A comprehensive literature search was conducted in PubMed, Scopus, and Web of Science databases. Relevant case reports, clinical studies, and reviews on the keywords "PIOM" and "PI" published from 2019 up to 2025 were included and qualitatively analyzed. Clinicopathologic characteristics are summarized as location and morphology, disease progression, histopathology, and degree of differentiation, and pathophysiological hypotheses involve inflammatory and electrochemical pathways, epithelial barrier dysfunction, molecular alterations, microbiome dysbiosis, and immune dysregulation. Current evidence remains limited and primarily anecdotal. Several studies suggest that chronic inflammation, titanium particle exposure, corrosion byproducts, and sustained tissue damage in peri-implant tissues may contribute to oncogenesis. While a direct causal link between PI and PIOM remains unproven, chronic peri-implant inflammation may contribute to malignancy development in predisposed individuals. Clinicians should consider a biopsy when peri-implant lesions exhibit atypical features, promptly.}, }
@article {pmid41754858, year = {2026}, author = {Bertin, L and Facchin, S and Barberio, B and Maniero, D and Lorenzon, G and Cesaroni, F and Zanconato, M and Romanelli, G and Francini-Pesenti, F and Busetto, L and Cananzi, M and Gaio, P and Bosa, L and Zingone, F and Gianolio, L and Damas, OM and Savarino, EV}, title = {Diet and Gut Microbiota in Inflammatory Bowel Disease: A Clinical and Nutritional Perspective.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {2}, pages = {}, pmid = {41754858}, issn = {1424-8247}, abstract = {Inflammatory bowel diseases, comprising Crohn's disease and ulcerative colitis, represent chronic inflammatory disorders with rising global incidence, underscoring the pivotal role of modifiable environmental factors in disease pathogenesis. Diet and intestinal microbiota have emerged as critical bidirectional therapeutic targets through complex interactions with host immune responses. Epidemiological evidence demonstrates that healthy and high fiber diets reduce disease risk, while ultra-processed foods and inflammatory dietary patterns increase susceptibility. Therapeutic nutritional interventions, including exclusive enteral nutrition, the Crohn's Disease Exclusion Diet combined with partial enteral nutrition, and the Mediterranean diet can induce and maintain clinical remission while promoting favorable microbiome modifications characterized by the enrichment of butyrate-producing taxa such as Faecalibacterium prausnitzii and Roseburia species, alongside a reduction in pathogenic Proteobacteria. Micronutrient deficiencies affect up to 78% of patients through malabsorption, chronic blood losses, dietary restrictions, and drug-nutrient interactions. Nutritional status significantly impacts surgical outcomes, with preoperative malnutrition and sarcopenia associated with increased postoperative complications, and it reciprocally influences biologic therapy response. Integration of personalized, microbiome-informed dietary strategies as complementary components of comprehensive treatment plans represents a promising therapeutic frontier, requiring multidisciplinary collaboration, rigorous clinical trials with standardized microbiome analyses, and precision nutrition algorithms accounting for disease phenotype, baseline microbial composition, and individual patient characteristics to optimize outcomes and improve quality of life.}, }
@article {pmid41754809, year = {2026}, author = {Krakowska, A and Skiba-Kurek, I and Zontek-Wilkowska, J and Koczurkiewicz-Adamczyk, P and Muszyńska, B and Skalski, T}, title = {The Use of Biomass from In Vitro Fungal Cultures as a Bioactive Ingredient with Antimicrobial Activity in Hydrogel Dressings.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {19}, number = {2}, pages = {}, pmid = {41754809}, issn = {1424-8247}, support = {NCN 2024/08/X/NZ7/01059//National Science Centre/ ; }, abstract = {Background/Objectives: Chronic wounds represent a significant clinical burden and require multimodal treatment strategies targeting inflammation, infection, moisture balance, and tissue remodeling, as defined by the TIME framework. This study aimed to evaluate the therapeutic potential of innovative hydrogel dressings enriched with fungal biomass, designed to exploit natural bioactive compounds-such as antimicrobial peptides and proteolytic enzymes-to enhance wound healing while maintaining high biocompatibility. Methods: Hydrogel dressings incorporating selected fungal biomasses were fabricated and characterized for physicochemical and biological performance. Key material properties relevant to wound care, including hydrophilicity and porosity, were analyzed to assess exudate management capacity and maintenance of a moist wound environment. Antimicrobial activity was tested against common wound pathogens, and species-pathogen interactions were evaluated using generalized linear modeling. In vitro biocompatibility was assessed using human keratinocytes and compared with conventional silver nanoparticle-based dressings. Results: The developed hydrogels demonstrated properties suitable for clinical application, including superhydrophilicity and high porosity, supporting effective exudate control and moisture retention. Significant broad-spectrum antimicrobial activity was observed, particularly against Staphylococcus aureus and Pseudomonas aeruginosa, with effects dependent on fungal species. Statistical modeling revealed highly significant interactions between fungal species and pathogens in inhibition zones (p < 0.001). Hydrogels containing Pleurotus ostreatus and Agaricus bisporus showed broad activity against Escherichia coli, P. aeruginosa, and S. aureus, whereas Enterococcus faecalis exhibited resistance. Fungal biomass-based dressings displayed superior keratinocyte biocompatibility compared to silver nanoparticle controls. Conclusions: Fungal biomass-reinforced hydrogels offer a promising, safer, multifunctional alternative for infected chronic wound management, supporting both antimicrobial action and tissue regeneration.}, }
@article {pmid41754522, year = {2026}, author = {Atkins, H and Stegman, N and Putonti, C}, title = {Diverse Temperate Coliphages of the Urinary Tract.}, journal = {Viruses}, volume = {18}, number = {2}, pages = {}, pmid = {41754522}, issn = {1999-4915}, support = {1R15AI171873-05/NH/NIH HHS/United States ; }, abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.}, }
@article {pmid41754473, year = {2026}, author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A}, title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754473}, issn = {2076-0817}, abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.}, }
@article {pmid41754458, year = {2026}, author = {Anderson, JG and Scarsella, E and Soltero-Rivera, M and Goldschmidt, S and Rojas, CA and Ganz, HH}, title = {First Description of Oral Microbiota in Domestic Cats Affected by Oral Squamous Cell Carcinoma.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754458}, issn = {2076-0817}, support = {annual grant 2022//Foundation for Veterinary Dentistry/ ; 5K12-CA138464//National Cancer Institute/National Institutes of Health/ ; UL1 TR001860/TR/NCATS NIH HHS/United States ; }, abstract = {Oral squamous cell carcinoma (OSCC) accounts for the majority of feline oral neoplasms and carries a poor prognosis; however, the oral microbiome in affected cats remains poorly characterized. This study aimed to preliminarily describe the oral bacterial communities of cats with OSCC and compare them with those of clinically healthy cats using DNA amplicon sequencing. Oral swabs were collected from cats with OSCC, including tumor surfaces, tumor cut surfaces, and clinically normal mucosa distant from the tumor (n = 20 total samples), and from the gingival margin of healthy cats (n = 12). DNA was extracted and full-length 16S rRNA gene sequencing was performed to assess microbial composition and diversity. Cats with OSCC exhibited significant alterations in oral microbiota compared with healthy controls, including reduced alpha diversity, distinct beta-diversity clustering, and consistent taxonomic shifts. Healthy cats displayed a relatively conserved core microbiome dominated by Porphyromonas spp., Bacteroides, Pasteurellaceae, Helcococcus, and Moraxella. In contrast, OSCC-associated samples showed increased relative abundances of anaerobic and disease-associated taxa, including Filifactor villosus, Bacteroides pyogenes, Odoribacter denticanis, Porphyromonas circumdentaria, and members of the Pasteurellaceae. These findings provide the first description of the oral microbiota associated with feline OSCC and demonstrate exploratory microbial differences between health and disease.}, }
@article {pmid41754428, year = {2026}, author = {Ugwu, CE and Akinsulie, OC and Ayandokun, TF and Ajibade, FA and Shahzad, S and Aliyu, VA and Oladoye, MJ and Idris, I and Obasi, KO and Edeh, JK and Olojede, AA and Ukauwa, CB and Adeyemi, MI and Ugwu, CC and Ugorji, LC}, title = {Mechanisms and Therapeutic Potential of Nutritional Immunity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754428}, issn = {2076-0817}, abstract = {Nutritional immunity is a major facet of host defense, wherein the host immune system strategically limits pathogen access to critical nutrients, including iron, zinc, vitamins, lipids, and amino acids, to repress microbial proliferation and virulence. This review provides a comprehensive synthesis of the molecular mechanisms that power nutrient immunity, including metal homeostasis, nutrient competition, transporter modulation, hormonal regulation, and direct antimicrobial actions. We examine nutrient-specific strategies employed by the host, such as iron-withholding mechanisms, vitamin deprivation, and copper-mediated toxicity. We also explore how diverse pathogens, including extracellular, intracellular, and eukaryotic pathogens, adapt to these hostile nutritional landscapes through siderophore diversification, regulatory integration, and metabolic rewiring. Comparative genomic analyses reveal convergent evolution in nutrient acquisition systems, illuminating the dynamic arms race between host restriction and microbial evasion. We examine the immunological mechanisms that regulate nutritional immunity. Further, we discuss the translational potential of nutritional immunity, cutting across nutrient-based therapies, host-directed interventions, and emerging diagnostic biomarkers. Finally, we suggest future directions that synergize nutritional immunity with microbiome ecology, global malnutrition, and personalized medicine. By elucidating the interconnection between metabolism and immunity, this review highlights the therapeutic promise of starving or toxifying the pathogen to save the host.}, }
@article {pmid41754400, year = {2026}, author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M}, title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, pmid = {41754400}, issn = {2076-0817}, abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.}, }
@article {pmid41754336, year = {2026}, author = {Haidri, I and Ullah, Q and Qasim, M and Amir, MA and Haider, W and Nguyen, HH and Promwee, A}, title = {Microbiome-Mediated Cd Stabilization in Chilli Pepper: Roles of Capsaicinoids and Cultivar Genetics Under Environmental Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, pmid = {41754336}, issn = {2223-7747}, support = {WU-CIA0 5205/2025//Walailak University under the international research collaboration scheme/ ; }, abstract = {Chilli pepper agroecosystems (Capsicum annuum L.) are increasingly threatened by cadmium (Cd) contamination, with emerging climatic stressors such as drought further exacerbating risks to food safety and crop productivity. This review synthesizes current evidence on microbiome-mediated Cd phytostabilisation in chilli pepper, with a particular focus on the roles of capsaicinoids and cultivar-specific genetic regulation in shaping rhizosphere microbial communities. Existing studies demonstrate that capsaicinoid-rich cultivars selectively recruit specialized rhizosphere microbes, enhancing root-level Cd sequestration and achieving Cd retention efficiencies of approximately 40-55%, thereby substantially restricting Cd translocation to edible fruit tissues. Multi-strain plant growth-promoting rhizobacteria (PGPR) consortia, especially when combined with structured organic amendments, have been reported to reduce fruit Cd and nickel (Ni) accumulation by more than 87% in contaminated soils. These responses are regulated by pungency-associated genetic loci, including Pun1 (pungency locus 1) and Pun4 (pungency locus 4) genes, which influence secondary metabolism and microbial assembly under metal stress conditions. The review highlights key knowledge gaps regarding the long-term stability of engineered rhizobiomes, the in situ dynamics of the Capsicum volatilome as a microbial recruitment signal, and the interactive effects of Cd contamination and drought in field environments. Overall, this synthesis provides a mechanistic framework for deploying high-pungency cultivars and microbiome-based strategies to improve Cd phytostabilisation, with important implications for sustainable chilli production in drought-prone, metal-contaminated agroecosystems.}, }
@article {pmid41754214, year = {2026}, author = {Churin, AA and Sokolyanskaya, LO and Lukina, AP and Karnachuk, OV}, title = {Current Concepts in Probiotic Safety and Efficacy.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040696}, pmid = {41754214}, issn = {2072-6643}, support = {25-24-00493//Russian Science Foundation/ ; }, abstract = {Background/Objectives: Advances in molecular biology, genetics, and microbiome research have significantly expanded our understanding of probiotic microorganisms and their interactions with human health, stimulating the development of both traditional and next-generation probiotic products. Although probiotics are widely used and generally considered safe for healthy individuals, accumulating evidence indicates that their safety profile varies significantly depending on the strain, dose, host, and context, with rare but clinically significant adverse events reported in vulnerable populations. Methods: This review summarizes current knowledge on the efficacy and safety of probiotics, analyzes limitations in clinical safety reporting, and compares regulatory frameworks governing the use of probiotics as dietary supplements, medicinal products, and live biotherapeutics. Particular attention is given to new genomic and computational approaches to safety assessment. Conclusions: Overall, the review emphasizes the need for coordinated regulation, rigorous clinical evidence, and integrated, modern safety assessment strategies to support the responsible expansion of probiotic use.}, }
@article {pmid41754202, year = {2026}, author = {Reytor-González, C and Sarno, G and Montalvan, M and Verde, L and Annunziata, G and Barrea, L and Muscogiuri, G and Simancas-Racines, D}, title = {Obesity, Bariatric Surgery, and Cancer Risk: Nutritional Perspectives and Long-Term Clinical Implications.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040685}, pmid = {41754202}, issn = {2072-6643}, abstract = {Obesity is recognized as a causal risk factor for the development of multiple cancers, with risk magnitude varying by tumor site, sex, life stage, and adipose tissue distribution. This narrative review synthesizes recent epidemiological evidence linking excess body fatness with cancer incidence and mortality and integrates the biological mechanisms that explain this association. Chronic low-grade inflammation, insulin resistance with compensatory hyperinsulinemia, dysregulation of adipose-derived hormones and sex steroids, impairment of anti-tumor immune responses, alterations in the gut microbiota, and remodeling of the tumor microenvironment collectively create conditions that favor tumor initiation and progression. Bariatric surgery is the most effective clinical intervention for achieving substantial and sustained weight loss in individuals with severe obesity, and growing evidence indicates that it is associated with a reduction in overall cancer risk and cancer-related mortality, particularly for malignancies strongly linked to obesity. However, the extent of this benefit differs by surgical technique and remains less consistent for colorectal cancer. Beyond metabolic improvements, bariatric surgery produces long-term changes in nutritional physiology that may also influence oncologic outcomes. Persistent deficiencies of micronutrients such as iron, folate, vitamin B12, vitamin D, and calcium can affect DNA synthesis, methylation, oxidative balance, and cellular repair. Altered protein and energy intake may contribute to loss of lean mass and reduced metabolic resilience, while changes in alcohol absorption and metabolism can increase systemic exposure to ethanol and its carcinogenic metabolites. In addition, bariatric surgery induces sustained remodeling of the gut microbiome and bile acid metabolism, which may further modulate tumorigenic signaling. Overall, the oncological impact of bariatric surgery reflects a balance between metabolic improvement and long-term nutritional management, underscoring the need for structured follow-up and targeted nutritional strategies to optimize cancer risk reduction.}, }
@article {pmid41754199, year = {2026}, author = {Arabi, T and Akbar, A and Yaqinuddin, A and Khan, MI and Arora, I}, title = {Cross-Cultural Nutritional Epigenomics: Diet and Microbiome Interactions Shaping Type 2 Diabetes in Arab and Western Populations.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040681}, pmid = {41754199}, issn = {2072-6643}, abstract = {In the Middle East and North Africa (MENA) region, the prevalence of Type 2 Diabetes (T2D) is 17-18%, substantially higher than the ~9-10% reported in Western populations, with some Gulf states approaching 25% in adults. Historically, Arab diets, characterized by high fiber intake from whole grains, legumes, and fermented dairy products, have contrasted markedly with the Western dietary pattern increasingly prevalent among urbanized Arab populations. These nutritional shifts have been associated with changes in gut microbial composition, including lower representation of short-chain fatty acid-producing bacteria and higher abundance of dysbiosis-associated taxa. Concurrently, diet-derived compounds and microbial metabolites have been associated with changes in DNA methylation, histone modifications, and non-coding RNA expression. Epigenome-wide association studies revealed both shared and population-specific methylation signatures in patients with T2D. However, integrated multi-omics studies remain limited in Arab populations, where the disease burden is highest. This review integrates emerging evidence on diet-linked epigenetic alterations, microbiome-associated metabolic pathways, and their intersection in potentially contributing to T2D risk and progression. Given the heterogeneity of T2D across populations, there is a pressing need for culturally contextualized precision medicine frameworks that integrate population-specific diet-microbiome-epigenome dynamics rather than extrapolating findings across populations. Additionally, this review synthesizes evidence that dietary patterns are associated with T2D-relevant pathways through the diet-microbiome-epigenome axis, with emphasis on Arab/MENA populations and Western comparator cohorts.}, }
@article {pmid41754197, year = {2026}, author = {Zhu, A and Bonja Geleto, F and Mohammed Ali, M and Ashenafi, H and Erko, B and Taye, B}, title = {Household Food Insecurity Alters Gut Microbiome Composition and Enriches Sutterella in Ethiopian Schoolchildren.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040680}, pmid = {41754197}, issn = {2072-6643}, support = {Picker ISI//Colgate University/ ; }, abstract = {Background: Household food insecurity (HFI) adversely affects child development by restricting caloric intake, dietary diversity, and food quality. Since diet is a key factor influencing the gut microbiome, HFI may negatively impact health by altering microbial communities. However, direct evidence linking HFI to changes in the gut microbiome is limited. Therefore, we investigated the effects of HFI as a composite variable and used individual HFI assessment questions as specific proxies for dietary deprivation on the gut microbiome in a group of Ethiopian schoolchildren. Methods: Fecal samples were collected from 57 school-aged children in Ethiopia, and microbial profiles were established using 16S rRNA amplicon paired-end sequencing. Food insecurity was assessed using the Household Food Insecurity Access Scale (HFIAS). Results: We observed no significant differences in alpha diversity across food security status (Wilcoxon p > 0.05). However, beta diversity analysis revealed a significant shift in microbiome composition between food-secure and food-insecure individuals (Bray-Curtis dissimilarity; PERMANOVA, p < 0.05). Further analyses of individual HFIAS questions as specific proxies for dietary deprivation showed that limited dietary variety, consumption of disliked foods, and reduced meal size were each associated with significant changes in microbial compositions (PERMANOVA; all q < 0.05). Differential abundance analyses consistently identified Sutterella as significantly more abundant among food-insecure participants (composite model q = 0.11; component-specific models q < 0.05). Additionally, a microbial feature-based machine learning model accurately predicted food security status (AUC = 0.81), with Sutterella emerging as the top predictive feature. Conclusions: Our findings suggest that food insecurity metrics are associated with alterations in gut microbial composition. The consistent enrichment of Sutterella in food-insecure children in this study suggests the need for future mechanistic studies to explore its role in mediating the effects of food insecurity.}, }
@article {pmid41754196, year = {2026}, author = {Qiu, Y and Laguna, JC and Alegret, M and Vilà, L}, title = {A Global Perspective on Metabolic Dysfunction-Associated Steatotic Liver Disease: From Molecular Mechanisms to Therapeutic Strategy Innovation.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040679}, pmid = {41754196}, issn = {2072-6643}, support = {PID2023-146140OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; 2021SGR-00345//Generalitat de Catalunya/ ; 202406910009//China Scholarship Council/ ; }, abstract = {Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent global health issue driven by metabolic syndrome, with cardiovascular disease being the leading cause of mortality. This review synthesizes current knowledge on its multifactorial pathogenesis, the impact of sexual dimorphism, and key experimental models. The progression of MASLD involves interconnected pathways including dysregulated de novo lipogenesis, insulin resistance, mitochondrial dysfunction, gut dysbiosis, ferroptosis, and genetic and epigenetic predispositions. These mechanisms not only promote hepatic injury but also accelerate atherosclerosis. Notably, MASLD exhibits significant sexual dimorphism, influenced by physiological differences, sex hormones, genetic factors, and the microbiome. The study of these complex processes relies mostly on dietary-induced animal models, particularly in rats, which effectively recapitulate features of the human disease. Given the multifaceted nature of MASLD, the therapeutic focus is shifting from monotherapies to combination or dual-target strategies. To enable this transition, refinement of preclinical models is essential to better understand and target this complex disorder.}, }
@article {pmid41754185, year = {2026}, author = {Alessa, H and Quinn, ME and Alhomidan, L and Ross, C and Kainadas, S and Brownson, E and MacDonald, J and Seenan, JP and Nichols, B and Koutsos, A and Gerasimidis, K}, title = {In Vitro Effects of Twelve Food Additives on Gut Microbiome and Its Fibre Fermentation Capacity in Adults with Crohn's Disease in Remission and Healthy Controls.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040668}, pmid = {41754185}, issn = {2072-6643}, support = {N/A//The Ministry of Education in Saudi Arabia, and Imam Abdulrahman Bin Faisal University in Dammam, Saudi Arabia, funded Hanoof Alessa's PhD/ ; }, abstract = {Background/Objectives: Animal studies have shown that food additives may adversely affect the gut microbiome. However, the effect of food additives on the microbiome in adults with Crohn's disease (CD) remains less explored. This study investigated the impact of food additives on gut microbiome and fibre fermentation capacity in adults with CD and healthy controls (HCs) using in vitro faecal fermentations. Methods: Faeces from 6 HCs and 6 patients with CD in clinical remission (Harvey Bradshaw Index < 5) were used for in vitro fermentation of a fibre mix with one of 12 food additives (calcium propionate, carboxymethylcellulose, carrageenan kappa, cinnamaldehyde, maltodextrin, polysorbate-80, potassium sorbate, sodium benzoate, sodium sulphite, titanium dioxide, turmeric, and xanthan gum). Short-chain fatty acids (SCFAs) were measured using gas chromatography, the microbiome was profiled with 16S rRNA amplicon sequencing and total bacterial load was measured with qPCR. Results: Maltodextrin increased acetate production in both groups. In HCs, turmeric increased acetate and butyrate production, sodium sulphite reduced acetate production, and maltodextrin reduced butyrate production. Microbiome Shannon α-diversity increased with titanium dioxide (both groups), and with carrageenan kappa only in patients with CD. In both groups, the addition of maltodextrin and polysorbate-80 induced significant shifts in microbiome structure (β-diversity). Significant shifts were seen with maltodextrin (HC: R[2] = 6.8%, p = 0.001; CD: R[2] = 5.1%, p = 0.004) and sodium sulphite (HC: R[2] = 6.9%, p = 0.001). Maltodextrin significantly decreased the estimated absolute abundance of Escherichia-Shigella in patients CD; sodium benzoate, potassium sorbate, and calcium propionate did so in HCs. Faecalibacterium decreased in the presence of polysorbate-80 in the HC and CD groups, as well as in the presence of maltodextrin in the CD group. Total bacterial load decreased with polysorbate-80, potassium sorbate, maltodextrin and calcium propionate in both groups. Xanthan gum decreased total bacterial load in HCs. Conclusion: Certain food additives significantly affected fibre fermentation capacity and microbiome structure, with only modest differences observed according to participants' health status.}, }
@article {pmid41754156, year = {2026}, author = {Carvalho, PA and Paciência, I and Moreira, A and de Castro Mendes, F}, title = {Air Pollution, Asthma and Diet: From Mechanisms to Prevention Strategies.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040639}, pmid = {41754156}, issn = {2072-6643}, abstract = {BACKGROUND/OBJECTIVES: Air pollution is a major environmental determinant of asthma morbidity and lung function impairment across the life course. Both outdoor and indoor exposures contribute to asthma development and exacerbations, impaired lung function growth, and accelerated decline, with heightened susceptibility during pregnancy and childhood. In this narrative review, we aimed to: (i) synthesize evidence on outdoor and indoor air pollution in asthma and lung function decline; (ii) describe key modulators of pollution-related risk; (iii) evaluate diet and supplementation as effect modifiers; and (iv) outline strategies and recommendations to mitigate pollution-related asthma burden.<br><br>METHODS: A narrative synthesis was conducted based on a comprehensive PubMed literature search through 2025, integrating evidence from observational and interventional studies evaluating habitual diet and nutritional supplementation as potential modifiers of the respiratory effects of indoor and outdoor air pollution.<br><br>RESULTS: We synthesized human observational and interventional studies associating outdoor and indoor air pollution with asthma and lung function outcomes, highlighted major susceptibility modulators and mechanistic pathways, and appraised emerging evidence that habitual diet and nutritional supplementation might modify pollutant-related respiratory effects. Mechanistic evidence supported dietary modulation through redox buffering, epithelial-immune pathways, lipid-mediated inflammatory balance, and microbiome-immune crosstalk. However, human evidence remained heterogeneous across pollutants, settings, dietary metrics, and endpoints.<br><br>CONCLUSIONS: Emissions reduction at source remained the cornerstone of prevention. Effective mitigation should be multi-level and equity-focused, combining structural air-quality improvements with pollution-aware asthma care and feasible household practices. Diet should be framed as a supportive, food-first resilience strategy, improving overall diet quality, fat quality, and fiber intake rather than a substitute for emissions reduction or guideline-based asthma management.}, }
@article {pmid41754155, year = {2026}, author = {He, J and Shan, L and Yu, L and Yu, L and Jiang, X and Shen, Y and Du, Z and Yu, R and Zhao, C and Du, X and Wang, H and Yang, R and Fang, C}, title = {Structural Insights and Metabolic Profiles of Oxidized Green Coffee Extract, and Its Impact on Obesity and Gut Microbiota in High-Fat Diet-Fed Mice.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040638}, pmid = {41754155}, issn = {2072-6643}, support = {Yunnan Internstion Joint Laboratory of Green Health Food (China &amp; Thailand) (202203AP140011)//Chongye Fang/ ; }, abstract = {Background: Obesity is a severe chronic disease impacting health, closely linked to intestinal microbiota. Gut microbiome significantly contributes to obesity and metabolic issues. This study aims to explore the structural characterization of two coffee extracts and their effects on gut microbiota disturbances caused by a high-fat diet (HFD). Methods: Male C57BL/6J mice were divided into four groups-normal diet (ND), high-fat diet (HFD), HFD supplemented with unroasted coffee extract (UC), and HFD supplemented with oxidized green coffee extract (GCE). Results: Structural characterization revealed that both extracts are polymeric phenolic compounds rich in hydroxyl and carboxyl groups. Full-target metabolomic analysis revealed significant metabolic differences between the extracts, with 499 differential metabolites identified: a total of 247 metabolites were upregulated and 252 were downregulated in GCE compared to UC. Supplementation with GCE reduced body weight gain and adipose tissue accumulation, improved dyslipidemia and insulin sensitivity, and enhanced hepatic antioxidant capacity in high-fat model mice. Gut microbial analysis showed that GCE significantly (p < 0.05) increased the growth of beneficial bacteria such as Prevotella, Butyricimonas, and Parabacteroides. Conclusions: Oxidized green coffee extract has the effect of lowering lipids and increasing intestinal beneficial bacteria.}, }
@article {pmid41754142, year = {2026}, author = {Moitra, P and Madan, J and Shah, K and Mandavkar, P and Joshi, R and Kalita, S and Udipi, SA}, title = {Almond Supplementation Improves Acne Lesions and Skin Microbial Diversity in Adults with Mild to Moderate Acne Vulgaris.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040625}, pmid = {41754142}, issn = {2072-6643}, support = {SH-22-Udipi-NR-01//Almond Board of California/ ; }, abstract = {OBJECTIVES: This randomized, controlled, parallel-group study was conducted to evaluate the effectiveness of daily almond consumption on acne lesion counts, skin hydration, sebum production, and skin microflora composition in 18-35-year-old young adults with acne vulgaris in Mumbai, India.<br><br>METHODS: A defined amount of whole, unsalted almonds with skin (60 g) was provided to the experimental group (n = 36). The control group (n = 38) received isocaloric cereal-pulse-based snack varieties. The primary endpoints were changes in inflammatory, non-inflammatory, and total acne lesion counts after 20 weeks of supplementation. Secondary endpoints included changes in facial sebum, hydration levels, skin morphology and microflora, and selected biochemical parameters.<br><br>RESULTS: At week 20, the almond group showed greater reductions in total lesion counts (-22.2% vs. -9.8%), inflammatory lesion counts (-8.3% vs. +12%), and non-inflammatory lesion counts (-26.1% vs. -20.4%) than controls. Objective lesion volume, area, and height measures for both single and clustered acne decreased in the almond group (p &#x2264; 0.001). Microbial diversity increased, with the Shannon index (2.6 to 3.4 (p = 0.039) and the Chao1 richness index (266.9 &#x2192; 835.2; p < 0.001) showing improvements at endline. Moreover, significant post-intervention changes in the psychosocial outcomes, such as the acne-related quality of life scores (p < 0.001) and anxiety symptoms (p = 0.016), were observed in the almond group.<br><br>CONCLUSIONS: Daily almond consumption reduced acne lesion count and improved skin microbial diversity and acne-specific quality of life, highlighting its potential to complement standard acne treatments and support skin health.}, }
@article {pmid41754141, year = {2026}, author = {Kou, R and Pan, C and Xing, X and Wang, J and Morrin, ST and Buck, RH and Li, X and Mao, Y and Wang, S}, title = {Long-Term Associations of Early-Life Human Milk Oligosaccharide Intake with Allergic Disease Development and Gut Microbiota Profiles in 5-Year-Old Children.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040624}, pmid = {41754141}, issn = {2072-6643}, abstract = {Background: Based on our extensive cohort study, the Maternal Nutrition and Infant Investigation (MUAI), this research investigated the associations between human milk oligosaccharide (HMO) intake during the postnatal period and allergic disease development and gut microbiome composition in early childhood through long-term follow-up. Methods: Human breast milk (HBM) samples at five lactation stages and fecal samples of infants and young children were collected. Children aged 5 years included in this study were categorized into allergic and non-allergic groups via standardized allergen testing. Results: The findings indicated that higher HMO intake levels across five distinct lactation periods may be linked to a reduced incidence of allergies in children. The consumption of six major structurally representative HMOs was significantly associated with alterations in the gut microbiota profiles of young children. Moreover, there were notable differences in gut microbiota composition between allergic and non-allergic children. Specifically, beneficial bacteria such as Bifidobacterium, Akkermansia, and Ruminococcus were significantly enriched, in addition to the levels of metabolite propionic acid, a beneficial short-chain fatty acid, which were notably higher in the non-allergic group. To further validate the relationship between Bifidobacterium abundance and early HMO intake, the analysis revealed that a differential strain biomarker, Bifidobacterium adolescentis (B. adolescentis), exhibited significant correlations with specific HMOs at different lactation stages, particularly showing a strong positive correlation with 2'-fucosyllactose (2'-FL) content. Conclusions: These findings suggest that early-life HMO intake is associated with long-term differences in allergic outcomes, potentially through modulation of gut microbiota composition, particularly the enrichment of B. adolescentis.}, }
@article {pmid41754137, year = {2026}, author = {Guo, Y and Wang, Q and Guo, H and Zhang, H and Wu, L and Li, X and Bian, X and Li, J and Ma, R}, title = {From Microbiota to Defense: The Preventive Effect and Mechanism of Total Flavonoids from Sea Buckthorn Leaves in DSS-Induced Colitis.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040620}, pmid = {41754137}, issn = {2072-6643}, support = {zyytd2024038//the Shanxi Health Committee/ ; 202203021221259//the Natural Science Foundation of Shanxi Province/ ; }, abstract = {OBJECTIVES: The main purpose of this study was to evaluate the potential preventive effect of Total Flavonoids from Sea Buckthorn Leaves (Fla) on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice from an integrated perspective of "gut microbiota-host interaction," and to elucidate its regulatory mechanism within the microbiota-metabolite-barrier-immune axis.<br><br>METHODS: A DSS-induced UC mouse model was established, and mice were randomly assigned into normal control, model, mesalazine, and Fla low, middle, and high-dose groups. Disease severity, colonic barrier integrity, inflammatory cytokines, gut microbiota composition, and short-chain fatty acid levels were evaluated using histopathological, molecular biological, and metabolomic analyses.<br><br>RESULT: Fla significantly ameliorated colonic damage and other pathological symptoms. It enhanced intestinal barrier integrity by upregulating ZO-1, E-cadherin, and MUC2 expression and suppressed inflammation by reducing TNF-&#x3b1; and IL-6 levels. Furthermore, Fla reshaped gut microbiota, increasing beneficial Akkermansia abundance, and elevated short-chain fatty acid (SCFA) production, with the most pronounced effects observed at the middle dose.<br><br>CONCLUSIONS: In summary, in this preventive model, Fla synergistically enhances intestinal barrier function and suppresses excessive local inflammatory responses by reshaping the gut microbiota and promoting SCFA production, ultimately alleviating UC. This study provides scientific evidence for the high-value utilization of sea buckthorn leaves (a by-product) and offers new insights for developing microbiome-based preventive strategies for UC.}, }
@article {pmid41754113, year = {2026}, author = {Kang, S and Sim, H and O'Keeffe, S and Park, JO and Seo, W and Koh, JS and Lee, MW and Song, IC and Lee, HJ and Jo, DY and Kang, YE and Yi, HS and Ryu, H}, title = {Stage-Dependent Metabolic Responses to Oral Nutritional Supplementation in Cancer Cachexia: A Single-Arm Pilot Study.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040597}, pmid = {41754113}, issn = {2072-6643}, abstract = {BACKGROUND/OBJECTIVES: Cancer cachexia is a multifactorial syndrome characterized by involuntary weight loss and muscle wasting, leading to impaired quality of life and poor clinical outcomes. Although oral nutritional supplements (ONS) are recommended to support inadequate oral intake during chemotherapy, their effects on underlying metabolic alterations and gut microbiome composition, particularly across different stages of cachexia remain unclear. This single-arm pilot study aimed to evaluate the feasibility and metabolic effects of an 8-week ONS intervention in patients with cancer cachexia undergoing chemotherapy.<br><br>METHODS: This study was conducted at the Chungnam National University Hospital, Daejeon, Republic of Korea between January 2023 and October 2023. The primary endpoints were feasibility outcomes, including adherence, tolerability, attrition rate, and ONS-related adverse events. Secondary outcomes included body composition, physical performance, biochemical markers, quality of life, plasma GDF-15 levels, serum metabolomics, and gut microbiome composition. Assessment of secondary outcomes and multi-omics profiling was performed at baseline and after 8 weeks. Patients were stratified into severe and non-severe cachexia groups and analyzed.<br><br>RESULTS: A total of 10 patients (median age 65 years, range 42-76) participated. Primary cancer types included cholangiocarcinoma (n = 4), colorectal (n = 4), and gallbladder cancer (n = 2). Adherence was 82%, with excellent tolerability and no ONS-related adverse events. Body composition, quality of life, and gut microbiome showed no significant changes. Hand-grip strength and walking-speed were slightly improved after 8 weeks intervention (p = 0.014 for hand-grip strength; p = 0.021 for walking-speed, Wilcoxon signed-rank test) in overall cohort. Metabolomics identified 10 metabolites, predominantly fatty acids, with significant between-group differential responses (p < 0.05, Mann-Whitney U test). Non-severe cachexia patients showed reductions in circulating fatty acids following ONS, consistent with attenuated lipolysis and reduced endogenous fat mobilization, whereas severe cachexia patients demonstrated increases, suggesting limited metabolic responsiveness to nutritional intervention. Fatty acid metabolism emerged as the predominant discriminatory pathway.<br><br>CONCLUSIONS: This study showed the feasibility of integrating ONS with multi-omics profiling. Our findings suggest that metabolic alterations might precede clinically detectable changes, potentially providing a rationale for early intervention. Specifically, certain fatty acids were identified as candidate biomarkers that warrant further validation in larger cohorts.}, }
@article {pmid41754110, year = {2026}, author = {Singh, N and Hosein, E and Virkud, YV and Keet, C and Kulis, M}, title = {The Gut Microbiome in the IgE-Mediated Food-Allergic Patient-A Narrative Review.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040593}, pmid = {41754110}, issn = {2072-6643}, abstract = {Food allergies (FA) are a major public health concern in both children and adults. Immunoglobulin E (IgE)-mediated FA is characterized by allergic reactions driven by allergen-specific IgE and the subsequent degranulation of mast cells and basophils. Current FA management primarily involves avoidance of allergen-containing food, and more recently, therapies such as oral immunotherapy (OIT), sublingual immunotherapy (SLIT), and the anti-IgE biologic omalizumab. However, these interventions are not curative. The gut microbiome has been implicated in the development and regulation of oral tolerance to food antigens. This narrative review explores the role of probiotics, fecal microbiota transplantation (FMT), dietary interventions, and the interaction between the microbiome and OIT as potential strategies to manage established FA. We also explore barriers to their proliferation as part of regular clinical care. We conclude that future research should (1) address how the microbiome interacts with immunotherapies other than OIT, (2) explore the role of novel microbiome-based treatments like FMT as potential adjuvants to existing food allergy therapeutics, and (3) focus on developing standardized protocols and endpoints for microbiome-based therapeutics.}, }
@article {pmid41754097, year = {2026}, author = {Hansen, B and Alvanou, E and Pavlou, MAS and Wilmes, P and Schneider, JG}, title = {Fasting and Nutrition as Promising Treatment Strategies for Women with Rheumatoid Arthritis in Transitional Hormonal Stages.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040580}, pmid = {41754097}, issn = {2072-6643}, support = {PRIDE/11823097//Luxembourg National Research Fund/ ; }, abstract = {Rheumatoid arthritis (RA) is a systemic and chronic autoimmune disease affecting about 1% of the global population, with a higher prevalence in women. Its treatment has been improved greatly over the past 30 years but there is no definitive cure available, and another unmet need exists for transitional hormonal stages such as pregnancy or menopause, which spurs the need to research new therapy options. In recent years, dietary interventions, particularly fasting and plant-based nutrition, have gained attention for their potential to alleviate RA symptoms. Fasting has been shown to reduce systemic inflammation, promote autophagy, and modulate immune cell activity, possibly leading to decreased joint pain and swelling. Nutritional strategies, such as anti-inflammatory and plant-based diets, have been shown to impact the gut microbiome and potentially support weight management, improve metabolic health, and reduce oxidative stress, all of which might contribute to better RA disease outcomes. Although the precise mechanisms remain under investigation, these approaches offer promising complementary strategies for enhancing RA management and improving patients' quality of life. This review explores the preventive and therapeutic potential of fasting and nutrition in RA, and their possible application in the context of hormonal fluctuations and transitional stages during a women's life.}, }
@article {pmid41754082, year = {2026}, author = {Smółka, L and Strugała, M and Blady, K and Pomianowski, B and Kursa, K and Stanek, A}, title = {Pathogenetic Gut Microbiota in Aortic Diseases: Evidence and Mechanisms Across Aneurysm, Dissection, and Inflammatory Aortopathies.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040565}, pmid = {41754082}, issn = {2072-6643}, abstract = {Aortic diseases, including abdominal aortic aneurysm (AAA), thoracic aortic aneurysm (TAA), aortic dissection (AD), and Takayasu arteritis (TAK), are characterized by vascular remodeling and chronic immune-inflammatory activation, with AD often representing an acute complication of long-standing aortic wall vulnerability. Increasing evidence suggests that gut dysbiosis, impaired intestinal barrier integrity, and microbiota-derived metabolites may contribute to aortic wall injury. We synthesized current evidence linking the gut microbiome to aortic diseases and explored potential translational implications. PubMed, Scopus, and Web of Science were searched for microbiome-related studies on AAA, TAA, AD, and TAK published up to December 2025. Human observational and interventional studies were integrated with relevant experimental research. The strongest evidence was identified for AAA, where multiple cohorts report gut dysbiosis and reduced microbial diversity. Translational studies have detected bacterial DNA and microbial products in blood, aneurysm wall, or intraluminal thrombus, consistent with barrier-related microbial signaling and vascular inflammation, although these low-biomass findings do not establish microbial viability or causality. Microbiota-derived mediators-including trimethylamine-N-oxide, lipopolysaccharides, short-chain fatty acids, and bile acid derivatives-interact with pathways involved in cytokine signaling, oxidative stress, innate immune activation, and extracellular matrix degradation. Evidence for TAA and AD remains limited and suggests mainly modifier effects, whereas early studies in TAK indicate disease-associated microbiome and metabolite alterations. Mendelian randomization analyses have explored genetically proxied microbiome-AAA associations; however, results are heterogeneous, and causal inference remains provisional. Overall, the gut microbiome emerges as a plausible modifier of aortic disease, with the greatest translational relevance in AAA, highlighting the need for longitudinal multi-compartment studies and targeted interventions with aortic endpoints.}, }
@article {pmid41754081, year = {2026}, author = {Grammatiki, M and Tsekmekidou, X and Koufakis, T and Kotsa, K}, title = {Nutritional Interventions in Type 1 Diabetes: Boosting Residual GLP-1 Responses-Is It an Option?.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040564}, pmid = {41754081}, issn = {2072-6643}, abstract = {Type 1 diabetes (T1D) is characterized by autoimmune beta-cell destruction and lifelong insulin dependence, yet early-stage disease (Stages 1-2) retains residual beta-cell function that may still respond to incretin signaling. Incretin hormones-mainly glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP)-enhance postprandial insulin secretion and suppress glucagon, and GLP-1 also exhibits beta-cell protective effects in preclinical models. Although the incretin effect is markedly reduced in established T1D, intestinal GLP-1 secretion is largely preserved, creating a mechanistic rationale for strategies that increase endogenous GLP-1 during the "residual function" window. This narrative review summarizes dietary and lifestyle interventions that may enhance endogenous GLP-1 responses and discusses their potential role as adjuncts to insulin therapy, particularly when combined with emerging beta-cell-preserving immunomodulatory approaches that may prolong early disease stages. Mechanistically, high-fiber diets may increase GLP-1 via microbiota-derived short-chain fatty acids acting on L-cell receptors; low-glycemic index carbohydrates may favor distal nutrient delivery and a GLP-1-dominant incretin profile; and Mediterranean dietary patterns may promote GLP-1 secretion through unsaturated fatty acids, fiber, and polyphenols, including potential DPP-4-modulating effects. This narrative review examines nutrition and lifestyle interventions modulating residual incretins to elongate early T1D stages and enhance glycemic control as insulin adjuncts, per Nutrients' Special Issue. Available evidence is strongest in non-T1D populations, with limited T1D-specific trials, highlighting the need for stage-targeted studies incorporating GLP-1 dynamics, C-peptide, glycemic variability, and microbiome outcomes.}, }
@article {pmid41754080, year = {2026}, author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F}, title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040563}, pmid = {41754080}, issn = {2072-6643}, support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; }, abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.}, }
@article {pmid41754077, year = {2026}, author = {Ashkanani, G and Rob, M and Yousef, M and Ashkanani, A and Al-Najjar, YA and Laws, S and Chaari, A}, title = {The Effects of Microbiome Modulating Therapies on Inflammatory Markers in Autoimmune Disease: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/nu18040560}, pmid = {41754077}, issn = {2072-6643}, abstract = {BACKGROUND: Autoimmune diseases (ADs) are a growing global health burden, driven by chronic inflammation and immune dysregulation. The gut-immune axis plays a central role in their pathogenesis, with dysbiosis linked to several conditions. This has prompted investigation into nutraceuticals such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation as adjunctive therapies.<br><br>METHODS: We conducted a systematic review and meta-analysis following PRISMA guidelines, searching PubMed, Embase, and Web of Science for randomized controlled trials evaluating these interventions in autoimmune diseases.<br><br>RESULTS: Twenty-eight randomized control trials (RCTs) involving 2002 patients across 11 countries met inclusion criteria. Across the included RCTs, pooled analyses demonstrated significant reductions in c-reactive protein (CRP) (SMD -0.67, 95% CI -1.00 to -0.33; I[2] = 80.8%) and Tumor necrosis factor-alpha (TNF-&#x3b1;) (SMD -1.81, 95% CI -2.67 to -0.94; I[2] = 96%), a significant increase in Interleukin-10 (IL-10) (SMD 2.65, 95% CI 0.64 to 4.66; I[2] = 98%), and no overall significant effect on Interleukin-6 (IL-6) (SMD -0.89, 95% CI -1.99 to 0.22; p = 0.12). The strongest evidence of benefit was observed in rheumatoid arthritis, multiple sclerosis, and inflammatory bowel disease. Pooled effects are limited by extreme between-study heterogeneity (I[2] 80-98%), leaving interpretation as exploratory rather than definitive. More limited or inconsistent findings were reported for systemic lupus erythematosus, hypothyroidism, axial spondylarthritis, and juvenile idiopathic arthritis. Heterogeneity in study design, probiotic strain selection, dosage, and treatment duration limited comparability across trials.<br><br>CONCLUSIONS: Overall, microbiome-targeted nutraceuticals appear promising for attenuating systemic inflammation in select autoimmune conditions, but results remain mixed. Larger, rigorously designed RCTs with standardized endpoints are needed to clarify efficacy, identify optimal formulations, and define patient populations most likely to benefit.}, }
@article {pmid41753774, year = {2026}, author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B}, title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020488}, pmid = {41753774}, issn = {2076-2607}, abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.}, }
@article {pmid41753768, year = {2026}, author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K}, title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020482}, pmid = {41753768}, issn = {2076-2607}, support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; }, abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.}, }
@article {pmid41753757, year = {2026}, author = {Zhou, J and Zhu, B and Bing, Z and Wang, T and Zhao, Y}, title = {The Gut-Liver Axis in MASLD: From Host-Microbiome Crosstalk to Precision Therapeutics.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020471}, pmid = {41753757}, issn = {2076-2607}, support = {T2341015//National Natural Science Foundation of China/ ; 32271182//National Natural Science Foundation of China/ ; 8257103456//National Natural Science Foundation of China/ ; 2024300382//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is an emerging global health challenge with limited effective therapeutic options. The gut microbiota, at the interface of host metabolism and immunity, acts as a critical disease modifier via the gut-liver axis. This review goes beyond cataloging its associations and synthesizes how intrinsic and extrinsic factors sculpt a permissive microbial ecosystem. These factors likely converge to establish a state of "metabolic dysbiosis", fueling MASLD progression through three core mechanisms: compromised intestinal barrier integrity with immune activation, dysregulation of key microbial metabolite axes, and direct hepatic insult from gut-derived products. Next, we evaluate the translational landscape through a mechanism-informed precision framework, with an emphasis on how microbiome-based interventions could be aligned with non-invasive biomarkers increasingly used for MASLD risk stratification and treatment monitoring. By integrating evidence across scales, this review aims to frame a roadmap from microbiome correlations to causality-driven, personalized therapeutic strategies for MASLD.}, }
@article {pmid41753756, year = {2026}, author = {Cano, RJ and García Menéndez, G}, title = {Why Clinical Trials of Microbiome-Targeted Interventions Often Fail to Support Health Claims: A Commentary on Probiotics and Translational Design.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020470}, pmid = {41753756}, issn = {2076-2607}, abstract = {The rapid expansion of probiotics and other microbiome-modulating interventions has been accompanied by a growing number of human clinical trials. However, despite frequent reports of statistically significant microbiome changes, relatively few studies generate evidence that convincingly supports health claims or translates into reproducible, clinically meaningful outcomes. This gap is often attributed to the inherent complexity and inter-individual variability of the gut microbiome; however, recurring shortcomings in trial design and interpretation likely play an equally important role. In this Commentary, we examine common failure modes that weaken the clinical validation of microbiome-mediated interventions. These include overreliance on descriptive microbiome metrics (e.g., alpha diversity and taxonomic shifts) as surrogate endpoints, misalignment between prespecified endpoints and the claims ultimately advanced, and excessive dependence on symptom-only outcomes in settings characterized by substantial placebo responsiveness. We further highlight how inadequate control of key confounders-particularly diet, antibiotic exposure, and concomitant medications-combined with endpoint overload and underpowered study designs, can obscure true biological signal and increase the risk of irreproducible findings. We argue that stronger evidence emerges when the microbiome is treated as a mechanistic mediator rather than a clinical endpoint. Trials are most interpretable when intended claims are prospectively defined, linked to explicit biological mechanisms, and evaluated using a hierarchy of endpoints that prioritizes host-relevant outcomes and objective biomarkers, with microbiome measures integrated to support mechanistic plausibility. Adoption of staged development pathways disciplined statistical planning, and transparent management of confounding variables can further improve reproducibility and clinical relevance.}, }
@article {pmid41753753, year = {2026}, author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J}, title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020467}, pmid = {41753753}, issn = {2076-2607}, abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.}, }
@article {pmid41753743, year = {2026}, author = {Zhao, P and Shi, B and Zhou, X and Zhao, Z and Hu, J and Zhang, X}, title = {Dietary Energy Levels Impact on Skin Microbiota and Metabolites of Yaks.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020457}, pmid = {41753743}, issn = {2076-2607}, support = {32302720//the National Natural Science Foundation of China/ ; GAU-KYQD-2022-18//the Gansu Agricultural University Public Recruitment Doctoral Research Start-up Fund/ ; }, abstract = {The study aims to investigate the skin microbiome composition of Yaks and the effects of different dietary nutrient levels on the skin microbiome diversity and metabolites. A total of 19 healthy Tianzhu White Yaks at two age stages (2.5 and 4.5 years old) were selected and fed either a high-energy diet (n = 9) or a low-energy diet (n = 10). After 90 days of feeding, skin microbiota and skin tissue metabolites were detected using 16S rRNA sequencing and LC-MS/MS untargeted metabolomics, respectively. The results showed: (1) the phyla Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidetes exhibited relatively high abundances in the skin of yaks, and the total abundance of these four phyla reached as high as 99.3%. Alpha diversity analysis indicated that the alpha diversity index of yak skin microbiota was significantly higher (p < 0.05) in the low-energy nutritional level group than in the high-energy nutritional level group in yaks of both 2.5 and 4.5 years of age. Principal coordinate analysis (PCoA) revealed a distinct separation of all skin microbiota samples into two clusters: the high-energy (H) and low-energy (L) groups. (2) A total of 114 differentially expressed metabolites were screened across both groups, significantly enriched (p < 0.05) in pathways including synaptic vesicle trafficking and glycerophospholipid metabolism; (3) Correlation analysis between microbiota and metabolites revealed significant positive correlations (p < 0.01) between Psychrobacter and choline, and between Corynebacterium and palmitic acid. In conclusion, A low-energy diet increases skin microbial diversity, which is beneficial for maintaining community stability; In contrast, a high-energy diet enriches bacterial genera such as Corynebacterium and Psychrobacter, enhancing functions related to antibacterial activity and barrier protection.}, }
@article {pmid41753733, year = {2026}, author = {Ihuț, A and Răducu, C and Ranta, M and Andrecan, A and Uiuiu, P}, title = {Gut Microbiome Health in Farm Animals and Fish: Implications for Human Health and the Risk of Gastrointestinal Diseases.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020447}, pmid = {41753733}, issn = {2076-2607}, abstract = {The gut microbiome is central to immune, metabolic, and gastrointestinal health across species. Dysbiosis disrupts microbial communities and is linked to inflammatory bowel disease, celiac disease, and other immune-mediated gastrointestinal disorders. This review addresses the central question of how diet- and environment-driven gut dysbiosis in farm animals and fish is transmitted through the food chain to influence human gastrointestinal health within a One Health framework. This review synthesizes recent evidence within the One Health framework, focusing on how diet- and environment-induced dysbiosis in farm animals and fish can influence human gastrointestinal health via the food chain. We highlight mechanisms of immune modulation, alterations in food products, and the risks of pathogen transmission and antimicrobial resistance. An important limitation of the current body of evidence is the lack of studies that comprehensively trace the proposed axis from animal gut dysbiosis to human health outcomes. Emerging interventions, including precision nutrition, probiotics, and microbiota-targeted therapies, show potential for restoring microbial balance, though translating these findings into clinical practice remains challenging. By integrating human, veterinary, and environmental perspectives, this work proposes a novel cross-species microbiome-diet-immune framework to guide future research and interventions, advancing One Health strategies for disease prevention, antimicrobial resistance mitigation, and sustainable gastrointestinal health.}, }
@article {pmid41753726, year = {2026}, author = {Kundnani, NR and Sharma, A and Levai, MC and Marin-Bancila, L and Georgescu, D and Botas, L and Chiriac, SD and Valcovici, M and Popa, MD}, title = {Early-Life β-Lactam Exposure and the Developing Microbiome: Clinical Relevance and Controversies.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020440}, pmid = {41753726}, issn = {2076-2607}, abstract = {Antibiotic-induced dysbiosis has been increasingly implicated in a range of pediatric outcomes, yet the concept remains variably defined and often inconsistently applied. The purpose of this review is to provide an overview and critical evaluation of the available data regarding the effects of early-life exposure to β-lactam antibiotics on the developing microbiome. We conducted a narrative review of experimental and epidemiological studies examining β-lactam exposure during pregnancy, the perinatal period, and early childhood was conducted. β-lactams induce reproducible alterations in microbial composition, diversity, and metabolic function, including decreases in Bifidobacterium and Lactobacillus and a relative increase in Enterobacteriaceae and other facultative anaerobes, especially in early life. Reduced microbial diversity and changed short-chain fatty acid-producing taxa often accompany these compositional changes. However, associations with immune, metabolic, and neurodevelopmental outcomes are heterogeneous and frequently confounded by indication host-related factors. Evidence for causality in humans remains limited despite strong mechanistic support from animal models. Current data support cautious interpretation, even though β-lactam-associated microbiome perturbations may contribute to disease susceptibility during vulnerable developmental windows. While mechanistic and longitudinal evidence continues to develop, antibiotic stewardship focused on appropriate indication and duration is still crucial.}, }
@article {pmid41753701, year = {2026}, author = {Zhao, J and Du, F and Zhu, J and Liu, G and Zhou, X and Zhang, Y and Rong, X}, title = {Bacterial Community Structure and FEAST Source Tracking of Endophytes in Vernonia anthelmintica (L.) Willd. from Southern Xinjiang, China.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020414}, pmid = {41753701}, issn = {2076-2607}, abstract = {Using 16S rRNA gene amplicon sequencing and FEAST microbial source tracking, this study characterized the bacterial communities in tissues (roots, stems, leaves, seeds) and associated soils (rhizosphere and bulk soil) of Vernonia anthelmintica, an important Uyghur medicinal plant endemic to arid southern Xinjiang. We found significantly higher bacterial diversity in soil than in plant tissues, with Pseudomonadota-dominated plant-associated communities and Actinobacteria co-dominating in soils. Bacterial community structures varied across plant compartments, with soil communities exhibiting greater stability and broader niche breadth. Critically, FEAST source tracking revealed that rhizosphere soil contributed 23.8%, 13.4%, 17.9%, and 10.8% of the bacterial communities in roots, stems, leaves, and seeds, respectively, identifying soil as the primary source of endophytic bacteria. These findings highlight the pivotal role of arid-region soil microbial diversity in shaping the unique endophytic microbiome of V. anthelmintica, providing a scientific basis for conserving soil microbial health to support its standardized cultivation and sustainable utilization in Uyghur medicine.}, }
@article {pmid41753691, year = {2026}, author = {Liu, B and Lu, T and Yao, T and Zhao, X and Yang, L}, title = {Developmental Stage-Driven Niche Differentiation and Assembly of Rhizosphere and Endophytic Bacterial Communities in Helianthus annuus Under Saline-Alkaline Stress.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020404}, pmid = {41753691}, issn = {2076-2607}, support = {2024LHMS04006//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; BR251306//Inner Mongolia Autonomous Region Direct University Basic Research Grant/ ; RZ2400001775//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; U23A2054//Joint Funds of the National Natural Science Foundation of China/ ; 2025KYPT0100; 2023YFHH0028//the Science and Technology Program of Inner Mongolia Autonomous Region/ ; 2025//Ecological Restoration of Degraded Grassland and High-Quality Development of Grassland Animal Husbandry/ ; }, abstract = {Soil salinization severely constrains agricultural productivity, while root-associated microbiota contribute to plant adaptation to saline-alkali stress. However, developmental assembly dynamics of rhizosphere and root endosphere bacterial communities remain insufficiently characterized in irrigation-driven saline-alkali agroecosystems such as the Hetao Plain of northern China. Here, Helianthus annuus plants were sampled at seedling, squaring, and flowering stages, and rhizosphere and root microbiota were analyzed using high-throughput amplicon sequencing integrated with soil physicochemical measurements, beta nearest taxon index-based community assembly inference, and co-occurrence network analysis. The rhizosphere maintained higher diversity, broader taxonomic heterogeneity, and persistently complex interaction networks, whereas the root endosphere exhibited progressive diversity reduction and compositional convergence during plant development. Developmental progression drove contrasting successional trajectories, with increasing rhizosphere complexity and endophytic convergence toward a Proteobacteria-dominated core, particularly Pseudomonas. Beta nearest taxon index analysis indicated mixed stochastic and dispersal-related processes in the rhizosphere but drift-dominated assembly in late-stage roots. Functional predictions revealed enhanced nitrogen-related metabolic potential during flowering, coinciding with enrichment and network centrality of Pseudomonas. These findings demonstrate stage-dependent spatial reorganization of sunflower root microbiomes under saline-alkali stress and provide a framework for identifying functionally relevant microbial groups for targeted microbiome-based agricultural management.}, }
@article {pmid41753678, year = {2026}, author = {Zhao, Q and Li, B and Liang, C and Wei, J and Ma, J and Qin, W}, title = {Fertility-Associated Soil Chemistry Predominantly Influence Gut Microbiota Diversity in Goitered Gazelles of the Qaidam Basin, China.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020391}, pmid = {41753678}, issn = {2076-2607}, support = {32160316//National Natural Science Foundation of China/ ; }, abstract = {This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) on samples of feces (n = 58), soil (n = 35), and water (n = 35) collected from six typical regions. We systematically revealed the mechanisms by which soil properties influence the gut microbiome of wildlife in an arid desert ecosystem based on source tracking and Multiple Regression on distance Matrices (MRM) analysis. The results showed that soil total phosphorus (TP) was significantly positively correlated with the α-diversity of gut microbiota (coefficient = 0.4/0.23/0.332; p < 0.05), while soil organic carbon (SOC) was significantly negatively correlated (coefficient = -0.44/-0.436; p < 0.05), indicating that soil nutrients indirectly predict host microbial diversity by regulating vegetation productivity and forage quality. β-diversity analysis further demonstrated that spatial heterogeneity in soil pH (coefficient = 0.3083; p < 0.05) and TP (coefficient = 0.227; p < 0.05) significantly drove the structural differentiation of gut microbial communities. Source-tracking results based on FEAST revealed significant regional differences in the proportional contribution of environmental microorganisms to the gut microbiota, with individuals in resource-poor habitats (ALK region) exhibiting higher input from soil microbes (8.0672% ± 6.9291%; p < 0.05). In conclusion, this study clarifies the ecological mechanism by which soil physicochemical properties regulate the diversity and composition of herbivore gut microbiota through a "soil-plant-food-gut microbiota" cascading pathway, providing important empirical evidence for understanding animal-microbe-environment interactions and adaptive evolution in extreme environments.}, }
@article {pmid41753674, year = {2026}, author = {Ece, G and Aktaş, A and Koyuncu Özyurt, &#xd6; and Demirbakan, H and Alışkan, HE and Sağlık, &#x130; and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T}, title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020387}, pmid = {41753674}, issn = {2076-2607}, abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.}, }
@article {pmid41753673, year = {2026}, author = {Petalas, K and Konstantinou, GN}, title = {Chronic Rhinosinusitis at the Interface of Type 2 Inflammation, Epithelial Barrier Dysfunction, and Microbiome Dysbiosis.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020386}, pmid = {41753673}, issn = {2076-2607}, abstract = {Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease of the nasal and paranasal sinus mucosa with substantial impact on quality of life. Although atopy and/or allergic rhinitis frequently coexist with CRS, often alongside type 2-skewed inflammation, the extent to which allergic mechanisms define a discrete CRS entity remains debated, in part due to inconsistent operational definitions and overlapping clinical phenotypes. In parallel, culture-independent sequencing studies have reframed CRS as a disorder of host-microbe interactions, with many cohorts reporting reduced sinonasal microbial diversity, enrichment of potentially pathogen taxa (including Staphylococcus aureus), and biofilm-associated community states. However, causality and directionality remain uncertain. In this narrative review, we synthesize evidence at the interface of epithelial barrier dysfunction, type 2 cytokine networks (IL-4/IL-13/IL-5), and microbiome dysbiosis, highlighting where data are consistent across studies versus where findings are heterogeneous or predominantly associative. We discuss representative allergy-associated CRS prototypes such as allergic fungal rhinosinusitis and central compartment atopic disease as clinical models to interrogate these interactions, while distinguishing them from non-IgE-mediated type 2 entities such as aspirin-exacerbated respiratory disease. We also summarize current data linking atopy to sinonasal microbial signatures and discuss emerging microbiome-directed interventions (topical probiotics, bacteriophages, and microbiota transfer concepts) alongside biologics and precision anti-inflammatory therapies. Finally, we highlight key knowledge gaps, including the limited endotype-resolved and longitudinal studies, variable allergic phenotyping in microbiome research, and the need for standardized definitions and biomarker-driven stratification to clarify clinical utility and to guide mechanism-informed therapeutic trials.}, }
@article {pmid41753667, year = {2026}, author = {Li, Y and Vigil, J and Pradhan, R and Zhu, J and Libault, M}, title = {Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020380}, pmid = {41753667}, issn = {2076-2607}, support = {2414183//National Science Foundation (NSF)/ ; 2425989//National Science Foundation (NSF)/ ; 2022-67013-36144//USDA National Institute of Food and Agriculture (USDA-NIFA)/ ; }, abstract = {Understanding the intimate interactions between plants and their microbiota at the cellular level is essential for unlocking the full potential of plant holobionts in agricultural systems. Traditional bulk and microbial community-level sequencing approaches reveal broad community patterns but fail to resolve how distinct plant cell types interact with or regulate microbial colonization, as well as the diverse antagonistic and synergistic interactions and responses existing between various microbial populations. Recent advances in single-cell and spatial multi-omics have transformed our understanding of plant cell identities as well as gene regulatory programs and their dynamic regulation in response to environmental stresses and plant development. In this review, we highlight the single-cell discoveries that uncover the plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation, particularly in roots, nodules, and leaves. We further discuss how integrating transcriptomic, epigenomic, and spatial data can reconstruct multilayered interaction networks that connect plant cell-type-specific regulatory states with microbial spatial niches and inter-kingdom signaling (e.g., ligand-receptor and metabolite exchange), providing a foundation for developing new strategies to engineer crop-microbiome interactions to support sustainable agriculture. We conclude by outlining key methodological challenges and future research priorities that point toward building a fully integrated cellular interactome of the plant holobiont.}, }
@article {pmid41753654, year = {2026}, author = {Hodzhev, Y and Zhelyazkova, V and Toshkova, N and Barashkova, AS and Tsafarova, B and Panaiotov, S and Stoev, P}, title = {Evaluation of the Bacterial Diversity in the World's Deepest Cave-Veryovkina, Arabika Massif, Western Caucasus.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020368}, pmid = {41753654}, issn = {2076-2607}, support = {KP-06-N-51/9-2021//Bulgarian Science Fund/ ; BG16RFPR002-1.014-0017//Procedure BG16RFPR002-1.014 "Sustainable development of Centers of Excellence and Centers of Competence, including specific infrastructures or their associations of the NRRI", Program "Research, Innovation and Digitalization for Smart Transformation 202/ ; }, abstract = {Veryovkina Cave is the world's deepest known cave (2212 m deep). It is located in the Arabika Massif of Gagra Mountain in the Western Caucasus. Its microbiome remains unknown because of difficulties in access. Ten sediment samples were collected at vertical depths ranging from 300 m to 2204 m; they varied by substrate type, moisture content, and visitor accessibility. Total microbial DNA was isolated, and 16S ribosomal gene metabarcoding was applied for taxonomic identification. Seven samples showed reliable content, whereas three samples indicated no recoverable reads. Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant phyla in total. Depth stratification of microbiota showed that (1) shallow wet clays were dominated by Acidimicrobia and Actinobacteria; (2) mid-depth wet clays showed the highest abundance of Nitrospira, Betaproteobacteria, and Vicinamibacter; and (3) deep, dry substrates were dominated by Thermoleophilia and Rubrobacteria. Multivariate analyses showed that substrate type and moisture tended to explain more variation in microbial abundance than depth or human activity. We demonstrate the presence of distinct ecological niches within the cave ecosystem, which emphasizes the role of local conditions in shaping microbial diversity.}, }
@article {pmid41753652, year = {2026}, author = {Adeyemi, OD and Nahashon, SN}, title = {Mitigating Salmonella in Poultry Using Probiotics: Mechanisms, Challenges, and Opportunities.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020365}, pmid = {41753652}, issn = {2076-2607}, abstract = {The global poultry industry continues to face significant challenges due to Salmonella infections, which pose severe public health concerns and economic losses. Recently, the reemergence of antimicrobial resistance has led to the restriction of antibiotic use in poultry, especially as growth promoters, thus accelerating the search for sustainable alternatives. Among these, probiotics have gained attention as potential candidates for improving poultry health and mitigating Salmonella colonization in the gut. This review summarizes the key mechanisms through which probiotics exert anti-Salmonella effects, including competitive exclusion, production of antimicrobial substances, reinforcement of the intestinal barrier, and modulation of host immune responses. Commonly used probiotic strains in poultry such as Lactobacillus and Bacillus are discussed, alongside emerging candidates derived from non-poultry hosts that may offer additional functional benefits. Despite encouraging findings, the use of probiotics in poultry faces several challenges, including strain-specific efficacy, variation in results across studies, environmental influences, and regulatory limitations. Therefore, we further explore future directions that are aimed at improving probiotic application in poultry production, such as microbiome-guided strain selection, advanced delivery systems, and combination therapies. Advancing our understanding of probiotic-pathogen-host interactions will be essential for optimizing probiotic use to enhance poultry health, reduce zoonotic transmission of Salmonella, and contribute to safer and more sustainable food systems.}, }
@article {pmid41753650, year = {2026}, author = {Wang, K and White, JF and Zhu, Z and Zhang, W and Li, X and Li, S}, title = {Desert Plant Seed Endophytes: A Reservoir of Stress-Adapted Bacillus Strains for Enhancing Wheat Salinity Tolerance.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020363}, pmid = {41753650}, issn = {2076-2607}, support = {25YFFA043//Gansu Provincial Key Research and Development Program/ ; }, abstract = {Land desertification poses a major ecological challenge and threatens agricultural productivity. This study investigated the seed endophytic microbiomes of desert plants as a potential resource for mitigating salt stress in crops. Using high-throughput sequencing, we characterized the bacterial and fungal communities within seeds of 12 desert plant species. Dominant taxa included Firmicutes (particularly Bacillus), Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota. Culturable bacteria were subsequently isolated from Haloxylon ammodendron (C.A.Mey.) Bunge (HB) and Hedysarum scoparium Fisch. &amp; C.A.Mey. (HSA) seeds. These isolates were screened for plant growth-promoting (PGP) traits and tolerance to salt (NaCl) and alkali (NaHCO3). Selected strains, including the high indole-3-acetic acid (IAA)-producing Bacillus sp. HB-4, were used to inoculate wheat (Triticum aestivum L.) under 150 mM NaCl or 150 mM NaHCO3 stress. Inoculation with strain HB-4 significantly improved wheat growth under stress. This improvement was associated with increased chlorophyll and proline content, enhanced activities of the antioxidant enzymes catalase and peroxidase, and reduced levels of malondialdehyde, a marker of oxidative damage. Our results demonstrate that desert plant seeds harbor taxonomically distinct and functionally resilient endophytes. The successful application of a desert-adapted Bacillus strain to alleviate salt stress in wheat highlights the potential of such microbiomes as a novel source of inoculants for sustainable agriculture in saline-affected regions.}, }
@article {pmid41753637, year = {2026}, author = {Zhao, J and Lu, Z and Wu, J and Wang, L and Huang, J and Yang, F}, title = {Microcin C7 Prevents Cyclophosphamide-Induced Immunosuppression and Intestinal Injury by Modulating T-Cell Differentiation and Gut Microbiota Composition in Mice.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020350}, pmid = {41753637}, issn = {2076-2607}, support = {2022YFC2105003//National Key Research and Development Program of China/ ; NCTIP-XD/B05//National Center of Technology Innovation for Pigs/ ; }, abstract = {Microcin C7 (McC7) is a ribosomally synthesized antimicrobial peptide that has emerged as a promising candidate due to its dual antibacterial and immunomodulatory activities. This study evaluated the preventive effect of McC7 against cyclophosphamide (CTX)-induced immunosuppression and intestinal injury. An immunosuppression model was established by intraperitoneal CTX injection in mice, which were randomly allocated into five groups (n = 15): a negative control, a CTX model group, and three McC7 treatment groups receiving dietary McC7 at 100, 200, or 400 mg/kg both before and during CTX exposure. Body weight and feed intake were monitored throughout the study. Organ indices, serum biochemical parameters, immune and antioxidant markers, and intestinal morphology were assessed. Splenic T-cell subsets were analyzed by flow cytometry, and gut microbiota composition was evaluated by 16S rRNA sequencing. McC7 supplementation significantly attenuated the CTX-induced reduction in body weight, feed intake, and organ indices, ameliorated markers of hepatic and renal injury, and restored the splenic CD4[+]/CD8[+] T-cell ratio. McC7 enhanced intestinal mucosal barrier integrity, increased the abundance of beneficial bacteria such as Candidatus Arthromitus and ASF356, and reduced the abundance of the potentially pathogenic genus Bilophila. In conclusion, our results demonstrate that McC7 alleviates CTX-induced immunosuppression by regulating T-cell differentiation, maintaining cytokine homeostasis, and modulating gut microbial composition to support intestinal health.}, }
@article {pmid41753636, year = {2026}, author = {Ma, J and Ning, X and Li, J and Dai, S and Sun, F and Li, H and Sun, S and Ding, Y}, title = {Metabolite-Mediated Alleviation of Iron Deficiency and Growth Promotion of Malus hupehensis by Bacillus licheniformis LCDD6 in Calcareous Soil.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020349}, pmid = {41753636}, issn = {2076-2607}, support = {2022TZXD0037//Key Research and Development Program of Shandong Province/ ; }, abstract = {Calcareous soils are typically deficient in essential nutrients such as iron, phosphorus, and potassium, which frequently results in nutrient deficiency in fruit trees. Bacillus licheniformis LCDD6 markedly enhanced Malus hupehensis seedling growth and plant iron nutrition in calcareous soil. This study aimed to elucidate the mechanism underlying these beneficial effects of strain LCDD6 under iron deficiency. Transcriptomic analysis revealed that iron deficiency induced metabolic reprogramming in strain LCDD6, characterized by a significant upregulation of genes involved in the biosynthesis of the siderophore bacillibactin and plant growth hormone indoleacetic acid (IAA). Consistently, metabolomic profiling identified bacillibactin and IAA as the dominant metabolites produced under iron-deficient conditions. A 60-day pot experiment further demonstrated that the cell-free fermentation broth of strain LCDD6 significantly enhanced plant growth and rhizosphere soil enzyme activities. The crude bacillibactin extract derived from the fermentation exerted the strongest effects on plant growth and iron accumulation, whereas IAA preferentially stimulated root development and promoted plant phosphorus accumulation. Additionally, different metabolites exerted distinct and selective effects on the rhizosphere microbial community, with fungi showing stronger and more metabolite-specific responses than bacteria. The crude bacillibactin extract enriched fungal taxa, particularly Coprinellus, which showed strong positive correlations with plant growth traits and iron accumulation, while Stachybotrys, enriched under IAA treatment, was positively correlated with plant phosphorus content. Overall, strain LCDD6 promotes plant growth under iron-deficient conditions through the coordinated action of multiple metabolites, with bacillibactin as the primary contributor and IAA providing complementary effects. These findings offer mechanistic insight and a scientific basis for developing Bacillus-based biofertilizers to improve nutrient acquisition in calcareous soils.}, }
@article {pmid41753617, year = {2026}, author = {Sekar, KPC and Schmiliver, B and Pieterick, PE and Cha, T and Patel, HA and Robinson, H and Kumar, P and Wu, DT and Jones, R and Goudy, S}, title = {Harnessing Microbiome-Mediated and Macrophage-Driven Mechanisms for Oral Wound Healing.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020330}, pmid = {41753617}, issn = {2076-2607}, abstract = {Oral mucosa healing is a complex process that involves the innate wound healing system, including the coagulation cascade, extracellular matrix remodeling, immune cell responses, and fibroblast and epithelial responses, within the context of a dynamic resident microbiome. Unlike cutaneous wounds, oral wounds heal rapidly with minimal scarring despite constant exposure to diverse microbial communities, saliva, and mechanical stress. Emerging evidence highlights the critical interplay between microbiome-mediated signaling and macrophage plasticity in shaping wound outcomes, suggesting that similar mechanisms operate within the oral cavity. Inflammation is an essential component of wound repair, and its resolution is necessary to promote tissue remodeling and functional regeneration. Macrophages play a central role in this transition through phenotype switching from a pro-inflammatory (M1) to a pro-resolving, anti-inflammatory (M2) state. This review synthesizes current understanding of the oral microbiome's influence on macrophage polarization across distinct stages of oral wound healing and examines microbial-based strategies that modulate the immune response to enhance repair. Significant knowledge gaps remain, including limited clinical translation, inter-individual variability in microbiome composition, and complete mechanistic insight into host-microbe immune interaction. Addressing these challenges enables the development of precision microbiome-based therapeutics that restore microbial balance, direct macrophage-driven regeneration, and improve outcomes in oral wounds and chronic inflammatory conditions.}, }
@article {pmid41753608, year = {2026}, author = {Casais, V and Pereira, J and Garcia, E and Coelho, C and Figueira, D and Ares, A and Tiago, I and Costa, J}, title = {Functional Profiling of Kiwifruit Phyllosphere Bacteria: Copper Resistance and Biocontrol Potential as a Foundation for Microbiome-Informed Strategies.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020321}, pmid = {41753608}, issn = {2076-2607}, support = {UIDB/04004/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Associated Laboratory TERRA LA/P/0092/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Community Initiative Action 1.1 Operational Groups "I9K-InovKiwi-Development of strategies for the sustainability of the kiwifruit sector through the creation of a value-added product"//PDR2020 and co-financed by the FEADER under the Portugal 2020 Partnership Agreement/ ; IPN//Fundo de Inova&#xe7;&#xe3;o, Tecnologia e Economia Circular/ ; }, abstract = {Bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to global kiwifruit production. Copper-based bactericides remain widely used, but increasing resistance highlights the urgency of developing sustainable alternatives. Understanding the functional capabilities of phyllosphere bacteria under copper pressure is critical for designing microbiome-informed management strategies. This study provides a culture-based functional inventory of bacteria associated with Actinidia chinensis var. deliciosa leaves from Portuguese orchards under long-term copper management, aiming to identify native taxa with traits relevant to plant health and resilience. A total of 1058 isolates were recovered and grouped into 261 Random Amplification of Polymorphic DNA (RAPD) clusters, representing 58 species across 29 genera. Representative strains were screened for Plant Growth-Promoting (PGP) traits (Indole-3-acetic acid (IAA), siderophore production, phosphate solubilization, ammonia production), copper tolerance, and in vitro antagonism against Psa. Copper resistance was widespread (53.3% of isolates with MIC ≥ 0.8 mM), including the first evidence of a highly copper-resistant PSA strain in Portuguese kiwifruit orchards and an exceptionally resistant non-pathogenic strain closely related to Erwinia iniecta (MIC 2.8 mM). A subset of 25 isolates combined all four PGP traits, and several also exhibited antagonism against Psa in vitro, among them Bacillus pumilus consistently supressed pathogen growth. Notably, antagonistic and multifunctional traits co-occurred in some isolates, highlighting promising candidates for integrated biocontrol strategies. Overall, the findings reveal a functionally diverse and copper-resilient collection of cultured bacteria, offering both challenges and opportunities for microbiome-based disease management. This work establishes a robust functional basis for subsequent in planta validation and the development of sustainable, microbiome-informed approaches for Psa control.}, }
@article {pmid41753597, year = {2026}, author = {Izquierdo-Jiménez, CM and Recuero, C and Maicas, S and Del Castillo-Madrigal, I}, title = {Indigenous Olive Orchard Bacteria as Biocontrol Agents: An Integrated Culture-Dependent and Soil Microbiome Approach.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020310}, pmid = {41753597}, issn = {2076-2607}, support = {No specific grant//SEIPASA/ ; }, abstract = {Olive orchard soils are a source of microorganisms capable of inhibiting major olive pathogens. In this study, rhizobacteria were isolated and characterized based on plant growth-promoting traits, and soil 16 rRNA gene sequencing analysis was performed to analyze microbial communities at two key olive phenological stages (flowering and fruit formation). Using a culture-dependent approach, a total of 90 bacterial isolates representing distinct colony morphotypes were recovered from olive soils, with 35 during the flowering stage and 55 during the fruit formation stage, indicating a higher cultivable diversity during the latter period. We identified some bacterial strains with antagonistic activity and observed phenology-related shifts in the soil microbiome. Using differential abundance analysis, we identified bacterial taxa that were significantly enriched or depleted during olive fruit formation. Overall, this study demonstrates that olive-associated bacteria harbor antagonistic potential against olive pathogens. The use of bacteria adapted to olive agroecosystems represents a promising strategy for sustainable disease management.}, }
@article {pmid41753594, year = {2026}, author = {Zhao, M and Chen, X and Liu, W and Li, Z and Li, W and Yang, F and Guo, Z and Li, Z and Tian, Y and Zhang, W and Zhang, G and Chen, T}, title = {Bioremediation of Saline-Alkali Soil Using a Waste Biomass-Functional Microorganism Composite Amendment and Preliminary Multi-Crop Field Validation.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020304}, pmid = {41753594}, issn = {2076-2607}, support = {25JRRA173//Natural Science Foundation of Gansu Province Project/ ; 2024ZY033//Qinghai Provincial Central Government Guide Local Science and Technology Devel-739 opment Project/ ; 2024//Undergraduate Key Teaching Reform Project of Lanzhou Jiaotong 740 University/ ; 2024//Graduate Students Key Teaching Reform Project for Graduate Students at Lan-741 zhou Jiaotong University/ ; 2025//Key Projects for Undergraduate Teaching Reform/ ; }, abstract = {Soil salinization threatens crop production; however, in multi-crop field systems, evidence for the effectiveness of waste biomass-functional microorganism composite amendments remains limited. Here, we developed a composite microbial soil conditioner (F2) using pine needles and crushed corn cobs as carriers combined with salt-tolerant strains Bacillus subtilis (K1), Azotobacter chroococcum (Y1), and Bacillus gelatinus (J3) to remediate moderately saline-alkali soil from central Gansu (pH 8.36 ± 0.18; EC 1658 ± 55.24 μS·cm[-1]). Saturation screening identified an optimal carrier ratio of pine needles:corn cobs = 1:2 and an inoculum ratio of K1:Y1:J3 = 1:2:1. In pot experiments, F2 increased soil organic matter and water-holding capacity, enhanced alkaline phosphatase, urease, and sucrase activities, and significantly reduced soil pH and EC. Maize seedling height and chlorophyll content increased by 53.87% and 38.88%, respectively. Amplicon-based microbiome profiling indicated enrichment of beneficial microbial taxa and strengthened primary metabolic functions under F2. Field validation across five crops (flax, potato, edible sunflower, sorghum, and maize) showed consistent growth and yield-related improvements. Overall, these results demonstrate that the biomass-microbe composite amendment effectively alleviates saline-alkali constraints by jointly improving soil properties, microbial functions, and crop performance.}, }
@article {pmid41753589, year = {2026}, author = {Xia, X and Yang, S and Song, X and Hao, C and Sun, H and Xu, X and Lu, X and Li, F}, title = {The Influence of Transgenic Maize on the Endophytic Microorganisms of Eisenia fetida.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020302}, pmid = {41753589}, issn = {2076-2607}, support = {ZR2021QC207//Shandong Province Natural Science Foundation Young Project/ ; 2023ZD04062//the Biological Breeding-Major Projects/ ; CXGC2025C05//The 2025 Annual Basic Research Task of the Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; }, abstract = {To evaluate the comprehensive ecological risks associated with transgenic plant residues, this study examined their impact on Eisenia fetida and their endogenous microorganisms. The results indicated that transgenic plant residues did not influence the survival or weight of E. fetida, but they significantly altered the microbial community structure at specific time points. Specifically, the diversity and structure of the fungal community exhibited significant changes on the 14th and 28th days after treatment. In contrast, the bacterial response was delayed, with 22 biomarkers, including Caproiciproducens, Lachnoclostridium, and Enterococcus, being specifically enriched on the 21st day. This study confirmed that transgenic plant residues can temporally reshape the microecology within E. fetida. The practical significance of this research lies in highlighting the importance of incorporating the microbiome into safety assessment frameworks, thereby providing a scientific foundation for developing more forward-looking ecological risk assessment standards.}, }
@article {pmid41753582, year = {2026}, author = {Pickup, RW and Ooi, PB and Agrawal, G and Atkinson, PM and Sanderson, J and Ali, RAR}, title = {Crohn's Disease in Malaysia: Could Application of the Precautionary Principle Reduce Future Incidence?.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020295}, pmid = {41753582}, issn = {2076-2607}, support = {STR-FCRI-LIVE-003-2022.//Lancaster University and Sunway University/ ; }, abstract = {Inflammatory bowel disease (IBD) comprises mainly Crohn's disease (CD) and Ulcerative Colitis (UC). The Western model suggests that environmental factors, immunological factors, the gut microbiome, and genetic disposition all contribute to the onset and sustained symptoms that define CD, although the pathogenesis of CD remains unresolved. Current studies propose that in individuals who are genetically susceptible, genetic factors linked to immune dysregulation, in combination with environmental exposure, can result in dysbiosis of the gut microbiome and intestinal barrier dysfunction, leading to immune dysregulation. In Malaysia, the incidence of IBD is rising with CD increasing disproportionally compared to UC, and the incidence of CD currently mirrors that of the United Kingdom in the 1930s, which now has one of the highest incidences worldwide. Given the suggested role of Mycobacterium avium subspecies paratuberculosis (MAP) in CD in Western countries, which is subject to some controversy, this review summarises for the first time the current evidence on genetic, environmental, and microbial factors that could contribute to the rise of Crohn's disease in Malaysia and proposes preventive approaches. We note the increasing reliance of Malaysia on imported cattle and milk products from areas of high Johne's Disease prevalence to meet increasing demand and changes in milk preferences in the Malaysian population, both key indicators for human-MAP exposure in the Western model. Therefore, should MAP be shown to be associated with CD in Malaysia, some preventative measures are suggested, such as screening imported and native beef and dairy cattle, dairy products and ultimately water, both recreational and potable.}, }
@article {pmid41753572, year = {2026}, author = {Lohbrunner, L and Baessler, C and Becker, E and Döhla, C and Droll, N and Hagen, RM and Klein, N and Mutters, NT and Reyhe, A and Weppler, R and Döhla, M}, title = {Hospital Wing Opening Sparks Antimicrobial Resistance in Wastewater Microbial Community Within the First Twelve Months.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020285}, pmid = {41753572}, issn = {2076-2607}, support = {Open Access Publication Fund//University of Bonn/ ; }, abstract = {Antimicrobial resistance (AMR) in hospital wastewater is a recognized public health concern, yet the dynamics of its emergence remain poorly understood. This study aimed to characterize the quantitative and qualitative changes in the microbial community of a newly built internal medicine intensive care hospital wing following the start of patient treatment. Wastewater samples were collected regularly from eight relevant sites, including seven patient-associated locations within the intensive care ward and the central sanitary sewer where all effluent converged. Culture-based analyses targeted the "ESCAPE-SO" bacterial and fungal groups ("Enterococci", "Staphylococci", "Candida", "Acinetobacter", "Pseudomonas", "Enterobacteriaceae", "Stenotrophomonas", "Others"). Comparisons were made between a 12-month pre-operation period (only flushing every 72 h to prevent contamination of the drinking water system) and the first 12 months of patient treatment. The results showed a significant increase in mean bacterial concentrations from 53 [0-349] CFU/mL before patient treatment to 8423 [3054-79,490] CFU/mL during patient treatment (p = 0.0224) with a particular focus on Pseudomonas spp. as the dominant genus. Resistance against all four main antibiotic classes of the WHO AWaRe essential "watch" list (carbapenems, third-generation cephalosporins, broad-spectrum penicillin and ciprofloxacin) emerged within the first twelve months and depended on the amount of prescribed antibiotics and the number of patients treated. These findings indicate that hospital activity drives rapid development of antimicrobial resistance in wastewater microbial communities, highlighting the critical role of clinical antibiotic use in shaping environmental resistomes. This study provides quantitative evidence that resistance can emerge within months of hospital operation, emphasizing the need for early monitoring and targeted interventions to mitigate the spread of AMR from hospital effluents into broader environmental systems.}, }
@article {pmid41753563, year = {2026}, author = {Ding, Y and Liu, A and Ma, B and Zhang, H and Zhang, C and Li, J and Han, J and Shi, C}, title = {Perinatal Antibiotic Timing Impairs Maternal IgG Transfer via FcRn and Shapes the Neonatal Gut Microbiome in Mice.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020276}, pmid = {41753563}, issn = {2076-2607}, abstract = {Perinatal antibiotic exposure poses a significant risk to maternal-offspring immune programming and infant gut microbiota development. This study investigated the time-specific effects of maternal cefoperazone sodium (CPZ) administration on IgG transfer and offspring gut microbiota in a murine model. Pregnant C57BL/6J mice were assigned to control (CON), gestational (G-CPZ), lactational (L-CPZ), and combined gestational/lactational (GL-CPZ) treatment groups. Results showed that all CPZ treatments significantly reduced IgG and its subtype levels in maternal serum, colostrum, and offspring serum (p < 0.05). Concurrently, mRNA expression of the neonatal Fc receptor (FcRn), critical for IgG transport, was downregulated in both maternal breast and offspring intestinal tissues (p < 0.05). Furthermore, 16S rRNA sequencing revealed that CPZ exposure altered offspring gut microbiota diversity and composition. Alpha diversity was reduced, particularly in the G-CPZ group, while beta diversity showed significant separation in L-CPZ and GL-CPZ groups (p < 0.05). Taxonomic shifts included decreased Bacteroidetes and Lactobacillus, and in the GL-CPZ group, a marked increase in Firmicutes and potential pathobionts like Enterococcus and Hungatella (p < 0.05). These findings demonstrate that perinatal antibiotic exposure, depending on its timing, impairs maternal-offspring IgG transfer via the FcRn pathway and induces distinct, persistent alterations in the offspring's gut microbiota, which may have implications for neonatal immunity and long-term health.}, }
@article {pmid41753553, year = {2026}, author = {Li, Y and Yu, Z and Cao, Q and Wang, H and Zhang, R and Liu, C and Wang, T and Wang, C}, title = {A Novel Approach to Biodegradation and Detoxification of Ricinine in Castor Meal: Relationship Between the Gut Microbiota and Microbial Metabolites of Hermetia illucens.}, journal = {Microorganisms}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/microorganisms14020265}, pmid = {41753553}, issn = {2076-2607}, support = {42407180, 42077357//National Natural Science Foundation of China/ ; NRGC202208//Hubei key Laboratory of Novel Reactor and Green Chemical Technology/ ; GCX2024006//Key Laboratory for Green Chemical Process of Ministry of Education/ ; 2024DJC045//Hubei Province Science and Technology Talent Service Enterprise Project/ ; }, abstract = {Hermetia illucens can digest toxic castor meal and tolerate ricinine stress. However, the underlying mechanisms of ricinine degradation and detoxification within the larval gut microbiome remain largely unknown. Here, the enhanced degradation kinetic process, and the roles of the gut bacterial community and metabolomics were investigated. When the ricinine content was 1000 mg kg[-1] in feeding substrate, larval development was not significantly affected. The ricinine degradation kinetics, facilitated by larval digestion, were significantly enhanced, reducing the degradation half-life to 5.13 days. The gut bacterial community structure adjusted in response to ricinine stress, suggesting that genera such as Dysgonomonas, Actinomyces, Phascolarctobacterium, Lachnoclostridium and Sedimentibacter might play key roles in ricinine resistance and degradation. Furthermore, the gut microbial metabolism responded to toxin stress, reflected by variations in metabolite expression and the enrichment of key metabolic pathways involved in amino acid and vitamin metabolism. This emphasizes the potential role of microbial metabolism in ricinine degradation and detoxification. The close association between gut bacteria and metabolites suggests a cooperative metabolic network within the gut microbiota, where bacteria may participate in ricinine degradation and detoxification either directly or through metabolic cooperation. These findings provide insights into host-microbe interactions and ricinine resistance, highlighting the need for further exploration into the microbiota's role in host metabolism and the development of new therapeutic strategies.}, }
@article {pmid41753276, year = {2026}, author = {Beca, AM and Folescu, R and Crăciun, AT and Olariu, L and Enatescu, I and Belei, B and Belei, O}, title = {Gut Microbiota Alterations and Dysbiosis Patterns in Pediatric Inflammatory Bowel Disease: Clinical Correlations and Therapeutic Impact.}, journal = {Journal of clinical medicine}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/jcm15041589}, pmid = {41753276}, issn = {2077-0383}, support = {Not applicable//Victor Babe&#x219; University of Medicine and Pharmacy Timi&#x219;oara/ ; }, abstract = {Background: Gut microbiota alterations are increasingly recognized as key contributors to the development and clinical course of inflammatory bowel disease (IBD), particularly in pediatric patients, in whom microbial maturation and immune regulation are still evolving. Objective: This study aimed to assess intestinal microbiota composition and dysbiosis severity in pediatric IBD, with comparative analyses according to disease phenotype (Crohn's disease versus ulcerative colitis) and therapeutic strategy (biologic versus non-biologic treatment). Methods: A prospective cohort of 60 pediatric patients diagnosed with IBD based on Porto criteria was evaluated. Fecal samples were obtained at baseline and after three months of combined standard IBD treatment and adjunct microbiota-targeted therapy, and were analyzed using an AI-assisted microbiota profiling platform. A semi-quantitative dysbiosis score was calculated based on the relative abundance of proinflammatory taxa and depletion of short-chain fatty acid (SCFA)-producing bacteria. Microbial parameters were correlated with clinical and therapeutic variables, including the Organism of Interest metric and the Gut Microbiota Index (GMI). Results: Dysbiosis severity was significantly higher in patients with Crohn's disease compared with ulcerative colitis (9.65 ± 1.44 vs. 8.42 ± 1.88, p = 0.037). Patients receiving biologic therapy showed a trend toward lower dysbiosis scores and improved microbial indices, although statistical significance was not reached. Severe dysbiosis was identified in 46.7% of the cohort. Strong positive correlations were observed between the dysbiosis score, Organism of Interest metric and GMI (r = 0.68-0.72, p < 0.01). Conclusions: Pediatric IBD is associated with a reproducible dysbiotic profile, more pronounced in Crohn's disease and partially modulated by biologic therapy. The observed correlations between microbiota-derived indices support their potential utility as complementary markers of intestinal microbial imbalance and disease activity.}, }
@article {pmid41753013, year = {2026}, author = {Crespo, J and Argos Vélez, P and Alonso-Peña, M and Cayón, L and Jiménez-González, C and Iruzubieta, P}, title = {MASLD Under the Umbrella of the Microbiota: A Narrative Review on Ecological Risk and Functional Transmissibility.}, journal = {Journal of clinical medicine}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/jcm15041325}, pmid = {41753013}, issn = {2077-0383}, support = {101095679//HORIZON-HLTH-2022-STAYHLTH-02/ ; PI22/01853//Fondo de In-601 vestigaciones Sanitarias, Instituto de Salud Carlos III, Spain/ ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease worldwide, distinguished by pronounced clinical heterogeneity and a frequent dissociation between metabolic risk factors and the degree of hepatic injury. These observations, together with the limited contribution of genetic heritability, have prompted a re-evaluation of the traditional conceptual framework of the disease. In this context, the question has emerged as to whether MASLD could be, at least in part, a transmissible condition. While there is no evidence to suggest that MASLD is contagious in humans, as no data support person-to-person transmission, gnotobiotic animal studies demonstrate that human gut microbiota can transfer susceptibility to steatosis, inflammation, and systemic metabolic disturbances through immunometabolic mechanisms, independent of host genetics. In parallel, human studies involving microbiota-targeted interventions support the concept that the gut ecosystem is a modifiable determinant of metabolic and hepatic phenotypes. Crucially, these findings do not imply natural transmission of disease, but rather underscore the functional plasticity of microbiota-host interactions. This narrative review integrates epidemiological, experimental, and clinical data to explore the hypothesis that MASLD may be functionally transmissible. MASLD is increasingly recognized as an eco-biological disease, where liver disease risk is not only shaped by host genetics and environment, but also by the ecological configuration and functional outputs of the gut microbiome. This perspective redefines disease susceptibility as, in part, context-dependent and microbiota-mediated, without implying infectiousness in the traditional sense.}, }
@article {pmid41752979, year = {2026}, author = {Schettini, G and Pieri, E and Rizzo, C and Giorgi, M and Mancini, V and Habib, N and Rovira, R and Centini, G}, title = {A Dive into the Invisible: The Vaginal and Endometrial Microbiota in Gynecologic and Obstetric Disorders: A Narrative Review.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/life16020344}, pmid = {41752979}, issn = {2075-1729}, abstract = {The human microbiota is increasingly recognized as a key component of women's reproductive health. This narrative review examines the vaginal, endometrial, and gut microbiota and their roles in the pathogenesis of gynecologic and obstetric disorders, aiming to integrate current evidence into a clinically relevant framework. We review intrinsic (genetic, hormonal, and immunological) and extrinsic (environmental, lifestyle, and pharmacological) factors shaping microbial composition, with particular focus on dysbiosis and the role of the gut estrobolome within the microbiome in estrogen metabolism. The review synthesizes data on microbiota alterations associated with endometriosis, adenomyosis, uterine fibroids, endometrial polyps and hyperplasia, gynecologic malignancies, pelvic inflammatory disease, bacterial vaginosis, infertility, and adverse obstetric outcomes, including preterm birth and fetal growth restriction. Methodological approaches used to characterize the reproductive tract microbiota, such as vaginal swabs, endometrial sampling, and fecal analysis, are critically discussed, together with limitations related to low-biomass environments and contamination risk. Evidence regarding therapeutic modulation of the microbiota, including antibiotics, probiotics, hormonal therapies, and emerging microbiota-based interventions, is summarized, alongside the impact of gynecologic surgery on microbial translocation and long-term microbial balance. Overall, the available literature supports an association between microbiota alterations and multiple reproductive conditions, although causality remains incompletely established. Further standardized and longitudinal studies are needed to clarify mechanisms and guide microbiota-informed diagnostic and therapeutic strategies.}, }
@article {pmid41752930, year = {2026}, author = {Glavina, A and Martić, D and Perko, MA and Mešin Delić, D and Tadin, A and Lešić, S and Šupe-Domić, D}, title = {The Oral Microbiome and Systemic Health: Current Insights into the Mouth-Body Connection.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/life16020294}, pmid = {41752930}, issn = {2075-1729}, abstract = {The oral cavity contains a complex and dynamic microbial ecosystem that plays a central role in maintaining both local and systemic homeostasis. Emerging evidence indicates that disturbances in oral microbial communities-including genetic and functional diversity within species-are associated not only with oral diseases but may also contribute to the development and progression of systemic diseases. This narrative review summarises the current state of knowledge on bidirectional interactions between oral microbial communities and major organ systems. A comprehensive search of PubMed/MEDLINE, Web of Science, Scopus, and Cochrane databases was conducted for studies published between 2019 and 2025, prioritising systematic reviews, meta-analyses, and high-quality mechanistic studies. Ultimately, 40 articles were included in the narrative synthesis. The results provide clear evidence of an association between oral dysbiosis and cardiovascular disease (CVD), type 2 diabetes mellitus (T2DM), chronic respiratory infections, and adverse pregnancy outcomes (APOs). Recent data also suggest links with neurodegenerative disorders, chronic kidney disease (CKD), autoimmune diseases, and cancer. Proposed mechanisms include transient or persistent bacteraemia, systemic inflammation caused by microbial metabolites and endotoxins, disruption of immune homeostasis, molecular mimicry, and modulation of host metabolic pathways. Despite growing evidence linking oral microbial communities to systemic health, most findings are based on observational studies, and causal relationships remain to be established through longitudinal and interventional research. Understanding the connection between the mouth and the body highlights the potential for targeting oral microbial activity, virulence factors, and host inflammatory responses in disease prevention and treatment.}, }
@article {pmid41752919, year = {2026}, author = {Suarez, B and Álvarez, AM and Mascardi, MF and Ramos, ALM and Woo, DH and Gutiérrez, MM and Alzueta, G and Basbus, MDC and Bruzone, S and Cuart, P and Dieuzeide, G and García, T and Escobar, O and Carulla, RDJ and Oviedo, C and Segura, N and Vera, ODV and Giunta, JN and Gadano, A and Trinks, J}, title = {Interactions Between the Gut Microbiome and Genetic and Clinical Risk Factors for Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) in Patients with Type 2 Diabetes Mellitus from Different Geographical Regions of Argentina.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/life16020283}, pmid = {41752919}, issn = {2075-1729}, support = {22920200100009CO//PUE CONICET/ ; 2023//Sociedad Argentina de Diabetes Translational Research Grant/ ; }, abstract = {Background: Local specific biomarkers for MASLD risk stratification are urgently needed in Argentina. Aim: The aim of the study was to characterize the interaction of gut microbiome signatures and genetic and clinical risk factors for MASLD in patients with diabetes from different regions of Argentina. Materials and Methods: We recruited 214 patients with diabetes from different regions of Argentina. Anthropometric, clinical, and lifestyle data were obtained from all participants, who also underwent abdominal ultrasound for MASLD diagnosis and oral swabbing. The PNPLA3 gene was amplified by PCR from the swabs, and the rs738409 genotype was determined via bidirectional sequencing. To profile the MASLD-associated microbiome, stool was collected from 170 participants. V4 16S rRNA gene sequencing was performed, and reads were analyzed using QIIME2 2024.10.1. R Studio 2023.05.1 was used for statistical analyses. Results: MASLD prevalence was 77.9%, with similar rates of occurrence in all regions represented. FIB-4 scores < 1.3 and > 2.67 were detected in 55.3% and 7.4% of patients, respectively. Half of the diabetic patients had the PNPLA3 GG genotype, with the highest rates occurring in patients from Northwestern Argentina (64.9%; p = 0.02 vs. Buenos Aires). The PNPLA3 GG genotype was an independent risk factor for FIB-4 score (p = 0.0008) and a protective factor against glycated hemoglobin (p = 0.004), fasting plasma glucose (p = 0.008), and cholesterol levels (p = 0.02). Marked regional differences were observed in microbiota diversity and composition in Argentina. After adjusting for geographical region, Negativibacillus genus was exclusively detected in diabetic patients with MASLD and GG carriers. The Catenibacterium genus was related to FIB-4 > 2.67. Short-chain fatty acid-producing bacteria were linked to the absence of MASLD. Conclusions: Although some geographical regions of Argentina were not represented in this study and these results therefore cannot be generalized to the country as a whole, these specific signatures could be useful as biomarkers for MASLD risk stratification in Argentines with diabetes.}, }
@article {pmid41752848, year = {2026}, author = {Liu, Y and Wang, K and Jiang, X and Wang, G}, title = {The Ratio of S[2-]/SO4[2-] Induces the Transference of Cadmium in Rhizosphere Soil, Soil Pore Water and Root Iron Plaque.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/life16020211}, pmid = {41752848}, issn = {2075-1729}, support = {2024HPYKFYB03//Key Laboratory for Lake Pollution Control of the Ministry of Ecology and Environment/ ; }, abstract = {Rice (Oryza sativa L.) readily accumulates cadmium (Cd), posing dietary exposure risks in populations dependent on rice-based diets. This study investigated how sulfur (S) redox processes regulate Cd mobility in S-deficient, Cd-contaminated paddy soil under waterlogged conditions. A pot experiment was conducted with two S treatments (-S and +S, 30 mg kg[-1]) throughout the rice growing season. S addition markedly increased pore water S[2-] concentrations during early growth (tillering) and mid-season (booting) and suppressed the diffusion of SO4[2-] from non-rhizosphere to rhizosphere at later stages (filling-maturity). Consequently, Cd in soil pore water was significantly lower in +S than -S treatments at all stages. Sulfur-amended soil showed a redistribution of Cd from labile fractions (exchangeable and carbonate-bound) to more stable fractions (Fe/Mn oxide-bound). Sulfur application also altered the rhizosphere microbiome: the relative abundance of sulfate-reducing bacteria (SRB) increased at the booting and filling stages, while sulfur-oxidizing bacteria (SOB) became more dominant at maturity. Additionally, +S enhanced Cd sequestration on rice root iron plaque by 32-67% during the grain-filling and maturity stages compared to -S. Throughout the rice growing period, redox-driven shifts in the S[2-]/SO4[2-] ratio emerged as a key control on Cd behavior, with low pe + pH (strongly reducing conditions) promoting Cd sulfide precipitation and high pe + pH (more oxidizing conditions) causing Cd remobilization.}, }
@article {pmid41752713, year = {2026}, author = {Filippini, M and Sozzi, J and de Góis Speck, NM and Fusco, I and Kesserling Tso, F and Dores, E and Farinelli, M}, title = {Efficacy and Safety of CO2 Laser Therapy Combined with Collagen Cream in Managing Vulvo-Vaginal Atrophy: A Randomized, Controlled Study on Symptom Relief and Microbiome Modulation.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {2}, pages = {}, doi = {10.3390/medicina62020314}, pmid = {41752713}, issn = {1648-9144}, abstract = {Background and Objectives: Vulvo-vaginal atrophy (VVA), a prevalent condition among postmenopausal women, significantly impairs quality of life through symptoms like vaginal dryness, dyspareunia, and burning. Non-hormonal treatments, such as CO2 laser therapy, have shown promise in managing VVA symptoms with minimal side effects. The addition of adjunctive treatments may enhance efficacy and mitigate possible adverse effects. To evaluate the combined efficacy and safety of CO2 laser therapy and a collagen-based cream in treating VVA and to explore their potential impact on the vaginal microbiome. Materials and Methods: This was a single-center, randomized, interventional. Sixty postmenopausal women diagnosed with VVA were randomized into two groups: a control group receiving laser-only treatment and a treatment group receiving laser therapy with daily collagen-based cream application. Primary outcome measures included symptom improvement on the Visual Analog Scale (VAS) for VVA-associated symptoms. Secondary outcomes involved microbiome composition analysis. Results: Both groups showed significant symptom improvement, with the combination therapy group demonstrating superior reductions in burning, dyspareunia, and vaginal dryness (p < 0.05). Microbiome analysis revealed increased levels of beneficial species (Lactobacillus iners and Lactobacillus crispatus) and decreased pathogenic bacteria (Gardnerella vaginalis and Atopobium vaginae) in the treatment group, though these changes were not statistically significant. Mild side effects, such as burning and swelling in the first days following the treatment, were less frequent in the combination therapy group, likely due to the anti-inflammatory effects of the collagen-based cream. Conclusions: This study provides evidence supporting the use of CO2 laser therapy with collagen-based cream as an effective and well-tolerated treatment for VVA in postmenopausal women, achieving significant symptom relief. The combined therapy approach holds potential for enhanced efficacy and reduced side effects compared to laser-only treatment, offering a promising alternative for women ineligible for hormone-based therapies.}, }
@article {pmid41752210, year = {2026}, author = {Mahmood, SM and Al-Nasrallah, HK and Aldossry, A and Al-Ansari, MM and Al-Alwan, M}, title = {Breast-Cancer-Derived Secretomes from MCF-7 Cells Modulate Bacterial Pathogenic Traits.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27042073}, pmid = {41752210}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital and Research Centre/ ; }, abstract = {Breast cancer is the most frequently diagnosed malignancy among women worldwide, with the luminal A subtype being the most prevalent. Several studies have reported a complex interplay between breast cancer cells and the local microbiome; however, the mechanisms by which tumor cell-secreted factors influence bacterial biological properties remain insufficiently explored. In this study, we established an in vitro model that partially recapitulates the luminal A breast cancer microenvironment by exposing three breast-associated bacterial species, Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, to conditioned media (CM) derived from MCF-7 (tumor) or MCF-10A (non-tumor control) cell lines. A combination of complementary approaches, including ultrastructural morphological assessment, biofilm formation assays, antimicrobial susceptibility testing, and virulence gene abundance profiling by genomic qPCR, was employed to reveal distinct tumor-microbiota interactions. Exposure to MCF-7 CM induced dose-dependent structural alterations in P. aeruginosa and E. faecalis, with pronounced membrane blebbing and structural disruption in E. faecalis. Biofilm formation was differentially modulated in a species- and concentration-dependent manner, with a persistent increase observed in E. coli. Antibiotic susceptibility profiles were selectively altered in E. faecalis, which displayed increased sensitivity to vancomycin, penicillin, and imipenem, along with decreased sensitivity to chloramphenicol. P. aeruginosa exhibited increased sensitivity to imipenem along with reduced sensitivity to meropenem and gentamicin, whereas no significant changes were observed in E. coli. qPCR analyses demonstrated that MCF-7 CM was associated with enrichment of multiple virulence-associated genes (e.g., lasB, exoS, pilB, plcH, fsrC, esp, fimH, and papG), reflecting enhanced pathogenic and adhesive potential. Collectively, these findings suggest that luminal A breast cancer-derived factors can reprogram microbial phenotypes in a species-specific manner, providing mechanistic insight into breast tumor-microbiome crosstalk and a platform to explore microbiome-targeted interventions.}, }
@article {pmid41752202, year = {2026}, author = {Jung, S}, title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27042068}, pmid = {41752202}, issn = {1422-0067}, support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; }, abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.}, }
@article {pmid41752141, year = {2026}, author = {Wu, Y and Wong, OWH and Chen, S and Wang, Y and Zhang, G and Gao, Y and Chan, FKL and Ng, SC and Su, Q}, title = {Gut Microbiome Mediates the Causal Link Between Autism Spectrum Disorder and Dietary Preferences: A Mendelian Randomization Study.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27042006}, pmid = {41752141}, issn = {1422-0067}, abstract = {Autism spectrum disorder (ASD) frequently co-occurs with malnutrition and gut dysbiosis, yet the underlying mechanisms remain poorly understood. Herein, this cross-sectional study first profiles dietary intake differences using dietary records from 210,874 participants (ASD = 232; non-ASD = 210,642; median age = 56.18) from the UK Biobank (UKB). Second, a bi-directional Mendelian Randomization (MR) approach serves to dissect relationships between ASD genetic susceptibility and dietary preferences by leveraging genome-wide association metadata from the iPSYCH-PGC (ASD) and UKB (dietary intake/food-liking traits). The same strategy is implemented to identify ASD-associated gut microbial species. Mediation analyses further assess the role of gut microbiota in the association between ASD and dietary preferences. Subjects with ASD exhibit higher consumption of cheese, processed meat, and oily fish, alongside lower intake of fruits, and demonstrate a preference for high-fat/salt and energy-dense foods. Additionally, the depletion of Turicibacter, Streptococcus, and Lachnospiraceae NK4A136 was causally related with ASD (all false discovery rate < 0.05; β = -0.15, β = -0.10, β = -0.093, respectively), which significantly mediates the ASD-associated elevated preference for high-fat/salt foods. In conclusion, ASD is associated with specific dietary preferences, likely mediated via gut microbiota, highlighting the future potential of gut microbiome-based therapeutics to modify eating disorders for ASD.}, }
@article {pmid41752122, year = {2026}, author = {Wang, SJ and Nian, HY and Chen, ZH and Cui, L}, title = {Human Microbiota-Associated Pig Models for Translational Microbiome Research: A Scoping Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041987}, pmid = {41752122}, issn = {1422-0067}, support = {23141900100//Science and Technology Commission of Shanghai Municipality/ ; }, abstract = {The human microbiota-associated (HMA) pig model provides a physiologically relevant platform that bridges preclinical and translational research. However, its use remains limited, with existing studies showing considerable variation in establishment methods. This scoping review systematically evaluates methodological frameworks, engraftment outcomes, and research applications of HMA pig models. Additionally, it highlights their strengths, limitations, and implications for future studies. We conducted a comprehensive literature search in PubMed, Web of Science, Scopus, and Directory of Open Access Journals, following PRISMA guidelines for Scoping Reviews. The review examines the methodological foundations of HMA pig model generation and proposes a minimal reporting framework to promote standardization. It synthesizes studies on human microbiota engraftment in pigs, identifying factors that influence colonization efficiency. Finally, it summarizes current applications, discusses persistent limitations and translational challenges, and outlines opportunities for future research. Overall, these integrated insights aim to foster standardized, reproducible protocols for HMA pig model preparation and guide advancements in the field.}, }
@article {pmid41752118, year = {2026}, author = {Kurdi, MA and Alotaibi, H and Alkhuraymi, AT and Aldahery, LN and Alhawaj, AF and Aldali, HJ}, title = {Amyotrophic Lateral Sclerosis (ALS) Genetics and Microbiota: A Comprehensive Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041978}, pmid = {41752118}, issn = {1422-0067}, abstract = {Amyotrophic Lateral Sclerosis (ALS) is a severe, progressive neurodegenerative disorder characterized by the loss of upper and lower motor neurons, affecting 0.5 to 2.6 per 100,000 people, with a median survival of 2 to 5 years. It is increasingly seen as a multisystem disorder, sharing essential clinicopathological features with Frontotemporal Dementia (FTD). This convergence arises from overlapping molecular processes, including severe oxidative stress, glutamate-mediated excitotoxicity, mitochondrial dysfunction, and widespread aggregated TDP-43 proteinopathy in both sporadic and familial cases. Several key genetic factors have been identified, particularly mutations in C9orf72, SOD1, TARDBP, and FUS, which serve as important targets for novel treatments, such as Tofersen, a recently approved SOD1-specific antisense oligonucleotide (ASO) gene therapy. Additionally, there is increasing evidence of the gut-brain connection. Dysbiosis, involving species such as Akkermansia muciniphila, and lower levels of neuroprotective metabolites, such as nicotinamide, may affect the course of the disease. As a result, treatment strategies are shifting toward a personalized approach. This includes using gene therapy, ranging from ASOs and RNA interference (RNAi) to new CRISPR-based genome editing. It also involves exploring microbiome-modulating treatments, such as specific probiotics and Fecal Microbiota Transplantation (FMT). While microbiome and gene therapies remain largely experimental, their potential is promising, as highlighted by the recent approval of Tofersen. These novel approaches could be further enhanced and guided by more robust diagnostic criteria and by investigating early multimodal treatment strategies to slow the progression of this complex disease.}, }
@article {pmid41751979, year = {2026}, author = {Eskildsen, J and Dong, M and Hanak, T and Madsen, CK and Holme, I and Plaszkó, T and Vestergård, M and Nicolaisen, M and Thordal-Christensen, H and Brinch-Pedersen, H}, title = {Novel CRISPR/Cas9-Derived mlo Alleles in Barley: Resistance to Powdery Mildew and Microbiome Implications.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041846}, pmid = {41751979}, issn = {1422-0067}, support = {NNF19OC0056580//Novo Nordisk Foundation/ ; BarleyMicroBreed, 101060057//EU Horizon research and innovation/ ; }, abstract = {Barley grown in temperate regions is often challenged by powdery mildew disease. An effective solution is mildew resistance locus o (mlo)-based resistance, which is monogenic, durable, and broad-spectrum. While the pleiotropic effects of mlo mutations on above-ground tissues are well documented, their impact on the root-associated microbiome remains underexplored. We utilized CRISPR/Cas9 to generate novel mlo mutant lines and evaluated their resistance to causal fungus Blumeria hordei. We further examined if mlo knockout has any impact on the overall root microbiome diversity and composition under field-like conditions and applied DESeq2 to compare the abundance of microbial taxa between mutants and wild type. We created five novel resistant mlo lines, including the first mutants with amino acid alterations in the protein's extracellular region. Mutant lines showed significantly reduced B. hordei colony formation (0.5-5%). While microbial alpha and beta diversity were not significantly altered, a few microbial taxa displayed time-dependent shifts in abundance. Overall, our study demonstrates the effectiveness of CRISPR/Cas9 in generating mlo-based resistance. Moreover, the study revealed functionally important residues in the protein's extracellular region. Finally, we present the first evidence of limited mlo-associated effects on root microbiome diversity and relative abundance of microbial taxa.}, }
@article {pmid41751912, year = {2026}, author = {Huang, S and Chaudhari, DS and Shukla, R and Kanani, P and Zeidan, RS and Lin, Y and Burrow, W and Mankowski, RT and Jain, S and Yadav, H}, title = {Global Microbiome: Core and Unique Signatures Across Diverse Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041776}, pmid = {41751912}, issn = {1422-0067}, abstract = {Earlier analyses evaluating patterns of gut microbiota in individuals from different geographies and age groups are heterogeneous in methodology, precluding broader conclusions about the relationship between the gut microbiome and geographic region, age, and clinical health. Here, we systematically conducted a meta-analysis of 16s rRNA gut microbiome sequencing data representing 10,878 samples across North America, Europe, Africa, Asia and Oceania. Our analysis included 27 countries and three age groups (neonate to age 17, or AG01; ages 18 to 64, or AG02; 65 and above, or AG03). We identified that Firmicutes, Bacteriodetes, and Proteobacteria constitute core phyla across geographic regions. A differing predominance of top families alongside core family Lachnospiracaeae across regions comprised unique microbiome signatures. Countries also differed in their relative abundances of Bifidobacterium, Faecalibacterium, Lactobacillus and Bacteroides. We found in our age analyses that Proteobacteria and Actinobacteria were the most abundant phyla in AG01, and Actinobacteria abundance declined across all continents with increasing age. The relative abundance of Bacteriodetes increased between AG01 and AG02. Enrichment of asthma-associated Enterobacterieaceae in AG01 was highest for North America, followed by Europe and then in Asia. We discuss the correlation of these gut microbial patterns in the context of dietary patterns, populations health, clinical health trends, and healthy aging.}, }
@article {pmid41751904, year = {2026}, author = {Katiraei, P and Frye, RE and Theoharides, TC}, title = {Gut-Brain Inflammation and Disrupted Homeostasis Due to Activation of Mast Cells and Microglia.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041768}, pmid = {41751904}, issn = {1422-0067}, abstract = {Recent data from the Centers for Disease Control (CDC) indicate that the incidence of Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by deficits in social communication and the presence of restricted interests and repetitive behaviors, has increased to 1 in 31 children. Individuals with ASD have a constellation of neurological, behavioral, sensory, feeding, gastrointestinal, and immunological issues. Even though there is some genetic component to the pathogenesis of ASD, accumulation of environmental and pathogenic toxins could contribute to disruption of the gut-blood-barrier (GBB) and blood-brain barrier (BBB) via activation of mast cells (MCs) and microglia, resulting in a chronic cycle of gut-brain inflammation. Here we discuss how various environmental, pathogenic, and stress factors can disrupt gut-brain homeostasis to create susceptibility and epigenetic effects that contribute to the development of ASD. We also suggest simple ways to address some of the key pathogenetic processes involved in ASD.}, }
@article {pmid41751903, year = {2026}, author = {Marton, J and Ciocan, RA and Bâldea, I and Gherman, ML and Gheban, D and Filip, A and Pașcalău, IR and Mihăileanu, FV and Pop, RM and Gherman, CD}, title = {Molecular Mechanisms, Dynamic Lesions, and Therapeutic Targets in Intestinal Ischemia-Reperfusion Injury: A Systematic Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041763}, pmid = {41751903}, issn = {1422-0067}, abstract = {Intestinal ischemia-reperfusion injury (IRI) represents a major cause of morbidity and mortality in abdominal surgery, trauma, and intestinal transplantation. The pathophysiological process involves a biphasic cascade that begins with ischemic hypoxia and progresses to amplified cellular and molecular injury upon reperfusion. This review synthesizes recent mechanistic insights regarding endothelial and microvascular dysfunction, epithelial barrier breakdown, microbiota-driven systemic propagation, and the involvement of oxidative/nitrosative stress and inflammatory signaling. The novelty of our review's approach is the focus on experimental and translational studies and correlation of the data with future directions for mechanistic research and clinical implementation. Despite promising preclinical results, heterogeneity in study protocols or/and model limitations make clinical translation challenging. Recent studies have demonstrated that mitochondria, tight junction proteins, adhesion molecules and innate immune receptors are critical determinants of lesion evolution. Based on these, the current therapeutic strategies include antioxidants, adenosine pathway modulators, dexmedetomidine, ischemic conditioning, hyperbaric oxygen therapy, and microbiota-targeted interventions. Since each mechanism is acting on distinct molecular pathways, a multimodal therapy that integrates redox modulation, endothelial protection, microbiome regulation, and the identification and employment of precision biomarkers is likely to improve outcomes. Beyond summarizing established molecular mechanisms, this review critically reassesses why decades of promising experimental strategies for intestinal ischemia-reperfusion injury has largely failed to translate into effective clinical therapies. By distinguishing context-dependent mechanisms from pathways with consistent translational relevance, we highlight key methodological and biological barriers limiting clinical applicability. Furthermore, we propose a temporally structured, multimodal therapeutic framework that integrates phase-specific pathophysiology with targeted interventions, aiming to inform future experimental design and improve translational success.}, }
@article {pmid41751881, year = {2026}, author = {Abd-Elgawad, MMM}, title = {Grasping Molecular Biology Mechanisms to Optimize Plant Resistance and Advance Microbiome Role Against Phytonematodes.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041744}, pmid = {41751881}, issn = {1422-0067}, support = {No. 47725//STDF/ ; }, abstract = {Plant-parasitic nematodes (PPNs) cause big crop losses globally. Safe/reliable methods for their durable management strategies can harness various beneficial relationships among the plant immune system and related microbiomes. Molecular mechanisms basic to these relations reveal wide arrays of significant roles for plant-healthy growth. This review focuses on such relations of microbiomes to prime and immunize plants against PPNs. It also highlights molecular issues facing PPN-resistant varieties with possible solutions such as genetic breeding/engineering, grafting, PPN-antagonistic root exudates, and novel resistant cultivars. These issues call for optimal uses of various widespread groups of microbiomes. Related plant signaling hormones and transcription factors that regulate gene expression and modulate nematode-responsive genes to ease positive/negative adaptation are presented. Exploring PPN-resistance genes, their activation mechanisms, and signaling networks offers a holistic grasp of plant defense related to biotic/abiotic factors. Such factors relevant to systemic acquired resistance (SAR) via plant-microbe interactions to manage PPNs are stressed. The microbiomes can be added as inoculants and/or steering the indigenous rhizosphere ones. Consequently, SAR is mediated by the accumulation of salicylic acid and the subsequent expression of pathogenesis-related genes. To activate SAR, adequate priming and induction of plant defense against PPNs would rely on closely linked factors. They mainly include the engaged microbiome species/strains, plant genotypes, existing fauna/flora, compatibility with other involved biologicals, and methods/rates of the inoculants. To operationalize improved plant resistance and the microbiome's usage, novel actionable insights for research and field applications are necessary. Synthesis of adequate screening techniques in plant breeding would better use multiple parameters (molecular and classical ones)-based ratings for PPN-host suitability designation. Sound statistical analyses and interpretation approaches can better identify genotypes with high-level, stable resistance to PPNs than the commonly used ones. Linking molecular mechanisms to consistent field relevance can be progressed via dissemination of many advanced techniques. The CRISPR/Cas9 system has been effective in knocking out both the OsHPP04 gene in rice to confer resistance against Meloidogyne graminicola and the GhiMLO3 gene in cotton to minimize the Rotylenchulus reniformis reproduction. Its genetic modifications in crops synthesized "transgene-free" PPN-resistant plants without decreased growth/yield. Characterizing microbiome species/strains needed to prime and immunize plants requires better molecular tools for fine-scale taxonomic resolution than the common ones used. The former can distinguish closely related ones that exhibit divergent phenotypes for key attributes like stability and production of enzymes and secondary metabolites. As PPN-control strategies via tritrophic interactions are more sensitive to the relevant settings than chemical nematicides, it is suggested herein to test these settings on a case-by-case basis to avoid erratic/contradictory results. Moreover, expanding the use of automated systems to expedite detection/count processes of PPN and related microbes with objectivity/accuracy is discussed. When PPNs and their related microbial distribution patterns were modeled, more aspects of their field distributions were discovered in order to optimize their integrated management. Hence, the feasibility of site-specific microbiome application in PPN-hotspot infections can be evaluated. The main technical challenges and controversies in the field are also addressed herein. Their conceptual revision based on harnessing novel techniques/tools is direly needed for future clear trends. This review also engages raising growers' awareness to leverage such strategies for enhancing plant resistance and advancing the microbiome role. Microbiomes enjoy wide spectrum efficacy, low fitness cost, and inheritance to next generations in durable agriculture.}, }
@article {pmid41751793, year = {2026}, author = {Ptáček, O and Musil, Z and Guarnieri, G and Vrbacká, A and Moudrá, P and Zlámalová, A and Röszlerová, P and Tonhajzer, M and Musil, V and Morelli, A and Zach, P}, title = {Amyotrophic Lateral Sclerosis: The State of the Art on Treatments and the Therapeutic Role of the Intestinal Microbiome in Human Studies.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041655}, pmid = {41751793}, issn = {1422-0067}, support = {Cooperatio 39 - Oncology and Haematology//Charles University/ ; Cooperatio 33-Intensive Care Medicine//Charles University/ ; Cooperatio 36-Medical Diagnostics and Basic Medical Sciences//Charles University/ ; #NEXTGENERATIONEU//European Commission/ ; MNESYS (PE0000006) - A Multiscale integrated approach to the study of the nervous system in health and disease (DR. 1553 11.10.2022)//Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP)/ ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a common neurodegenerative disorder; to date, there is no long-term effective treatment. Recently, a relationship has been discovered between the human intestinal microbiome and the pathogenesis of ALS, on which basis faecal microbiota transplantation (FMT) has been proposed as a potential treatment for ALS. In this review, we compare three existing case studies examining the effect of FMT on the course of ALS, highlighting differences in methodology and results. In two of the studies, a halt in the progression of ALS symptoms was observed following FMT, accompanied by improvement in patient health. However, in the third and largest study, no significant effect of FMT was observed. The possible explanation for this discrepancy may be the intentional depletion of intestinal microorganisms using antibiotics prior to FMT in the third study. Future studies and/or completion of the ongoing clinical studies will help clarify the therapeutic effectiveness of FMT in ALS patients.}, }
@article {pmid41751759, year = {2026}, author = {Jovandaric, MZ and Babic, S and Milincic, M and Medjo, B and Raus, M and Krstic, M and Tiric, D}, title = {Microbiome, Epigenetics, and Nutritional Factors in Shaping Perinatal Pregnancy Outcomes.}, journal = {International journal of molecular sciences}, volume = {27}, number = {4}, pages = {}, doi = {10.3390/ijms27041622}, pmid = {41751759}, issn = {1422-0067}, abstract = {Maternal nutrition and gut microbiome composition are central regulators of fetal development and perinatal outcomes, modulating immune signaling, oxidative balance, and epigenetic programming. The authors searched PubMed, Scopus, the Cochrane Library, and Web of Science for full-text, peer-reviewed articles published in English between 2010 and 2025, using keywords relevant to maternal diet, gut microbiome, epigenetic modifications, oxidative stress, reactive oxygen species (ROS), short-chain fatty acids (SCFAs), placental function, and perinatal outcomes. Selected studies provided detailed insights into how maternal dietary patterns and microbiome-derived metabolites influence placental function, fetal growth, and neonatal health. Integration of the microbiome, epigenetics, and nutritional factors reveals key molecular and metabolic networks that shape perinatal health. Targeted modulation of these networks provides a foundation for personalized strategies to improve neonatal outcomes.}, }
@article {pmid41751475, year = {2026}, author = {Papaneophytou, C}, title = {Phytochemical Quorum-Sensing Inhibitors Against Bacterial Pathogens: Mechanisms of Action and Translational Challenges.}, journal = {Current issues in molecular biology}, volume = {48}, number = {2}, pages = {}, pmid = {41751475}, issn = {1467-3045}, abstract = {Antimicrobial resistance is a critical global health challenge, driven by the rapid emergence of multidrug-resistant bacterial pathogens and exacerbated by extensive antibiotic use, which imposes intense selective pressure and disrupts host-associated microbial communities. In this context, quorum sensing (QS), a conserved molecular communication system that coordinates population-level gene regulation, virulence expression, and biofilm development, has emerged as an attractive target for anti-virulence intervention. A growing body of evidence indicates that phytochemicals, such as curcumin, carvacrol, carnosol, eugenol, and chlorogenic acid, can modulate key QS pathways, including acyl-homoserine lactone-, autoinducing peptide-, and LuxS/AI-2-mediated signaling, thereby attenuating pathogenic behaviors at sub-inhibitory concentrations that do not directly impair bacterial viability. Despite this promise, the translational development of phytochemical-based QS inhibitors remains limited. Because QS also regulates cooperative and homeostatic functions in beneficial bacteria, QS-targeted interventions raise concerns about microbiome disruption and ecological imbalance. Furthermore, the literature is marked by substantial methodological heterogeneity, reliance on indirect phenotypic endpoints, limited molecular target validation, and insufficient assessment of toxicity, bioavailability, and pharmacokinetics. The predominance of simplified in vitro models further constrains extrapolation to complex host-associated and polymicrobial environments. This review critically examines the molecular mechanisms underlying phytochemical modulation of bacterial QS, synthesizes pathogen-focused experimental evidence, and evaluates key translational challenges arising from QS conservation, microbiome considerations, and methodological limitations. Addressing these barriers through mechanism-resolved experimentation, standardized evaluation frameworks, and microbiome-aware testing strategies will be essential for advancing phytochemical QS inhibitors toward clinically and industrially relevant anti-virulence applications.}, }
@article {pmid41751448, year = {2026}, author = {Xu, Y and Zhang, L and Gao, Z and Shi, Z and Li, P and Xu, R and Cui, J}, title = {Genotype-Specific Rhizosphere Microbiome Assembly Mediates Biochar-Induced Salt Tolerance in Sorghum.}, journal = {Current issues in molecular biology}, volume = {48}, number = {2}, pages = {}, pmid = {41751448}, issn = {1467-3045}, support = {YFD1000700 and YFD1000702//The National Key Research and Development Program of China/ ; }, abstract = {Sorghum genotypes differentially shape their rhizosphere microbiomes to cope with salt stress; however, the modulatory role of biochar in this genotype-specific plant-microbe interplay remains unclear. In this study, we investigated how salt-sensitive (Henong 16, HN16) and salt-tolerant (Jizaonuo 1, JZN) sorghum genotypes leverage biochar to assemble distinct functional rhizosphere microbiomes under salt stress (5 g kg[-1] NaCl). Biochar application (20 g kg[-1]) alleviated ionic stress by reducing soil electrical conductivity (EC decreased by 46% in HN16) and enhanced soil fertility through increased organic matter (SOM increased by 26% in JZN). 16S rRNA gene sequencing revealed that biochar selectively enriched genotype-specific, stress-resistant taxa. The salt-sensitive HN16 primarily recruited Sporosarcina (a genus reported to exhibit salt tolerance and nitrogen-fixing capabilities) and Intrasporangiaceae, thereby rapidly establishing a rhizosphere barrier. In contrast, the salt-tolerant JZN consistently enriched Salinimicrobium (an extreme halophile) and the family LWQ8, forming more complex and stable co-occurrence networks with a higher proportion of positive correlations (81%). Plant genotype was the primary determinant of core microbiome assembly: Bacillus and Arthrobacter dominated in HN16, whereas Sphingomonas and Streptomyces prevailed in JZN. Biochar reinforced this genotype-specific assembly by modulating soil pH and SOM, which were identified as key drivers of microbial community divergence. Importantly, these biochar-shaped microbial modules showed significant positive correlations with increased plant biomass. Our findings demonstrate that biochar enhances salt tolerance not merely by improving soil properties, but primarily by facilitating the deterministic assembly of genotype-specific, functional rhizosphere microbiomes. This mechanistic insight shifts the paradigm of biochar from a universal soil amendment to a precision tool for rhizosphere engineering, providing a genotype-aware foundation for enhancing salinity resilience in sustainable agriculture.}, }
@article {pmid41751427, year = {2026}, author = {Nair, DG and B Nair, D and Weiskirchen, R}, title = {Reconstructing Liver Fibrosis: 3D Human Models, Microbiome Interfaces, and Therapeutic Innovation.}, journal = {Current issues in molecular biology}, volume = {48}, number = {2}, pages = {}, pmid = {41751427}, issn = {1467-3045}, abstract = {Liver fibrosis is a significant consequence of severe liver injury resulting from viral hepatitis, alcohol, and metabolic dysfunction. Progressive fibrosis and ultimate cirrhosis are leading causes of morbidity and mortality worldwide, generally irreversible and poorly targeted by current therapies. Traditional in vitro models and animal models mostly fail to fully recapitulate human multicellular crosstalk, extracellular matrix (ECM) remodeling, and the chronic, immune modulated nature of the disease. Recent advances in three-dimensional (3D) cell culture models including organoids, spheroids, bioprinted constructs, and organ-on-a-chip systems are advantageous for reconstructing cellular diversity and mechanical microenvironments to understand pathophysiology and aid in drug discovery. Emerging multi-organ models are capable of incorporating microbiome derived cues and using multi-omics readouts and imaging-enabled mechanistic dissection for more predictive anti-fibrotic screening. These technologies align well with the recent Modernization 3.0 regulation and New Approach Methodologies by the Food and Drug Administration (FDA) and recent EU Pharmaceutical Reform. This review summarizes the pathophysiology of liver fibrosis, the current landscape of 3D human liver models, and examines how microbiome interfaces modulate fibrogenesis.}, }
@article {pmid41751385, year = {2026}, author = {Mallol-Simmonds, M and Parra-Lucares, A and Canete, I and Avila, C and Pena-Silva, J and Bustamante, S}, title = {Heart Failure in the Molecular Era: Redefining Our Understanding of Disease Mechanisms and Perspectives.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020486}, pmid = {41751385}, issn = {2227-9059}, abstract = {Heart failure (HF) is a global health challenge characterized by the heart's inability to satisfy metabolic demands, driven by renin-angiotensin-aldosterone system (RAAS) overactivation, a neurohormonal imbalance, and emerging mechanisms like the gut-heart axis and mitochondrial dysfunction. Affecting over 6 million adults in the US alone, HF incurs a 5-year mortality rate of 50% and escalating costs projected to double by 2030. This review examines HF's molecular paradigms, integrating established pathways with advances in omics, stem cell therapy, genetic modification, and personalized medicine. The RAAS blockade remains central, yet its efficacy is limited in HF with preserved ejection fraction (HFpEF). Stem cell therapies (mesenchymal and induced pluripotent stem cells) show regenerative potential but face poor retention (<10% survival at 30 days). CRISPR/Cas9 offers precision, though off-target effects persist. The gut microbiome, via trimethylamine N-oxide, exacerbates inflammation, while omics technologies promise biomarkers for tailored treatments. Challenges include translating these innovations into practice, particularly for HFpEF. Future directions involve novel HFpEF therapies, enhanced stem cell delivery, precise genetic tools, and microbiome interventions, supported with artificial intelligence. By 2030, these advances could shift HF management toward regeneration, contingent on overcoming translational barriers through global collaboration.}, }
@article {pmid41751356, year = {2026}, author = {Lee, K and Kim, H and Wang, JH}, title = {Clinical Evidence Linking the Gut Microbiome and Functional Dyspepsia: A Systematic Review and Meta-Analysis.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020457}, pmid = {41751356}, issn = {2227-9059}, support = {NRF-2022M3A9E4017033//National Research Foundation of Korea/ ; 2020R1F1A1074155//National Research Foundation of Korea/ ; }, abstract = {Background/Objectives: Accumulating evidence and clinical observations suggest that the gut microbiome plays a crucial role in functional dyspepsia (FD). However, the precise characterization of this relationship is unclear. This systematic review and meta-analysis aimed to elucidate the potential role of the gut microbiome in FD based on evidence from published clinical studies. Methods: A comprehensive search of three databases (PubMed, Google Scholar, and Web of Science) was conducted, and 17 relevant clinical studies, including 8 observational studies and 9 interventional studies, published up to September 2025, were identified. Data on the gut microbiome and FD were extracted and subjected to meta-analysis. Results: Meta-analysis revealed no significant differences in gut microbiota α- or β-diversity between patients with FD and healthy controls (Shannon index: standardized mean difference [SMD] = -0.12, 95% confidence interval [CI] -0.90 to 0.67, I[2] = 88%). In contrast, effective interventions induced notable shifts in the microbial community structure (pooled SMD = 0.27, 95% CI -0.28 to -0.83, I[2] = 58%). These shifts were accompanied by increased short-chain fatty acid (SCFA) production and intestinal tight-junction protein levels, which coincided with improved FD symptoms. Conclusions: Although no significant differences in the gut microbiota were detected between patients with FD and healthy controls, interventions in patients with FD induced marked changes in the microbial community. Modulation of gut microbiota-related metabolites, such as SCFAs, may represent a promising therapeutic strategy for the management of FD.}, }
@article {pmid41751285, year = {2026}, author = {Xia, W and Wang, S and Xu, Y and Hua, H and Guo, R and Zhou, B}, title = {The Microbial Profile of Keloid Tissue: A Potential Biomarker for Lesion Activity.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020386}, pmid = {41751285}, issn = {2227-9059}, support = {No.82073472//National Natural Science Foundation of China/ ; }, abstract = {Background: Keloids can extend beyond the boundaries of the original wound and often cause itching or pain. Although the skin microbiome is known to influence various skin conditions, it is still unclear how the microbiota inside keloid tissues differ between active and inactive stages. Methods: We enrolled 43 patients with active keloids and 20 patients with inactive lesions. Tissue samples were collected from keloids and from nearby normal skin. In active lesions, both the relatively unstable and stable regions were also sampled. Microbial composition and predicted functions were analyzed using 16S Ribosomal RNA (rRNA) sequencing and standard bioinformatic approaches. Results: Active keloids exhibited a distinct microbial profile compared to normal skin. Acinetobacter and Pseudomonas were more abundant in active lesions, while Cutibacterium was more common in normal skin. Functional prediction also indicated changes in lipid-related pathways in active lesions. In contrast, inactive keloids showed no significant differences from normal skin, and different regions within active lesions had similar microbial features. Conclusions: This study indicates that alterations in the microbiota are linked to the activity of keloids. Potential microbiome-based translational pathways should be explored for monitoring and managing keloid activity in the future.}, }
@article {pmid41751236, year = {2026}, author = {Yang, X and Song, J and Zhang, H and Jiang, N and Zhang, D and Li, Z and Fan, Y and Zhou, Y and Tian, W and Zhang, J and Ma, W and Wang, X}, title = {Radiological Phenotypes of Bronchiectasis Based on Airway Generation.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020337}, pmid = {41751236}, issn = {2227-9059}, support = {No.82270021//National Natural Science Foundation of China/ ; }, abstract = {Background: High-resolution computed tomography reveals a marked radiological heterogeneity in bronchiectasis; however, the clinical characteristics have not been clearly elucidated. Method: We conducted a prospective observational cohort of 334 bronchiectasis patients at Wuhan Union Hospital. Patients were classified into distal airway (DA) and proximal-intermediate airway (PIA) phenotypes and followed every six months for exacerbations. Clinical, inflammatory, microbial, and metabolic features were compared between groups. Results: Among 334 patients, 206 were classified as DA and 128 as PIA. Most allergic bronchopulmonary aspergillosis cases belonged to the PIA group (p < 0.001). The DA group showed a lower FEV1%pred (p = 0.010) and Bhalla scores (p < 0.001), higher BSI (p = 0.003) and FACED scores (p < 0.001), more frequent exacerbations (p = 0.002), and a greater prevalence of Pseudomonas aeruginosa (PA) colonization (p < 0.001). Radiologically, the DA group exhibited more extensive structural lung damage (all p < 0.05). Inflammatory profiling showed higher neutrophil counts (p = 0.047) and elevated CRP levels (p = 0.006) in DA, whereas the PIA group was characterized by eosinophilic inflammation (p = 0.026); no significant differences were observed in inflammatory cytokine levels. Microbial interaction network analysis revealed distinct ecological structures between phenotypes. The PIA group showed strong negative correlations with Streptococcus, Rothia, and other commensal taxa, whereas the DA group exhibited no significant associations between Pseudomonas aeruginosa and other species. Furthermore, metabolomic analyses revealed elevated 4-hydroxynonenal levels in the DA group, which also experienced a higher rate of acute exacerbations during follow-up (p = 0.003). Conclusions: Distinct radiological phenotypes based on airway generation in bronchiectasis are associated with different clinical severity, inflammatory profiles, and microbiome features which enable personalized bronchiectasis management.}, }
@article {pmid41751214, year = {2026}, author = {Garzon-Escamilla, N and Medina-Cardena, M and Roy, P and Trent, J and Jamous, J and Somesan, Y and Denslow, SJ}, title = {Mechanistic Links Between the Gut Microbiome and Longevity Therapeutics.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020316}, pmid = {41751214}, issn = {2227-9059}, abstract = {Aging is a multifactorial biological process marked by the progressive decline in cellular and physiological functions, increasing susceptibility to chronic diseases and mortality. Recent research has identified the gut microbiome as a key modulator of aging, influencing immune regulation, metabolic homeostasis, and neuroendocrine signaling. A diverse and balanced gut microbiota promotes healthspan by supporting gut barrier integrity, nutrient metabolism, and anti-inflammatory responses, whereas dysbiosis contributes to the onset and progression of age-related diseases, including neurodegeneration, cardiovascular conditions, cancer, and metabolic disorders. Currently, anti-aging interventions targeting key aging pathways, such as insulin/IGF-1 signaling, mTOR, AMPK, and sirtuins, are a major focus in the field of geroscience. Compounds such as metformin, rapamycin, anti-inflammatories, GLP-1 agonists, senolytics, spermidine, SGLT2 inhibitors, and sirtuin activators have shown lifespan extension in animal models. In humans, some of these interventions are associated with improvements in healthspan-related outcomes, including metabolic, cardiovascular, musculoskeletal, respiratory, cognitive and ocular functions. Notably, the gut microbiome may serve as both a mediator and modulator of these interventions, influencing drug metabolism, efficacy, and host responses. This review synthesizes current evidence on the gut microbiome's role in aging, examining its role as both mediator and modulator of longevity interventions and how microbiome-associated mechanisms intersect with emerging anti-aging therapeutics.}, }
@article {pmid41751210, year = {2026}, author = {Zhang, X and Wang, T and Liu, Y and Miao, S and Liu, P and Guo, Y and Cai, J and Zhang, C}, title = {Multi-Omics Profiling of mTBI-Induced Gut-Brain Axis Disruption: A Preliminary Study for Biomarker Screening and Mechanistic Exploration.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020311}, pmid = {41751210}, issn = {2227-9059}, support = {No.82371895//National Natural Science Foundation of China/ ; No.CX20250345//Hunan Provincial Postgraduate Research Innovation Project/ ; No. 2025ZZTS0312//the Graduate Innovation Project of Central South University/ ; }, abstract = {Background/Objectives: Mild Traumatic Brain Injury (mTBI) is a prevalent form of cranial trauma that can elicit a range of acute and chronic neuropsychiatric symptoms, and may increase the risk of neurodegenerative diseases. Its accurate identification remains a significant challenge in the field of forensic medicine. This study aimed to identify differential gut microbiota as potential biomarkers following mTBI and to preliminarily explore the association between alterations in gut microbiota and brain metabolites. Methods: An animal model was used to induce mTBI in male Sprague-Dawley (SD) rats. Dynamic changes in the gut microbiota and brain metabolites were analyzed via 16S rRNA sequencing and untargeted metabolomics. Results: Key discriminative taxa included Staphylococcus, Streptococcus, and Aeromonadaceae. Concurrently, brain metabolites, such as C24:1 Sphingomyelin and Thioetheramide PC, exhibited significant alterations. Multi-omics integration revealed that these changes were strongly correlated; in addition, a pathway analysis implicated disruptions in short-chain fatty acid and glycerophospholipid metabolism, which were linked to the regulation of inflammatory factors. Conclusions: This study demonstrates that mTBI induces distinct, time-dependent alterations in both the gut microbiota and brain metabolome, thereby providing a novel direction for research into the forensic diagnosis and mechanistic investigation of mTBI. Future studies are warranted to validate these potential biomarkers in human cohorts and to further elucidate the causal mechanisms underlying gut-brain axis interactions.}, }
@article {pmid41751197, year = {2026}, author = {Bullegas, A and Shaforostova, I and Seipel, K and Kronig, MN and Nilius, H and Bacher, U and Pabst, T}, title = {Antibiotic Use Before CAR-T Treatment Is Associated with Inferior Outcomes in DLBCL Lymphoma Patients.}, journal = {Biomedicines}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biomedicines14020298}, pmid = {41751197}, issn = {2227-9059}, abstract = {Background/Objectives: CAR-T-cell therapy has become a key treatment for relapsed or refractory hematologic malignancies such as diffuse large B-cell lymphoma (r/r DLBCL), although patient outcomes differ considerably. The intestinal microbiome has been proposed as an important factor influencing CAR-T-cell therapy efficacy; accordingly, antibiotic exposure, which may induce dysbiosis, has been associated with inferior outcomes after CAR-T-cell therapy. Methods: We retrospectively analyzed clinical data from 140 patients to assess the impact of infection-related antibiotic therapy prior to CAR-T-cell therapy, stratifying them into two cohorts: 67 patients with previous antibiotic exposure and 73 without exposure. Results: Patients exposed to antibiotics prior to CAR-T therapy had significantly reduced progression-free survival (p = 0.016) and overall survival (p = 0.002) compared to those without exposure. Multiple antibiotic courses and shorter intervals between the last antibiotic treatment and CAR-T-cell therapy were linked to poorer outcomes. Conclusions: Our data suggest that pre-CAR-T-cell-therapy antibiotic exposure is associated with inferior outcomes, although it remains unclear whether this effect is causal or reflects underlying patient comorbidities. These findings highlight the need for further studies investigating the role of antibiotic-induced dysbiosis on CAR-T-cell therapy efficacy.}, }
@article {pmid41751143, year = {2026}, author = {Chen, J and Ma, L and Zhang, Z and An, F and Li, X and Li, B and An, T and Wang, L}, title = {Rumen-Protected Glucose Supplementation Enhances Yak Calf Growth Through Gut Microbiota-Metabolic Interactions.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040683}, pmid = {41751143}, issn = {2076-2615}, support = {2021YFYZ0001//the "14th Five-Year Cattle Breeding Public Relations" Project on Innovation of High-Quality Cattle Breeding Materials and Methods and Selection of New Varieties/ ; 2025YFHZ0277//Project of Sichuan Provincial Department of Science and Technology/ ; 2025ZNSFSC0979//the Natural Science Foundation of Sichuan Province/ ; }, abstract = {Alleviating negative energy balance in perinatal yaks is a critical challenge for safeguarding the health of both dams and calves and achieving sustainable development of yak husbandry. While RPG supplementation represents an effective nutritional strategy, its transgenerational benefits, particularly the long-term effects on offspring calf development through maternal intervention, remain largely unexplored. In the present study, low-dose RPG (150 g d[-1], L-RPG, n = 6) markedly improved milk composition, elevating protein, fat, lactose, and gross energy contents (p < 0.05), and enhance calf weight gain (21.74%) with activation of the somatotropic axis (increased GH, IGF-1, etc.). Calves in this group also exhibited enhanced antioxidant capacity (higher SOD, CAT, and T-AOC) and improved immune regulation (lower IL-6, TNF-α). Multi-omics analyses revealed that L-RPG enriched beneficial taxa such as Solbacillus, Citricoccus, and Akkermansia muciniphila, optimized the hindgut microbiome, and upregulated serum metabolites including di-O-methylfraxetin and phenylalanyl-histidine. Integrated microbiota-metabolite profiling demonstrated significant cross-talk between the altered bacteria and metabolites. Collectively, supplementing dams with 150 g d[-1] RPG improves milk quality, modulates the calf gut microbiota, and reshapes host metabolism, thereby synergistically promoting offspring growth. Our findings provide a comprehensive "maternal nutrition-microbiota-metabolism" framework for understanding RPG's mode of action and furnish both theoretical insights and practical guidance for dam-calf health management in yak production systems.}, }
@article {pmid41751133, year = {2026}, author = {Dou, X and Zhang, G and Dong, X and Wang, C and Dong, W and Ding, X and Wang, H and Mei, Y and Jiao, H and Ren, M}, title = {Intestinal Microbiota and Probiotic Characteristics of Two Indigenous Chicken Breeds (Hotan Black Chicken and Baicheng You Chicken) from the Tarim Basin.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040672}, pmid = {41751133}, issn = {2076-2615}, support = {2024ZD105//the Science and Technology Plan Project of the Xinjiang Production and Construction Corps/ ; 32560040//the National Natural Science Foundation of China/ ; TDGRI202306//Graduate Innovation Project of Tarim University/ ; XJARS-12-06//Modern Agricultural Industry Technology System of Xinjiang Uygur Autonomous Region/ ; 2022NC118//Science and Technology Achievement Transformation Demonstration Project of Xinjiang Uygur Autonomous Region/ ; 202510757003//Undergraduate Innovation and Entrepreneurship Training Program of Tarim University/ ; }, abstract = {Drawing on two indigenous chicken breeds that have adapted for centuries to the hyper-arid Tarim Basin, namely the Baicheng You Chicken and Hotan Black Chicken, this study provides a high-resolution map of their gut microbiota across the duodenum, jejunum, ileum and cecum and subsequently isolates putative probiotic strains from cecal contents using conventional culture techniques. In the duodenum, Lactobacillus dominated Hotan Black Chicken (43.16%), whereas Ligilactobacillus prevailed in Baicheng You Chicken (37.03%). This segregation persisted in the jejunum, with Lactobacillus accounting for 62.55% of Hotan Black Chicken reads and Ligilactobacillus accounting for 60.76% reads in Baicheng You Chicken. The ileal core of Hotan Black Chicken remained Lactobacillus (50.63%), while Baicheng You Chicken shifted to Enterococcus (32.37%). In the cecum, both breeds converged on the Rikenellaceae RC9 gut group as the single dominant lineage (Hotan Black Chicken, 46.87%; Baicheng You Chicken, 46.23%). At the genus level, Hotan Black Chicken was enriched in Lactobacillus and Ligilactobacillus, whereas Baicheng You Chicken harbored a greater proportion of Enterococcus. Concurrently, eight strains with in vitro probiotic attributes were isolated, four from each breed, identified as Ligilactobacillus salivarius, Limosilactobacillus reuteri, Lactobacillus gallinarum, Enterococcus lactis, Enterococcus faecium, Enterococcus faecalis, and Bacillus velezensis. This study deciphers the intestinal microbiome of two native Tarim Basin chicken breeds, Hotan Black Chicken and Baicheng You Chicken, and mines them for autochthonous probiotic strains. The obtained dataset has established a foundational resource for poultry-related probiotics adapted to extremely arid environments, providing theoretical insights and practical value for poultry nutritionists in water-scarce regions in the future.}, }
@article {pmid41751122, year = {2026}, author = {Yuan, X and Su, X and Zhuang, D and Zhou, H and Tang, Z and Li, C and Wang, J and Shi, B and Luo, Y and Li, S and Zhao, F}, title = {Gut Microbiome Signatures of Aging Associated with Intramuscular Fat Deposition in Tan Sheep.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040661}, pmid = {41751122}, issn = {2076-2615}, support = {2023-QN-186//Lanzhou Youth Science and Technology Talent Innovation Project/ ; Gaufx-03Y0//Fuxi Young Talents Fund of Gansu Agricultural University/ ; GAUXKTD-2022-21//Discipline Team Project of Gansu Agricultural University/ ; 0722019//Research Fund Project of Gansu Agricultural University/ ; }, abstract = {Intramuscular fat (IMF) content determines marbling levels and influences the sensory and edible qualities of livestock meat. Its deposition is influenced by the animal's age and gut microbial community. This study assessed age-related differences in IMF deposition and shifts in gut microbiota between yearlings (1-year-old) and mature (4-year-old) grazing Tan sheep. Then correlations among these factors were examined to investigate the potential role of gut bacteria in IMF deposition. The results demonstrated that mature sheep exhibited higher IMF content in shoulder and rump muscles (p < 0.05), elevated serum lipid levels (p < 0.001), and increased lipolytic enzyme abundances in the liver and pancreas (p < 0.05), compared with yearlings. In contrast, the concentrations of acetate and propionate in ruminal and colonic contents were lower in mature sheep (p < 0.05), despite a higher abundance of lipolytic and synthetic enzymes in colonic content (p < 0.05). Gut microbial diversity differed between age groups, particularly in the rumen and colon, with clear shifts in specific bacterial taxa. Correlation analyses revealed that the abundance of Copromorpha and RUG420 in the colon were positively correlated with IMF content in shoulder and rump muscles, and serum lipid levels (including free fatty acids, FFA; low-density lipoprotein, LDL; high-density lipoprotein, HDL; and very-low-density lipoprotein, VLDL), but negatively correlated with propionate content (|r| > 0.45, FDR < 0.05). Conversely, the abundance of Cryptobacteroides in the colon was negatively correlated with IMF content in shoulder muscle (r < -0.6, FDR < 0.05), and with the levels of triglyceride (TG), LDL, HDL, and VLDL, while showing positive correlations with acetate and propionate contents (r > 0.45, FDR < 0.05). These findings highlight the potential role of specific colon bacteria (Copromorpha, RUG420, and UBA5905) in IMF deposition, identifying them as candidate bacteria for further investigation regarding their effects on meat quality.}, }
@article {pmid41751121, year = {2026}, author = {Aguilar, MG and Tuminello, J and Godke, A and Tashakkori, A and Settle, A and Rhim, H and Dickson, L and Matthews, KL and Yacoub, M and Zapanta, K and Krumbeck, JA and Mitchell, MA}, title = {Effects of Two Different Dietary Calcium Concentrations on Bone Density and Skin Microbiome in Lemur Tree Frogs (Agalychnis lemur).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040660}, pmid = {41751121}, issn = {2076-2615}, support = {AWD-AM221256//LSU ACRES/ ; }, abstract = {The lemur tree frog (Agalychnis lemur), a critically endangered species, can benefit from ex situ conservation programs; however, managing amphibians under human care presents challenges, including the provision of appropriate nutrition. House crickets (Acheta domesticus), a common feeder insect, have an inverse calcium to phosphorus ratio (Ca:P; 0.15:1) and low calcium content (<0.3%). While gut-loading crickets with an 8% calcium diet can improve their calcium concentrations, no study has assessed the effects of dietary calcium on bone development in Agalychnis spp. Moreover, no study has examined how diet impacts the gut-skin axis and skin microbiome of these frogs. This study examined how crickets gut-loaded with either a 1.3% or 8% calcium diet affected lemur tree frog bone density and skin microbiome. We hypothesized that frogs consuming the 8% calcium diet would exhibit significantly higher Hounsfield units (HU; bone density) over time, as measured by micro-computed tomography (mCT), and that dietary calcium concentration would have no effect on skin bacterial and fungi microbiomes. Eleven juvenile lemur tree frogs underwent mCT scans at baseline and 90 and 180 days. Total body volume of interest analysis showed a significant increase in HU in the 8% calcium group compared to the 1.3% group (F = 9.9, p = 0.01). There was no significant difference noted in the alpha or beta diversities for the bacterial and fungal microbiomes between dietary groups. This study provides the first evidence of dietary calcium's impact on bone density in lemur tree frogs, offering valuable insights for improving ex situ management of this species.}, }
@article {pmid41751100, year = {2026}, author = {Yang, L and Xu, Z and Liu, D}, title = {The Effects of Dual-Yeast Compound Preparation on the Intestinal Health and Metabolism of Lambs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040637}, pmid = {41751100}, issn = {2076-2615}, support = {NDYB2022-5//Inner Mongolia Agricultural University High-level/excellent Doctoral Talent Introduction Research Project/ ; BR230118//University Basic Scientific Research Business Expenses Project-Young Teachers Research Ability Enhancement Fund Project, 2023 Financial Funds/ ; 2025MS03114//Natural Science Foundation of Inner Mongolia Autonomous Region Project/ ; SYKJZD202302//Discipline Project of College of Veterinary Medicine, Inner Mongolia Agricultural University/ ; }, abstract = {Microecological preparations exert beneficial effects on the health of young ruminant animals; however, the mechanism is unclear. As a result, the present study analyzed the effects of yeast cultures on the growth properties, microbiome, and metabolism of weaned lambs. In this study, a total of 20 weaned lambs were randomly, stochastically divided into four teams: the control group (Group A) were fed a basic diet; Group B were fed with Saccharomyces cerevisiae BC strain culture (30 g/head/d); Group C were fed with Kluyveromyces marquez XR4 strain culture (30 g/head/d); Group D were fed with a composite culture of the two yeast strains (30 g/head/d). The study lasted for 40 days, with daily records of lamb feed intake and weight. Lamb feces were collected regularly for metagenomic sequencing and metabolomics analysis. The average daily weight gain and average daily yield of Group D lambs were significantly higher than those of Group A lambs (p < 0.01). The feed utilization rate in the yeast-fed groups was considerably higher than in the control group (p < 0.05), indicating that the addition of yeast crops to lamb feed might improve lamb feed performance. Bacteroides and the mTOR signaling pathway were dramatically enriched in the intestines of weaned lambs in the yeast-culture-fed groups, and their expression levels of ketones and benzoic acid compounds were significantly upregulated. These results indicated that yeast culture had excellent effects on weaned lambs in regulating immunological functioning and the intestinal environment, protecting the enteric mucosal barrier, improving digestion and nutritional absorption, and enhancing antioxidant function. In summary, adding yeast culture to weaned lamb feed can generate a positive effect on its productivity performance and gut health. These findings provide novel insights into promoting the health of young ruminants.}, }
@article {pmid41751034, year = {2026}, author = {Wang, J and Cheng, M and Huang, F and Chen, L and Xu, W and Cai, J and Chen, Z and Zhao, Y and Zhang, X}, title = {Metagenomic-Metabolomic Integration Reveals Gut Microbiota Dynamics and Metabolic Changes in Super-Geriatric Captive Giant Pandas.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040575}, pmid = {41751034}, issn = {2076-2615}, support = {2025ZNSFSC0252//the Science and Technology Project of Sichuan Province/ ; }, abstract = {Age-related changes throughout the lifespan are known to influence gut microbiota composition, microbial functional potential, and host-associated metabolic processes. Understanding these age-related variations is important for elucidating their potential physiological implications at different life stages. However, information regarding the gut microbiome and metabolomic characteristics of super-geriatric captive giant pandas (Ailuropoda melanoleuca) remains limited. In this study, fecal samples were collected from adult and super-geriatric captive giant pandas and analyzed using metagenomic sequencing combined with untargeted metabolomics. The gut microbiota of super-geriatric individuals exhibited a marked decrease in Bacillota and an enrichment of Pseudomonadota compared with adult individuals. Functional profiling revealed age-associated shifts in microbial metabolic potential, with a transition from biosynthesis-dominated pathways toward pathways related to substrate degradation and energy utilization. Metabolomic analyses further revealed pronounced metabolic alterations in super-geriatric giant pandas, including elevated levels of unsaturated fatty acids and changes in bile acid-related metabolites. Alterations in gut microbiota composition, particularly the relative enrichment of Pseudomonadota-associated taxa, were associated with inflammation-related metabolic features. Collectively, these findings indicate coordinated changes in gut microbial composition and metabolic profiles during aging. Overall, this study characterizes age-associated alterations in gut microbiota structure and fecal metabolic signatures in super-geriatric captive giant pandas, providing a scientific basis for future studies on microbiota-metabolism interactions and for improving nutritional management and health monitoring strategies in aged individuals of this endangered species.}, }
@article {pmid41751010, year = {2026}, author = {Jiang, G and Zhang, Y and Kamunga, EM and Feng, W and Xu, Y and Li, J and Zhang, Z and Tang, Y}, title = {Physiological and Intestinal Microbiota Analyses Offer Insights into the Analysis of Differential Residual Feed Intake in Jian Carp (Cyprinus carpio var. Jian).}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040548}, pmid = {41751010}, issn = {2076-2615}, support = {NO. 2025JBFR05//the earmarked fund for Central Public-interest Scientific Institution Basal Research Fund, Freshwater Fisheries Research Center, CAFS/ ; CAFS [2023TD40]//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; HBCT2023230203//Hebei Province Modern Agriculture Industry Technology System Freshwater Aquaculture Innovation Team/ ; CAFS [2024JBFR09]//Central Public-interest Scientific Institution Basal Research Fund/ ; }, abstract = {Feed efficiency (FE) is a critical economic trait in aquatic species. This study aimed to assess the effects of residual feed intake (RFI) divergence on growth performance, as well as antioxidant, digestive, and immune capacities. Additionally, intestinal microbiome was also employed to reveal the mechanism affecting the RFI in Jian carp. After the 8-week culture period, 12 fish (25 ± 1.05 g) each from the highest and lowest RFI extremes were selected as the HRFI and LRFI groups, respectively, for detailed physiological and microbial analysis. In terms of growth performance, the RFI, FCR, and DFI were found to be significantly lower in the LRFI group (p < 0.001), whereas no differences were observed in the ADG, BWG, SGR, HIS, VSI, and CF (p > 0.05). For physiological performance, the activities of digestive enzymes (protease, lipase and amylase) and antioxidant enzymes (T-AOC, SOD, CAT, GPx) were significantly higher in the LRFI group than in the HRFI group (p < 0.001). In line with this, the integrity of the intestinal tissue in the LRFI group was also superior to that in the HRFI group. Furthermore, the expressions of immune-related genes (LEP, GHR, AGPR, NPY) followed the same pattern. However, the expression of the CCK gene was significantly higher in the HRFI group (p < 0.001). There was no significant difference in the total lipid and fatty acids contents of muscle between the RFI groups (p > 0.05). Microbiota analysis indicated that the LRFI group harbored a higher relative abundance of several microbial taxa often associated with beneficial metabolic functions, including s Cetobacterium_sp_ZOR0034, unidentified_Chloroplast, Chloroplast, and Mangrovibacter. KEGG functional enrichment analysis indicated that the functions of these microbiota were primarily associated with metabolic processes. Collectively, these results demonstrate that improved feed efficiency in Jian carp is collaboratively driven by enhanced physiological status (digestion, antioxidant, immunity) and a beneficial shift in gut microbiota. This study provides an integrated perspective for understanding the regulatory mechanisms of RFI and offers potential microbiota-targeted strategies for feed efficiency improvement in aquaculture.}, }
@article {pmid41751009, year = {2026}, author = {Kim, M and Cho, HY and Park, E and Lee, KE and Park, C and Yoon, JS}, title = {Effects of Canine-Derived Bifidobacterium animalis subsp. lactis DS008 Culture Supernatants on In Vitro Canine Keratinocytes.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/ani16040547}, pmid = {41751009}, issn = {2076-2615}, support = {no applicable//COSMAX BTI/ ; }, abstract = {Microorganisms residing on the skin play a crucial role in maintaining both the integrity of the skin barrier and immune function. This study examined the effects of culture supernatants from canine-derived Bifidobacterium animalis subsp. lactis DS008 on canine keratinocytes in vitro. To induce cytokine production, canine progenitor epidermal keratinocytes (CPEK) were indirectly co-cultured with Malassezia pachydermatis using an insert well system to prevent direct cell-to-yeast contact, and CPEK were supplemented with 0.1%, 1%, and 10% of DS008 supernatants. mRNA expression levels of tumor necrosis factor-α (TNF-α), interleukin (IL)-13, thymic stromal lymphopoietin (TSLP), IL-31, and keratin 10 were analyzed by real-time PCR. The protein concentrations of TSLP and IL-31 were measured by ELISA. Additionally, DS008 supernatants were applied to reconstructed canine epidermis (RCE) models exposed to lipopolysaccharide to evaluate changes in epidermal architecture. Treatment with DS008 supernatants showed significant reductions in mRNA expression of TNF-α, IL-13, TSLP, and IL-31, as well as decreased protein levels of TSLP and IL-31. Furthermore, keratin 10 mRNA expression was significantly increased, and RCE analysis demonstrated that DS008 supernatants ameliorated stratum corneum deformation. These findings suggest that postbiotics derived from canine-derived Bifidobacterium animalis subsp. lactis DS008 is a potential candidate with anti-inflammatory properties.}, }
@article {pmid41750908, year = {2026}, author = {Zhu, X and Han, B and Hu, A and Bi, J and Wang, W and Ye, Y and Xue, F and Zhang, C}, title = {Licorice Flavonoid Extract Ameliorates Intestine Damage in Ulcerative Colitis via MAPK/NF-κB Signaling Modulation and Gut Microbiome Remodeling.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040716}, pmid = {41750908}, issn = {2304-8158}, support = {BK20233003//Jiangsu Basic Research Center for Synthetic Biology/ ; 2024ZB779//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 32402267//National Natural Science Foundation of China/ ; CX (23)1015//Jiangsu Agricultural Science and Technology Innovation Fund/ ; }, abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease of unknown etiology, characterized by non-specific colonic inflammation. Licorice (Glycyrrhiza uralensis Fisch.), a food-medicine dual-use botanical, exhibits anti-inflammatory, antioxidant, and immunomodulatory properties, suggesting therapeutic potential for UC. However, the specific bioactive components of licorice and their underlying mechanisms of action require further elucidation. In this study, we investigated the efficacy and mechanisms of licorice flavonoid extract (LF) in a dextran sulfate sodium (DSS)-induced murine model of UC. The results demonstrated that oral administration of LF significantly alleviated disease pathology indices, reduced colon shortening, and improved histopathological colon damage. LF treatment suppressed the production of pro-inflammatory cytokines, likely through inhibiting the phosphorylation of MAPK and NF-κB p65, while upregulating PPARγ expression. Additionally, LF intervention restored gut microbial diversity, increasing the abundance of beneficial taxa such as Bacteroidetes and Firmicutes. The chemical characterization of LF revealed that 15 flavonoid compounds contribute to its therapeutic basis. These findings demonstrate that LF mitigates UC via integrated anti-inflammatory, immunomodulatory, and microbiota-regulating mechanisms, highlighting its potential as a natural therapeutic agent for UC management.}, }
@article {pmid41750904, year = {2026}, author = {Schoder, D}, title = {Honey Fraud as a Moving Analytical Target: Omics-Informed Authentication Within a Multi-Layer Analytical Framework.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040712}, pmid = {41750904}, issn = {2304-8158}, abstract = {Honey fraud represents a persistent and analytically challenging form of food adulteration, driven by globalised supply chains, strong economic incentives and asymmetries in regulatory oversight and analytical capacity. Conventional physicochemical, spectroscopic and isotopic methods provide legally robust tools for routine control, yet increasingly struggle to detect sophisticated adulteration strategies that are compositionally optimised to mimic authentic honey profiles. These challenges are amplified in a global context, where heterogeneous enforcement landscapes and fragmented analytical infrastructures create exploitable vulnerabilities across international trade networks. This narrative review synthesises current knowledge on honey fraud typologies and critically evaluates established analytical approaches alongside emerging omics-based authentication strategies, including genomics, metabolomics, proteomics and microbiome profiling. Omics-based approaches extend authenticity assessment beyond single-marker paradigms by capturing multidimensional biological and compositional signatures, thereby improving sensitivity to subtle and system-aware fraud (i.e., adulteration strategies that adapt to prevailing analytical detection methods and regulatory thresholds) strategies. To maintain evidentiary clarity, this review explicitly distinguishes between analytically demonstrated vulnerabilities, technically feasible adulteration scenarios and fraud practices documented in regulatory or enforcement contexts. Advanced technology-driven strategies are therefore discussed as potential system-level risks rather than confirmed large-scale honey fraud cases. This differentiation not only safeguards evidentiary precision but also highlights the structural limits of purely analytical solutions. Beyond analytical performance, honey authentication is framed as a systemic challenge embedded in global food systems. This review highlights the need for integrated, data-driven and scalable authentication frameworks that align analytical innovation with reference harmonisation, governance structures and international regulatory cooperation to support resilient and globally robust honey authenticity control.}, }
@article {pmid41750879, year = {2026}, author = {Samantaray, P and Saha, S}, title = {Decoding the Microbial Diversity of Indian Fermented Foods: Integrating Ethnobiology, Multi-Omics and Functional Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040687}, pmid = {41750879}, issn = {2304-8158}, support = {SRMAP/URG/SEED/2023-24/049//SRM University Andhra Pradesh/ ; }, abstract = {India's diverse culinary heritage includes a wide spectrum of traditional fermented foods that harbour complex microbial communities essential for flavour development, preservation, and nutritional enhancement. These microorganisms-primarily lactic acid bacteria, yeasts, and molds-contribute functional properties that extend beyond food transformation to confer health benefits, including probiotic potential and metabolic regulation. This review integrates classical microbiological studies with modern molecular approaches such as metagenomics, metatranscriptomics, and metabolomics to elucidate the microbial diversity of Indian fermented foods. It highlights how geography, substrates, and ethnic traditions shape region-specific microbial consortia sustained through long-standing ethno-microbiological practices. Special focus is given to the glycemic modulation achieved through microbial fermentation, wherein organic acid production and resistant starch formation lower glycemic index and improve glucose metabolism. These processes, along with enhanced nutrient bioavailability, vitamin synthesis, and immunomodulation, illustrate the broader functional potential of fermentation. The review also examines interactions between food-borne microbes and the human gut microbiota, underscoring implications for personalized nutrition. Finally, it discusses modernization and commercialization strategies and outlines future directions involving multi-omics integration, indigenous starter cultures, and microbiome-based innovations to harness India's microbial heritage for improved health and sustainable food development.}, }
@article {pmid41750856, year = {2026}, author = {Gabriele, M and Peres Fabbri, L and Ventimiglia, M and Łepecka, A}, title = {From Waste to Worth: The Role of Fermentation in a Sustainable Future.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040664}, pmid = {41750856}, issn = {2304-8158}, abstract = {Fermentation, one of the oldest biotransformation processes, has become a key element of contemporary sustainable biotechnology. In modern food systems, it enables the simultaneous resolution of environmental, nutritional, and economic challenges by converting agricultural and food residues into high-value-added products, such as bioactive compounds, organic acids, biofuels, enzymes, and proteins. Consistent with the concept of a circular bioeconomy, fermentation supports resource recycling, waste minimization, and greenhouse gas reduction, contributing to the achievement of selected United Nations Sustainable Development Goals (SDGs). The importance of fermentation extends beyond its environmental aspects-fermented foods and postbiotics support the modulation of the gut microbiome, strengthen immunity, and can act as a preventative measure against metabolic and inflammatory conditions. Simultaneously, the dynamic development of precision fermentation and synthetic biology enables the design of microorganisms that produce specific food ingredients without the use of animals or traditional agriculture, paving the way for more responsible production and consumption. This review presents the categories of organic residues valorized through fermentation, explains their role in circular food and healthcare systems, and identifies key technological and regulatory barriers limiting the scaling of this approach. Collectively, fermentation emerges as a biotechnology platform with significant transformative potential for future sustainable food systems.}, }
@article {pmid41750828, year = {2026}, author = {Zhang, J and Li, Y and Cai, M and Xiao, J and Liu, Y and Wu, B and Qianrige,  and Ma, Z and Xiang, H and Feng, X and Chen, S}, title = {Exercise-Related Personality Traits Are Associated with Gut Microbiome Composition and Meat Quality in Qingyuan Partridge Chickens.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/foods15040636}, pmid = {41750828}, issn = {2304-8158}, support = {2024A151501233//Natural Science Foundation of Guangdong Province/ ; 2023ZD0406401//Major projects in agricultural biology breeding/ ; }, abstract = {Chicken meat quality is primarily determined by genetics and nutrition, but recent evidence suggests that animal personality traits and the gut microbiota may also play crucial roles through their influence on muscle development and metabolism. However, the specific mechanisms linking behavior, gut microbiota, and meat flavor remain largely unexplored, particularly in native chicken breeds like the Qingyuan partridge chicken. This study investigated associations between personality traits, gut microbiome composition, metabolite profiles, and meat quality in 200 female Qingyuan partridge chickens. Chickens were monitored for daily step counts from 70 to 120 days of age and divided into three experimental groups: high-exercise (HE), moderate-exercise (ME), and low-exercise (LE). Behavioral tests (open-field, T-maze) revealed HE chickens exhibited enhanced exploration (p < 0.05), reduced latency to move (p < 0.05), and higher learning success rates (p < 0.05) compared to LE counterparts. Meat quality analysis showed HE chickens had brighter breast muscle (L* value, p < 0.05), firmer thigh muscle (shear force, p < 0.05), and reduced intramuscular fat (p < 0.01) relative to LE chickens. Gut microbiome profiling indicated HE chickens showed enrichment of beneficial taxa like Bifidobacterium (p < 0.01) and Intestinimonas (p < 0.05), alongside reduced levels of opportunistic pathogens such as Staphylococcus (p < 0.05). Metabolomic analysis (LC-MS) highlighted upregulated pathways including phenylalanine metabolism and tryptophan-serotonin signaling (VIP ≥ 1.0, p < 0.05). These findings confirm that exercise-related personality traits are associated with improved meat quality and flavor, with correlations linked to gut microbiota and metabolite remodeling, providing novel insights for optimizing poultry meat quality in commercial production.}, }
@article {pmid41750781, year = {2026}, author = {Bogdan-Andreescu, CF and Bubulac, L and Albu, CC and Slăvescu, DA and Bănăţeanu, AM and Botoacă, O and Muşat, GC and Tudor, V and Cadar, E and Păcurar, M}, title = {Toward Smart Salivary Diagnostics: A Comprehensive Review of Heavy Metal Biomarkers and Digital Risk Modeling.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/diagnostics16040635}, pmid = {41750781}, issn = {2075-4418}, abstract = {Background: Saliva has been identified as a valuable diagnostic biofluid due to its non-invasive collection and its capacity to reflect oral and systemic biological processes. Advances in analytical chemistry, biosensing technologies, and artificial intelligence (AI)-assisted data integration have broadened the applications of salivary diagnostics. Among salivary exposome components, heavy metals such as lead, cadmium, mercury, nickel, chromium, arsenic, and aluminum serve as biologically and clinically relevant indicators of environmental exposure, toxic burden, and disease-associated molecular disorders. Methods: This structured review integrates clinical, experimental, and translational studies published between January 2020 and January 2026 that examined salivary heavy metal profiling in relation to oral health. Evidence was identified using systematic searches of PubMed/MEDLINE and supplementary sources. Studies were qualitatively assessed regarding analytical methodologies, reported concentration ranges, biological mechanisms, disease associations, and the development of digital and AI-assisted diagnostic applications. Results: Thirteen human clinical studies and six animal or in vivo investigations met the inclusion criteria. Across these studies, altered salivary metal profiles were linked to oxidative stress, inflammatory signaling, immune dysregulation, microbiome disturbances, and genotoxic markers relevant to periodontal disease, oral mucosal pathology, and the risk of oral squamous cell carcinoma. Inductively coupled plasma mass spectrometry was the predominant analytical platform, while emerging biosensor technologies showed potential for rapid detection and monitoring. Digital and AI-based approaches were identified as promising tools for integrating metallomic data with clinical and molecular biomarkers to support exposure-informed risk stratification. Conclusions: Salivary heavy metal profiling represents a biologically informative, non-invasive method for exposure-aware risk assessment in oral health. Although current clinical translation is limited by methodological variability, small cohort sizes, and the lack of standardized reference ranges, integration with digital biosensing platforms and explainable AI frameworks might facilitate scalable, precision-oriented salivary diagnostics.}, }
@article {pmid41750603, year = {2026}, author = {Herrera-Quintana, L and Iturbe-Sanz, P and Olivares-Arancibia, J and Vázquez-Lorente, H and Plaza-Diaz, J}, title = {Interplay of Microbiome, Oxidative Stress and Inflammation in Health and Disease.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020222}, pmid = {41750603}, issn = {2076-3921}, abstract = {The human microbiome plays a crucial role in health, being involved in both physiological and pathological processes. The highly dynamic microbiome composition is shaped by different factors, which also may affect host-microbe interactions. Although this relationship is complex and incompletely understood, the interplay between the microbiome, oxidative stress and inflammation is increasingly recognized. Microbial metabolites and specific probiotic strains contribute to maintaining redox homeostasis through multiple pathways, such as regulating the immune system and inflammatory processes or influencing mitochondrial reactive oxygen species production and antioxidant signaling pathways. Oxidative stress and inflammation, in turn, may affect the microbiome by altering microbial diversity and function. These disturbances are believed to create a vicious cycle that further disrupts homeostasis and promotes the appearance of different diseases. This review synthesizes current evidence on the interplay between the microbiome, oxidative stress, and inflammation, highlighting its relevance to both physiological and pathological states.}, }
@article {pmid41750591, year = {2026}, author = {Fang, X and Zhu, L and Bing, X and Li, Z and Liu, X and Liu, B and Sun, C and Zheng, X and Liu, B}, title = {Alleviating Effects of Three Heat-Inactivated Enterococcus faecalis Strains Against Growth Suppression, Oxidative Stress and Gut Microbiome Dysbiosis in Macrobrachium rosenbergii Fed with Sesame Meal-Replaced Fish Meal Diet.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020210}, pmid = {41750591}, issn = {2076-3921}, abstract = {This study evaluated the alleviating effects of three heat-inactivated Enterococcus faecalis strains on growth suppression, oxidative stress, and gut microbiome dysbiosis in Macrobrachium rosenbergii-fed sesame meal-substituted fish meal diets. The trial comprised a control group (CT), low fish meal group (LF), and LF fed with three postbiotic-supplemented groups (LF+HK-448, LF+HK-798, LF+HK-804). Results demonstrated that compared with the CT group, the LF diet significantly decreased weight gain rate, specific growth rate, hepatopancreatic total nitric oxide synthase and inducible nitric oxide synthase, while increased feed conversion ratio, nitric oxide, and malondialdehyde contents. Among the postbiotics, LF+HK-804 group conferred the most pronounced compensatory growth and significantly improved oxidative stress and immune markers, as evidenced by elevated WGR, SGR, HSI, and flesh percentage, reduced MDA, and the down-regulation of Toll and Relish alongside the upregulation of peroxiredoxin-5. Intestinal microbiota analysis showed the group of LF+HK-804 improved microbial diversity and richness, specifically by increasing Firmicutes and decreasing Habeamium and Sphingomonas. Metabolomics identified 11 key differential metabolites related to amino acid, energy, and fatty acid metabolism. Correlation analysis further revealed that Gemmatimonadetes, WD2101_soil_group, and Sphingomonas were negatively correlated with phospholipids and positively correlated with glycoside and fatty acid metabolites. Moreover, immunometabolic correlation analysis segregated the metabolic response of microbiota into two distinct profiles: one potentiating a reactive oxygen/nitrogen species-antioxidant defense, and the other favoring a Dorsal/Relish-mediated transcriptional response. In conclusion, E. faecalis 804 can promote growth, alleviate oxidative damage, enhance immunity, and regulate intestinal microbiota and metabolic capacity in M. rosenbergii, showing great potential as a postbiotic.}, }
@article {pmid41750580, year = {2026}, author = {Prokopidis, K and Burke, A and Altinpinar, BG and Farahani, SJ and Khaiyat, O and Lip, GYH and Sankaranarayanan, R and Pekovic-Vaughan, V and Muhamadali, H and Isanejad, M}, title = {Associations Between Gut Microbiota and Mitochondrial Metabolites, with Growth Differentiation Factor-15 as a Marker of Oxidative Stress in Heart Failure vs. Healthy Ageing.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020199}, pmid = {41750580}, issn = {2076-3921}, abstract = {Growth differentiation factor-15 (GDF-15) is an established marker of oxidative stress and a general stress-response mitokines. In this study, we aim to investigate the association of GDF-15 with the metabolic signature of gut and mitochondrial activity in HF and ageing population. A total of 25 HF (67.9 ± 10.0 years) and 29 age-matched healthy participants (HPs) (67.8 ± 11.1 years) were recruited and underwent detailed body composition assessment via dual X-ray absorptiometry; total fat mass and appendicular lean soft tissue index (ALSTI/body mass index (BMI)) were calculated. Utilizing semi-targeted Gas Chromatography-Mass Spectrometry on fasting plasma, a panel of gut microbial-derived (e.g., hippuric acid, indole derivatives, and sarcosine) and tricarboxylic acid cycle metabolites was identified. Results showed higher GDF-15 tertiles were associated with greater HF prevalence, fat mass, NT-proBNP, and TNF-α (p < 0.05). Gut-derived metabolites exhibited phenotype-specific patterns; 3-hydroxyindole predicted higher fat mass in HP; hippuric acid was inversely related in HF; and sarcosine correlated with GDF-15 only in HP. In HF, GDF-15 was strongly driven by pyruvic and fumaric acid, indicating disease-specific mitochondrial stress. In conclusion, these observed associations could be evaluated in future mechanistic studies as sensitive biomarkers of systemic oxidative stress markers, informing potential microbiome-targeted therapeutic avenues.}, }
@article {pmid41750556, year = {2026}, author = {Wu, X and Mu, B and Li, G and Du, R and Park, S}, title = {Gut Microbial Composition, Oxidative Stress, and Immunity in Metabolic Disease: Toward Personalized Interventions.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020175}, pmid = {41750556}, issn = {2076-3921}, support = {RS-2023-00208567//National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT/ ; }, abstract = {This review examines how distinct gut microbial community configurations-characterized by differential enrichment of Bacteroides, Prevotella, Ruminococcus, Bifidobacterium, and Lachnospira-may be associated with variations in host redox homeostasis through microbiota-derived metabolites, including short-chain fatty acids, secondary bile acids, and tryptophan derivatives. These compositional patterns represent reproducible features across populations and correlate with differential disease susceptibility in metabolic disorders. While microbial communities exist along compositional continua rather than discrete clusters, stratification based on dominant patterns offers a pragmatic framework for interpreting large-scale microbiome datasets and guiding precision nutrition interventions. Observational evidence suggests Bacteroides-enriched communities may associate with pro-inflammatory signatures, whereas Prevotella- Ruminococcus, Proteobacteria, Bifidobacterium, and Lachnospira-enriched configurations may exhibit anti-inflammatory or antioxidant characteristics in certain populations. However, inter-population variability and species- and strain-level heterogeneity limit generalization. Condition-dependent effects are exemplified by Prevotella copri, which demonstrates pro-inflammatory responses in specific settings despite beneficial profiles in others. When dysbiosis compromises intestinal barrier integrity, microbial translocation may amplify chronic oxidative stress and immune activation. We evaluate therapeutic potential of beneficial genera including Lactobacillus and Bifidobacterium while examining the dose-dependent, context-specific, and sometimes paradoxical effects of key metabolites. Microbiota-stratified therapeutic strategies-personalizing dietary, probiotic, or prebiotic interventions to baseline community composition-show promise but remain at proof-of-concept stage. Current evidence derives predominantly from cross-sectional and preclinical studies; prospective interventional trials linking community stratification with oxidative stress biomarkers remain scarce. The community-redox relationships presented constitute a hypothesis-generating framework supported by mechanistic plausibility and observational associations, rather than established causal pathways. Future research should prioritize intervention studies assessing whether aligning therapeutic approaches with baseline microbial configurations improves outcomes in oxidative stress-related metabolic disorders.}, }
@article {pmid41750555, year = {2026}, author = {Moustakli, E and Messini, C and Potiris, A and Zikopoulos, A and Arkoulis, I and Kozonis, A and Karampitsakos, T and Machairoudias, P and Machairiotis, N and Antsaklis, P and Panagopoulos, P and Stavros, S and Domali, E}, title = {The Gut-Extracellular Vesicle-Mitochondria Axis in Reproductive Aging: Antioxidant and Anti-Senescence Mechanisms.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020174}, pmid = {41750555}, issn = {2076-3921}, abstract = {Cellular senescence, mitochondrial dysfunction, and cumulative oxidative stress (OS) are the main causes of the progressive decreases in oocyte and sperm quality that define reproductive age. There is growing evidence that these processes are controlled by systemic variables, such as metabolites produced from the gut microbiome and extracellular vesicle (EV)-mediated intercellular communication, rather than being exclusively regulated at the tissue level. Antioxidant enzymes, regulatory microRNAs, and bioactive lipids that regulate mitochondrial redox balance, mitophagy, and inflammatory signaling are transported by EVs derived from reproductive organs, stem cells, immune cells, and the gut microbiota. Concurrently, microbiome-derived metabolites such as urolithin A, short-chain fatty acids, and polyphenol derivatives enhance mitochondrial quality control, activate antioxidant pathways, and suppress senescence-associated secretory phenotypes. This narrative review integrates the most recent research on the relationship between redox homeostasis, mitochondrial function, gut microbiota activity, and EV signaling in the context of male and female reproductive aging. We propose an emerging gut-EV-mitochondria axis as a unified framework through which systemic metabolic and antioxidant signals affect gamete competence, reproductive tissue function, and fertility longevity. Finally, we discuss therapeutic implications, including microbiome modulation, EV-based interventions, and senotherapeutic strategies, highlighting key knowledge gaps and future research directions necessary for clinical translation.}, }
@article {pmid41750539, year = {2026}, author = {Semenescu, I and Bora, L and Dușe, AO and Watz, CG and Avram, &#x218; and Berkó, S and Olteanu, GE and Căta, A and Diaconeasa, Z and Minda, DI and Dehelean, CA and Muntean, D and Danciu, C}, title = {Formulation and Biological Evaluation of Glycyrrhiza glabra L. Methanolic Extract: An Exploratory Study in the Context of Rosacea.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antiox15020158}, pmid = {41750539}, issn = {2076-3921}, abstract = {Rosacea is a chronic inflammatory skin disorder characterized by oxidative stress, innate immune dysregulation, vascular instability, and microbiome-related triggers. Glycyrrhiza glabra (Gg, licorice) root contains phenolics and triterpenoids with antioxidant, anti-inflammatory, antimicrobial, and anti-angiogenic properties that may benefit rosacea-prone skin. Xanthan-gum hydrogels containing 2% methanolic Gg extract (S1, S2) were prepared and characterized. Rheology, in vitro release, and in vitro permeation were evaluated, with the aim of assessing their suitability as topical formulations for rosacea-prone skin. Antioxidant activity was assessed using DPPH, ABTS, and FRAP assays. Antimicrobial effects were tested against S. pyogenes, S. aureus, and C. acnes. Safety and bioactivity were examined through HaCaT keratinocyte assays (MTT, Neutral Red, LDH), the HET-CAM irritation test, and the CAM angiogenesis assay. Immunocytochemistry was performed on rosacea-related inflammatory markers. Both hydrogels showed suitable rheology, sustained release, and preserved strong antioxidant activity. Moderate antimicrobial effects were observed, particularly against S. pyogenes and C. acnes. HaCaT cell viability remained above 84% for the S2 formulation at the highest concentration (200 µg/mL), indicating improved cytocompatibility compared with formulation S1. The hydrogels were non-irritant in the HET-CAM model and reduced neovascularization in the CAM assay, with a more sustained effect observed for formulation S2. Immunohistochemistry supported potential modulation of inflammatory pathways relevant to rosacea, evidencing suppressed VEGF expression and preserved CD44-mediated integrity, particularly in the Labrasol-based formulation (S2), while Caspase-3 staining indicated a controlled apoptotic profile. Overall, Gg hydrogels are safe, biocompatible, non-irritant, and exhibit antioxidant, antimicrobial, and anti-angiogenic activities, supporting their potential as biocompatible topical formulations with antioxidant and pathway-modulating properties relevant to the biological features associated with rosacea, while underscoring the importance of formulation design.}, }
@article {pmid41750436, year = {2026}, author = {Napier, BA and Allegretti, JR and Feuerstadt, P and Kelly, CR and Van Hise, NW and Jäger, R and Stuivenberg, GA and Kassam, Z and Reid, G}, title = {Multi-Species Synbiotic Supplementation After Antibiotics Promotes Recovery of Microbial Diversity and Function, and Increases Gut Barrier Integrity: A Randomized, Placebo-Controlled Trial.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antibiotics15020138}, pmid = {41750436}, issn = {2079-6382}, support = {N/A//Seed Health, Inc./ ; }, abstract = {Background: Antibiotics are essential for treating infections; however, they disrupt the microbiome and key microbiome-dependent functions. Clinical evidence is mixed for probiotic supplementation following antibiotics due to product heterogeneity and inconsistencies in evaluating biological mechanisms that drive clinical consequences. Accordingly, this study investigates the effects of a multi-species synbiotic on gut microbiome composition and function, and gut barrier integrity, during and following antibiotics. Methods: In a randomized, placebo-controlled trial designed to assess proof-of-mechanism, healthy adult participants received a daily synbiotic (53.6 billion AFU multi-species probiotic and 400 mg Indian pomegranate extract; DS-01) or matching placebo for 91 days. All participants also received ciprofloxacin (500 mg orally twice daily) and metronidazole (500 mg orally three times daily) for the first 7 days. Samples were collected at baseline and Days 7, 14, 49, and 91. Endpoints included fecal microbiome composition, fecal acetate and butyrate levels, urinary Urolithin A (UroA), serum p-cresol sulfate (pCS), gut barrier integrity, and safety. Results: The multi-species synbiotic significantly increased the alpha-diversity of Bifidobacterium and Lactobacillus at all timepoints compared to placebo, including short-term (Day 7, p < 0.0001) and end-of-study (Day 91, p < 0.001). The multi-species synbiotic enhanced recovery of native beneficial microbes, including butyrate-producing species and a novel Oscillospiraceae species (UMGS1312 sp900550625, p < 0.001). Beneficial microbiome-dependent metabolites increased, including fecal butyrate (119%, p < 0.05), fecal acetate (62%, p < 0.01), and UroA (13,008%, p < 0.05), whereas detrimental metabolite pCS decreased (68%, p < 0.05) compared to placebo. Functionally, the multi-species synbiotic improved gut barrier integrity rapidly (Day 7; 305%, p < 0.05) and over the long-term (Day 91; 161%, p < 0.05) compared to placebo. Conclusions: During and after antibiotics, this multi-species synbiotic promotes recovery of gut microbiome diversity and native beneficial microbes, microbiome metabolite recovery, and gut barrier function, all of which underpin antibiotic-associated gastrointestinal symptoms.}, }
@article {pmid41750432, year = {2026}, author = {Olszewska, N and Guzel, T and Milner, A and Paluszkiewicz, P and Podsiadły, E and Słodkowski, M}, title = {Should Preoperative Biliary Decontamination Be Considered to Minimize Morbidity and Mortality Following Pancreatoduodenectomy?.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antibiotics15020134}, pmid = {41750432}, issn = {2079-6382}, abstract = {BACKGROUND: Pancreatoduodenectomy (PD) remains the fundamental treatment for periampullary malignancies but is associated with considerable morbidity (20-50%) and mortality (2-7%). Bacteriobilia contributes to unfavourable postoperative outcomes. Current antibiotic prophylaxis recommendations endorse first-generation cephalosporins, which often fail to adequately target pathogens most frequently isolated from bile. To date, no specific guidelines for preoperative targeted antibiotic therapy have been established, although tailoring such strategies to the bile microbiome may improve surgical outcomes. This study aimed to characterize bile microbiology in patients undergoing PD for pancreatic ductal adenocarcinoma (PDAC), evaluating potential antibiotherapy regimens that provide effective coverage against the most frequently isolated pathogens.<br><br>METHODS: A retrospective cohort analysis of 725 patients surgically treated for pancreatic tumours at a high-volume pancreatic surgery center between 2017 and 2022 was performed. To minimize heterogeneity, study was restricted to 138 patients who underwent PD with histopathological confirmed PDAC. Intraoperative bile cultures were assessed.<br><br>RESULTS: Patients with bacteriobilia likewise experienced worse outcomes: higher 5-year mortality (OR 3.01, p = 0.007), greater overall postoperative pancreatic fistula (POPF) occurrence (OR 2.54, p = 0.044) and wound infections (OR 2.90, p = 0.038). Among bile microbiome the highest susceptibility rates were observed for combination of amoxicillin/clavulanic acid with gentamicin, while the lowest were noted for cephalosporin-metronidazole regimen (93.6% vs. 30.2%, respectively).<br><br>CONCLUSIONS: Bacteriobilia contributes to postoperative complications and serves as a predictor of poorer survival after PD. Standard perioperative antibiotic prophylaxis in PD is insufficient. Based on our findings, perioperative antibiotic therapy with amoxicillin/clavulanic acid and gentamicin combination appears to provide superior coverage and may improve postoperative morbidity and overall survival following PD.}, }
@article {pmid41750427, year = {2026}, author = {Bellato, E and Longo, F and Menotti, F and Mariani, R and Massobrio, L and Bartolotti, V and Villavicencio, H and Mandras, N and Bondi, A and Curtoni, A and Castoldi, F and Banche, G and Allizond, V}, title = {Pathogen Profiling in Reverse Total Shoulder Arthroplasty: Virulence Traits of Clinical Isolates Before and After Intraoperative Povidone-Iodine Irrigation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/antibiotics15020129}, pmid = {41750427}, issn = {2079-6382}, support = {RF = 106691/2023.1748//Fondazione CRT/ ; 17th SECEC Research Grant 2023//European Society for Surgery of the Shoulder and the Elbow/ ; }, abstract = {Background/Objectives: Reverse total shoulder arthroplasty (RTSA), a commonly performed procedure in elderly patients with osteoarthritis, is frequently complicated by postoperative infections-primarily caused by Cutibacterium acnes and coagulase-negative staphylococci (CoNS)-which remain a major clinical challenge. While standard antiseptic skin protocols can reduce the bacterial load at the surgical site, they often fail to achieve complete eradication, particularly with C. acnes, a resident species of the shoulder microbiome. Recent evidence indicates that intraoperative povidone-iodine irrigation is effective in significantly decreasing microbial burden; however, a thorough characterization of the virulence factors of the isolated strains remains essential. Methods: A total of 187 clinical strains isolated immediately after RTSA were characterized with respect to their antibiotic resistance profiles and biofilm-forming capacity, and the impact of intraoperative povidone-iodine irrigation on the reduction in bacteria that express these virulence traits was evaluated. Results: Of the 120 C. acnes isolates, 97.67% were susceptible to the tested antimicrobial agents, while only 3.33% exhibited resistance, specifically to clindamycin. In contrast, 53% of CoNS isolates were classified as susceptible, whereas the remaining 47% demonstrated multidrug resistance. Biofilm production was detected in 24% (29/120) of C. acnes and 39% (25/64) of CoNS isolates, with a statistically significant reduction observed after irrigation only for C. acnes. No association was found between biofilm formation and clindamycin resistance in C. acnes, likely due to the low number of resistant isolates. Conversely, among CoNS, a correlation was observed, with the 17.2% of biofilm-producing strains also exhibiting resistance to antimicrobial agents. Conclusions: Notwithstanding the presence of these virulence factors, povidone-iodine irrigation proved effective in substantially reducing the number of bacterial isolates recovered at the surgical site without selecting for strains with enhanced pathogenicity. Notably, the majority of resistant bacteria were detected prior to intraoperative irrigation. This intraoperative procedure may be a key approach to reducing prosthetic joint infections frequently caused by more virulent pathogens, which are unlikely to be selected following this disinfection strategy.}, }
@article {pmid41750320, year = {2026}, author = {Moroz, SM and Negru, AG and Luca, S and Valcovici, M and Baba, M and Lupu, AM and Lascu, A and Lighezan, DF and Mozos, I}, title = {Metabolic Drivers of Valve Calcification and Atrial Remodeling in Calcific Aortic Stenosis.}, journal = {Biomolecules}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/biom16020251}, pmid = {41750320}, issn = {2218-273X}, abstract = {AS, one of the most common forms of valvular heart disease, requiring intervention in aging populations in Europe and North America, has traditionally been viewed as a passive, degenerative condition. However, growing evidence supports a paradigm shift toward recognizing AS as an active metabolic and inflammatory disorder. This narrative review synthesizes experimental, translational, and clinical evidence published between 2015 and 2025 examining metabolic mechanisms linking valvular calcification and atrial remodeling in AS and discusses their clinical relevance in the context of transcatheter aortic valve replacement (TAVR). We discussed classical pathways involving mineral metabolism and vitamin signaling, alongside emerging roles of lipid oxidation, mitochondrial dysfunction, epigenetic regulation, and gut microbiome-derived metabolites. Further, metabolomic signatures associated with disease severity and post-TAVR outcomes were reviewed, highlighting the predominantly associative nature and current limitations of these data. Although valve replacement remains the only effective therapy for advanced AS, metabolic and multi-omics insights may improve future risk stratification and mechanistic understanding. Metabolomic profiling could be integrated at multiple points in the clinical pathway for aortic stenosis and TAVR-most promisingly for pre-procedural risk stratification. The present paper focuses on an integrative framework in which valvular calcification and atrial remodeling are viewed within a broader context of metabolic dysregulation. Future research should aim to translate molecular biomarkers into real-world diagnostics and targeted interventions.}, }
@article {pmid41750271, year = {2026}, author = {Yumoto, T and Obara, T and Naito, H and Nakao, A}, title = {Targeting the Gut in Sepsis: Therapeutic Potential of Medical Gases.}, journal = {Biomolecules}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/biom16020199}, pmid = {41750271}, issn = {2218-273X}, support = {24K12199//JSPS KAKENHI/ ; }, abstract = {Sepsis is a life-threatening condition characterized by a dysregulated host response to infection, often resulting in multiorgan dysfunction. Among affected systems, the gastrointestinal tract plays a central role in sepsis progression by promoting systemic inflammation through impaired barrier function, immune imbalance, and microbiome alterations. Recent research has identified selected medical gases and gasotransmitters as promising therapeutic candidates for preserving gut integrity in sepsis. In particular, hydrogen, carbon monoxide, and hydrogen sulfide exhibit antioxidative, anti-inflammatory, and cytoprotective properties. These gases act through defined molecular pathways, including activation of Nrf2, inhibition of NF-κB, and preservation of tight junction integrity, thereby supporting intestinal barrier function. In addition, they influence immune cell phenotypes and autophagy, with indirect effects on the gut microbiome. Although most supporting evidence derives from preclinical models, translational findings and emerging safety data highlight the potential of gut-targeted gas-based strategies. This review summarizes current mechanistic and translational evidence for gut-protective medical gases in sepsis and discusses their integration into future organ-specific and mechanism-based therapeutic approaches.}, }
@article {pmid41750126, year = {2026}, author = {Leigh, K and Ray, SK}, title = {Exosomes as Specific Vehicles for Delivery of Combination Therapies for Inhibiting Autophagy and Inducing Apoptosis in MYCN-Amplified Neuroblastoma Displaying Gut Dysbiosis: Current Challenges and Future Opportunities.}, journal = {Brain sciences}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/brainsci16020125}, pmid = {41750126}, issn = {2076-3425}, abstract = {Neuroblastoma is a highly aggressive pediatric malignancy originating from neural crest progenitor cells, predominantly in the adrenal medulla. Amplification of the MYCN oncogene occurs in 20-30% of all neuroblastoma cases and approximately 50% of high-risk tumors, strongly correlating with poor prognosis, relapse, and multidrug resistance. MYCN-driven oncogenesis promotes tumor progression by suppressing apoptotic signaling and enhancing survival pathways, including autophagy-a key mechanism underlying resistance to chemotherapy and immunotherapy. This review examines current therapeutic strategies and resistance mechanisms in MYCN-amplified neuroblastoma, while introducing emerging approaches utilizing exosomes as precision drug delivery systems. Exosomes, nanoscale extracellular vesicles secreted by the tumor cells, exhibit natural tropism and can be engineered to selectively target neuroblastoma-specific biomarkers such as glypican-2 (GPC2), which is highly expressed in MYCN-amplified tumors. Leveraging this property, neuroblastoma-derived exosomes can be purified, modified, and loaded with small interfering RNA (siRNA) to silence MYCN expression, combined with chloroquine-an FDA-approved autophagy inhibitor-to simultaneously inhibit autophagy and induce apoptotic signaling. This dual-targeted approach aims to overcome drug resistance, reduce off-target toxicity, and enhance therapeutic efficacy through exosome-mediated specificity. Furthermore, gut dysbiosis has emerged as a critical factor influencing tumor progression and diminishing treatment efficacy in MYCN-amplified neuroblastoma. We propose integrating microbiota-derived exosomes engineered to deliver anti-inflammatory microRNAs (miRNAs) to the gut mucosa, restoring eubiosis and potentiating systemic anti-tumor responses. Collectively, exosome-based strategies represent a paradigm shift in formulating combination therapies, offering a multifaceted approach to target MYCN amplification, inhibit autophagy, induce apoptosis, and modulate the tumor-microbiome axis. These innovations hold significant promise for improving clinical outcomes in high-risk MYCN-amplified neuroblastoma patients.}, }
@article {pmid41749862, year = {2026}, author = {Morishita, A and Oura, K and Tai, H and Yano, R and Nakahara, M and Tadokoro, T and Fujita, K and Mimura, S and Tani, J and Tatsuta, M and Himoto, T and Kobara, H}, title = {Advances in the Therapeutic Landscape of Hepatocellular Carcinoma: Current Strategies and Future Perspectives.}, journal = {Cancers}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/cancers18040609}, pmid = {41749862}, issn = {2072-6694}, abstract = {Hepatocellular carcinoma (HCC) is the most common primary liver cancer and a major cause of cancer mortality worldwide. Because HCC usually arises in cirrhotic livers, prognosis is shaped by the dual threats of tumor progression and hepatic decompensation, requiring treatment decisions that balance anticancer efficacy with preservation of liver function, portal hypertension control, and quality of life. In recent years, management has shifted from a predominantly locoregional approach to an integrated continuum that spans curative resection, ablation, and transplantation; refined transarterial and radiotherapy techniques; and modern systemic therapy dominated by immunotherapy-based combinations. These advances have improved response rates, enabled downstaging and conversion in selected patients, and expanded opportunities for sequential and multimodal treatment. However, challenges persist, including therapeutic decision-making in patients with Child-Pugh B liver function, lack of robust predictive biomarkers, and resistance after initial response. Emerging tools-liquid biopsy, radiomics, AI-assisted imaging, and microbiome modulation-may support future precision strategies and optimized treatment allocation. In this review, we summarize current evidence guiding staging and therapy selection, outline practical considerations across curative, locoregional, and systemic modalities, and discuss evolving biomarkers and next-generation immunotherapy as key steps toward more personalized, durable, and equitable global HCC care.}, }
@article {pmid41749850, year = {2026}, author = {Pertiwi, TH and Suraya, R and Akashi, M and Nagano, T}, title = {The Role of the Oral Microbiome in Modulating Therapeutic Outcomes in Lung Cancer: Key Commensals and Clinical Implications.}, journal = {Cancers}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/cancers18040591}, pmid = {41749850}, issn = {2072-6694}, abstract = {Lung cancer remains one of the deadliest forms of cancer worldwide; thus, there is an urgent need to continually devise new strategies to effectively treat this condition. In this review, we will discuss one of the previously less studied but important aspects of the oral microbiome in both accelerating the development of lung cancer and modulating the efficacy of its treatment modalities. Herein, following an exhaustive search of available databases, we summarize the current knowledge on the association between oral microbiota and lung cancer, focusing on its impact on the efficacy and complications of widely used lung cancer treatments, including surgery, radiotherapy, chemotherapy, and immunotherapy. We also discuss the evidence supporting the use of oral microbiome-targeting interventions in improving outcomes in lung cancer, both preclinically and clinically, and conclude that the full potential of modulating oral dysbiosis in lung cancer has yet to be realized, requiring broader and larger-scale studies in the future. We hope that this review will highlight the importance of an often-forgotten aspect of lung cancer treatment optimization.}, }
@article {pmid41749750, year = {2026}, author = {Wang, R and Xie, Y and Liu, C and Jing, Y and Yang, X and Sun, Q}, title = {Therapeutic Efficacy of Floating Electrode-Dielectric Barrier Discharge Plasma in Experimental Periodontitis: A Pilot Study.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/bioengineering13020211}, pmid = {41749750}, issn = {2306-5354}, support = {2023-NHLHCRF-YXHZ-TJMS-07//National High Level Hospital Clinical Research Funding/ ; }, abstract = {Periodontitis is a chronic inflammatory disease characterized by dysbiotic biofilms and host-mediated destruction of periodontal tissues. This study evaluated the efficacy of a novel needle-shaped floating electrode-dielectric barrier discharge (FE-DBD) plasma probe in treating experimental periodontitis. Using a split-mouth design in a rat model of ligature-induced periodontitis, subgingival microbiome changes were analyzed via 16S rRNA sequencing, while gene expression of inflammatory mediators and osteoclastogenic factors was quantified by qRT-PCR. Histopathological evaluation and osteoclast activity were assessed through H&amp;E and TRAP staining, respectively. FE-DBD treatment significantly shifted the subgingival microbiome by reducing pathobionts such as Bacteroidota and Fusobacteriota and increasing health-associated taxa including Proteobacteria and Actinobacteriota. The therapy also exerted immunomodulatory effects by suppressing pro-inflammatory genes (TNF-α, ICAM-1, CCL2) and elevating anti-inflammatory IL-10 expression. Moreover, FE-DBD favorably modulated bone remodeling by downregulating RANK and RANKL, upregulating OPG, and raising the OPG/RANKL ratio 3.72-fold, accompanied by reduced inflammatory infiltration and osteoclast numbers. These findings demonstrate that FE-DBD plasma effectively ameliorates periodontitis by simultaneously targeting pathogenic biofilms, host inflammation, and osteoclastogenesis, highlighting its potential as a multifaceted adjunctive therapy for periodontal disease.}, }
@article {pmid41749685, year = {2026}, author = {Zhu, Y and Tang, Y and Qi, X and Zhu, X}, title = {Transformer Models, Graph Networks, and Generative AI in Gut Microbiome Research: A Narrative Review.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/bioengineering13020144}, pmid = {41749685}, issn = {2306-5354}, support = {Grant No. LCMYZHYX-KFKT202303//Open Project of the Sichuan Provincial Key Laboratory for Clinical Immunology and Translational Medicine/ ; Grant No. 2022JC03//Scientific Research Foundation of Chengdu Women's and Children's Central Hospital/ ; }, abstract = {BACKGROUND: The rapid advancement in artificial intelligence (AI) has fundamentally reshaped gut microbiome research by enabling high-resolution analysis of complex, high-dimensional microbial communities and their functional interactions with the human host.<br><br>OBJECTIVE: This narrative review aims to synthesize recent methodological advances in AI-driven gut microbiome research and to evaluate their translational relevance for therapeutic optimization, personalized nutrition, and precision medicine.<br><br>METHODS: A narrative literature review was conducted using PubMed, Google Scholar, Web of Science, and IEEE Xplore, focusing on peer-reviewed studies published between approximately 2015 and early 2025. Representative articles were selected based on relevance to AI methodologies applied to gut microbiome analysis, including machine learning, deep learning, transformer-based models, graph neural networks, generative AI, and multi-omics integration frameworks. Additional seminal studies were identified through manual screening of reference lists.<br><br>RESULTS: The reviewed literature demonstrates that AI enables robust identification of diagnostic microbial signatures, prediction of individual responses to microbiome-targeted therapies, and design of personalized nutritional and pharmacological interventions using in silico simulations and digital twin models. AI-driven multi-omics integration-encompassing metagenomics, metatranscriptomics, metabolomics, proteomics, and clinical data-has improved functional interpretation of host-microbiome interactions and enhanced predictive performance across diverse disease contexts. For example, AI-guided personalized nutrition models have achieved AUC exceeding 0.8 for predicting postprandial glycemic responses, while community-scale metabolic modeling frameworks have accurately forecast individualized short-chain fatty acid production.<br><br>CONCLUSIONS: Despite substantial progress, key challenges remain, including data heterogeneity, limited model interpretability, population bias, and barriers to clinical deployment. Future research should prioritize standardized data pipelines, explainable and privacy-preserving AI frameworks, and broader population representation. Collectively, these advances position AI as a cornerstone technology for translating gut microbiome data into actionable insights for diagnostics, therapeutics, and precision nutrition.}, }
@article {pmid41749649, year = {2026}, author = {Pawłowski, P and Zaj, N and Iwaniszczuk, K and Grzelka, I and Makuch, W and Samardakiewicz-Kirol, E and Kościołek, A and Samardakiewicz, M}, title = {Personalizing Nutritional Therapy in Pediatric Oncology: The Role of Gut Microbiome Profiling and Metabolomics in Mitigating Mucositis and Enhancing Immune Response to Chemotherapy.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/children13020293}, pmid = {41749649}, issn = {2227-9067}, abstract = {INTRODUCTION: Intensive chemotherapy protocols and hematopoietic stem cell transplantation (HSCT) in children with cancer frequently lead to severe complications, such as mucositis and immune dysfunction. A growing body of evidence indicates that these complications are closely associated with the patient's nutritional status and the composition of the gut microbiome, which becomes profoundly destabilized as a result of cytotoxic therapy and antibiotic use.<br><br>BACKGROUND: The aim of this review is to critically evaluate the current state of knowledge on the interplay between gut dysbiosis, metabolomic profiles-with particular emphasis on short-chain fatty acids (SCFAs)-and treatment-related toxicity in pediatric patients, as well as to delineate pathways toward personalized nutritional therapy.<br><br>METHODS: A narrative review was conducted, including clinical and preclinical studies published between January 2015 and October 2025. PubMed/MEDLINE, Embase, Cochrane Library, and other databases were searched, focusing on changes in microbiome composition, correlations between gut-derived metabolites and the severity of complications (sepsis, graft-versus-host disease [GvHD], mucositis), and the effects of targeted nutritional interventions (probiotics, prebiotics, postbiotics, and fecal microbiota transplantation [FMT]) on microbiome modulation during anticancer therapy.<br><br>RESULTS: The analysis demonstrates that pediatric oncologic treatment leads to a marked reduction in microbial diversity, including the loss of protective Clostridiales taxa (e.g., Faecalibacterium), accompanied by an overgrowth of Proteobacteria pathobionts. Metabolomic profiling indicates that low SCFA levels (e.g., butyrate < 20-50 &#xb5;mol/g) are a strong predictor of severe mucositis, prolonged neutropenia, and an increased risk of sepsis. Interventions aimed at restoring eubiosis and enhancing SCFA production show potential in strengthening the intestinal barrier, modulating immune responses, and enabling maintenance of the planned relative dose intensity (RDI) of chemotherapy by reducing treatment-related toxicity.<br><br>CONCLUSIONS: Gut microbiome profiling and fecal metabolomics represent promising prognostic tools in pediatric oncology. There is an urgent need for further research employing "omics"-based approaches to develop precise, individually tailored nutritional protocols. Such strategies, including postbiotics and FMT, may minimize treatment-related adverse effects and improve long-term clinical outcomes in pediatric patients.}, }
@article {pmid41749544, year = {2026}, author = {Alamoudi, A and Bahammam, HA}, title = {Mapping the ECC-Saliva Neuroimmune Axis Using AI: A System-Level Framework.}, journal = {Children (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/children13020185}, pmid = {41749544}, issn = {2227-9067}, abstract = {BACKGROUND/OBJECTIVES: Early childhood caries (ECC) and saliva have been studied across disparate domains, including microbiome, fluoride, immune, oxidative-stress, and neuroendocrine research. However, the ECC-saliva literature has not previously been mapped as a connected system using modern natural language processing (NLP). This study treats PubMed titles and abstracts as data to identify major themes, emerging topics, and candidate neuroimmune axes in ECC-saliva research.<br><br>METHODS: Using the NCBI E-utilities API, we retrieved 298 PubMed records (2000-2025) matching ("early childhood caries" [Title/Abstract]) AND saliva [Title/Abstract]. Text was cleaned with spaCy and embedded using a transformer encoder; BERTopic combined UMAP dimensionality reduction and HDBSCAN clustering to derive thematic topics. We summarised topics with class-based TF-IDF, constructed keyword co-occurrence networks, defined an internal topic-level Novelty Index (semantic distance plus temporal dispersion), and mapped high-novelty topics to gene ontology and Reactome pathways using g:Profiler. Prophet was used to model temporal trends and forecast topic-level publication trajectories. Finally, we generated a fully synthetic neuroimmune salivary dataset, based on realistic ranges from the literature, to illustrate how the identified axes could be operationalised in future ECC cohorts.<br><br>RESULTS: Seven coherent ECC-saliva topics were identified, including classical microbiome and fluoride domains as well as antioxidant/redox, proteomic, peptide immunity, and Candida-biofilm themes. High-novelty topics clustered around total antioxidant capacity, glutathione peroxidase, superoxide dismutase, and peptide-based host defence. Keyword networks and ontology enrichment highlighted "Detoxification of Reactive Oxygen Species", "cellular oxidant detoxification", and cytokine-mediated signalling as central processes. Temporal forecasting suggested plateauing growth for classical epidemiology and fluoride topics, with steeper projected increases for antioxidant and peptide-immunity themes. A co-mention heatmap revealed a literature-level Candida-cytokine-neuroendocrine triad (e.g., Candida albicans, IL-6/TNF, cortisol), which we propose as a testable neuro-immunometabolic hypothesis rather than a confirmed mechanism.<br><br>CONCLUSIONS: AI-assisted topic modelling and network analysis provide a reproducible, bibliometric map of ECC-saliva research that highlights underexplored antioxidant/redox and neuroimmune salivary axes. The synthetic neuroimmune dataset and modelling pipeline are illustrative only, but together with the literature map, they offer a structured agenda for future ECC cohorts and mechanistic studies.}, }
@article {pmid41749387, year = {2026}, author = {Neubauer, V and Aditya, S and Quijada, NM and Wetzels, SU and Dzieciol, M and Pourazad, P and Zebeli, Q and Selberherr, E}, title = {Dynamics of the milk microbial community during subacute ruminal acidosis with or without intramammary lipopolysaccharide challenge in dairy cows.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41749387}, issn = {2524-4671}, abstract = {BACKGROUND: Lipopolysaccharides (LPS) from pathogenic Gram-negative bacteria play a key role in the pathophysiology of mastitis. Subacute ruminal acidosis (SARA) induces rumen dysbiosis, leading to LPS translocation and systemic immune activation. This study investigated the effects of a high-grain diet and intramammary LPS challenge on the milk microbiome of dairy cows. Cows were first fed a baseline control diet (day-7 to d-1; CON; 40% grain; n = 18). On d1, 12 cows were switched to a SARA diet (60% grain). On d30, six SARA (SARA_LPS) and the six CON cows (CON_LPS) were challenged intramammarily with LPS, while the other six SARA cows received a placebo (SARA_PLA). No CON_PLA group was enrolled. Milk samples were collected on d-2 (before feeding challenge), d30 (after feeding challenge; before LPS), and d32 (after LPS), and analysed using 16S rRNA gene amplicon sequencing and qPCR.<br><br>RESULTS: During the feeding phases, more genera (70.1%) increased in CON than SARA cows, whereas more (65.3%) genera decreased their relative abundance in SARA compared to CON (p&#x2009;<&#x2009;0.001). This decline persisted in SARA_PLA cows, with more genera (62.4%) decreasing their abundance (p&#x2009;<&#x2009;0.001). However, LPS injection reversed the trend of the feeding effect, with more genera (79.3%) increasing in SARA_LPS cows in comparison to the other two groups, while more genera (85.5%) decreased in CON_LPS (p&#x2009;<&#x2009;0.001) in comparison to the other two groups. Alpha diversity correlated positively with bacterial cell equivalents. Of all genera, 22.1% correlated negatively with milk amyloid A (MAA), which increased post-LPS injection, 21.7% positively with lactose, and 13.4% positively with milk urea. SCC showed significant differences in beta-diversity, but no distinct visual clustering nor many correlations.<br><br>CONCLUSION: The microbial dynamics suggest that high-grain diet and the LPS injection influence the milk bacterial community. More taxa correlated with MAA than with SCC, suggesting that MAA may better reflect immune-microbial interactions in milk. A roughage-rich diet promoted higher microbial abundance, whereas high-grain feeding reduced abundance over the timespan of 30&#x2009;days. Intramammary LPS challenge decreased absolute abundance in CON but increased it in SARA cows, suggesting a diet-dependent immune modulation of the mammary environment. These findings indicate that mammary gland epithelial integrity and immune mediators jointly shape the milk microbiome under metabolic and inflammatory stress.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00499-5.}, }
@article {pmid41749299, year = {2026}, author = {Nordmeyer, SC and Anderson, TJC and Le Clec'h, W and Chevalier, FD}, title = {Limited impact of schistosome infection on Biomphalaria glabrata snail microbiomes.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07299-z}, pmid = {41749299}, issn = {1756-3305}, support = {R01AI133749/NH/NIH HHS/United States ; R21AI171601/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The microbiome of disease vectors can be a key determinant of their ability to transmit parasites. Conversely, parasite infection may modify vector microbiomes. We explore the interactions between the Biomphalaria glabrata snail microbiome and the blood fluke Schistosoma mansoni, responsible for an estimated 200,000 human deaths each year. We have previously shown that the snail hemolymph (i.e. blood) and organs harbor a diverse microbiome. Here, we investigate the impact of schistosome infection on snail microbiomes, hypothesizing that invading schistosomes can alter the snail microbiomes in both composition and abundance over the course of infection, as developing schistosome parasites are in close contact with the host tissues.<br><br>METHODS: We generated cohorts of uninfected and S. mansoni-infected snails. We collected snail hemolymph and hepatopancreas (i.e. liver) at eight timepoints during the pre-patent and patent periods of schistosome infection. We quantified bacterial density using qPCR and profiled the microbiome composition of all samples by sequencing the V4 region of the 16S rRNA.<br><br>RESULTS: Surprisingly, schistosome infection had no effect on bacterial density and limited effect on the microbiome composition, affecting mainly the hemolymph during the pre-patent period (at days 7 and 21). Organ and hemolymph microbiomes were relatively stable over time for both infected and uninfected snail cohorts. The sample type (hemolymph, hepatopancreas) was the major driver of the differences observed in microbiome composition.<br><br>CONCLUSIONS: The limited impact of schistosome infection on the host snail microbiomes might be explained by the long-term interaction of the two partners. Further investigations into the interactions among snails, their microbiomes and schistosome parasites may suggest strategies to disrupt the parasite lifecycle and, consequently, schistosomiasis transmission.}, }
@article {pmid41749281, year = {2026}, author = {Diemer, S and Kozjek, K and Påhlman, LI}, title = {Cystic fibrosis-related diabetes is associated with reduced airway microbial diversity.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03598-2}, pmid = {41749281}, issn = {1465-993X}, }
@article {pmid41749276, year = {2026}, author = {Bozack, AK and Perez-Garcia, J and Rifas-Shiman, S and Zhou, Y and Sordillo, J and Lee, JJ and Coull, B and Lai, PS and Oken, E and Hivert, MF and Gold, DR and Cardenas, A}, title = {Interplay of the nasal microbiome and epigenome among adolescents.}, journal = {Clinical epigenetics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13148-026-02093-1}, pmid = {41749276}, issn = {1868-7083}, support = {K99ES035109/ES/NIEHS NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R01ES031259/ES/NIEHS NIH HHS/United States ; UH3OD023286//NIH Office of the Director/ ; R01HD034568//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, abstract = {BACKGROUND: The respiratory microbiome, including that of the nasal cavity, is involved in host defense and airway pathophysiology. Interactions of the microbiome with the host immune system may impact health and disease susceptibility through changes in the epigenome. In this study, we aimed to analyze cross-sectional associations of nasal microbiome composition and the nasal epigenome among adolescents in the Project Viva cohort (N = 372, mean age: 13.0 years). We collected nasal swabs from anterior nares, profiled the microbiome by 16 S rRNA gene sequencing, and grouped samples into 6 clusters using partitioning around medoids. Nasal cell DNA methylation was measured with the Illumina MethylationEPIC BeadChip. In an epigenome-wide association study, we tested for associations of microbiome cluster assignment and DNA methylation using robust linear models adjusting sociodemographics, season, batch, and surrogates of cell type composition. Among significant loci, we conducted differential abundance analysis to identify individual bacterial genera associated with DNA methylation levels.<br><br>RESULTS: A total of 45 loci had differential methylation between two or more microbiome clusters (pBonferroni< 0.05). Methylation differences between clusters ranged from 0.20 to 12.45% (median&#x2009;=&#x2009;0.95%). Differentially methylated loci were near genes related to asthma (ITPR2, MAPK1), lung function (FKBP11), mitochondrial function (MRPL20, SPTBN1), inflammation (C3), and immune function (N4BP3, EIF5). The abundance of individual taxa, particularly Propionibacterium, was associated with methylation at 15 of these loci (FDR&#x2009;<&#x2009;0.05). In addition, we found greater Corynebacterium abundance was associated with lower nasal epigenetic aging (FDR&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Our findings support the hypothesis that the nasal microbiome is associated with small-to-modest variation in the nasal epigenome. Future research is needed to investigate how the relationship between the nasal microbiome and epigenome is impacted by environmental exposures, as well as the health effects of microbial and epigenetic variation in early life and across the life course.}, }
@article {pmid41749264, year = {2026}, author = {Li, L and Cai, F and Liu, Z and Mo, W and Zhang, J and Qin, J and Liang, C and Xu, H and Liu, S and Tang, S and Peng, P and Liang, J and Ruan, H and Qin, R and Luo, F and Xiong, G and Yang, C and Zou, J and Liu, S and Geng, Y and Huang, J}, title = {Cross-kingdom microbial interactions in the gut during inflammatory bowel disease.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07692-3}, pmid = {41749264}, issn = {1479-5876}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is characterized by chronic, relapsing inflammation of the gastrointestinal tract. Recent studies emphasize the importance of gut microbiome dysbiosis in IBD pathogenesis, where interactions among bacteria, fungi, protozoa, and viruses contribute to inflammation, immune modulation, and epithelial barrier disruption.<br><br>METHODS: A comprehensive narrative literature review was conducted, focusing on human data and preclinical studies. Biomedical databases were searched for research related to microbial communities and their role in IBD development, specifically targeting microbial metabolites, gut fungi, protozoa, and viruses. Relevant studies were analyzed to assess their impact on immune pathways and microbial interactions.<br><br>RESULTS: The review reveals how different microbial kingdoms collaborate through bacteria-fungi, bacteria-protozoa, and phage-bacteria interactions, influencing metabolite production and immune system function. Specific microbial metabolites like short-chain fatty acids (SCFAs), indoles, bile acids, and others play significant roles in regulating mucosal immunity and barrier function. Disruptions in these interactions lead to chronic inflammation and contribute to disease progression. Multi-kingdom therapies, including probiotics, yeast-based treatments, and fecal microbiota transplantation (FMT), show promise but face challenges due to clinical variability.<br><br>CONCLUSION: Understanding IBD as a disruption of microbial ecosystems enables the development of personalized treatment strategies. Multi-omics studies and microbiome-based interventions targeting specific microbial interactions hold potential for more effective, individualized therapies in IBD management. However, further research and larger clinical trials are necessary for translating these findings into routine clinical practice.}, }
@article {pmid41749195, year = {2026}, author = {Kim, SK and Ku, IY and Han, SJ}, title = {Association of PCR-based oral bacterial profiles with fluorescence-detected plaque and caries experience in 3-year-old children: a cross-sectional study.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-07968-6}, pmid = {41749195}, issn = {1472-6831}, }
@article {pmid41748989, year = {2026}, author = {Minty, M and Lê, S and Addi, M and Canceill, T and Thomas, C and Loubieres, P and Burcelin, R and Blasco-Baque, V}, title = {Live tissue microbiota and bacterial translocation: mechanisms and translational perspectives in cardiometabolic diseases.}, journal = {Reviews in endocrine &amp; metabolic disorders}, volume = {}, number = {}, pages = {}, pmid = {41748989}, issn = {1573-2606}, abstract = {The long-standing view of sterile internal tissues has been challenged by accumulating evidence that microbial material, and under specific conditions, viable bacteria may translocate from the gut and oral cavity into metabolic and cardiovascular tissues. This review synthesizes current knowledge on the mechanisms underlying bacterial translocation and its implications for cardiometabolic disease, complemented by original experimental data. Dysbiosis and epithelial barrier disruption facilitate the passage of microbial components and, in some settings, culturable bacteria across mucosal surfaces, triggering local and systemic inflammation. In our murine models, high-fat feeding markedly increased the recovery of culturable bacteria from visceral adipose tissue and spleen, with tissue-specific bacterial signatures enriched in pro-inflammatory taxa. GFP-labelled E. coli translocated more abundantly under metabolic stress, while CD14 deficiency significantly reduced dissemination, highlighting the role of LPS-CD14 signaling. Clinical studies consistently report bacterial DNA and, in some cases, viable bacteria in adipose tissue, liver, atherosclerotic plaques, and heart valves, correlating with immune cell infiltration, cytokine production, and disease severity. However, because internal organs are low-biomass environments, interpretation requires stringent contamination controls and orthogonal evidence of viability and localization. Together, these findings support bacterial translocation as a plausible contributor to chronic low-grade inflammation, insulin resistance, and cardiometabolic pathology. Targeting microbial translocation through barrier reinforcement, microbiota modulation, and metabolite inhibition may offer novel preventive and therapeutic strategies that warrant careful validation.}, }
@article {pmid41748906, year = {2026}, author = {Servetas, SL and Gierz, KS and Hoffmann, D and Ravel, J and Jackson, SA}, title = {Evaluating the analytical performance of direct-to-consumer gut microbiome testing services.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41748906}, issn = {2399-3642}, abstract = {Consumer interest in personal microbiome health has given rise to numerous direct-to-consumer (DTC) microbiome testing services despite questions regarding their analytical and clinical validity, and consumer safety. These tests straddle the line between more strictly regulated medical devices and minimally regulated general health and wellness products; a distinction that may not be readily apparent to consumers. To assess the current state of the industry, we evaluated the performance of seven DTC gut microbiome testing services using a standardized NIST-developed human fecal material. Our results reveal major discrepancies, both within and across the different service providers. Significantly, we found variability between providers was on the same scale as biological variability between different donors. We attribute the observed differences to methodological variability and lack of sufficient quality control. Additionally, we highlight that analytical performance is a prerequisite for making sound clinical recommendations. Our results demonstrate the need for standards to ensure analytical validity and consumer confidence.}, }
@article {pmid41748831, year = {2026}, author = {Moreno, DS and Carvalho, JP and Murray, E and Colombo, NSR and Lamas, A and Cobas, AC and Hill, C and Azeredo, J and Domingues, L}, title = {Evaluation of the delivery of an anti-Listeria endolysin via CRISPR-Cas9 engineered probiotic Saccharomyces boulardii.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41748831}, issn = {1432-0614}, abstract = {Listeriosis is a foodborne infection caused by Listeria monocytogenes that causes febrile gastroenteritis and central nervous system infections and that can often lead to fatality. Upon consumption of contaminated food, Listeria is able to survive a number of gastrointestinal stressors, including competition with the host microbiota. The emergence of antibiotic-resistant clones of L. monocytogenes, together with the side effects of antibiotic treatment, highlights the need for alternatives or additives for its treatment and prevention. Saccharomyces boulardii is a probiotic yeast that is often used alongside antibiotics to minimize side effects since it is not affected by them as a result of its eukaryotic nature. Furthermore, it can be engineered to produce a wide range of molecules. We previously engineered Saccharomyces cerevisiae through CRISPR-Cas9 integration to produce Ply511, a bacteriophage endolysin active against L. monocytogenes, showing the potential of engineered yeast to produce endolysins for biocontrol. In this study, we extended this approach to the probiotic yeast S. boulardii and directly compared the two yeasts as secretion hosts for Ply511. Using a simulated human gastrointestinal environment, we evaluated their ability to retain endolysin activity and reduce L. monocytogenes levels. We then tested the cell extracts from both yeasts in a bacterial consortium termed SImplified HUman intestinal MIcrobiota (SIHUMI), confirming a specificity for Listeria. Finally, we evaluated their activity in a simulated intestinal fermentation using fecal samples from human donors. Overall, this study demonstrates the potential of delivering endolysins to the gut via engineered probiotic S. boulardii. KEY POINTS: CRISPR-Cas9-engineered S. boulardii and S. cerevisiae were compared, both allowing the expression and activity of endolysin Ply511 against L. monocytogenes. Endolysin Ply511 retained its activity against L. monocytogenes in simulated gastrointestinal digestion and was specific against Listeria in a bacterial consortium termed SImplified HUman intestinal MIcrobiota (SIHUMI). Using fecal samples from human donors, the anti-Listeria effect was reduced potentially due to the lower metabolic activity of S. boulardii and the higher competition with the intestinal microbiome.}, }
@article {pmid41748753, year = {2026}, author = {Paredes, J and Schmiester, M and Jenq, R and van den Brink, MRM}, title = {The intestinal microbiota as a key modulator of acute graft-versus-host disease.}, journal = {Nature reviews. Cancer}, volume = {}, number = {}, pages = {}, pmid = {41748753}, issn = {1474-1768}, abstract = {Although allogeneic haematopoietic cell transplantation (allo-HCT) is a curative therapy for various malignant diseases, severe complications such as graft-versus-host disease (GVHD) limit its use. The intestinal microbiome has long been known to modulate allo-HCT outcomes. Studies in the past two decades alone have uncovered a complex interplay between the microbial repertoire and the host immune system during allo-HCT. Preclinical studies have characterized the crosstalk between the microbiome and the immune response of the host, discovered associations between microbial taxa and the integrity of the mucosal intestinal barrier, and investigated the role of microbial metabolites in GVHD. Clinical studies have demonstrated that dysbiosis is an independent predictor of both transplantation-related and GVHD-related mortality, and ongoing trials are investigating microbiota-focused approaches to improve clinical outcomes and reduce GVHD severity after allo-HCT, paving the way for therapeutic applications of microbiome research. We anticipate that these insights will support the development of personalized therapies for patients receiving allo-HCT, integrating microbiome profiles with individual risk data. In this Review, we summarize current preclinical and clinical studies, providing a comprehensive account of translational efforts in this highly dynamic field.}, }
@article {pmid41748638, year = {2026}, author = {Qunli, R and Xiaolan, L and Jingtong, W and Qian, W and Fangzhou, L and Bin, Z and Pan, G and Yingzhe, L and Menglin, S and Zhongjia, T and Bin, C and Jianguo, L}, title = {Network pharmacology, molecular docking, and in vivo experiments reveal the effects of Polygonati Rhizoma on periodontitis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40597-1}, pmid = {41748638}, issn = {2045-2322}, support = {gzwkj2023-520//Science and Technology Fund Project of Guizhou Provincial Health and Wellness Committee/ ; (Qianzhi Gaopei [2026] 2)//Key Projects for Promoting the Utilization of Intellectual Property in Guizhou Province/ ; (Zunshi Kehe SYS [2025]1)//Zunyi Laboratory of Oral Diseases Research/ ; }, abstract = {This study explores Polygonati Rhizoma's therapeutic potential against periodontitis using network pharmacology, molecular docking, and experimental validation to uncover its mechanisms. Active ingredients and targets of Polygonati Rhizoma were sourced from TCMSP and DrugBank, while periodontitis-related targets were retrieved from GeneCards, DisGeNET, and PharmGKB. Core targets were identified via Venny 2.1, and a compound-target network was built using Cytoscape. GO/KEGG analyses and molecular docking were performed. A periodontitis mouse model (C57BL/6) was treated with 500 mg/kg Polygonati Rhizoma or water (control). Post-treatment, tissues and serum were analyzed. Twelve active ingredients in Polygonati Rhizoma (e.g., diosgenin, baicalein) exerted therapeutic effects by targeting core proteins such as MMP9, PPARG, and ESR1, and modulating signaling pathways including PI3K/AKT, IL-17/TNF, and HIF-1. In vivo experiments showed that Polygonati Rhizoma significantly suppressed serum IL-6 and TNF-α levels (P < 0.01), alleviated alveolar bone resorption, and reduced inflammatory infiltration in periodontal tissues of periodontitis mice. Additionally, Polygonati Rhizoma ameliorated histopathological damage in the liver and intestine, modulated the gut microbiota structure by increasing the abundance of Prevotella, and enriched ABC transporter-related functions. Polygonati Rhizoma alleviated alveolar bone loss in a periodontitis mouse model, suppressed inflammation by targeting MMP9, PPARG, and ESR1 via the PI3K/AKT, IL-17/TNF, and HIF-1 signaling pathways, reduced the levels of pro-inflammatory cytokines (IL-6/TNF-α), and modulated the gut microbiota composition. Modulation of the gut microbiome was associated with attenuated systemic inflammation, suggesting a potential role in the therapeutic effects of Polygonati Rhizoma.}, }
@article {pmid41748627, year = {2026}, author = {Huang, Z and Petersen, JM}, title = {Recovery of metagenome-assembled genomes from Spartina alterniflora root microbiome in Fujian Province, China.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-06914-z}, pmid = {41748627}, issn = {2052-4463}, support = {2025J01967//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, abstract = {The saltmarsh cordgrass Spartina alterniflora proliferates along the coast of China. Like all plants, S. alterniflora hosts a specific microbiome that plays crucial roles in sustaining plant growth and health. Till now, very few studies have investigated the root microbiome of S. alterniflora in China, where it is considered an invasive pest. Here, ~350 Gbp metagenomes of S. alterniflora were generated from 8 sampling sites in South Fujian Province, China. 798 bacterial metagenome-assembled genomes (MAGs) and 7 archaeal MAGs were obtained, which were de-replicated into 205 and 3 representative genomes at a 95% ANI cutoff. The recovered bacterial MAGs mainly belonged to Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Campylobacterota. Sedimenticolaceae were prevalent at all sampling sites, accounting for 4-30% of the corresponding MAGs. These genomic datasets provide a new resource for investigating S. alterniflora root microbiomes, particularly valuable considering current efforts to eradicate this species in China.}, }
@article {pmid41748590, year = {2026}, author = {Sharma, S and Woodworth, B and Yang, B and Duan, N and Pheko, M and Moutsopoulos, N and Emiola, A}, title = {Quantitative mapping of pseudouridines in bacterial RNA.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70073-3}, pmid = {41748590}, issn = {2041-1723}, abstract = {RNA pseudouridylation is one of the most prevalent post-transcriptional modifications, occurring universally across all organisms. Although pseudouridines have been extensively studied in bacterial tRNAs and rRNAs, their presence and role in bacterial mRNA remain poorly characterized. Here, we used a bisulfite-based deep sequencing approach to provide a comprehensive and quantitative measurement of bacterial pseudouridines using E. coli, to provide proof of concept. We identified 1,954 high-confidence sites in 1,331 transcripts, which is 29 times above previous estimates and representing almost 30% of the transcriptome. Furthermore, pseudouridines were significantly associated with mRNA stability and enriched in transcripts associated with secondary metabolite production and adaptation to diverse environments. Finally, we mapped pseudouridines in oral microbiome samples of human subjects, demonstrating the broad applicability of our approach in complex microbiomes. This way, we observe that, although uridines are required for modification, mRNAs from GC-rich bacteria harbored more pseudouridine sites than AT-rich genomes in our dataset. Altogether, our work highlights the advantages of mapping bacterial pseudouridines and provides a tool to study posttranscription regulation in microbial communities.}, }
@article {pmid41748585, year = {2026}, author = {Lu, W and Wong, OWH and Zhu, J and Chen, S and Tun, HM and Wan, Y and Xu, Z and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Wong, S and Chan, D and Chan, FKL and Su, Q and Ng, SC}, title = {Gut microbiome composition and strain-sharing in multiplex autism spectrum disorder families.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70142-7}, pmid = {41748585}, issn = {2041-1723}, abstract = {Autism spectrum disorder (ASD) is associated with alteration of gut microbiome, but the influence of familial structure on it remains poorly understood. We investigate gut microbiota across 429 children from multiplex families with multiple affected children, simplex families with one affected child, and single-child ASD families, alongside typically developing controls. We found that children from multiplex families exhibit the most distinct microbiome compositions. Cohabiting siblings in ASD families display higher microbiome similarity than those in healthy families, with a clear gradient in strain-sharing rates that is highest in multiplex, intermediate in simplex, and lowest in healthy siblings. This increased sharing involves specific taxa with reported opportunistic pathogenic potential, such as Eubacterium rectale, alongside reduced sharing of the commensal bacterium Bacteroides xylanisolvens. This suggests that their gut microbiome configurations, which are potentially influenced by shared environmental and host factors, are associated with increased persistence or detectability of specific bacterial strains. Our results underscore the significant contribution of family type to microbial heterogeneity in ASD and provide a hypothesis-generating context for future studies to explore the role of the shared microbial environment in a familial context.}, }
@article {pmid41748159, year = {2026}, author = {Liu, W and Lu, Y and Ng, SC and Chan, FK and Sung, JJ and Yu, J}, title = {Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337280}, pmid = {41748159}, issn = {1468-3288}, abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored.<br><br>OBJECTIVE: We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application.<br><br>DESIGN: We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice.<br><br>RESULTS: We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%).<br><br>CONCLUSION: Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.}, }
@article {pmid41748098, year = {2026}, author = {Jawale, N and Shenberger, J and Shetty, AK and Gunasekaran, V and Garg, PM}, title = {NEC-associated Bronchopulmonary Dysplasia and the Gut-Lung Axis in Preterm infants.}, journal = {American journal of perinatology}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2821-3458}, pmid = {41748098}, issn = {1098-8785}, support = {U54GM115428/GM/NIGMS NIH HHS/United States ; }, abstract = {Prevailing evidence establishes the influence of an infant's gut microbiota on immune responses and associated intestinal disorders. The role of functional programming of effector immune cells at extra-intestinal mucosal sites, particularly the lung, is increasing in interest. Animal and human studies show that microbial ligands and metabolites produced by the gut microbiome shape respiratory immunity, while lung directed insults, in turn, influence gut microbiome function. Common connections between development of gut and lung microbiomes and reciprocal signaling between the two organ systems has reinforced the concept of a gut-lung axis. In that context, this review evaluates the mechanistic evidence associating preterm acute lung injury to the development of necrotizing enterocolitis, and subsequently, to the progression to chronic lung disease or bronchopulmonary dysplasia. By focusing on mediators involved in this gut-lung crosstalk, we seek to highlight avenues to prevent or reduce the severity of two of the major morbidities of prematurity.}, }
@article {pmid41748043, year = {2026}, author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG}, title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {113079}, doi = {10.1016/j.exger.2026.113079}, pmid = {41748043}, issn = {1873-6815}, abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.}, }
@article {pmid41748030, year = {2026}, author = {Dong, W and Ren, X and Qu, X and Li, J and Li, M and Wang, S and Liu, P and Sun, J and Jiang, L and Li, H and Wang, C and Zhang, Z}, title = {Maternal intestinal dysbiosis mediated by sevoflurane exposure during pregnancy leads to altered gut microbiota and metabolites and cognitive dysfunction in the offspring.}, journal = {Neurotoxicology}, volume = {}, number = {}, pages = {103413}, doi = {10.1016/j.neuro.2026.103413}, pmid = {41748030}, issn = {1872-9711}, abstract = {Prenatal exposure to anesthetic drugs, such as sevoflurane, may exert a long-lasting impact on neurological function in the offspring. This study aims to investigate the consequence of prenatal sevoflurane exposure on cognitive function in offspring mice. C57BL/6J mice of 2-3 months of age were housed under standard environmental conditions. Pregnant mice were randomly assigned to receive either sevoflurane exposure or to serve as control group. Behavioral tests conducted included the novel object recognition test and the Morris water maze test. During the terminal phase of the experiment, fecal samples from the mother and offspring, as well as serum and hippocampal samples from the offspring, were collected for microbiome and metabolomic analyses. Behavioral experiments showed that cognitive function was impaired in the offspring mice of the anesthetized group. In addition, sevoflurane altered the gut microbiota composition in pregnant mice and their offspring, with reduced Prevotella abundance in the anesthetized group. Metabolomics analyses showed that anesthetized and control offspring also exhibited significant differences in metabolites in fecal, serum, and hippocampal samples, particularly in the glycerophospholipid metabolism pathway. Further correlation analyses showed a significant correlation between the gut microbiota (especially Prevotella) and differential metabolites in the hippocampus. These results indicate that prenatal sevoflurane exposure disrupts gut microbiota and metabolic pathways, potentially contributing to cognitive deficits in offspring via the gut-brain axis, highlighting risks of anesthesia during pregnancy on fetal neurodevelopment.}, }
@article {pmid41748020, year = {2026}, author = {Edslev, SM and Liu, CM and Lo, BZS and Meiniche, H and Lilje, B and Park, DE and Rendboe, A and Pham, T and Salazar, JE and Toudahl, T and Ingham, AC and Aziz, M and Bartels, MD and Andersen, PS and Skov, RL and Price, LB and Stegger, M}, title = {Changes in nasal and throat microbiota composition during and after mupirocin and chlorhexidine decolonisation treatment in asymptomatic MRSA carriers: a longitudinal observational study.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.020}, pmid = {41748020}, issn = {1469-0691}, abstract = {OBJECTIVES: Decolonisation treatment of asymptomatic methicillin-resistant Staphylococcus aureus (MRSA) carriage is recommended as a preventive measure in several countries, including Denmark. This study aimed to investigate the temporal dynamics of the nasal and throat microbiota in MRSA carriers undergoing decolonisation treatment and to assess bacterial changes associated with treatment success.<br><br>METHODS: Adults with asymptomatic nasal MRSA carriage (n=34) were included in this prospective observational study. Participants underwent a 5-day decolonisation regimen consisting of 2% mupirocin nasal ointment and daily skin cleansing with 4% chlorhexidine soap. Nasal and throat samples were collected at multiple time points from baseline to 6 months post-treatment and analysed by 16S rRNA gene sequencing. A reference group of untreated community-dwelling adults (n=116) served as comparison.<br><br>RESULTS: At one-month follow-up, 21 of 34 participants (62%) were successfully decolonized, while 13 (38%) remained MRSA-positive at one or more body sites. At baseline, no nasal bacterial taxa were significantly associated with nasal MRSA decolonisation outcome. The nasal bacterial community changed significantly within the first 2 days of treatment and remained distinct from the baseline composition for 30 days, both among those with successful decolonisation and those who remained colonized with MRSA. Nasal community state types (CSTs) characterized by S. aureus, coagulase-negative staphylococci, Moraxella, and Dolosigranulum became less prevalent during treatment, whereas CSTs dominated by Corynebacterium and Cutibacterium increased in prevalence. Among successfully decolonised participants, the nasal microbiota at 3 and 6 months post-treatment continued to differ from baseline and from the reference group, mainly due to a sustained depletion of Dolosigranulum and Moraxella. In contrast, the throat microbiota showed only short-term compositional changes.<br><br>CONCLUSIONS: Decolonisation treatment significantly alters the nasal microbiota, with both short-term and persistent effects. Future strategies could consider supplementation with beneficial nasal commensals, like Dolosigranulum, after treatment to promote microbiome recovery.}, }
@article {pmid41748019, year = {2026}, author = {Piccinno, G and Asnicar, F}, title = {Advanced computational analysis in metagenomic studies to support precision medicine.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.018}, pmid = {41748019}, issn = {1469-0691}, abstract = {BACKGROUND: The human microbiome has been linked to host health and is suggested to play a direct role in the onset of certain human diseases, as well as in impacting treatment efficacy. Characterizing the microbiome composition and its interaction with the host is now supported by an established, continuously improving set of bioinformatic and statistical resources that enable reproducible answers to fundamental questions about microbiome sample composition and its association with sample and host information. Extensive evidence highlighted that, in a non-diseased state, the microbiome composition is determined by multiple factors, including the acquisition of microbes at birth, lifestyle, dietary patterns, social interactions, antibiotic use, or probiotic intake, among others. In disease states, the microbiome may alter its composition and, in some cases, present specific biomarkers, as in colorectal cancer. Some microbiome components have also been associated with improved immunotherapy response in clinical oncology, suggesting a potential beneficial role for certain species and supporting the use of the microbiome as an additional therapeutic tool in these scenarios.<br><br>OBJECTIVES: This review summarizes computational approaches for microbiome characterization, highlights key findings on microbiome-disease associations, and provides a perspective on directions and open questions relevant to address in the future.<br><br>SOURCES: We selected scientific studies and reviews, published in peer-reviewed journals, based on their impact in the field and relevance to the topic of this manuscript. Literature selection was conducted by reviewing scientific publications retrieved from major scientific databases, such as PubMed, and by combining with the authors' knowledge of the literature.<br><br>CONTENT: Here we review computational approaches to characterize and model the microbiome's structure in health and disease and discuss multi-cohort data analysis, integration, and validation methods.<br><br>IMPLICATIONS: Improved microbiome characterization supports precision medicine by informing prevention or treatment, leveraging refined microbiome signature and modulation strategies.}, }
@article {pmid41748016, year = {2026}, author = {de Gaay Fortman, DPE and Kullberg, RFJ and Wiersinga, WJ and Haak, BW}, title = {Dynamics of the gut and lung microbiota in severe infections: from observational studies to therapeutic strategies.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.02.016}, pmid = {41748016}, issn = {1469-0691}, abstract = {BACKGROUND: Severe infections and sepsis are characterized by a disruption of intestinal and respiratory microbial communities. Loss of obligate gut anaerobes and depletion of immunomodulatory metabolites disrupt mucosal integrity, impair immune homeostasis, and increase susceptibility to secondary infection and organ failure.<br><br>OBJECTIVES: To summarize the current understanding of gut and lung microbiome dynamics during severe infections, describe immunometabolic crosstalk along the gut-lung axis, and identify microbiome-targeted strategies to improve outcomes.<br><br>SOURCES: Peer-reviewed preclinical and clinical studies on microbiota composition, metabolite signaling, and therapeutic modulation in severe infections published up to October 2025.<br><br>CONTENT: In health, obligate anaerobes such as Faecalibacterium and Blautia species are thought to support mucosal homeostasis through short-chain fatty acids, secondary bile acids, and tryptophan-derived indoles that calibrate systemic immunity and suppress overgrowth of opportunistic pathogens. Sepsis-associated inflammation, hypoperfusion, and antibiotic exposure deplete obligate anaerobes, shifting the gut ecosystem toward Enterococcus, Enterobacterales, and Candida species, accompanied by disruption of metabolite-mediated immune homeostasis. The lungs, which contain their own low biomass microbiota, similarly undergo a loss of diversity with overrepresentation of Proteobacteria during critical illness, a pattern that has been linked to impaired alveolar immunity and adverse outcomes. Experimental studies indicate that gut-derived metabolites and migrating immune cells shape pulmonary responses, while loss of gut-lung compartmentalization may permit bacterial translocation and contribute to systemic inflammation. Defined live anaerobic consortia and postbiotics represent promising experimental strategies to restore microbial balance during severe infections, but the most immediate opportunity lies in antibiotic stewardship that limits unnecessary anaerobe-active coverage.<br><br>IMPLICATIONS: The obligately anaerobic microbiome is central to host-pathogen interactions in severe infection. Preserving and restoring anaerobic and pulmonary microbial communities through rational antimicrobial use and mechanistically informed microbiome-based interventions may improve outcomes and recovery after critical illness.}, }
@article {pmid41748012, year = {2026}, author = {Zhang, ML and Jin, WL}, title = {Dysregulated energy homeostasis at the crossroads of cancer-depression comorbidity: A brain-body-tumor interaction perspective.}, journal = {Cancer letters}, volume = {645}, number = {}, pages = {218351}, doi = {10.1016/j.canlet.2026.218351}, pmid = {41748012}, issn = {1872-7980}, abstract = {Cancer-depression comorbidity (CDC), the bidirectional and clinically consequential coexistence of cancer and major depressive disorder, represents a particularly severe and prognostically adverse clinical state. Compared with either condition alone, patients with CDC show poorer adherence to anticancer treatment, reduced quality of life, and increased all-cause and cancer-specific mortality. Epidemiological evidence suggests that depression may raise long-term risk for several cancers, while cancer itself frequently precipitates depressive syndromes, supporting a reciprocal relationship between the two conditions. In this Review, we propose that CDC is best conceptualized not as two separate entities but as a unified disorder of systemic energy homeostasis. We present a brain-body-tumor interaction perspective and outline a tri-level regulatory model linking central energy-sensing circuits and neuroendocrine control with peripheral metabolic allocation and tumor microenvironmental demands. Central to this model is the dysregulated energy homeostasis, wherein chronic stress, inflammation, and tumor burden progressively erode bioenergetic capacity across the brain and body. Mitochondrial dysfunction serves as the key integrator and executor of these insults, linking cellular ATP failure to systemic catabolism, immune dysfunction, and depressive phenotypes. Finally, we highlight that therapies targeting energy homeostasis, including mitochondrial support, metabolic and immunometabolic reprogramming, nutritional or microbiome based approaches, and behavioral interventions, may provide dual benefits for both cancer control and mood regulation in CDC.}, }
@article {pmid41747877, year = {2026}, author = {Waghmare, A and Rahangadale, S and Khare, K and Taksande, B and Umekar, M and Mangrulkar, S}, title = {Interweaving microglial senescence and gut microbiome dynamics in Alzheimer's disease - Mechanisms and therapeutic frontiers.}, journal = {Molecular and cellular neurosciences}, volume = {}, number = {}, pages = {104075}, doi = {10.1016/j.mcn.2026.104075}, pmid = {41747877}, issn = {1095-9327}, abstract = {Alzheimer's disease (AD), a prevalent neurodegenerative disorder characterized by cognitive impairment and neuronal degeneration, is increasingly recognized as being driven not only by the traditional amyloid-beta and tau pathologies but also by persistent neuroinflammation and systemic immune dysregulation. Emerging evidence implicates microglia senescence and gut microbiota dysbiosis is critical contributors to the neuroinflammatory landscape. Senescent microglia marked by reduced phagocytic ability and a pro-inflammatory secretory profile, are unable to clear pathogenic stimuli, thereby intensifying neuronal damage. Simultaneously, gut dysbiosis, characterized by a reduction in beneficial bacteria and an increase in endotoxin-producing species, elevates systemic inflammation and compromises the intestinal and blood brain barrier. Microbial metabolites, such as short-chain fatty acids (SCFAs) and lipopolysaccharides (LPS), affect microglial activation through the gut-brain axis, primarily via the TLR4/NF-κB and NLRP3 inflammasome pathways, thus promoting microglial senescence and exacerbating AD pathology. Therapeutic approaches that target these interacting pathways are rejuvenation of microglia with senolytics and stimulation of TREM2; regulation of gut microbiota with probiotics, prebiotics, lifestyle modification, dietary intervention; and fecal microbiota transplantation. Precision medicine approaches incorporating microbiome profiling and immunogenetic analysis will enhance these treatments. This review combines mechanistic insight into microglial aging and gut-brain interaction, emphasizes their synergistic role in AD pathogenesis, and delineates integrated therapeutic strategies. Dissection of the gut-microglia axis can reveal novel targets for early intervention to counteract neuroinflammation, improve cognitive function, and slow disease progression in AD.}, }
@article {pmid41747787, year = {2026}, author = {Yiğit, &#x130;K and Türsen, &#xdc; and Türsen, B and Solak, B and Bakay, &#xd6;SK and Kroumpouzos, G}, title = {Probiotics for Skin Aging and Skin Conditions in the Elderly.}, journal = {Clinics in dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clindermatol.2026.02.016}, pmid = {41747787}, issn = {1879-1131}, abstract = {Skin aging is increasingly recognized as a process associated with the microbiome, characterized by barrier dysfunction, chronic low-grade inflammation, and degradation of the extracellular matrix. Current evidence suggests that age-related changes in both skin and gut microbiota contribute to "inflammaging" and impaired cutaneous homeostasis through the gut-skin axis. In recent years, probiotics, prebiotics, and postbiotics have emerged as potential modulators of skin aging. Probiotics, in particular, are noted for their ability to modulate the gut-skin axis, decrease inflammation, and promote skin rejuvenation. In this discussion, we highlight current evidence on the role of probiotic-based interventions in skin aging and geriatric dermatoses. Probiotics, prebiotics, and postbiotics modulate skin aging by restoring microbial balance, enhancing barrier integrity, and regulating immune and oxidative pathways, particularly through the gut-skin axis. Topical formulations act locally by reinforcing tight junctions, increasing ceramide synthesis, and suppressing inflammatory mediators and matrix metalloproteinases, whereas oral probiotics exert their effects by modulating gut dysbiosis, reducing systemic inflammation, and improving extracellular matrix homeostasis. Clinical studies have shown improvements in skin hydration, elasticity, wrinkle depth, photoprotection, and wound healing. Although there have been promising results, several challenges remain about strain specificity, formulation stability, regulatory constraints on viable organisms, and the paucity of powered randomized clinical trials. Overall, microbiome-targeted interventions hold promise as a strategy for reducing age-related skin changes and managing skin conditions in the elderly.}, }
@article {pmid41747778, year = {2026}, author = {Dubois, L and Chaussard, A and Seksik, P and Nancey, S and Nachury, M and Treton, X and Buisson, A and Carbonnel, F and Fumery, M and Peyrin-Biroulet, L and Boureille, A and Hebuterne, X and Serrero, M and Louis, E and Blanc, P and Brot, L and Rolhion, N and Vermeire, S and Manichanh, C and Fossmark, R and Bezault, M and Uzzan, M and ,  and Allez, M and Sokol, H}, title = {Uncovering the dynamics of mucosa-associated microbiota in post-operative recurrence of Crohn's disease.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.01.043}, pmid = {41747778}, issn = {1528-0012}, abstract = {BACKGROUND: About 50 to 75% of Crohn's Disease patients (CD) need bowel resection. Postoperative recurrence of Crohn's disease is frequent. Here, we investigate the evolution of the mucosa-associated microbiota along the Rutgeerts score measuring endoscopic recurrence after surgery.<br><br>METHODS: We used 16S rRNA and ITS2 sequencing to profile the mucosa-associated microbiota of biopsies from CD patients at the time of surgery (M0, n=139) and later, at the time of endoscopic assessment of recurrence (M6, n=125).<br><br>RESULTS: While the effect of surgery and recurrence were moderate on the overall microbiota composition, we identified specific microbial signatures displaying differential relative abundance when accounting for clinical covariates. The relative abundance of certain species, notably a decrease of Faecalibacterium prausnitzii, or increase of Akkermansia muciniphila, was differentially associated with a whole range of Rutgeerts score or with more specific scores characterizing the inflammation of the anastomosis or the ileum. In addition, machine learning performances were impacted by the consideration of the Rutgeerts score as a multilevel prediction instead of a binary classification, further confirming the need to consider its full range. Finally, we investigated the community dynamics, which highlighted a denser network organisation after surgery and in the absence of recurrence, along with changes in keystone species.<br><br>CONCLUSION: Altogether, these results provide further understanding of the effects of ileal resection patients with CD and show that disease recurrence is a dynamic process characterized by several waves of changes in the microbiota composition.}, }
@article {pmid41747730, year = {2026}, author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C}, title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2026.01.021}, pmid = {41747730}, issn = {1097-4172}, abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.}, }
@article {pmid41747725, year = {2026}, author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z}, title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.002}, pmid = {41747725}, issn = {1934-6069}, abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.}, }
@article {pmid41747724, year = {2026}, author = {Xu, D and Xia, A and Huang, R and Huang, Y and Zhao, B and Shen, Q and Wang, G and Wang, Q and Liu, H and Huang, L and Xu, JR and Jiang, C}, title = {Bacterial entrapment of a fungal carbon repressor prevents plant colonization.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.02.001}, pmid = {41747724}, issn = {1934-6069}, abstract = {Carbon catabolite repression (CCR) acts as a switch, reprogramming nutrient utilization in fungal pathogens during the growth-to-colonization transition. However, whether this regulatory system can be exploited by other microbes remains unknown. Here, we demonstrate that Pseudomonas CXZ-8 attenuates the virulence of Fusarium graminearum by hijacking fungal CCR. CXZ-8 disrupts the infection-induced nuclear-to-cytoplasmic relocalization of the CCR master regulator FgCreA, thereby suppressing FCO1 expression, which is crucial for both host cell wall degradation and nutrient acquisition. This interference also benefits the bacterium by preventing the accumulation of host-derived indole derivatives and fungal mycotoxins that threaten its survival. Notably, approximately 20% of field-isolated bacteria exhibit similar FgCreA-stabilizing activity. Furthermore, we assembled a microbial consortium enriched for CCR-targeting bacteria, which conferred broad-spectrum disease resistance in field trials. These findings reveal a novel mode of interkingdom interference and establish CCR as a conserved microbial vulnerability, with implications for sustainable, microbiome-based crop protection.}, }
@article {pmid41747696, year = {2026}, author = {Shen, S and Zhou, Y and Zhao, R and Liu, M and Fu, W and Zhao, S and Yan, C and Gao, Q and Zhang, D and Wang, Y and Jia, H and Wei, Y}, title = {Microplastic-pathogen interactions differentially modulate tomato Fusarium wilt severity: The dependence of polymer biodegradability.}, journal = {Journal of hazardous materials}, volume = {506}, number = {}, pages = {141594}, doi = {10.1016/j.jhazmat.2026.141594}, pmid = {41747696}, issn = {1873-3336}, abstract = {Microplastics (MPs) are pervasively present in agricultural soils, adversely affecting rhizosphere ecology and plant physiology; however, their influence on soil-borne pathogens and crop health remains poorly understood. Here, we systematically investigate the effects of exogenous MPs on Fusarium oxysporum f. sp. lycopersici (FOL) colonization, virulence and antagonistic network in tomato rhizosphere using hydroponic, soil-based, and in vitro co-culture assays. We found that conventional polyethylene (PE) exacerbated wilt severity by 19 %, whereas biodegradable polylactic acid (PLA) reduced it by 14 %. This divergence arose from MP-mediated pathogen colonization patterns: PE adhered to root surfaces and facilitated colonization, whereas PLA leachates generated during degradation suppressed growth. Gas chromatography-mass spectrometry analysis and in vitro antifungal assays identified two key antifungal pathways: the intermediate L-lactide induced rhizosphere acidification, and the leached plasticizer tris(2-butoxyethyl) phosphate, which exhibited direct antifungal activity (minimum inhibitory concentration = 50 mg·L[-1]; inhibition rate = 15.5 %). Transcriptomic profiling revealed that PE upregulated N transport and metabolism genes in FOL, whereas PLA downregulated the expression of the plant cell wall-degrading enzyme gene FOXG_11947 (log2 fold change = -3.18), reducing β-1,3-glucanase activity by 75.5 %, and consequently impairing pathogen virulence toward the host roots. Beyond singular interaction with FOL, PLA shifted rhizosphere microbiome toward an antagonistic network, which consequently reduced Fusarium abundance by 1.31 %. Our findings establish a polymer-dependent mechanism by which MPs regulate soil-borne disease and underscore an underappreciated co-exposure threat, providing a scientific basis for sustainable plastic use in agriculture.}, }
@article {pmid41747651, year = {2026}, author = {Xiao, R and He, Y and Mao, X and Sun, L and Ao, L and Wang, L and Zhai, Q and Zhao, J and Chen, W and Wang, G and Guo, J}, title = {A multi-strain probiotic formulation alleviates chronic constipation in middle-aged and older adults: A randomized, double-blind, placebo-controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {59}, number = {}, pages = {106598}, doi = {10.1016/j.clnu.2026.106598}, pmid = {41747651}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: Chronic constipation is prevalent among middle-aged and older adults, with current interventions often limited by modest efficacy and adverse effects. Probiotics have emerged as a safe, promising modality; we aimed to evaluate a 28-day multi-strain probiotic in this population using clinical and mechanistic endpoints.<br><br>METHODS: We conducted a randomized, double-blind, placebo-controlled trial in adults with chronic constipation: 132 were randomized (probiotics n = 66; placebo n = 66), and 100 completed per protocol (50/50).The primary endpoint was weekly complete spontaneous bowel movements (CSBMs) at day 28; secondary endpoints included Bristol Stool Form Scale (BSFS), Patient Assessment of Constipation Symptoms (PAC-SYM), bloating scores, and multi-omics profiling (gut microbiota and fecal metabolites at days 0/14/28), with targeted fecal short-chain fatty acids (SCFAs). A pre-specified responder was defined as week-4 CSBMs &#x2265;3 and increases &#x2265;1 from baseline.<br><br>RESULTS: At day 28, probiotics yielded higher CSBMs than placebo (4.53 &#xb1; 1.17 vs 2.40 &#xb1; 1.01, P < 0.0001), improved stool form (higher BSFS), reduced PAC-SYM, and markedly alleviated bloating (0.70 &#xb1; 0.46 vs 2.60 &#xb1; 0.93, P < 0.0001). Microbiologically, &#x3b1;-diversity increased and &#x3b2;-diversity separated between groups at days 14 and 28 (PERMANOVA P = 0.003 and 0.001); Faecalibacterium, Lactobacillus, and Bifidobacterium increased, whereas Enterobacter, Collinsella, and Oscillibacter declined. Untargeted metabolomics indicated enrichment of SCFA biosynthetic pathways (butanoate/propanoate), and targeted assays confirmed higher fecal acetate and butyrate at day 28 (P < 0.01 and P < 0.05), with no significant change in propionate or valerate (both P > 0.05). Responder rates were 88 % (44/50) with probiotics versus 26 % (13/50) with placebo; within the probiotic arm, &#x394;Faecalibacterium and &#x394;butyrate correlated positively with &#x394;CSBM, while &#x394;Enterobacter correlated negatively.<br><br>CONCLUSIONS: In middle-aged and older adults with chronic constipation, a 28-day multi-strain probiotic significantly increases bowel movement frequency, improves symptoms-especially bloating-and favorably remodels gut microbiota and SCFA-related pathways, supporting its use as a nutritional intervention.<br><br>TRIAL REGISTRATION: ChiCTR2200065905.}, }
@article {pmid41747600, year = {2026}, author = {Ghasemzadeh, N and Nejati, ST and Kazemi, KS and Emrahoglu, S and Masouleh, SS and Safarzadeh, D and Irannejadrankouhi, S and Tabari, MAK}, title = {NLRP3 inflammasome as a therapeutic target in oral squamous cell carcinoma: implications for tumorigenesis and immunomodulation.}, journal = {International immunopharmacology}, volume = {175}, number = {}, pages = {116432}, doi = {10.1016/j.intimp.2026.116432}, pmid = {41747600}, issn = {1878-1705}, abstract = {Oral squamous cell carcinoma (OSCC) is a prevalent and aggressive malignancy strongly influenced by chronic inflammation. Central to this process is the NLRP3 inflammasome, a cytosolic multiprotein complex that senses cellular stress and mediates the maturation of pro-inflammatory cytokines such as IL-1β and IL-18. Recent studies highlight NLRP3's dual role in OSCC pathogenesis, contributing to tumor progression, immune evasion, and therapy resistance, while also possessing potential tumor-suppressive capabilities via pyroptosis induction. NLRP3 activation promotes epithelial-mesenchymal transition, lymphangiogenesis, and chemoresistance through signaling networks involving SOAT1, miR-22, and PRDX1. Additionally, it regulates the tumor immune microenvironment by modulating tumor-associated macrophages, neutrophils, and cytokines like IL-6 and IL-1β. Oral pathogens further shape this landscape by influencing NLRP3 activity, linking the microbiome to carcinogenesis. Despite its protumoral functions, NLRP3 can stimulate anti-tumor immunity under certain conditions, making it a complex therapeutic target. Emerging strategies to modulate NLRP3 include small-molecule inhibitors (e.g., MCC950, BAY-117082), plant-derived compounds (e.g., oridonin, Bacopa monnieri), and immunotherapy approaches, including intratumoral NLRP3 agonists combined with checkpoint blockade. This review synthesizes the multifaceted roles of NLRP3 in OSCC, highlighting its centrality in inflammation-driven tumor biology and its promise as a therapeutic target. Understanding the contextual duality of NLRP3 activation is critical for developing precision therapies that disrupt its tumor-supportive effects while preserving or enhancing its immunogenic functions.}, }
@article {pmid41747440, year = {2026}, author = {Eryılmaz, HS and Günal-Köroğlu, D and Ozkan, G and Öztekin, S and Capanoglu, E}, title = {Honey-associated microorganisms and antimicrobial activity: Probiotic, synbiotic, and postbiotic properties.}, journal = {International journal of food microbiology}, volume = {452}, number = {}, pages = {111686}, doi = {10.1016/j.ijfoodmicro.2026.111686}, pmid = {41747440}, issn = {1879-3460}, abstract = {Honey harbors a diverse microbial ecosystem, including Lactobacillaceae, Bacillaceae, and fructophilic lactic acid bacteria (FLAB), as well as selected yeasts, which collectively contribute to gut health, immune modulation, and antimicrobial activity. These honey-associated microorganisms exhibit probiotic-like traits such as acid and bile tolerance, pathogen inhibition, and adhesion-related properties, suggesting potential functional relevance, although most evidence currently derives from in vitro and preclinical studies. Unlike previous reports, this review integrates both probiotic and postbiotic mechanisms of honey-associated microorganisms with the effects of processing and storage on microbial viability and functional compounds, providing a mechanistic perspective on their biological actions. Raw honey maintains superior microbial diversity and antibacterial properties, largely driven by organic acids, bacteriocins, antimicrobial peptides, and exopolysaccharides produced by resident microorganisms; however, these properties can be partially lost during thermal processing due to reduced microbial viability and enzyme activity. In this context, emerging alternative technologies, such as ultrasound, microwave, and high-pressure treatments, offer promising strategies to ensure microbial safety while preserving honey's bioactive integrity, including probiotic and postbiotic functionality, as well as synbiotic potential. Additionally, honey-derived microorganisms produce enzymes, prebiotics, and secondary metabolites that contribute to its functional potential. The magnitude and profile of these effects vary according to geographic origin, botanical source and bee-related factors. By combining insights on microbial diversity, functional metabolites, and emerging preservation strategies, this review provides a unique and integrative perspective on harnessing honey's probiotic, synbiotic and postbiotic potential, while highlighting current knowledge gaps, future research needs, and opportunities for the development of honey-based functional foods and biotechnological applications. Future research should prioritize strain-level safety assessment, standardization of isolation and identification methods, validation of health effects through well-designed clinical studies, and the optimization of processing strategies to enable the industrial application of honey-derived probiotics, synbiotics, and postbiotics.}, }
@article {pmid41747420, year = {2026}, author = {Dong, H and Wang, X and Ma, T and Shan, T and He, W and Zhang, G and Xia, Z and Yang, W and Chen, L and Niu, P and Chen, T}, title = {The impact of microbiome dysbiosis on manganese-induced neurotoxicity: Brain metabolomics and multi-organ 16S rRNA profiling in mice.}, journal = {Ecotoxicology and environmental safety}, volume = {312}, number = {}, pages = {119931}, doi = {10.1016/j.ecoenv.2026.119931}, pmid = {41747420}, issn = {1090-2414}, abstract = {Manganese (Mn) is an essential metal but becomes neurotoxic upon excessive exposure. Although emerging evidence links Mn toxicity to gut microbiome alterations, little is known about how Mn affects microbial communities across multiple mucosal sites or how these changes relate to brain metabolism. This study aimed to investigate the impact of long-term Mn exposure on microbiota across the oral, nasal, lung, and gut compartments and its association with striatal metabolic alterations. The mice were intranasally exposed to MnCl2 for four months. Microbiota composition was profiled by 16S rRNA sequencing, and striatal metabolites were assessed by untargeted LC-MS metabolomics. Correlation analyses were performed to identify multisite metabolite-microbiota interaction networks. Chronic Mn exposure impaired locomotor function and elevated serum Mn levels. Mn induced significant dysbiosis across all examined sites, characterized by reduced beneficial taxa (e.g., Butyricicoccus, Blautia) and increased conditionally pathogenic taxa (e.g., Alistipes, Stenotrophomonas, Xanthomonadaceae). Some taxa responded across multiple sites but exhibited compartment-specific patterns. Striatal metabolomics revealed perturbations in amino acid and lipid metabolism. Cross-site correlation analyses identified a coordinated metabolite-microbiota network, with gut taxa showing the strongest associations, while oral, lung, and nasal taxa also contributed to the systemic metabolic variability. These findings demonstrate that chronic Mn exposure disrupts microbial homeostasis across multiple compartments and alters key brain metabolic pathways. Overall, this study provides an integrative framework highlighting a multi-organ microbial axis potentially associated with Mn neurotoxicity.}, }
@article {pmid41747184, year = {2026}, author = {Tomar, AK and Jha, N and Priyadarshini, E and Gautam, R and Nirala, JP and Rajamani, P}, title = {Effects of industrial, scientific, and medical (ISM) band frequency 2.45 GHz on membrane integrity and oxidative stress of human skin bacteria.}, journal = {International journal of radiation biology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09553002.2026.2636305}, pmid = {41747184}, issn = {1362-3095}, abstract = {PURPOSE: To investigate the effects of 2.45 GHz radiofrequency radiation (RFR) on oxidative stress and membrane integrity of human skin bacteria.<br><br>MATERIALS AND METHODS: Cultures of Staphylococcus epidermidis, Micrococcus luteus, and Enterobacter cloacae were exposed to 2.45&#x2009;GHz RFR. Oxidative stress was assessed by quantifying hydroxyl (&#x2022;OH) and superoxide (O2&#x2022;[-]) radicals and total intracellular ROS (DCFH2-DA assay). Lipid peroxidation (MDA levels) and protein carbonyl content were measured as oxidative damage markers. Membrane integrity was examined by SEM and TEM imaging and by evaluating protein and carbohydrate leakage. All experiments were performed with at least three independent biological replicates.<br><br>RESULTS: RFR-exposed bacteria exhibited a marked increase in ROS generation compared to sham and control groups. Total intracellular ROS, hydroxyl radicals, and superoxide radicals were significantly elevated (&#x223c; 2 fold), indicating strong oxidative stress induction. This biochemical stress correlated with structural alterations: SEM and TEM revealed disrupted cell membranes and cytoplasmic disorganization. Functionally, exposed bacteria showed enhanced membrane permeability, evidenced by substantial leakage of proteins and carbohydrates into the extracellular environment. Furthermore, oxidative damage was confirmed biochemically, with significantly elevated malondialdehyde (MDA >1.5 fold) levels reflecting lipid peroxidation, and increased protein carbonyl (>2 fold) content indicating oxidative modification of proteins. These effects were consistent across all three bacterial species, although E. cloacae demonstrated more pronounced damages. Collectively, these findings highlight a clear link between RFR-induced ROS overproduction, oxidative macromolecular damage, and compromised cellular integrity.<br><br>CONCLUSIONS: Exposure to 2.45&#x2009;GHz RFR induces oxidative stress, membrane disruption, and macromolecular leakage in skin-associated bacteria, suggesting possible risks to skin microbiome stability under high-RFR environments.}, }
@article {pmid41747050, year = {2026}, author = {Corral López, R and Bonachela, JA and Dominguez-Bello, MG and Manhart, M and Levin, SA and Blaser, MJ and Muñoz, MA}, title = {Imbalance in gut microbial interactions as a marker of health and disease.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6788}, pages = {890-895}, doi = {10.1126/science.ady1729}, pmid = {41747050}, issn = {1095-9203}, abstract = {Imbalances in the human gut microbiome, or dysbioses, are associated with multiple diseases but remain poorly understood. Existing biomarkers of dysbiosis fail to capture the ecological mechanisms that differentiate healthy from diseased microbiomes. We have developed a metric, the ecological network balance index (ENBI), that quantifies the balance between positive and negative microbial interactions. This metric was inspired by the phenomenology observed in a model for gut microbiome dynamics that we introduce in this work, which revealed alternative stable states with distinct emergent microbial communities: a healthy state dominated by negative interactions and a dysbiotic state dominated by positive interactions. The ENBI robustly differentiates these states in both simulated and empirical datasets spanning multiple diseases and correlates with disease progression in conditions such as colorectal cancer, which underscores its potential as a diagnostic tool.}, }
@article {pmid41747025, year = {2026}, author = {Kaur, L and Bell, TH and Sadeghi, J and Hockett, KL}, title = {Disease-Suppressive Phyllosphere Microbiomes: A Perspective on Microbiome Transplantation for Sustainable Agriculture.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-03-25-0116-PER}, pmid = {41747025}, issn = {0031-949X}, abstract = {The plant-associated microbiome is a key contributor to plant health, influencing nutrition, stress tolerance, and disease outcomes. Manipulating these microbiomes is a potentially powerful tool for plant disease management. However, the implementation of direct plant microbiome manipulation is rare, in contrast to medical fields, in which microbiome transplantation has been a growing focus of research for several decades, particularly for treatment of conditions like Clostridioides difficile induced diarrhea and bacterial vaginosis. This concept has more recently gained attention in agriculture, as rhizosphere microbiome transplants are being tested for their ability to promote crop health and productivity. A few research groups have also explored the potential of transplanting phyllosphere microbiomes to combat foliar phytopathogens. Microbiome transplantation could occur either as a direct transplant or following iterative passaging, in which beneficial traits are gradually enhanced through multiple transfers in set environments. In this Perspective, we discuss the concept and potential applications of phyllosphere microbiome transplantation to develop disease-suppressive microbiomes, including recent advances, and offer insights into its prospects for enhancing the sustainability of plant disease management. Before realizing the full potential of disease-suppressive phyllosphere microbiomes, however, several challenges need to be addressed, including establishment of standardized protocols, elimination of pathogens from the microbiome, and regulatory considerations.}, }
@article {pmid41747011, year = {2026}, author = {Zhuo, Y and Yu, L and Jiang, C and Wang, K}, title = {Understanding the Role of Gut Microbial Enzyme in CMD.}, journal = {Circulation research}, volume = {138}, number = {5}, pages = {e326979}, doi = {10.1161/CIRCRESAHA.125.326979}, pmid = {41747011}, issn = {1524-4571}, abstract = {Cardiometabolic diseases (CMDs) refer to a broad spectrum of interconnected disorders, including heart attack, obesity, diabetes, atherosclerosis, and metabolic dysfunction-associated steatohepatitis, which represent the leading cause of mortality worldwide. In recent years, research on the role of gut microbiota in the pathogenesis of CMD has gradually shifted from correlation-based observations to mechanistic explorations. Within this context, microbial enzymes have gained increasing attention as key regulatory factors. These enzymes not only participate in the metabolic regulation of microorganisms themselves but also directly mediate host-microbe interactions, influencing the onset and progression of CMD. Specifically, microbial enzymes play a central role in CMD by modulating the homeostasis of key host metabolites such as cholesterol, generating bioactive molecules with metabolic and immunoregulatory functions, and participating in drug responses and the metabolic transformation of other xenobiotics. These enzymes provide novel and well-defined molecular targets for developing precision intervention strategies targeting the gut microbiota-such as enzyme replacement therapy, the design of enzyme agonists or inhibitors, and in vivo gene editing-thereby holding promise for advancing CMD prevention and treatment strategies toward greater specificity and controllability. This review systematically summarizes key microbial enzymes involved in the metabolism of endobiotics, including amino acids, peptides, and purines, and xenobiotics such as drugs, elucidating their specific mechanisms and functions in the development of CMD, strategies for mining these microbial enzymes, and the challenges and future of microbial enzyme-based interventions.}, }
@article {pmid41747008, year = {2026}, author = {Liao, Y and Hao, Y and Wu, X and Yang, R and Wu, M and Tian, R and Wang, Z and Deng, X and Li, J and Liu, J}, title = {Absolute Quantification of Full-Length 16S rRNA Amplicon Sequencing and Metabolomic Profiling of Red-Stipe Disease in Morel Fruiting Bodies.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-12-25-0388-R}, pmid = {41747008}, issn = {0031-949X}, abstract = {Morel (Morchella spp.) is one of the most valuable edible and medicinal fungi globally. Red-stipe disease severely impairs morel quality and yield, although its causative pathogens remain unclear. To investigate changes in morel fruiting bodies during red-stipe disease, this study employed absolute quantification full-length sequencing and metabolomics. Red-stipe disease significantly altered bacterial communities. All α-diversity indices increased except the Pielou evenness index. Absolute abundances of Pseudomonas, Carnobacterium, Stenotrophomonas, and Sphingobacterium were elevated and identified as potential pathogenic candidates. Co-occurrence network complexity was higher in diseased samples than in healthy samples. Metabolomics revealed that red-stipe disease affected metabolite accumulation. A total of 868 metabolites were upregulated, including Anabasine, Dinoprost, 4-Nitrophenyl β-D-Glucopyranosiduronic Acid, Glucotropaeolin, and Homocamptothecin. By contrast, 928 metabolites were downregulated, including Cimifugin, Defibrotide, D-Sedoheptulose 7-Phosphate, 1-O-Feruloyl-β-D-Glucose, and Geniposide. Differential metabolites were primarily classified as amino acids, peptides and analogues, and carbohydrates and carbohydrate conjugates. They were mainly enriched in the biosynthesis of cofactors, tryptophan metabolism, ABC transporters, D-amino acid metabolism, and nucleotide metabolism KEGG pathways. This study revealed distinct bacterial and metabolic alterations associated with red-stipe disease in morel fruiting bodies. The findings provide foundational data for identifying causative agents and elucidating metabolic mechanisms underlying nutrient composition changes in diseased morels.}, }
@article {pmid41746998, year = {2026}, author = {Khan, A and Ahmad, A and Badshah, F and Ali, M and Khan, MS and Naz, W and Ibánez-Arancibia, E and De Los Ríos-Escalante, PR and Yassin, MT}, title = {Immunoinformatics-driven design of multi-epitope vaccine targeting antibiotic-resistant Salmonella typhimurium.}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0342426}, pmid = {41746998}, issn = {1932-6203}, abstract = {Salmonella typhimurium, a Gram-negative bacterium, is a significant cause of gastroenteritis worldwide, with outbreaks occurring in diverse regions. Despite its global impact, there is currently no vaccine for human use against this pathogen. Complicating treatment efforts, S. typhimurium has exhibited resistance to multiple antibiotics, posing challenges to effectively managing infections. Given its prevalence and unresolved antibiotic resistance-associated global health burden, urgent attention is required to develop a genuinely effective vaccine. Using the S. typhimurium complete proteome data, vaccinomics-assisted immunoinformatics techniques were employed in the current investigation to find possible vaccine candidates. Candidate proteins were identified based on essentiality, lack of homology with the human proteome, and absence from the gut microbiome. Using a reverse vaccinology methodology, four antigenic outer membrane proteins were ranked in order of priority for lead epitope prediction. To boost immune responses against the intended vaccination, lead B and T-cell epitopes were coupled with appropriate linker and adjuvant peptide sequences to create multiepitope-based chimeric vaccines. The ST-MEVC construct was ranked according to several immunological, physicochemical, and immune receptor docking scores. Immune simulation predicted a strong immunogenic response for the proposed vaccine formulation. Molecular dynamics simulations analysis confirmed stable molecular interactions between the primary vaccine construct and the host receptors. The ST-MEVC construct's feasible cloning potential within the E. coli expression system was anticipated by in silico restriction and cloning studies. The proposed vaccine design is expected to elicit more robust immune responses against S. typhimurium infections and will be safer, more efficacious, and more promising for investigation using in vitro/in vivo assays.}, }
@article {pmid41746826, year = {2026}, author = {Belcher, T and Stevens, EJ}, title = {Pathogens as commensals: microbial priming of the immune system and heterologous protection.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {2}, pages = {}, pmid = {41746826}, issn = {1465-2080}, abstract = {Exposure to microbes is essential to promote the development of the host's immune system. Commensal microbes (i.e. the microbiota) which are acquired early in life play a vital role in immune priming. Whilst many organisms within the microbiota are harmless, some can be considered opportunistic pathogens. Examples include Staphylococcus aureus, Streptococcus pneumoniae and Pseudomonas aeruginosa, and these organisms can also contribute to the development of a healthy host immune system. At the extreme end of the spectrum, pathogens which typically do not form part of the microbiota (e.g. Mycobacterium tuberculosis, Bordetella pertussis and Salmonella Typhimurium) have been shown to provide cross-protection against infectious and non-infectious diseases in mice. Attenuated strains of these pathogens, such as BPZE1, could have clinical applications, whilst Bacillus Calmette-Guérin, a live-attenuated Mycobacterium bovis strain, has been shown to have non-specific effects against cancers and other diseases. A wide range of organisms, from harmless microbiota to potentially life-threatening infections, interact with the host immune system and can prime or modulate the immune response in different ways. In this review, we discuss the important role that pathogens, including opportunistic components of the microbiota, play in the development and maintenance of host immunity to a wide range of infectious and non-infectious diseases.}, }
@article {pmid41746758, year = {2026}, author = {Holt, B and Comizzoli, P}, title = {Reproductive science and wildlife conservation: the knowns and unknowns!.}, journal = {Reproduction &amp; fertility}, volume = {}, number = {}, pages = {}, doi = {10.1530/RAF-25-0135}, pmid = {41746758}, issn = {2633-8386}, abstract = {ABSTRACT: Conservation biologists specializing in reproductive science for the support of threatened species are hampered by many knowledge gaps. One of the objectives of this review is to point out a few of those gaps. We discuss the surprising observation that modern genomic technologies are revealing inaccuracies in the identification of cryptic species, which is critically important for wildlife biobank management or where reproductive interventions are required. If confronted with a familiar species, but of unfamiliar origin, it would be unwise to assume that every aspect of their reproductive biology is exactly as expected. Serious gaps in detailed knowledge can mislead the biologist, and new projects and species are therefore usually hampered by unforeseen problems. Developmental plasticity is one of the key processes behind species diversity, whereby instead of embryos always developing along inflexible pathways, it is now clear that embryonic development can be modified by modulating gene expression through epigenetic mechanisms. In some cases, animals can improve their survival by migrating to optimal feeding or breeding grounds. Others can exploit reproductive delays that relax the synchrony that normally forces mating, or insemination, to occur at the same time as ovulation. While genetic properties such as inbreeding are known to modulate reproductive success, more recent research shows that even the microbiome can influence mammalian fertility. It is therefore becoming clearer that, not only has evolution resulted in a bewildering diversity of reproductive adaptations, but that attempts to support wildlife have to be backed up by a great deal of fundamental knowledge.<br><br>LAY SUMMARY: All animal species, past and present alike, are the products of evolution, and although they have diversified in multiple directions, they currently occupy niches that optimize their future chances of survival. While animal evolution as an abstract concept usually brings to mind a series of changes taking place over long timescales, recent advances in developmental biology have shown that many animal species can also adapt surprisingly rapidly if their environment changes. For example, some tadpoles and fish embryos can sense that their watery habitat is drying out, whereupon they can either accelerate their development, or bury themselves in mud until the waters return. How do they do it? While biologists are gradually discovering the mechanisms behind these, and other, unexpected responses confront biologists every day with knowledge gaps that have to be filled. Here we explore some of these gaps and their influence on efforts to protect threatened species.}, }
@article {pmid41746598, year = {2026}, author = {Li Pomi, F and Di Domenico, EG and Pimpinelli, F and Vaccaro, M and Borgia, F and Fargnoli, MC}, title = {Actinic Keratosis at the Crossroads of Inflammation and Cutaneous Dysbiosis.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {41746598}, issn = {2193-8210}, support = {RC 2026//Ministero della Salute/ ; }, abstract = {Actinic keratosis (AK) represents an early stage of keratinocyte carcinogenesis and has long been attributed primarily to cumulative ultraviolet (UV) radiation-induced genetic damage. However, increasing evidence suggests that AK arises within a complex cutaneous microenvironment, in which chronic inflammation, oxidative stress, immune dysregulation, and alterations of the skin microbiota interact to promote and sustain field cancerization. UV exposure not only drives mutational events in epidermal keratinocytes, but also disrupts barrier integrity and local immune surveillance, reshaping microbial community structure on photodamaged skin. Recent studies reveal a characteristic profile in AK, characterized by reduced microbial diversity, depletion of protective commensals, and enrichment of opportunistic taxa, most notably Staphylococcus aureus. Experimental and clinical data suggest that S. aureus may act as a microbial cofactor in AK by amplifying proinflammatory and pro-oxidant signaling, inducing genotoxic stress, impairing DNA repair pathways, and modulating local immune responses in a manner consistent with early carcinogenic progression. Concurrent loss of commensal bacteria and fungi with immunomodulatory functions may further destabilize epidermal homeostasis, potentially reinforcing a self-perpetuating inflammatory loop. This perspective review synthesizes current molecular, immunologic, and microbial evidence to elucidate the role of host-microbe interactions in AK arising on chronically UV-exposed skin. Finally, we discuss how targeting inflammation-microbiota crosstalk may open new opportunities for risk stratification, prevention, and therapeutic intervention across the AK-cutaneous squamous cell carcinoma spectrum.}, }
@article {pmid41746338, year = {2026}, author = {Calvanese, CM and Valentino, V and De Prisco, A and Allesina, S and Amoruso, A and Deidda, F and Visciglia, A and Ercolini, D and Pane, M and De Filippis, F}, title = {Women's health is a team effort: probiogenomics supports the development of a multi-species vaginal probiotic.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-026-06107-2}, pmid = {41746338}, issn = {1420-9071}, }
@article {pmid41746264, year = {2026}, author = {Martínez-Gregorio, H and Vallejo-Lecuona, F and Ambriz-Barrera, F and Ruiz-De-La-Cruz, M and Morales-Valdez, JA and Rojas-Jiménez, EA and Jiménez-Martínez, MS and Monroy-Pérez, E and Paniagua-Contreras, GL and Díaz-Velásquez, CE and Vaca-Paniagua, F}, title = {Integrative Analysis of Bacterial Diversity in Patients with Type 2 Diabetes Mellitus and Periodontitis Using a Case-Control Microbiome Approach.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag051}, pmid = {41746264}, issn = {1365-2672}, abstract = {AIM: Type 2 diabetes mellitus (T2DM) is a risk factor for periodontitis; however, its relationship with the oral microbiome remains poorly defined. Here, we characterize taxonomic composition and predicted microbial functions in the salivary microbiome of T2DM and non-diabetic patients with periodontitis, while evaluating the influence of disease stage, smoking, and sex.<br><br>METHODS AND RESULTS: We analyzed saliva from 100 periodontitis patients (50 T2DM, 50 non-diabetic controls) using 16S rRNA V3-V4 sequencing, selecting a screened, deliberately balanced cohort to ensure robust comparison. &#x3b1;-diversity did not differ significantly across diabetes status, disease stage, smoking, or sex. However, &#x3b2;-diversity analysis revealed a statistically significant differences in microbial community composition between T2DM and non-diabetic controls (R2&#xa0;=&#xa0;0.016, p&#xa0;=&#xa0;0.029). Differential abundance analysis showed enrichment of Neisseria (p&#xa0;=&#xa0;0.02, Wilcoxon test with Bonferroni correction) and Corynebacterium matruchotii (p&#xa0;=&#xa0;0.002) in T2DM patients, whereas Haemophilus sputorum was enriched in mild periodontitis. Among smokers, Neisseria elongata (p&#xa0;=&#xa0;0.009) was more abundant than in non-smokers. Female patients exhibited higher abundances of Haemophilus, Neisseria, Gemella, Aggregatibacter, Corynebacterium, and Cardiobacterium (p&#xa0;<&#xa0;0.02), whereas Megasphaera was enriched in males (p&#xa0;=&#xa0;0.04). PICRUSt-based predictions indicated TDM2-associated enrichment of pathway related to virulence, nutrient acquisition, and pyridoxal-5'-phosphate biosynthesis, particularly in moderate and severe periodontitis.<br><br>CONCLUSIONS: T2DM is associated with distinct shifts in salivary microbial composition and predicted function, revealing taxa and pathways linked to periodontitis.}, }
@article {pmid41745979, year = {2026}, author = {Park, C and Kim, H and Yoon, J and Nam, A}, title = {Characterization and Comparative Analysis of Gut Microbiomes in Fourteen Parrot Species.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745979}, issn = {2306-7381}, abstract = {Although the gut microbiome constitutes a key component of vertebrate physiology, comparative baseline data for companion birds, particularly parrots, remain limited. Therefore, this study profiled the fecal gut microbiota of 31 privately owned companion parrots representing 14 psittacine species maintained in indoor household environments for >6 months. Amplicons targeting the V3-V4 region of the 16S rRNA gene were sequenced, denoised into amplicon sequence variants using QIIME 2 with DADA2, and taxonomically assigned against the SILVA v132 database. Community composition was broadly dominated by Firmicutes and Proteobacteria, with recurrent detection of Lactobacillus across most samples, consistent with a potential core component of the gut microbiome of captive parrots. Taken together, this study provides an exploratory comparative snapshot of fecal gut microbiota across diverse companion parrot species and establishes baseline reference data for future research linking diet, husbandry practices, and health to microbiome variation, including longitudinal and wild-captive comparative investigations.}, }
@article {pmid41745976, year = {2026}, author = {Németh, K and Tóth, I and Lányi, K and Schilling-Tóth, BM and Csorba, S and Žura Žaja, I and Sterczer, &#xc1;}, title = {The Collaborative Collapse: Bile Acid Dysmetabolism as a Central Pathogenic Driver in Canine and Feline Multi-Systemic Disorders-From Mechanisms to Precision Therapeutics.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745976}, issn = {2306-7381}, support = {SRF-003//University of Veterinary Medicine Budapest/ ; 2025-2.1.1-EK&#xd6;P-2025-00022//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; }, abstract = {Veterinary metabolomics has redefined bile acids (BAs) from simple digestive surfactants to systemic endocrine signals within a microbial-host metabolic axis. This review aims to evaluate how BA dysmetabolism acts as a central pathogenic factor in canine and feline disease. We analyze the BA pool's integrity, which depends on a specialized functional guild, primarily Peptacetobacter hiranonis, responsible for 7α-dehydroxylation. We delineate two principal pathological profiles: (1) microbial collapse, characterized by secondary bile acid (SBA) depletion and compromised farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5) signaling, which exacerbates inflammation in chronic enteropathy (CE), protein-losing enteropathy (PLE), and exocrine pancreatic insufficiency (EPI); and (2) hepato-biliary spillover, wherein host-induced dysfunction results in primary bile acid (PBA) excess. Recent data have linked these disruptions to skeletal health, feline renal fibrosis, cardiac remodeling in myxomatous mitral valve disease (MMVD), and neuroinflammation in epilepsy and hepatic encephalopathy. The discovery of microbially conjugated bile acids (MCBAs) and microbial extracellular vesicles (MEVs) reveals highly specific, vesicle-mediated communication pathways impacting systemic health. Diagnostic protocols should prioritize functional profiling, including the dysbiosis index (DI), serum conjugated BA analysis, and SBA/PBA ratios. Clinical management is moving beyond empirical fecal microbiota transplantation (FMT), towards precision synthetic microbial consortia (SynComs), neuroprotective BAs like tauroursodeoxycholic acid (TUDCA), and molecular postbiotics to restore the collaborative metabolome.}, }
@article {pmid41745919, year = {2026}, author = {Elmagzoub, WA and Weidmann, M and Elnaiem, MHE and Dennig, A and Waller, U and Bernhard, A and Junhold, J and Abd El Wahed, A and Truyen, U and Ceruti, A}, title = {Microbiome as a Tool to Monitor Aquarium Systems.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745919}, issn = {2306-7381}, abstract = {The bacterial microbiome in aquaria plays an essential role in system stability by metabolizing toxic compounds like ammonia. This study monitored microbiome changes in seven zoo aquatic systems during their first year to assess responses to external influences. Over one year (October 2021-October 2022), water and swab samples were collected from one seawater tank and six filtration systems at regular intervals. Bacterial cultivation included total bacterial counts. Metagenomic analysis was performed on samples corresponding to environmental events using Oxford Nanopore sequencing. Taxonomical analysis at the phylum and genus levels used EPI2ME software. Diversity analyses and statistical tests were performed using R. Total bacterial counts increased steadily after inoculation and stabilized by the end of the collection period. Diversity analysis revealed significant differences within and between freshwater and saltwater tanks. Each aquarium exhibited a distinct bacterial community with frequent compositional changes. Despite environmental conditions and maintenance interventions and resulting disturbances that affected the microbiome, the overall nitrifying capacity remained unaffected. Nitrifying taxa emerged as potential indicators for environmental effects. Combined with investigations of ecological function, next-generation sequencing could facilitate the development of aquarium management protocols, ultimately improving fish welfare.}, }
@article {pmid41745912, year = {2026}, author = {Chen, Q and Liu, Y and Zhu, W and Aye, H and Li, R and Hou, Z and Liu, D and Yin, Y and Tao, J and Xu, J}, title = {Relationship Between Histomonas meleagridis Infection and Cecal Intestinal Microbiota of Chickens.}, journal = {Veterinary sciences}, volume = {13}, number = {2}, pages = {}, pmid = {41745912}, issn = {2306-7381}, support = {31772727//National Natural Science Foundation of China/ ; }, abstract = {Histomonosis, caused by Histomonas meleagridis, leads to economic losses in the poultry and livestock industry. In recent years, studies on the role of intestinal microbiota in host physiological health have attracted growing attention. Understanding the changes in gut bacterial communities of chickens is crucial for improving poultry and livestock production. This study investigated the impact of Histomonas meleagridis infection on the growth performance, overall health, and cecal microbiota composition of chickens. Body weight changes and pathological alterations were assessed at different time points post-infection through animal experiments, with 7 days post-infection defined as the early stage and 14 days as the peak stage of infection. Cecal content samples were collected from the 7-day control group (G1), 7-day infected group (G2), 14-day control group (G3), and 14-day infected group (G4) for 16S rRNA sequencing analysis. The microbial diversity analysis revealed that H. meleagridis infection altered the number of microbial species in the cecal microbiota of chickens. The alpha diversity index was significantly reduced (p < 0.05), and principal coordinate analysis (PCoA) revealed significant structural differences between infected and control groups (p = 0.001). Taxonomic composition analysis showed that beneficial gut bacteria, such as Firmicutes and Lactobacillus spp., decreased in abundance, whereas Bacteroidota, Proteobacteria, Escherichia spp., and Fusobacterium mortiferum were enriched in the infected group. LEfSe analysis indicated that G1 was enriched with Oscillospiraceae and Blautia; G2 with Christensenellaceae; G3 with Verrucomicrobia and Lactobacillus aviarius; and G4 with Proteobacteria and Fusobacteria. In conclusion, H. meleagridis infection markedly altered the cecal microbiota composition by shifting the relative abundances of beneficial and pathogenic bacteria, resulting in reduced microbial diversity.}, }
@article {pmid41745726, year = {2026}, author = {Xie, J and He, W and Qiu, M and Lin, J and Shu, H and Wang, J and Liu, L}, title = {Field-Evolved Resistance to Bt Cry Toxins in Lepidopteran Pests: Insights into Multilayered Regulatory Mechanisms and Next-Generation Management Strategies.}, journal = {Toxins}, volume = {18}, number = {2}, pages = {}, pmid = {41745726}, issn = {2072-6651}, support = {32102289//National Natural Science Foundation of China/ ; 2025AFB458//Natural Science Foundation of Hubei Province/ ; T2024039//Hubei Provincial Higher Education Outstanding Young and Middle-aged Scientific and Technological Innovation Team Project/ ; }, abstract = {Bt Cry toxins remain the cornerstone of transgenic crop protection against Lepidopteran pests, yet field-evolved resistance, particularly in invasive species such as Spodoptera frugiperda and Helicoverpa armigera, can threaten their long-term efficacy. This review presents a comprehensive and unified mechanistic framework that synthesizes current understanding of Bt Cry toxin modes of action and the complex, multilayered regulatory mechanisms of field-evolved resistance. Beyond the classical pore-formation model, emerging evidence highlights signal transduction cascades, immune evasion via suppression of Toll/IMD pathways, and tripartite toxin-host-microbiota interactions that can dynamically modulate protoxin activation and receptor accessibility. Resistance arises from target-site alterations (e.g., ABCC2/ABCC3, Cadherin mutations), altered midgut protease profiles, enhanced immune regeneration, and microbiota-mediated detoxification, orchestrated by transcription factor networks (GATA, FoxA, FTZ-F1), constitutive MAPK hyperactivation (especially MAP4K4-driven cascades), along with preliminary emerging findings on non-coding RNA involvement. Countermeasures now integrate synergistic Cry/Vip pyramiding, CRISPR/Cas9-validated receptor knockouts revealing functional redundancy, Domain III chimerization (e.g., Cry1A.105), phage-assisted continuous evolution (PACE), and the emerging application of AlphaFold3 for structure-guided rational redesign of resistance-breaking variants. Future sustainability hinges on system-level integration of single-cell transcriptomics, midgut-specific CRISPR screens, microbiome engineering, and AI-accelerated protein design to preempt resistance trajectories and secure Bt biotechnology within integrated resistance and pest management frameworks.}, }
@article {pmid41745621, year = {2026}, author = {Pérez-Rocher, B and Reyes-Prieto, M and Ruiz-Ruiz, S and Palmer-Rodríguez, P and Castro, JA and Moya, A and Llabrés-Segura, M}, title = {Topological and Functional Diversity of Gut Microbiota Metabolism Across the Human Lifespan.}, journal = {Metabolites}, volume = {16}, number = {2}, pages = {}, pmid = {41745621}, issn = {2218-1989}, support = {PID2019-105969GB-I00//Spanish Ministry of Economy, Industry and Competitiveness/ ; PGC2018-096956-B-C43//Spanish Ministry of Science and Innovation, the Agencia Estatal de Investigaci&#xf3;n (AEI) and the European Regional Development Fund (ERDF)/ ; PID2021-126114NB-C44//MCIN/AEI/10.13039/501100011033/ ; }, abstract = {Background: The human gut microbiota plays a central role in host physiology by influencing digestion, immune function, and metabolism. Characterizing age-associated differences in the organization of microbial metabolism may provide insights into functional variation in the gut microbiome across the human lifespan. Methods: Gut microbiota metabolic organization was analyzed in a cohort of 30 individuals spanning three age groups (infants, adults, and elderly individuals) and comprising 156 stool samples. Community metabolic networks were reconstructed using the metabolic Directed Acyclic Graph (m-DAG) framework derived from KEGG Ortholog annotations. Network topology was characterized to assess whether the resulting networks conform to previously described global structural patterns and to examine age-associated variability. Pairwise m-DAG dissimilarities were computed, and hierarchical clustering was applied to evaluate similarities among samples. Results: All samples revealed a conserved global network organization, alongside marked variability in specific structural features. Hierarchical clustering did not strictly reflect chronological age. A homogeneous cluster composed exclusively of adult samples was identified, whereas elderly samples were distributed across two clusters, one grouping with adults and the other with infants. Exploratory discriminative analyses identified functional reactions contributing to the separation between the adult cluster and the remaining samples, indicating age-associated differences in metabolic network organization. Conclusions: Gut microbiota metabolic networks in adults tend to exhibit lower redundancy and structural complexity, whereas those in infant and elderly samples display more heterogeneous network configurations. This network-based analysis provides a functional perspective on age-associated variation in gut microbiota metabolism and offers a framework for future integrative studies.}, }
@article {pmid41745619, year = {2026}, author = {Liu, S and Wu, D and Ma, W and Wang, T and Yan, B and Ge, Y and Xiong, F and Wang, H and Kang, C}, title = {Metabolomics and Microbiomics Reveal the Cultivation-Dependent Divergence in Ginsenoside Biosynthesis and Rhizosphere Ecology of Panax ginseng.}, journal = {Metabolites}, volume = {16}, number = {2}, pages = {}, pmid = {41745619}, issn = {2218-1989}, support = {2023YFC3503802//National Key Research and Development Program of China/ ; CI2024E003, CI2024C010YNL//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; ZXKT25043//Fundamental Research Funds for the Central public welfare research institutes/ ; }, abstract = {Background: Cultivation environments impose distinct abiotic and biotic stresses that act as primary drivers reshaping the metabolic profile and microbiome assembly of medicinal plants. This study investigates the impact of simulative habitat versus arched greenhouse cultivation on the synthesis of bioactive ginsenosides and the associated root microbiome structure in Panax ginseng. Methods: A combined metabolomics and microbiomics approach was applied to compare ginsenoside accumulation and rhizosphere microbial community composition under the two cultivation modes. Results: Ginseng from simulative habitat cultivation exhibited significantly higher ginsenoside content, particularly ginsenoside Re, compared to arched greenhouse cultivation, with this advantage being more pronounced in long-term cultivation. Microbiome profiling revealed that specific taxa, including Bradyrhizobium, were strongly enriched in simulative habitats and positively correlated with enhanced ginsenoside accumulation, suggesting a microbiome-mediated mechanism for metabolic plasticity. In contrast, arched greenhouse cultivation was associated with a more complex microbial structure characterized by increased negative interactions, which may compromise metabolic quality. Conclusions: These findings, utilizing multi-omics correlations, provide a theoretical basis for optimizing Panax ginseng quality through ecological cultivation strategies that leverage stress-responsive microbe-metabolite interactions.}, }
@article {pmid41745580, year = {2026}, author = {Zhong, R and Lin, Z and Jin, B and Wang, X and Mu, H and Hu, J and Li, Q and Dou, P and Liu, X and Hu, C and Xu, G and Tan, G}, title = {Exploratory Analysis of Gut Microbiome and Metabolic Profile Changes Following Lenvatinib and Anti-PD-1 Combination Therapy in Liver Cancer.}, journal = {Metabolites}, volume = {16}, number = {2}, pages = {}, pmid = {41745580}, issn = {2218-1989}, support = {DMU-1&amp;DICP UN202203//The Medical and Industry Joint Innovation Programs/ ; No. 81972217//The National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: Lenvatinib combined with anti-PD-1 therapy has shown promise in the treatment of hepatocellular carcinoma (HCC). The study evaluates changes in gut microbiota (GM) and metabolites during HCC treatment with lenvatinib combined with anti-PD-1. Methods: An HCC mouse model was established via diethylnitrosamine (DEN) injection, and the mice were then treated with lenvatinib, anti-PD-1, or their combination. GM composition and structural changes were assessed by 16S rDNA sequencing, and metabolite abundance by liquid chromatography-mass spectrometry (LC-MS). Results: Significant alterations in GM and metabolites were observed in the HCC group compared to the control group, and compared with the HCC group, both monotherapy and combination therapy resulted in varying degrees of GM and metabolites rebalancing. Specifically, compared to the HCC group, lenvatinib combined with anti-PD-1 therapy decreased the abundance of GM, including p_Patescibacteria, g_Lactobacillus, g_Clostridium_sensu_stricto_1, g_Eubacterium_siraeum_group, and g_Desulfovibrio, while the abundance of g_Prevotella_7 increased. Metabolite changes included increased 4-pyridoxic acid, deoxycholic acid, and taurochenodesoxycholic acid, and decreased myristic acid, oleic acid, riboflavin, and uric acid. Conclusions: HCC induces substantial alterations in the GM and metabolic profile of mice. Lenvatinib combined with anti-PD-1 treatment partially modulates these dysregulations. The relevant GM and metabolites may be associated with the efficacy of combined therapy and could serve as potential markers for further investigation.}, }
@article {pmid41745391, year = {2026}, author = {Kaltsas, A and Pournaras, S and Giannakodimos, I and Markou, E and Stavropoulos, M and Papaharitou, S and Dimitriadis, F and Zachariou, A and Sofikitis, N and Chrisofos, M}, title = {Probiotics as Microbiome Modulators in Male Infertility: Rethinking Dysbiosis Across the Gut-Testis Axis.}, journal = {Journal of personalized medicine}, volume = {16}, number = {2}, pages = {}, pmid = {41745391}, issn = {2075-4426}, abstract = {Male infertility contributes substantially to couple infertility, and a large proportion of cases remain idiopathic. Dysbiosis within the gut, seminal, and urinary microbiomes has been associated with impaired semen parameters, reproductive tract inflammation, and oxidative stress. This narrative review, informed by a structured literature search, summarizes current evidence for the gut-testis axis and the androbactome in male infertility and discusses mechanistic pathways linking microbial imbalance to sperm dysfunction. Proposed mechanisms include immune activation, increased oxidative stress, endocrine and metabolic perturbations, and disruption of epithelial barriers, including the blood-testis barrier. Early clinical trials report that selected probiotic or synbiotic formulations may be associated with improvements in one or more World Health Organization (WHO) semen parameters and with reductions in oxidative or inflammatory biomarkers (surrogate laboratory endpoints; pregnancy and live-birth outcomes are rarely reported and remain unproven) in selected populations, such as idiopathic infertility and the post-varicocelectomy setting. Given patient heterogeneity, a personalized approach requires prespecified clinical phenotypes and measurable monitoring targets, rather than indiscriminate supplementation. At present, probiotics should be considered an adjunct rather than a stand-alone therapy. Well-designed, contamination-aware microbiome studies and adequately powered randomized trials with clinically meaningful endpoints, including pregnancy and live birth, are required before routine clinical implementation. This synthesis is intended to support personalized counseling and trial design by clarifying candidate phenotypes, appropriate monitoring endpoints, and realistic limitations of current evidence.}, }
@article {pmid41745272, year = {2026}, author = {Pan, X and Ibrahim, M and Zhou, L and Ullah, A and Ali, A and Gao, D}, title = {Synergistic Effects of Arbuscular Mycorrhizal Fungi and Mycorrhiza Helper Bacteria Alter Cucumber Rhizosphere Fungal Community and Reduce Soil Cadmium Contamination.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745272}, issn = {2309-608X}, support = {32472818//National Natural Science Foundation of China/ ; 2022MD713726//China Postdoctoral Science Foundation/ ; LBH-Z22004//Postdoctoral Science Foundation of Heilongjiang Province/ ; }, abstract = {Cadmium (Cd) contamination in agricultural soils severely impairs plant growth, disrupts microbial communities, and threatens food safety due to its high toxicity and mobility. Conventional remediation methods are often expensive and environmentally unsustainable. In contrast, plant-microbiome interactions offer an eco-friendly solution to reduce Cd accumulation and improve plant growth. Arbuscular mycorrhizal fungi (AMF) and mycorrhiza helper bacteria (MHB) are known to improve plant growth and resilience in Cd-contaminated soils. However, the mechanisms by which AMF and MHB co-inoculation could reduce soil Cd contamination by altering the rhizosphere fungal community remain unclear. This study aimed to evaluate how co-inoculation with AMF (Funneliformis mosseae) and MHB (Alcaligenes faecalis) affects plant Cd uptake and soil Cd content, and how it reshapes the cucumber rhizosphere fungal community. A greenhouse experiment was conducted with four treatments: CK (no inoculation), Fm (AMF inoculation), Af (MHB inoculation), and FA (AMF + MHB co-inoculation). Co-inoculation with AMF and MHB (FA) significantly reduced Cd concentrations in both plant tissues and soil. Fungal communities were profiled using Illumina MiSeq sequencing of the ITS region, and diversity metrics and structural changes were assessed through PCoA and DESeq2. Co-inoculation (FA) significantly reshaped the fungal community, increasing the relative abundances of beneficial phyla such as Mortierellomycota, Basidiomycota and Glomeromycota, while decreasing the abundance of potentially pathogenic Ascomycota. Double inoculation with AMF and MHB also enhanced fungal diversity, as measured by the Simpson index, and enriched specific OTUs. This study uncovers the mechanisms through which AMF-MHB co-inoculation reduces Cd concentrations in both plants and soil by altering the cucumber rhizosphere fungal community composition. These findings demonstrate that AMF-MHB co-inoculation is an effective, biologically driven strategy for remediating Cd-contaminated soils by restructuring cucumber rhizosphere fungal communities.}, }
@article {pmid41745266, year = {2026}, author = {Yuan, Y and Feng, Z and Song, H and Yuan, A and Chang, L and Zou, Y and Dashdorj, M and Bian, Z}, title = {Effects of Powdered and Granular AMF on Maize Growth Under Low Fertilizer Conditions.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745266}, issn = {2309-608X}, support = {2024YFC3909300//National Key R&amp;D Program/ ; 202304290000011//Key R&amp;D Program of Shanxi Province/ ; GZSTCKP [2025]019//Science and Technology Program of Shanxi Province/ ; 202523anull050017//Anhui Provincial Science and Technology Innovation and Development Program/ ; }, abstract = {Excessive fertilizer use drives soil degradation and resource waste. This study investigates how arbuscular mycorrhizal fungi (AMF) formulations (powder vs. granular) optimize maize (Zea mays L.) yield, soil microbiome, and economic benefits under 50% and 75% fertilizer reduction. Field trials showed that the AMF powder formulation under 50% fertilizer reduction (AP50) increased maize yield by 14.67%. This increase was associated with rapid root colonization (85.3%), enhanced phosphorus availability, and the recruitment of beneficial fungi such as Mortierellomycota. Granular formulation at 75% reduction (AG75) achieved 7.18% yield gain via sustained symbiosis. Fungal communities exhibited greater sensitivity to fertilization than bacteria (Chao1, p = 0.0094), with AMF suppressing Fusarium by 42% while enriching functional taxa (Actinobacteria, Mortierellomycota). Economic analysis confirms that AP50 (30,435 CNY/ha) and AG75 (26,954 CNY/ha) yield higher net profits, where CNY denotes Chinese Yuan. Powder formulations maximize immediate benefits in medium- to low-fertility soils, whereas granules support long-term soil health in high-organic systems, providing a precision strategy for sustainable agriculture.}, }
@article {pmid41745122, year = {2026}, author = {Naito, K and Tomii, A and Ishii, K and Shimizu, H}, title = {Indole-3-Acetic Acid and Skatole Exert Opposing Effects on MDR1 Proteostasis in Human Colonic Epithelial Cells: A Molecular Basis for the Gut Microbial Metabolic Switch.}, journal = {Journal of xenobiotics}, volume = {16}, number = {1}, pages = {}, pmid = {41745122}, issn = {2039-4713}, support = {JP21H03356//Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {The escalating consumption of red meat is a potent environmental risk factor for inflammatory bowel disease (IBD), which is characterized by compromised expression of the xenobiotic transporter P-glycoprotein (MDR1/ABCB1). While gut microbiota metabolize dietary tryptophan into diverse indole derivatives that function as aryl hydrocarbon receptor (AhR) ligands, their differential regulation of MDR1 remains an unresolved AhR paradox. Here, we investigated the mechanisms by which two distinct metabolites, indole-3-acetic acid (IAA) and skatole, regulate MDR1 expression in human colonic epithelial Caco-2 cells. We observed that IAA selectively enhances MDR1 protein stability via an AhR-dependent pathway without inducing de novo transcription, suggesting a mechanism we term enhanced proteostasis mediated by the AhR-Hsp90 complex. Conversely, skatole, a toxic dysbiotic metabolite linked to red meat intake, triggered a time-dependent depletion of MDR1 and potently abrogated the protective efficacy of IAA. Our findings are consistent with a model in which skatole acts as a putative structural disruptor, potentially destabilizing the chaperone complex essential for MDR1 integrity. This destruction is facilitated by a key bacterial enzyme, indoleacetate decarboxylase (IAD), which is a pH-dependent metabolic switch in the gut. The modern Western diet, characterized by high protein and low fiber content, elevates colonic pH, thereby activating IAD to convert protective IAA into toxic skatole. These findings provide a molecular framework for the red meat-microbiome-barrier failure axis and highlight the restoration of the IAA/skatole balance through dietary intervention as a promising therapeutic strategy.}, }
@article {pmid41745115, year = {2026}, author = {Novacescu, D and Cut, TG and Baloi, A and Herlo, A and Luput-Andrica, IM and Saizu, AE and Uzum, A and Mot, MD and Zara, F and Sandesc, D and Lazureanu, VE and Marinescu, A}, title = {Gut Microbiome Recovery in Clostridioides difficile Infection Patients Receiving Multi-Strain Probiotics During Convalescence: A Prospective Pilot Series of Longitudinal Dynamics.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41745115}, issn = {2079-9721}, abstract = {Background/Objectives:Clostridioides difficile infection (CDI) is a major healthcare-associated infection associated with profound antibiotic-induced gut microbiome disruption that frequently persists after clinical resolution. This pilot study aimed to characterize early post-infectious gut microbiome recovery following an inaugural CDI episode and to descriptively assess microbiome remodeling during adjunctive multi-strain probiotic supplementation. Methods: Adult patients with mild-to-moderate CDI were prospectively enrolled after completing standard antimicrobial therapy and received a 30-day course of a high-potency, 10-strain probiotic formulation. Stool samples were collected before and after supplementation and analyzed using 16S rRNA gene sequencing with microbiome-inferred functional profiling, alongside targeted screening for enteric protozoa and yeasts. Results: Five patients completed paired analyses. At baseline, all patients exhibited severe dysbiosis characterized by markedly reduced microbial diversity, depletion of Actinobacteria and short-chain fatty acid-producing taxa, expansion of Proteobacteria, and unfavorable inferred metabolic signatures. After supplementation, four of five patients were observed to exhibit increased microbial diversity and partial improvement in global dysbiosis indices. Microbiome recovery was heterogeneous and non-linear, involving variable reductions in Proteobacteria, recovery of Actinobacteria, or both, with incomplete normalization of taxonomic balances and inferred functions. Enterotype shifts were observed in three patients, consistent with ecological reorganization rather than full restoration. Baseline protozoal colonization resolved in affected patients, while fungal dynamics showed clearance or species-level replacement. No early CDI recurrences were observed during follow-up. Conclusions: Interpretation is limited by the single-arm design without a control group, which precludes distinguishing supplementation-associated changes from natural post-antibiotic recovery. Even so, our findings highlight the complexity and inter-individual variability of early post-CDI microbiome recovery and support further investigation of integrative microbiome profiling to describe post-infectious dysbiosis dynamics.}, }
@article {pmid41745080, year = {2026}, author = {Kumar, S and Himanshu,  and Gaur, P and Ahmad, S and Puri, P and Raj, VS and Pandey, RP}, title = {Microbiota Transplantation as a Future Novel Therapeutic Strategy Approach.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41745080}, issn = {2079-9721}, abstract = {Bacterial vaginosis (BV) is a leading cause of genital discomfort among women globally, and it arises from dysbiosis of the vaginal ecosystem characterized by the overgrowth of pathogenic bacteria. Current therapeutic strategies primarily rely on antibiotics and/or probiotics, which demonstrate clinical efficacy but are frequently associated with limitations such as antimicrobial resistance, high recurrence rates, and incomplete restoration of a healthy vaginal microbiota. Inspired by the success of fecal microbiota transplantation in gastrointestinal disorders, vaginal microbiome transplantation (VMT) from healthy donors has emerged as a potential alternative therapeutic approach for BV. However, experimental and early clinical studies indicate that VMT efficacy is not uniform across individuals, with considerable inter-individual variability in treatment outcomes. Host genetic factors, baseline vaginal microbial composition, immune status, and environmental influences are likely to modulate therapeutic success, underscoring the need for personalized interventions. This article critically evaluates the shortcomings of existing standardized treatments, highlights the potential advantages and challenges of VMT, and discusses emerging, precision-based therapeutic strategies for BV in light of recent research advances and ongoing clinical trials worldwide.}, }
@article {pmid41745076, year = {2026}, author = {Murmu, M and Singh, R and Gaikwad, R and Banodkar, A and Barage, S and Sudhakara, P and Santhosh Kumar, AW}, title = {Comparative Analysis of Oral Microbiome in Indian Type 2 Diabetes Mellitus (T2DM) and Periodontitis Cohorts.}, journal = {Diseases (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {41745076}, issn = {2079-9721}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) and periodontitis are highly prevalent immune-inflammatory diseases that interact bidirectionally. However, how early-onset T2DM, periodontitis, and adverse lifestyle behaviors collectively remodel the gingival plaque microbiome at the ecological network level remains poorly understood in Indian populations.<br><br>METHODS: A cross-sectional 16S rRNA gene (V3-V4) sequencing study was conducted on supragingival and subgingival plaque from 60 adults (30-40 years) recruited in Mumbai. Participants were categorized as healthy (H, n = 10), periodontitis (P, n = 10), T2DM (n = 20), and T2DM with periodontitis (T2DM_P, n = 20). Comprehensive demographic, anthropometric, metabolic, periodontal, dietary, lifestyle, and oral hygiene data were collected. Sequence data were processed using QIIME2-DADA2, followed by diversity, differential abundance, and genus-level co-occurrence network analyses (Spearman |r| &#x2265; 0.6, FDR < 0.05; core prevalence &#x2265; 70%).<br><br>RESULTS: &#x3b1;-diversity showed no marked depletion across groups, whereas Bray-Curtis &#x3b2;-diversity revealed significant global separation, with maximal dissimilarity between H and T2DM_P. Healthy individuals with favorable lifestyle behaviors harbored scaffold-forming taxa such as Corynebacterium matruchotii, Lautropia mirabilis, and Capnocytophaga spp. In contrast, P and T2DM_P groups showed enrichment of proteolytic, inflammation-adapted genera including Porphyromonas, Tannerella, Treponema, Fretibacterium, Peptostreptococcus, and Selenomonas. Network analysis revealed a shift from commensal-rich modular networks to densely connected, keystone-centered disease modules.<br><br>CONCLUSION: Early-onset T2DM and periodontitis, particularly under adverse lifestyle behaviors, reorganize plaque microbial composition and interaction architecture rather than depleting diversity, highlighting plaque-based keystone taxa and networks as targets for microbiome-informed risk stratification and integrated medical-dental-lifestyle interventions.}, }
@article {pmid41745051, year = {2026}, author = {Marinescu, GA and Rotaru-Zavaleanu, AD and Trasca, ET and Caluianu, EI and Taisescu, O and Gresita, A and Musat, MI and Radulescu, D and Mercut, R and Taisescu, CI}, title = {Hydrogel-Based Therapeutic Strategies for Post-Cholecystectomy NAFLD: Targeting Bile Acid Signaling, Gut Microbiota, Inflammation, and Hepatic Fibrosis.}, journal = {Gels (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {41745051}, issn = {2310-2861}, abstract = {Post-cholecystectomy non-alcoholic fatty liver disease (NAFLD), now encompassed within metabolic dysfunction-associated steatotic liver disease (MASLD), is increasingly linked to persistent disruption of bile acid kinetics and gut-liver axis signaling after gallbladder removal. Continuous bile delivery to the intestine reshapes the bile acid pool, perturbs FXR-FGF19/TGR5 pathways, remodels gut microbiota, and compromises epithelial barrier integrity, collectively promoting portal endotoxemia, chronic hepatic inflammation, and fibrogenic remodeling. Hydrogel-based biomaterials offer a mechanistically aligned therapeutic platform for this setting because they enable localized, sustained, and stimuli-responsive interventions at intestinal or hepatic sites. Functional hydrogels can sequester excess bile acids, protect and deliver probiotics/prebiotics/postbiotics, reinforce mucosal barrier function, and provide controlled release of anti-inflammatory or antifibrotic agents with reduced systemic exposure. In this review, we map emerging hydrogel strategies relevant to post-cholecystectomy NAFLD across four pathogenic nodes, bile acid dysregulation, dysbiosis, inflammation, and fibrosis, and highlight design principles (polymer chemistry, charge/hydrophobicity balance, mucoadhesion, and pH/redox/enzyme responsiveness) that enable targeted modulation of the gut-liver axis. Finally, we identify key translational gaps, including the lack of post-cholecystectomy-specific experimental models and standardized outcome measures integrating bile acid profiling, microbiome readouts, and hepatic histology. Hydrogel technologies represent a promising route toward localized and multimodal therapy in metabolic liver disease, warranting focused preclinical validation and clinical development.}, }
@article {pmid41744821, year = {2026}, author = {Luboń, W and Świerczyńska, M and Jadczyk-Sorek, K and Wyględowska-Promieńska, D}, title = {Autoimmune Ocular Surface Disorders: From Molecular Immunopathogenesis to Regenerative and Surgical Therapeutics.}, journal = {Cells}, volume = {15}, number = {4}, pages = {}, pmid = {41744821}, issn = {2073-4409}, abstract = {Autoimmune ocular surface diseases represent a complex group of disorders in which systemic immune dysregulation triggers chronic inflammation, epithelial dysfunction, and progressive tissue fibrosis. Systemic lupus erythematosus, primary Sjögren's syndrome, and ocular cicatricial pemphigoid are the principal entities linking systemic autoimmunity to ocular surface pathology. These conditions share convergent mechanisms-including dysregulated cytokine signaling (IFN-I, IL-6, and IL-17), complement activation, and epithelial-mesenchymal transition-culminating in tear film instability and visual impairment. Recent advances in molecular immunology and omics profiling have elucidated disease-specific pathways and identified actionable therapeutic targets. Conventional immunosuppressants such as corticosteroids and cyclosporine remain fundamental, yet emerging biologics targeting BAFF, IFNAR, and JAK/STAT signaling-alongside regenerative strategies employing mesenchymal and induced pluripotent stem cells-are transforming disease management. Parallel innovations in amniotic membrane transplantation, keratoprosthesis, and bioengineered corneal scaffolds integrate structural reconstruction with immune modulation. Furthermore, the convergence of multi-omics analytics, artificial intelligence-assisted diagnostics, and microbiome-based immunomodulation heralds a new era of precision ophthalmology. This review synthesizes current molecular insights, clinical observations, and translational advances that collectively redefine autoimmune ocular surface diseases-from chronic inflammatory disorders into a targetable, regenerative, and potentially reversible spectrum of conditions.}, }
@article {pmid41744722, year = {2026}, author = {Cai, H and Wang, D and Zhao, Y and Yang, C}, title = {Recent Advances in Microfluidic Chip Technology for Laboratory Medicine: Innovations and Artificial Intelligence Integration.}, journal = {Biosensors}, volume = {16}, number = {2}, pages = {}, pmid = {41744722}, issn = {2079-6374}, support = {2024JJ13PT070//Dalian Science and Technology Innovation Fund Program/ ; DMU-2&amp;DICP UN202410//United Foundation for Dalian Institute of Chemical Physics, Chinese Academy of Sciences and the Second Hospital of Dalian Medical University/ ; 2024ZDJH01PT084//Dalian Life and Health Field Guidance Program Project/ ; 2025-MSLH-196//Liaoning Provincial Science and Technology Plan Joint Program Project/ ; }, abstract = {Microfluidic chip technologies, also known as lab-on-a-chip systems, have profoundly transformed laboratory medicine by enabling the miniaturization, automation, and rapid processing of complex diagnostic assays using minimal sample volumes. Recent advances in chip design, fabrication methods-including 3D printing, modular and flexible substrates-and biosensor integration have significantly enhanced the performance, sensitivity, and clinical applicability of these devices. Integration of advanced biosensors allows for real-time detection of circulating tumor cells, nucleic acids, and exosomes, supporting innovative applications in cancer diagnostics, infectious disease detection, point-of-care testing (POCT), personalized medicine, and therapeutic monitoring. Notably, the convergence of microfluidics with artificial intelligence (AI) and machine learning has amplified device automation, reliability, and analytical power, resulting in "smart" diagnostic platforms capable of self-optimization, automated analysis, and clinical decision support. Emerging applications in fields such as neuroscience diagnostics and microbiome profiling further highlight the broad potential of microfluidic technology. Here, we present findings from a comprehensive review of recent innovations in microfluidic chip design and fabrication, advances in biosensor and AI integration, and their clinical applications in laboratory medicine. We also discuss current challenges in manufacturing, clinical validation, and system integration, as well as future directions for translating next-generation microfluidic technologies into routine clinical and public health practice.}, }
@article {pmid41744683, year = {2026}, author = {Gong, Y and Wu, G and Tavarez, S and Zhao, C and Zhao, L and Ghosh, S}, title = {Dietary fiber fermentation restores microbiome resilience to oxygen stress in a host-independent ex vivo model.}, journal = {mBio}, volume = {}, number = {}, pages = {e0393425}, doi = {10.1128/mbio.03934-25}, pmid = {41744683}, issn = {2150-7511}, abstract = {Gut dysbiosis is often driven by the loss of beneficial obligate anaerobes and the overgrowth of pathobiont facultative anaerobes, a shift perpetuated by oxygen buildup in the gut lumen. We hypothesized that dietary fibers could restore microbiome resilience to oxygen disruption by fueling short-chain fatty acid (SCFA) production and acidifying the environment to inhibit the blooming of pathobiont facultative anaerobes. To test this hypothesis independent of the host, fecal samples from healthy donors were cultured ex vivo under four conditions: Control, Oxygen-only (5%), Fiber-only, and Oxygen+Fiber. Guild-level analysis of 16S rRNA gene V4 region sequencing revealed that oxygen alone drove a significant expansion of co-abundant groups (CAGs; CAG2, CAG3) with facultative anaerobes, specifically amplicon sequence variants (ASVs) from Enterobacteriaceae. However, fiber supplementation under microaerophilic conditions fueled robust SCFA production and lowered pH, which effectively suppressed these oxygen-promoted pathobionts. Crucially, fiber restored the abundance of guilds (CAG15, CAG17) with key SCFA-producing obligate anaerobes, such as Eubacterium and Roseburia, which were otherwise inhibited by oxygen. Furthermore, we identified a unique guild (CAG19) containing Bifidobacterium that thrived specifically in the oxygen-fiber environment, suggesting a transitional role in restoring homeostasis. These findings demonstrate that dietary fibers can directly restore microbiome resilience against oxygen stress, offering a mechanistic strategy for managing dysbiosis-related conditions.IMPORTANCEThis study demonstrates that dietary fibers can protect short-chain fatty acid (SCFA)-producing obligate anaerobes under microaerophilic conditions in a host-independent manner. Unlike antioxidants that scavenge oxygen, fibers provide fermentable substrates that fuel microbial metabolism, lowering pH and creating a chemical environment that suppresses oxygen-tolerant pathobionts. Using an ex vivo fermentation model, we show that fiber drives the emergence of a Bifidobacterium-centered "transitional guild" that promotes the recovery of strict anaerobes, highlighting a microbe-fueled resilience mechanism. These findings reveal how dietary fibers directly stabilize the microbial community and support targeted high-fiber interventions to prevent dysbiosis.}, }
@article {pmid41744675, year = {2026}, author = {Liu, Y and Zeng, F and Hao, Z and Li, J and Han, S and Han, M and Feng, C and Dong, J and He, Y}, title = {Microbial Differences in Rhizospheric and Ednophytic Microbiota in Healthy Chinese Yam Roots and Those Affected by Yam End Black Disease.}, journal = {Biology}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/biology15040366}, pmid = {41744675}, issn = {2079-7737}, support = {2017YFD0201600//National key Research and Development Program/ ; HBCT2018060204//Modern Agricultural Industry Technology System of Hebei Province/ ; }, abstract = {Yam end black disease (YEBD) is a devastating soil-borne disease that severely compromises the yield of Chinese yam (Dioscorea opposita Thunb.). Despite its agricultural importance, the etiological agents and molecular mechanisms underlying YEBD remain poorly understood. In this study, we employed an integrated multi-omics approach, combining transcriptomics and microbiome analysis, to dissect the host responses and microbial shifts associated with YEBD. De novo transcriptome assembly revealed significant enrichment of differentially expressed genes involved in polyamine metabolism and hormone signaling pathways. Microbiome profiling identified a substantial increase in nematodes (Meloidogyne spp.) in diseased samples, which correlated negatively with the beneficial fungus Cladosporium. Bacterial community analysis showed an increase in Proteobacteria and Bacteroidetes and a decrease in Actinobacteria and Firmicutes in YEBD-affected roots. Notably, the rhizosphere microbiome was less affected than the endophytic community, suggesting that internal microbial dysbiosis plays a critical role in disease progression. These findings provide new insights into the interactions among yam, nematodes, and microbes, offering potential strategies for biocontrol and disease management.}, }
@article {pmid41744668, year = {2026}, author = {Ren, Y and Zhang, B and Jin, H and Yang, X and Xu, Z and Yuan, Y and Hua, C and Yan, Z and Qin, B}, title = {Community Structure and Soil Environmental Drivers of Rhizosphere and Root Endophytic Microbiota of Polygonum divaricatum in a Temperate Grassland.}, journal = {Biology}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/biology15040359}, pmid = {41744668}, issn = {2079-7737}, abstract = {Understanding the ecological drivers of plant-associated microbiota is essential for predicting grassland ecosystem resilience. This study aimed to characterize the community structure, functional potential, and soil environmental drivers of rhizosphere and root endophytic microbiota associated with Polygonum divaricatum across three Hulunbuir Grassland sites. A nested sampling design was applied with three replicated plots per site, from which paired rhizosphere soil and root samples were collected. Each sample represented a composite of 15 plants, yielding six samples per site (total n = 18) and allowing the separation of compartmental and environmental effects on community assembly. P. divaricatum plays a key role in nutrient cycling and soil stability; however, its rhizosphere and root microbiomes remain poorly characterized. Fungal diversity was consistently higher in the root endosphere, whereas bacterial diversity was greater in rhizosphere soils. Fungal assemblages were dominated by Ascomycota and Mortierellomycota, primarily represented by Mortierella and Trichoderma, while bacterial communities were dominated by Actinomycetota and Pseudomonadota, enriched in Bradyrhizobium and Pseudonocardia. Community differentiation reflected strong compartmental filtering and responses to soil pH, organic carbon, nitrogen, and enzyme activities. Functional prediction indicated clear compartmental partitioning: in the rhizosphere, bacterial communities were enriched in pathways related to carbon and nitrogen metabolism and secondary metabolite biosynthesis, whereas in the root endosphere, functional profiles were more associated with transport, uptake, and fermentation; fungal communities were dominated by saprotrophic and symbiotrophic guilds. These findings demonstrate that soil biochemical gradients and host-driven filtering jointly structure the P. divaricatum microbiome, providing ecological insights into plant-microbe-soil interactions and the maintenance of grassland ecosystem stability.}, }
@article {pmid41744504, year = {2026}, author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T}, title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137325}, doi = {10.1128/msystems.01373-25}, pmid = {41744504}, issn = {2379-5077}, abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.<br><br>IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.}, }
@article {pmid41744501, year = {2026}, author = {Whitham, JM and Goller, CC}, title = {Improving knowledge of metagenome-assembled genomes (MAGs) through bioinformatics and article annotation.}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0022625}, doi = {10.1128/jmbe.00226-25}, pmid = {41744501}, issn = {1935-7877}, abstract = {DNA from microbial communities can be sequenced and assembled to gain insight into the microbes that may be present in unique environments. Powerful computational tools, combined with more accessible sequencing technologies, have enabled metagenome-assembled genome (MAG) analysis in course-based settings. However, the computational methods and assumptions surrounding the creation of MAGs, as well as their application in understanding microbes in biomes, are often complex and intimidating to new users. The metagenomics course we designed enrolls undergraduate and graduate students in a half-semester lab experience. We hypothesized that collaborative annotation of specific bioinformatics research articles, paired with student application of tools using guided case studies on the powerful KBase bioinformatics web platform, would enhance learning of key MAG concepts. Student learning outcomes on conceptual quizzes, as well as learner perceptions of the assignment and confidence in using KBase and other bioinformatics tools, were analyzed. Assessments and surveys of student perceptions were collected over several semesters using consistent assignments, readings, and KBase narratives. Learning gains were identified for specific MAG analysis concepts and data interpretation. Nevertheless, misconceptions continue, and confidence in bioinformatics approaches varies. Additional exploration of qualitative data may suggest concepts to reinforce and resources to support learners. Combining KBase, collaborative annotation of primary literature, guided case studies, and aligned assessments effectively promotes students' conceptual and mechanistic understanding of MAGs and the assumptions underlying their creation and use.}, }
@article {pmid41744445, year = {2026}, author = {Ciesielski, S and Babis, W and Żarski, D and Gomułka, P and Hliwa, P}, title = {Does the manipulation of light conditions affect the gut microbiome of Eurasian perch (Perca fluviatilis L.) in a recirculating aquaculture system?.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70373}, pmid = {41744445}, issn = {1095-8649}, support = {00002-6521.1-OR1400004/17/20//Eurasian Maritime and Fisheries Fund/ ; }, abstract = {An important element of modern aquaculture is the creation of optimal environmental conditions for economically profitable fish farming, as only such conditions can guarantee a high growth rate and the welfare of the fish. One of the most important factors is the photoperiod, which has a substantial influence on the circadian rhythm, as it is a direct modulator of physiological functions. It has been reported that the photoperiod affects the microbiome of fish, which could potentially serve as an indicator of their welfare. Therefore, the main aim of this study was to determine the possible effects of shortening and lengthening daylight on the gut microbiome of Eurasian perch (Perca fluviatilis L.) in a recirculating aquaculture system. Our study indicates that rearing the fish in very short daylight for 2 months has no significant effects on their biomass and length; however, long daylight reduced the specific growth rate in comparison to the control group. Furthermore, no significant differences in the structure of the gut microbiome were observed. Importantly, potential differences in the structure of the gut microbiome of fish kept under different light conditions could be masked by the possibility of bacterial transfer between tanks within individual recirculation systems. Nevertheless, discriminant analysis showed that the abundance of Flavobacterium sp. and members of the Microbacteriaceae family was significantly increased in the group of fish reared in the dark for 22 h compared to the control group. Similarly, Pseudopropionibacterium sp. was identified as a significant biomarker between the group of fish reared in the light for 24 h and the control group. These results expand our understanding of the influence of the gut microbiome on the welfare of fish in aquaculture.}, }
@article {pmid41744425, year = {2026}, author = {Sandeep, G and Pahari, S and Nayak, V and Gundamaraju, R and Mishra, P and Misra, A}, title = {The Gut-Prostate Axis: Decoding the Interplay of Environmental Factors, Microbial Metabolites, and Hormonal Regulation in Prostate Cancer Pathogenesis.}, journal = {Technology in cancer research &amp; treatment}, volume = {25}, number = {}, pages = {15330338261424322}, doi = {10.1177/15330338261424322}, pmid = {41744425}, issn = {1533-0338}, abstract = {Prostate cancer remains one of the most common malignancies in men, with its progression strongly influenced by androgen signaling. While genetic alterations are well-documented in prostate cancer, growing evidence highlights the contribution of environmental factors, particularly diet and the gut microbiome, in modulating disease risk and therapy response. The gut microbiota plays a crucial role in regulating host metabolism, immune responses, and hormone activity. Recent findings suggest that specific microbial communities influence androgen biosynthesis and metabolism through enzymes such as β-glucuronidase, altering systemic androgen availability and imp acting tumor progression. Additionally, microbial metabolites, including short-chain fatty acids, secondary bile acids, and bacterial genotoxins, can affect inflammatory pathways and cellular signaling relevant to prostate tumorigenesis. Experimental studies also indicate that modifying the gut microbiota through dietary interventions, probiotics, or fecal microbiota transplantation can influence tumor growth and improve responses to immunotherapy and hormone-based treatments. In this review we present the current knowledge on gut-prostate axis, examine the mechanistic links between microbial activity and prostate cancer biology, and discuss emerging microbiome-based strategies as potential therapies. A deeper understanding of this bidirectional crosstalk could pave the way for microbiome-informed approaches to prevention, diagnosis, and personalized treatment of prostate cancer.}, }
@article {pmid41743827, year = {2025}, author = {Ward, S and Cox, OT and Roggiani, S and Crowley, T and Turroni, S and Melgar, S and O'Connor, R}, title = {Loss of the PDLIM2 protein during chronic colitis promotes inflammation, impaired epithelium recovery, alterations to the microbiome and oxidative stress.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1720162}, pmid = {41743827}, issn = {1664-2392}, abstract = {INTRODUCTION: Ulcerative colitis (UC) involves impaired wound healing processes contributing to sustained immune and microbial interactions that aggravate intestinal injury and may progress to colitis-associated cancer (CAC). Here we investigated whether PDLIM2, a known regulator of both epithelial and immune cell fate, contributes to colitis progression.<br><br>METHODS: PDLIM2 knockout mice (-/-) and wildtype littermates (+/+) were assessed for responses to dextran sodium sulphate (DSS)-induced colitis, and to aoxymethane +DSS. Microbiota were assessed using 16s rRNA amplicon sequencing. Mechanistic studies were carried out in Caco-2 cell cultures, and in silico analysis was carried out on single cell RNA sequencing data from patients with Ulcerative colitis or Crohn's disease.<br><br>RESULTS AND DISCUSSION: Compared to PDLIM2 +/+ mice, PDLIM2 -/- mice exhibited exacerbated and unresolved epithelial damage and inflammation accompanied by immune cell infiltration, which was precluded sufficient time to observe tunour development. PDLIM2 -/- mice exhibited altered basal gut microbial diversity, composition and predicted functionality compared to +/+ mice. Interestingly, in +/+ mice, PDLIM2 expression was lost over the course of DSS-induced colitis. Mechanistic studies in Caco-2 enterocyte cell cultures demonstrated that PDLIM2 suppression resulted in impaired cell adhesion signalling and sustained oxidative stress. In silico analysis of single cell RNA seq data sets from patients with ulcerative colitis and Crohn's disease demonstrated that although PDLIM2 was clearly expressed in normal human colonic epithelial enterocyte populations, its expression declined in both ulcerative colitis and Crohn's disease. We conclude that PDLIM2 is necessary for intestinal homeostasis through regulation of cell adhesion and antioxidant pathways, while loss of PDLIM2 sustains inflammation and epithelial damage.}, }
@article {pmid41743807, year = {2026}, author = {Zhou, H and Jiang, S and Zhang, L and Zhao, J and Zhou, T and Zhang, L and Ma, Y and Liu, S and You, Z and Li, F and Chen, S and Chen, L and Wang, Q and Xing, X and Chen, W and Li, D}, title = {Impact of Ozone Exposure on Oral Microbiome: A Controlled, Randomized, Crossover Trial.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {236-245}, pmid = {41743807}, issn = {2833-8278}, abstract = {Environmental ozone pollution may adversely impact human health, while dysbiosis is implicated in various health outcomes. However, the effects of ozone exposure on the human microbiome remain unclear. This study conducted a controlled, randomized, crossover ozone exposure trial with 29 participants exposed to filtered air and ozone. Oral microbiome samples were collected for 16S rRNA sequencing. A mixed-effects model was used to analyze the impact of ozone exposure on the diversity and composition of the oral microbiome, as well as their association with lung functions. The results showed that the ozone concentration remained stable at 5 ± 5.1 parts per billion (ppb) under filtered air and 282.2 ± 44 ppb during ozone exposure. Acute ozone exposure significantly impaired lung function and reduced oral microbiome diversity, with forced vital capacity (FVC) decreasing by 0.41 L, expiratory volume in one second (FEV1) by 0.36 L, and peak expiratory flow (PEF) by 0.81 L, while observed species richness (Sobs), abundance-based coverage estimator (Ace), and chao indices (Chao) decreased by 21.83, 22.24, and 21.87%, respectively. Males exhibited greater sensitivity to ozone exposure than females, reflected in both reduced lung function and alterations in the oral microbiome. The altered microbiome was mainly enriched in metabolic pathways. Among the microbiome, Treponema medium exhibited a significant correlation and mediating effect on ozone-induced lung function impairment, which may serve as a sensitive indicator of changes in lung function. These findings provide new insights into the health effects caused by ozone exposure.}, }
@article {pmid41743802, year = {2026}, author = {Wei, H and Xu, Y and Jin, B and Zhao, X and Yang, X and Guan, Q and Gao, B and Zhang, Z and Sun, H and Ye, Y and Ikeda, A and Xia, Y}, title = {Population-Level Amplicon and Metagenomic Analyses Uncover Distinct Effects of Landscape-Level Pesticides on the Maternal Gut Microbiome.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {2}, pages = {246-258}, pmid = {41743802}, issn = {2833-8278}, abstract = {The environment dominates over host genetics in shaping the gut microbiome, which plays a pivotal role in modulating human health. Experimental evidence supports the notion that exposure to pesticides could perturb the gut microbiome, and the toxicant-induced dysbiosis may affect host homeostasis. However, the field of human studies, especially in early life, is still in its infancy. We aimed to evaluate the effects of landscape pesticide exposure on the maternal gut microbiome. Here, we assessed the blood levels of a broad array of pesticides in 405 pregnant women. Gut microbial compositions and functional profiles were assessed by using both 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. Microbial alpha diversity indices were regressed on host and environmental factors using linear models. Differences in overall microbial compositions were evaluated by using univariable permutational multivariate analyses of variance (PERMANOVA) with Bray-Curtis dissimilarities. All pesticides, as well as other host and environmental factors, were correlated to the gut microbiome at the phylum, genus, species, and pathway levels employing the multivariable regression models adjusted for the potential covariates, respectively. The joint effects of the mixture of pesticide exposure on the gut microbiome were investigated using quantile g-computation. Microbial ecological networks were constructed via Spearman correlations to explore species co-occurrence patterns related to pesticide exposure. Significant associations were observed between exposure to various pesticides individually or as a mixture and maternal gut microbiome features. Specific taxa and pathways were enriched or depleted in response to varying pesticide concentrations, indicating the potential exposure-response relationships. Notably, mirex exposure showed a positive correlation with both the relative abundance of Blautia_wexlerae and the sucrose biosynthesis II pathway. Microbial co-occurrence network analyses revealed marked shifts in species interactions associated with increasing levels of pesticide exposure. Mediation analyses further identified a greater number of microbial taxa, particularly Blautia_wexlerae, as significant mediators linking pesticide exposure to alterations in microbial functional pathways. Our large-scale amplicon and metagenomic analyses unraveled the extensive impacts of landscape-level pesticides on the maternal gut microbiome. Further observational and experimental research is warranted to validate our findings as well as to elucidate whether and how these microbial changes affect maternal and offspring health.}, }
@article {pmid41743643, year = {2026}, author = {Markfeld, M and Talpaz, I and Biton, B and Maheriniaina Randriamoria, T and Soarimalala, V and Goodman, SM and Nunn, CL and Titcomb, G and Pilosof, S}, title = {Host traits and environmental factors shape infection heterogeneity in wild rat-protozoa networks.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag026}, pmid = {41743643}, issn = {2730-6151}, abstract = {The occurrence of microbes in animal hosts is highly heterogeneous, shaped by interactions among host traits, environmental context, and microbial diversity. Understanding this heterogeneity is particularly critical for endoparasite infections, where some hosts harbor diverse, high-burden assemblages that elevate disease spread and spillover risk. Yet the mechanisms underlying such heterogeneity remain poorly understood in wild systems, especially at the individual-host level. We addressed this challenge by studying protozoan infections in introduced black rats (Rattus rattus) across environmental gradients in Madagascar. Using network-based stochastic block modeling, we identified three infection profiles capturing meaningful variation in protozoan richness and composition, providing a structured framework for understanding heterogeneity. To uncover the predictors of these profiles, we trained machine-learning models incorporating host traits with environmental variables. Our models consistently outperformed no-skill baselines, with host traits contributing [Formula: see text]40% more to predictions than environmental factors. Body mass and gut microbiome composition emerged as the strongest host predictors, while rat and other non-native species densities were the most influential environmental predictors. These results show that infection heterogeneity arises from the interplay of intrinsic host traits and extrinsic environmental conditions. Our approach illustrates how combining network analysis with predictive modeling can (i) uncover latent heterogeneity in host-microbe associations, (ii) identify the relative contribution of the factors driving this heterogeneity, and (iii) predict host infection profiles. Our framework advances microbial ecology by linking host traits, microbial communities, and environmental context, while also informing disease ecology at human-animal interfaces where zoonotic pathogens circulate.}, }
@article {pmid41743568, year = {2026}, author = {Ekunseitan, DA and Famuyide, IM and Adelusi, OO and Ayoola, AA}, title = {Editorial: Ethnomedicinal strategies for controlling pathogen colonization in livestock: integrating traditional practices into modern livestock health management.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1793301}, pmid = {41743568}, issn = {2297-1769}, }
@article {pmid41743357, year = {2026}, author = {Xixi, NA and Karamanolis, G and Vlachogianni, EE and Voulgaris, T and Sokou, R and Volaki, P and Paliatsiou, S and Iliodromiti, Z and Iacovidou, N and Boutsikou, T}, title = {The effect of gestational weight gain on the infant gut microbiome- a systematic review of the literature.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1751708}, pmid = {41743357}, issn = {2235-2988}, abstract = {INTRODUCTION: Maternal weight status and gestational weight gain (GWG) critically affect maternal and neonatal health. The infant gut microbiome is a key predictor of short- and long-term child health. Therefore, investigating how maternal weight characteristics influence the composition and establishment of the infant's gut microbiome is essential.<br><br>OBJECTIVE: To evaluate the impact of excessive GWG on the infant gut microbiome.<br><br>METHODOLOGY: PubMed and Scopus were systematically searched for studies on GWG from September 1[st] until October 1[st], 2025. Data on infant gut microbiome characteristics and their relation to maternal weight change during pregnancy were extracted. The systematic review is registered in PROSPERO (CRD 420251181399).<br><br>RESULTS: A total of 15 studies met the inclusion criteria and were included in this review. Excessive Gestational Weight Gain (EGWG) consistently appeared to impair infant gut microbial alpha diversity, an effect that persisted up to 12 months. Taxonomically, EGWG caused a shift away from beneficial Bacteroides toward opportunistic/pathogenic genera (e.g., C. difficile). The negative effects are synergistically exacerbated by co-occurring Gestational Diabetes Mellitus (GDM) and are functionally characterized by an independent shift toward microbial carbohydrate degradation and vitamin synthesis pathways. Clinically, this EGWG-induced dysbiosis is linked to increased early childhood weight gain.<br><br>CONCLUSION: EGWG is an independent, critical determinant of persistent infant gut dysbiosis, characterized by taxonomic and functional shifts. These findings establish EGWG as a key modifiable maternal factor, linking gestational health to infant gut microbiome and health.<br><br>https://www.crd.york.ac.uk/PROSPERO/view/CRD420251181399, identifier: CRD 420251181399.}, }
@article {pmid41743327, year = {2026}, author = {Loke, P and Lee, SC and Tee, MZ and Shen, Z and Er, YX and Neelam, R and Cadwell, K and Lim, Y and Segre, J}, title = {Functional divergence of the gut microbiome associated with lifestyle and helminth infection in Indigenous Peninsular Malaysian.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7706316/v1}, pmid = {41743327}, issn = {2693-5015}, abstract = {Gut microbiome catalogs from Indigenous Southeast Asian populations remain underrepresented. Here, we integrated metagenomic and metatranscriptomic data from Indigenous Orang Asli (OA) in Peninsular Malaysia and urban residents of Kuala Lumpur (KL), together with immune profiling, to investigate gut microbial activity and functions associated with lifestyle and helminth infection. Prevotella showed significantly higher transcriptional activity in OA, whereas Bacteroides was more active in KL, corresponding to distinct immune signatures. Microbial genome-wide association studies (mGWAS) revealed Prevotella copri_A variants were linked to lifestyle and host immunity, while Blautia strain variation was associated with helminth infection. Malaysian metagenome-assembled genomes (MAGs) uncovered 307 novel species, predominantly within Clostridia. Among these, the novel HGM13006 species were enriched with genes for starch and sucrose metabolism, and the novel Ruminococcus_D species in flagellar assembly and chemotaxis. Together, these findings provide function-level insights into gut microbiome variation associated with lifestyle and helminth infection in an indigenous population.}, }
@article {pmid41743241, year = {2026}, author = {Paymani, Z and Nazari, M and Mirnia, K and Sangsari, R and Ebrahimi, M and Haghighi, F}, title = {Rethinking Neonatal Vaccination Policies: A Neuroimmune Perspective.}, journal = {Iranian journal of medical sciences}, volume = {51}, number = {2}, pages = {84-103}, pmid = {41743241}, issn = {1735-3688}, abstract = {Neonatal vaccination is a cornerstone of early-life infectious disease prevention. However, the timing and safety of these interventions require careful consideration. This review explored the neuroimmune implications of early immunization, with a specific focus on the interplay between the developing immune and nervous systems. We examined potential mechanisms through which vaccine-induced immune activation might influence brain development, through epigenetic modifications and sustained cytokine responses, particularly involving interleukin-6 (IL-6). The discussion addressed concerns related to immune overstimulation, regulatory T-cell suppression, and microbiome disruption, considering their potential links to autoimmune and neurodevelopmental disorders. In light of the identified evidence gaps, we advocate for a cautious, individualized vaccination approach guided by the "As Low and Late As Reasonably Achievable" (ALLARA) principle. This strategy aimed to balance robust protection against infectious diseases with the imperative of safeguarding lifelong neurological and immunological health.}, }
@article {pmid41743204, year = {2026}, author = {Xu, K and Guan, P and Du, W and Zeng, H and Chen, M and Lv, Z and Liu, Y and Shao, M and Qu, B}, title = {Warming outweighs nitrogen deposition in shaping rhizosphere microbial structure involved in carbon, nitrogen, and phosphorus cycling in Ambrosia trifida.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1686326}, pmid = {41743204}, issn = {1664-462X}, abstract = {INTRODUCTION: Ambrosia trifida, a harmful invasive plant, poses significant ecological and economic threats and is expected to spread further under future warming and nitrogen deposition scenarios. According to plant-soil feedback and enhanced mutualist hypothesis, invasive plants may gain a competitive edge by recruiting specific microorganisms. However, little is known about the composition and functional potential of its rhizosphere microbiome.<br><br>METHODS: In this study, we combined metagenomics with widely targeted metabolomics to investigate the interactions between root exudates and soil microbial communities under experimental warming and nitrogen deposition.<br><br>RESULTS AND DISCUSSION: The results showed that warming and nitrogen addition together promoted biomass accumulation. And their combination enhanced soil nutrient content. Warming increased the abundance of functional genes involved in carbon fixation (e.g., acs, acsA, PCCA, MUT), whereas nitrogen addition suppressed nitrification and denitrification genes. Warming also enhanced the abundance of genes related to inorganic phosphate solubilization (ppk, ppx), phosphorus mineralization (phnPP, phnF, glpQ), and phosphorus transport (pstBC, ugpABCE). Functionally, warming increased the relative abundance of beneficial taxa such as Sphingomicrobium, Massilia, and Nocardioides, while reducing Pseudomonas, Trinickia, and Rhizomicrobium. Nitrogen deposition had a comparatively weaker effect on the functional microbial community. Correlation analysis between metabolites and functional genes suggested that alkaloids, organic acids, and phenolic compounds may be key drivers of microbial functional shifts. Overall, our findings demonstrate that warming has a greater influence than nitrogen deposition on shaping the rhizosphere soil microbial community and enhancing nutrient cycling functions, potentially increasing the risk of A. trifida invasion under future climate change.}, }
@article {pmid41743194, year = {2026}, author = {Obeagu, EI}, title = {Novel Microbiome-Driven Approaches to Counteract Chemotherapy-Induced Mucositis in Breast Cancer Patients.}, journal = {Breast cancer (Dove Medical Press)}, volume = {18}, number = {}, pages = {590718}, pmid = {41743194}, issn = {1179-1314}, abstract = {Chemotherapy-induced mucositis (CIM) is a clinically important toxicity in breast cancer care that adversely affects oral and gastrointestinal mucosa, quality of life, nutritional status, and treatment tolerability. While CIM is less frequently dose-limiting in contemporary standard regimens (eg, AC-T, TC) compared with hematologic and neurotoxicities, it remains a significant supportive care challenge, particularly in dose-dense schedules, older cytotoxic protocols, and with selected targeted agents and antibody-drug conjugates. Emerging evidence indicates that chemotherapy-associated dysbiosis can amplify mucosal inflammation and barrier dysfunction, acting as a modifier of injury rather than the primary driver, which is direct epithelial cytotoxicity. A narrative review was conducted using structured searches of PubMed/Medline, Scopus, and Web of Science up to 2025 to identify preclinical and clinical studies addressing the pathobiology of CIM, chemotherapy-associated microbiome perturbations in breast cancer, and microbiome-targeted preventive or therapeutic strategies. Evidence was synthesized qualitatively, with explicit distinction between mechanistic preclinical data and emerging clinical findings. Chemotherapy induces reproducible alterations in oral and gut microbial communities, characterized by reduced microbial diversity, depletion of commensal taxa involved in epithelial homeostasis, and relative expansion of pathobionts. Preclinical models demonstrate that dysbiosis can exacerbate inflammatory signaling, impair epithelial repair, and increase susceptibility to ulceration and infection. Early-phase clinical studies and small randomized trials in heterogeneous oncology populations suggest that selected probiotics, prebiotics, and dietary interventions may modestly attenuate the incidence or severity of mucositis, although robust breast cancer-specific evidence remains limited. More advanced approaches, including postbiotics, fecal microbiota-based strategies, and engineered live biotherapeutics, are largely investigational. CIM in breast cancer is a multifactorial toxicity primarily driven by direct chemotherapy-induced epithelial injury, with the microbiome functioning as an important biological modifier of inflammation, barrier integrity, and mucosal repair. Microbiome-targeted interventions represent a promising adjunct to conventional supportive care rather than a stand-alone solution. Well-designed, breast cancer-specific clinical trials incorporating longitudinal microbiome and metabolomic profiling are required to define clinical efficacy, safety, and patient subgroups most likely to benefit from precision microbiome modulation.}, }
@article {pmid41743137, year = {2026}, author = {Shan, F and Leng, C and Xiao, Y and Zhang, X and Tang, M and Yi, Y and Tang, J}, title = {Root triterpenoid metabolites drive the assembly and feedback regulation of the rhizosphere microbiome during flowering to senescence in Rhododendron hybridum 'Yangmeihong'.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753104}, pmid = {41743137}, issn = {1664-302X}, abstract = {The flowering-to-senescence transition is a critical developmental period in ornamental plants, yet the interplay between root metabolites and the rhizosphere microbiome during this process remains poorly characterized. Integrating metabolomic and microbiomic analyses of Rhododendron hybridum, we investigated their dynamic interactions. Our analyses revealed both the root metabolome and rhizosphere microbiome exhibited significant temporal dynamics. Differential metabolites significantly enriched in sesquiterpenoid and triterpenoid biosynthesis, while microbial α-diversity peaked at full bloom before declining. The rhizosphere microbial network complexity decreased from flowering to senescence, accompanied by a shift in community assembly from stochastic to more deterministic processes. Furthermore, root metabolites mediated stage-specific assembly of the rhizosphere microbiome. Specifically, seven volatile terpenoids, upregulated during senescence, were significantly correlated with 77 microbial taxa, including putative plant growth-promoting bacteria. Functional prediction suggested that these interacting microbial taxa are potentially involved in sulfur cycling, methionine biosynthesis, and nucleic acid metabolism, indicating a potential role in feedback regulation during senescence. Our findings demonstrate that root triterpenoid metabolites are pivotal in driving rhizosphere microbiome assembly and may receive functional feedback, providing novel insights into microbiome-mediated regulation of floral development and senescence.}, }
@article {pmid41743010, year = {2026}, author = {Álvarez-Montero, X and Mercado-Reyes, I and Castillo-Chamba, W and Gordillo, G and Santos-Ordóñez, E and Portalanza, D and Saeteros-Hernández, A}, title = {Metabarcoding insights into the fungal diversity and biotechnological potential of mangrove sediments in Ecuador's Reserva Ecológica Manglares Churute.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1710970}, pmid = {41743010}, issn = {2673-6128}, abstract = {Mangrove ecosystems are biodiversity hotspots and vital carbon sinks, yet their fungal communities-key drivers of nutrient cycling and ecosystem resilience-remain largely unexplored in the Neotropics. This is particularly true for Ecuador's protected reserves, where no molecular census of sediment fungi exists. To address this gap, we conducted the first metabarcoding survey of the fungal microbiome in the sediments of the Reserva Ecológica Manglares Churute (REMC), a critical mangrove habitat under increasing anthropogenic pressure. This is the first molecular study to characterize fungal communities in the mangrove sediments of the Reserva Ecológica Manglares Churute (REMC) in the neotropical context of Ecuador, using metabarcoding. The fungal community was dominated by Ascomycota (68%) and Basidiomycota (30%), with minor contributions from Mortierellomycota, Chytridiomycota, and Mucoromycota (<0.1%), and 2.10% unclassified at the phylum level. The most diverse sample (2005L2-69) had a Shannon index of 2.166. Rarefaction curves indicated that additional sampling could reveal more fungal diversity. Fungal assemblages were similar across samples, with minor variations linked to environmental factors. Predominant classes included Dothideomycetes, Agaricomycetes, and Eurotiomycetes. At the genus level, Ascochyta (27%), Antrodia (24%), and Talaromyces (17%) were the most abundant. The presence of genera such as Talaromyces and Penicillium highlights their biotechnological potential, like antibacterial properties. At the same time, the abundance of Ascochyta, a phytopathogen, suggests potential stress or disease susceptibility in this area of REMC. This research provides an essential preliminary overview of the mycobiome in this underexplored region and identifies principal taxa of ecological and biotechnological importance. Furthermore, this investigation, conducted in a specific area of REMC sediments, employs metabarcoding analysis utilizing ITS86-ITS4 primers in Neotropical mangroves, thereby contributing to the global understanding of mangrove microbiomes.}, }
@article {pmid41742841, year = {2026}, author = {Wang, Y and Wu, H and Qu, M and Zhang, C and Xu, Z and Pei, Y and Zhao, C and Wang, J and Ma, S and Lyu, N and Xu, X and Bi, Y and Zhu, B and Gao, GF}, title = {A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e74581}, doi = {10.1002/advs.74581}, pmid = {41742841}, issn = {2198-3844}, support = {2023YFC2307101//National Key Research and Development Program of China/ ; 235200810058//Project for Young Scientists of the Joint Funds of Science and Technology Research and Development Plan of Henan Province, China/ ; 30501278//Young TopNotch Talents Foundation of Henan Agricultural University/ ; }, abstract = {Migratory birds play an important role in the spread of antimicrobial resistance (AMR); however, gaps in surveillance data from vital regions along migratory flyways across China limit the detection of emergent threats. Here, we assembled 340 metagenomes from 52 bird species covering 11 provincial administrative districts in China, presenting a specialized migratory microbial genome and gene catalog to archive the genomic and functional diversity of gut microbiomes in wild birds. This comprehensive migratory bird microbial genome and gene (MBGG) catalog includes 5823 metagenome-assembled genomes (MAGs), 13 072 plasmid sequences, and 44 974 viral genomes, which represent 1709 candidate species spanning 36 phyla. The catalog also contains over 20 million non-redundant protein-encoding genes, the use of which is confirmed by the mining of 15 678 secondary metabolite biosynthetic gene clusters, 1814 known antibiotic resistance genes, and 7219 virulence factors. The number of clinically critical ARGs identified in Grus japonensis was the highest, followed by Cygnus cygnus and Sibirionetta formosa, which indicated that these species are hotspot species of clinically critical AMR dissemination. Moreover, we mapped the profile of bacterial zoonotic/opportunistic pathogens carried by wild birds and evaluated their associations with publicly available genomes. Finally, the precise migratory movements for 10 bird species using a global positioning system tracking system help to assess the movement of microorganisms and AMR risk. Collectively, this valuable resource provides the basis for the integration and unification of global wild bird microbiomes, timely sharing, and assessing the uncertainty of migratory microbiomes in the future.}, }
@article {pmid41742575, year = {2026}, author = {Fernandes, EL and Souza, RBMS and Santos, LNA and Lima, LS and Silva, HL and Oliveira, SG and Félix, AP}, title = {Longitudinal study of diet digestibility, microbiome, and gut fermentation metabolites in growing dogs.}, journal = {Journal of veterinary internal medicine}, volume = {40}, number = {1}, pages = {}, doi = {10.1093/jvimsj/aalag001}, pmid = {41742575}, issn = {1939-1676}, abstract = {BACKGROUND: Puppies have particular characteristics due to gastrointestinal immaturity, influencing physiological processes.<br><br>HYPOTHESIS/OBJECTIVES: Evaluate the effects of age and consumption on apparent diet digestibility coefficients (ADC), fecal characteristics, fermentation metabolites, and fecal microbiome in growing dogs.<br><br>ANIMALS: Eight dogs were evaluated at 2, 5, 8, 11, and 14&#xa0;months old in experiment 1 and 12 dogs at 14&#xa0;months old in experiment 2.<br><br>METHODS: This was a prospective experimental study. Dietary ADC, fecal characteristics, fermentation metabolites, and fecal microbiome were evaluated in 2 experiments: the first analyzed the effect of age, and the second, the effect of consumption in 2 groups: adult intake (AI) and puppy intake (PI).<br><br>RESULTS: Older dogs had lower ADC of dry matter (DM), ether extract, and metabolizable energy, and higher ADC of crude protein (CP) (P&#xa0;<&#xa0;.05). Younger dogs had lower fecal DM and fecal score and higher fecal production (P&#xa0;<&#xa0;.05). Older dogs had higher fecal concentrations of short-chain fatty acids and indoles and lower concentrations of branched-chain fatty acids (BCFA) (P&#xa0;<&#xa0;.05). Dogs aged between 2 and 5&#xa0;months had a higher fecal abundance of Streptococcus and Escherichia coli and lower abundance of Turicibacter and Peptacetobacter (P&#xa0;<&#xa0;.05). The ADC of DM, organic matter, and CP were lower in PI dogs than in AI dogs (P&#xa0;<&#xa0;.05). The AI dogs had higher fecal DM and fecal score and lower fecal production (P&#xa0;<&#xa0;.05). Puppy intake dogs had higher fecal concentrations of ammonia and BCFA and a higher abundance of Streptococcus and a lower abundance of Blautia (P&#xa0;<&#xa0;.05).<br><br>Age and feed intake influence the ADC of nutrients and energy, the fecal microbiome, and fermentation metabolites, with the microbiota stabilizing after 8&#xa0;months of age in dogs.}, }
@article {pmid41742321, year = {2026}, author = {Mazzoni, C and Ochana, BL and Orlanski-Meyer, E and Ya'acov, AB and Focht, G and Harpenas, E and Shmorak, S and Ledder, O and Lev-Tzion, R and Shemer, R and Shteyer, E and Dor, Y and Yassour, M}, title = {Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02344-6}, pmid = {41742321}, issn = {2049-2618}, abstract = {BACKGROUND: Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized as a non-invasive way to profile the gut microbiome, and both clinical practice and research on inflammatory bowel diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, excessive immune cell recruitment and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics.<br><br>METHODS: We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of pediatric IBD patients and controls (Pediatric cohort, N&#x2009;=&#x2009;134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large complementary external cohort including adult IBD patients and controls (Adult cohort, N&#x2009;=&#x2009;689 adults, the Netherlands), not only to compare microbial patterns across the age spectrum, but also to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomic sequencing.<br><br>RESULTS: We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage, and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD cohorts.<br><br>CONCLUSIONS: The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients. Video Abstract.}, }
@article {pmid41742234, year = {2026}, author = {Matsumoto, M and Miura, O and Moriya, T and Ogino, H and Hirayama, M and Mitsui, A and Hirayama, T and Ebisuno, Y and Kaneko, M and Satomi, Y and Nio, Y}, title = {Cross-organ multi-omics profiling of microbiome and metabolome along the gut-liver axis in MASH model mice induced by western diet and MC4R knockout.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00813-9}, pmid = {41742234}, issn = {1757-4749}, }
@article {pmid41742177, year = {2026}, author = {Moon, SW and Kim, M and Kim, EY and Kang, C and Shin, JH and Kim, K and Won, S and Yi, H and Jung, JY}, title = {Longitudinal change of lung microbiome in chronic obstructive pulmonary disease: a prospective cohort study.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-025-03471-8}, pmid = {41742177}, issn = {1465-993X}, support = {RS-2025-25459824//Korea Health Industry Development Institute/Republic of Korea ; RS-2021-KE001387//Korean Ministry of Environment/ ; 2022R1A2C1007966//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: The lung microbiome is increasingly implicated in chronic obstructive pulmonary disease (COPD) pathogenesis. However, its long-term dynamics and interactions with key clinical features-including inhaled corticosteroid (ICS) use, smoking, and lung function-remain poorly defined.<br><br>METHODS: We conducted a prospective two-year study of 43 Korean male patients with COPD who provided sputum samples annually (n&#x2009;=&#x2009;129). Bacterial communities were profiled using 16S rRNA gene sequencing. Associations between microbial composition and clinical characteristics-including inhaled corticosteroid (ICS) use, smoking status, lung function (FEV&#x2081;), and recent exacerbations-were evaluated using negative binomial mixed models (NBMMs) with and without time interaction terms, adjusting for potential confounders.<br><br>RESULTS: At baseline, overall microbial diversity did not significantly differ between patients with COPD and ex-smoker controls without airflow limitation; however, several low-abundance genera showed differential abundance. Cross-sectional NBMMs revealed that ICS use, current smoking, and reduced FEV&#x2081; % predicted were associated with distinct taxonomic profiles. ICS use was associated with reduced relative abundances of Veillonella, Catonella, and Saccharimonas. Persistent smoking was linked to increased abundances of Actinomyces and Bulleidia and decreased Lautropia. Patients with FEV&#x2081; % predicted < 50% exhibited lower Alloprevotella levels. In longitudinal models, ICS use was associated with increasing temporal trends in Megasphaera and Alloprevotella. Persistent smokers showed attenuated changes in Butyrivibrio and Pseudomonas, while those with severe airflow limitation exhibited increased Bacteroides and decreased Atopobium, Gemella, Kingella, and Tannerella over time. Acute exacerbations were not significantly associated with microbial composition at baseline or during follow-up.<br><br>CONCLUSIONS: Clinical factors in COPD are associated with distinct temporal shifts in the airway microbiome of patients with COPD. Longitudinal profiling combined with NBMMs with time-interaction terms revealed subtle microbial shifts with potential clinical implications that were not evident in cross-sectional analyses. These findings underscore the potential utility of temporal microbiome signatures in stratifying COPD patients and guiding future therapeutic strategies.}, }
@article {pmid41742010, year = {2026}, author = {Sobhy, EE and Ezzeldin, S and Karam, A and Galal, A and Mokhtar, A and Anwar, W and Abou-Elmagd, A and Magdeldin, S and Enany, S}, title = {Functional microbial shifts and host-microbiome crosstalk in colorectal cancer: insights from a metaproteomic approach.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04807-0}, pmid = {41742010}, issn = {1471-2180}, abstract = {Colorectal cancer (CRC) incidence is increasing in many low- and middle-income countries, including Egypt, partly due to urbanization and lifestyle changes. Metaproteomic approaches remain underutilized in these settings. In this study, we applied fecal metaproteomics in Egyptian CRC patients to characterize disease-associated protein expression patterns, explore host-microbiota functional interactions, and identify metabolic pathways that are altered in the CRC gut environment. Stool samples from 10 CRC patients and 10 healthy controls were analyzed. A total of 441 differentially expressed proteins (DEPs) were identified, of which 406 were consensus proteins overlapping across fold-change analysis, Wilcoxon testing, and PLS-DA. Differential microbial protein expression was primarily associated with core metabolic functions, including carbohydrate, amino acid, and nucleotide transport. Notably, proteins from Segatella copri were markedly suppressed in CRC patients. Functional analysis revealed upregulation of microbial proteins related to DPP-4 and cysteine metabolism, suggesting a possible role of microbiome-derived enzymes in colorectal cancer-associated metabolic and immune modulation, without direct evidence of host translocation.}, }
@article {pmid41741786, year = {2026}, author = {Flinn, H and Marshall, A and Holcomb, M and Burke, M and Kara, G and Cruz-Pineda, L and Soriano, S and Treangen, TJ and Villapol, S}, title = {Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09737-1}, pmid = {41741786}, issn = {2399-3642}, support = {R56AG080920//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; EF-2126387//NSF | BIO | Division of Emerging Frontiers (EF)/ ; }, abstract = {Traumatic brain injury induces neuroinflammation and gut microbiome dysbiosis, yet the effects of short-term antibiotic treatment on these processes remain poorly understood. To address this, male mice received controlled brain injuries followed by a brief course of oral antibiotics. Antibiotic treatment reduced bacterial abundance in feces and altered microbial diversity, with more pronounced shifts after two injuries. Despite this disruption, antibiotic-treated mice exhibited smaller lesion volumes, reduced cell death, attenuated microglial and macrophage activation, lower pro-inflammatory cytokine levels, and decreased astrogliosis and peripheral immune cell infiltration compared with vehicle-treated mice after two injuries. In the gut, increasing injury severity was associated with villus shortening and loss of mucus-producing cells, and antibiotic treatment further modified these injury-related changes. Circulating levels of short-chain fatty acids and associated microbial metabolic functions were reduced by antibiotic exposure. In contrast, germ-free mice showed increased lesion volumes and exacerbated gliosis following brain injury. Long-read metagenomic sequencing identified Parasutterella excrementihominis and Lactobacillus johnsonii as taxa that persisted despite antibiotic treatment. Collectively, these results suggest that antibiotics can reduce brain damage after injury through mechanisms not explained by short-chain fatty acids, while also highlighting potential drawbacks of altering the gut microbiome.}, }
@article {pmid41741644, year = {2026}, author = {Wiederkehr, F and Paoli, L and Richter, D and Racunica, D and Ruscheweyh, HJ and Sperfeld, M and O'Brien, J and Miravet-Verde, S and Streiff, AB and Ransome, J and Chepkirui, C and Priest, T and Sintsova, A and Salazar, G and Bistolas, KSI and Sawyer, T and Labadie, K and Mayer, KI and Perdereau, A and Reddy, MM and Moulin, C and Boissin, E and Bourdin, G and Cailliau, J and Iwankow, G and Poulain, J and Romac, S and ,  and Planes, S and Allemand, D and Agostini, S and Bowler, C and Douville, E and Forcioli, D and Galand, PE and Lombard, F and Oliveira, PH and Thomas, OP and Vega Thurber, R and Troublé, R and Voolstra, CR and Wincker, P and Ziegler, M and Piel, J and Sunagawa, S}, title = {Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {41741644}, issn = {1476-4687}, abstract = {Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services[1]. They are reservoirs of bioactive metabolites, many produced by microorganisms associated with reef invertebrate hosts[2]. However, for the keystone species of coral reefs-the reef-building corals-we still lack a systematic assessment of their microbially encoded biosynthetic potential and the molecular resources at stake due to the alarming decline in reef biodiversity. Here we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands throughout the Pacific Ocean (Tara Pacific expedition)[3]. By contextualizing our analyses with the microbiomes of other reef species, we found that only 10% of the 4,224 microbial species and less than 1% of the 645 species exclusively identified in Tara Pacific samples had genomic information available. Furthermore, the biosynthetic potential of reef-building coral microbiomes rivalled or surpassed that of traditional natural product sources such as sponges. Among the biosynthetically rich bacteria in the reef microbiome, we identified new groups of Acidobacteriota that encode previously unknown enzymology, in turn opening promising avenues for functional protein engineering. Together, this study underscores the importance of conserving coral reefs as vital reservoirs of molecular diversity.}, }
@article {pmid41741537, year = {2026}, author = {Aouabed, Z and Therrien, V and Bouaoune, MA and Bakhtyari, M and Hijri, M and Makarenkov, V}, title = {Soil microbiome prediction using traditional machine learning and deep learning models.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-39537-w}, pmid = {41741537}, issn = {2045-2322}, }
@article {pmid41741520, year = {2026}, author = {Valadez-Ingersoll, M and Bodnar, CA and Feng, EX and Wong, A and Gilmore, TD and Davies, SW}, title = {Symbiotic state affects microbiome recovery in a facultatively symbiotic cnidarian.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-38684-4}, pmid = {41741520}, issn = {2045-2322}, support = {NRT DGE 1735087//National Science Foundation/ ; IOS-1937650//National Science Foundation/ ; }, abstract = {Cnidarian holobionts consist of host cells, algal symbionts, and a complex microbiome residing in and on host tissue and algal symbionts. To investigate interactions among these three partners, we used antibiotics to deplete the microbiome of the facultatively symbiotic sea anemone Exaiptasia pallida (Aiptasia) in both symbiotic and aposymbiotic states and profiled 16S bacterial communities throughout recovery. We assessed host molecular response to microbiome depletion and recovery using RNA-seq and Western blotting of immune transcription factor NF-κB. 16S results demonstrate that, following depletion, symbiotic Aiptasia readily reestablished bacterial communities similar to control anemones. However, aposymbiotic Aiptasia microbiomes failed to reestablish control-level microbiomes even after seven days of recovery, highlighting differences between symbiotic states. Specifically, Endozoicomonadaceae reestablished to control levels in symbiotic, but not aposymbiotic, Aiptasia, suggesting a close physical association between Endozoicomonadaceae and algal symbionts. Molecular analyses showed that, during antibiotic recovery, host immune system gene expression was downregulated, but NF-κB protein levels increased, suggesting mechanisms for microbiome reestablishment following disruption. This study demonstrates the dynamics of microbiome recovery and how microbiome community members influence host gene expression in a cnidarian, providing a foundation for future research involving pairwise interactions between microorganisms and hosts.}, }
@article {pmid41741460, year = {2026}, author = {Lin, Y and Kouraki, A and Cheetham, NJ and Louca, P and Bowyer, RC and Pope, R and Asnicar, F and Zhang, X and Visconti, A and Falchi, M and Spector, TD and Segata, N and Valdes, AM and Menni, C}, title = {Gut microbiome composition and function reflect socioeconomic deprivation.}, journal = {NPJ biofilms and microbiomes}, volume = {12}, number = {1}, pages = {}, pmid = {41741460}, issn = {2055-5008}, support = {MR/W026813/1 and MR/Y010175/1//UKRI/MRC grants/ ; }, abstract = {Socioeconomic status (SES) correlates with adverse health outcomes, but the underlying biological mechanisms remain unclear. We examined how area-level deprivation (Townsend Deprivation Index) influences gut microbiome composition and function and whether the gut microbiome mediates the effects of deprivation on metabolic and mental health. A total of 1390 females from TwinsUK with shotgun metagenomes were included in this study. We found that higher Townsend deprivation was associated with reduced alpha diversity (Beta [95% CI] = -1.60 [-3.00, -0.21]) and distinct microbial composition shifts (PERMANOVA P = 0.001). Twelve species and 22 functional pathways were linked to deprivation, distinguishing between deprivation groups (AUC = 0.725-0.744), with altered energy metabolism in deprived individuals. Townsend deprivation was associated with anxiety (OR [95%CI] = 1.09 [1.01, 1.18]) and diabetes (OR [95% CI] = 1.16 [1.03, 1.30]). Importantly, Intestinimonas massiliensis and Lawsonibacter sp_NSJ_51 partially mediate the effect of anxiety. Lawsonibacter sp_NSJ_51 also mediated the deprivation-diabetes association. These findings suggest that socioeconomic deprivation influences microbiome composition and function, mediating disparities in metabolic and mental health.}, }
@article {pmid41741450, year = {2026}, author = {Hesse, RD and Dinsdale, EA}, title = {The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00939-3}, pmid = {41741450}, issn = {2055-5008}, abstract = {Marine animal epidermal surfaces act as a transitional viral habitat-an epidermal ecotone-between tissues and the environment, supporting diverse tripartite relationships between animals, microbes, and viruses, which have yet to be investigated. In this review, we synthesize the viral ecology of marine animal epidermal tissues, surfaces, and aura biomes to identify knowledge gaps and highlight the value of marine animal epidermis as a novel model system for microbiome research.}, }
@article {pmid41741396, year = {2026}, author = {Garcia-Guevara, F and Resink, T and Clasen, F and Uhlén, M and Achour, A and Shoaie, S}, title = {Temporal dynamics of gut biosynthetic gene clusters link persistent colonization and engraftment in fecal microbiota transplantation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2634469}, doi = {10.1080/19490976.2026.2634469}, pmid = {41741396}, issn = {1949-0984}, abstract = {The human gut microbiome carries a large array of biosynthetic gene clusters (BGCs) that encode the production of secondary metabolites, yet their temporal dynamics and role during microbial colonization remain largely unexplored. Here, we tracked BGCs profile over time in a cohort of healthy adults, and identified two distinct groups: persistent, which are stable over time, and transient, which are more sporadic. Functional annotations indicated persistent gene clusters are enriched in antibiotic resistance mechanisms, while transient ones more frequently carry virulence-associated genes. We then examined colonization of these two groups in the context of fecal microbiome transplantation. Our results show that persistent gene clusters exhibit higher colonization rates than transient ones. These findings contribute to our understanding of how microbial metabolites influence host health, potentially guiding future therapeutic strategies targeting the microbiome.}, }
@article {pmid41741392, year = {2026}, author = {Yilmaz, B and Moulin, S and Heimgartner, B and Li, H and Geuking, M and Juillerat, P and Misselwitz, B and Macpherson, AJ and Wiest, R}, title = {Spatial mapping of human colonic niches reveals rapid, mucus-specific microbiota disruption after bowel cleansing.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2635866}, doi = {10.1080/19490976.2026.2635866}, pmid = {41741392}, issn = {1949-0984}, abstract = {Bowel preparation is routinely performed before colonoscopy, yet its immediate effects on the spatial organization of the colonic microbiota at the mucosal interface remain poorly resolved. Here, we introduce a high-resolution endoscopic mucus-harvesting approach, combined with luminal aspirates and mucosal biopsies, to generate a high-resolution, within-subject trajectory of microbiota alterations across distinct colonic niches in healthy adults over the first 24 hours after purging. While luminal bacterial communities remained remarkably stable, with no significant changes in alpha or beta diversity and proportional washout of taxa. In contrast, mucus-associated and mucosal communities underwent a rapid but reversible ecological restructuring, characterized by immediate post-cleansing shifts in composition and transient blooms of Proteobacteria, particularly Enterobacteriaceae. These perturbations were strongest in the 0-12-hour window and varied by individual, consistent with the dominance of personalized baseline microbial signatures. Critically, spatially resolved sampling revealed a key refinement: the Enterobacteriaceae expansion was confined almost exclusively to the superficial mucus layer, a glycan-rich, dynamically oxygenated compartment that is particularly susceptible to mechanical disturbance during lavage, whereas deeper mucus and mucosa-associated communities remained comparatively stable. By 24 hours, both mucosal and mucus-associated microbiota had largely returned to their individualized pre-cleansing configurations, indicating rapid ecosystem resilience and suggesting that the deeper mucus layer functions as a protected microbial reservoir that reseeds the epithelium and lumen once normal physiology is restored. This compartment-specific recovery trajectory contrasts with the prolonged dysbiosis typically observed after antibiotics or infection, underscoring the need for spatially precise sampling to interpret microbiome data collected during clinical endoscopy. Together, these findings establish an endoscopic strategy for probing microbe-mucus interactions in humans and provide a conceptual and methodological framework for interpreting microbiome data obtained during clinical endoscopy.}, }
@article {pmid41740714, year = {2026}, author = {Santos, ML and Mateo, SG and Martí, PR and Homedes, CS}, title = {CAN GUT MICROBIOME INFLUENCE ANEMIA DUE TO GASTROINTESTINAL LOSSES?.}, journal = {Gastroenterologia y hepatologia}, volume = {}, number = {}, pages = {502706}, doi = {10.1016/j.gastrohep.2026.502706}, pmid = {41740714}, issn = {0210-5705}, }
@article {pmid41740703, year = {2026}, author = {Garrigós, M and Jiménez-Peñuela, J and Saavedra, I and Veiga, J and García-López, MJ and Garrido, M and Ruiz-López, MJ and Figuerola, J and Moreno-Indias, I and Martínez-de la Puente, J}, title = {Interactions between urbanization, malaria infection and avian cloacal microbiome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124073}, doi = {10.1016/j.envres.2026.124073}, pmid = {41740703}, issn = {1096-0953}, abstract = {Urbanization, a major component of global change, has drastically modified the landscape, and is generally associated with biodiversity loss. Pollutants and low-quality food resources, among other urban stressors, can alter the physiology of urban-dwelling birds, ultimately affecting their interactions with other organisms, including pathogens and symbiotic microorganisms. The house sparrow (Passer domesticus) is one of the most common passerine species closely associated with anthropized environments. Here, we explored the association between the level of habitat urbanization, avian malaria infection (Plasmodium and Haemoproteus are grouped together in this study) and their combined effects on the composition of the cloacal microbiome of wild house sparrows. Urban birds showed a lower parasite prevalence than those from natural and rural habitats. In addition, the association between avian malaria infection and avian cloacal bacterial-microbiome composition depended on the habitat type. In natural habitats, infected birds showed a nearly significant increase in bacterial richness and significant differences in the relative abundance of various taxa, compared to uninfected individuals. In contrast, infection status was not associated with any microbiome parameter in birds from rural and urban habitats. In conclusion, habitat type is associated with avian malaria prevalence in house sparrows and may modulate the relationship between parasite infection and the bacterial composition of avian cloacal microbiome.}, }
@article {pmid41740635, year = {2026}, author = {Hsu, CY and Almajidi, YQ and Abohassan, M and Gafarov, R and Basunduwah, TS and Hjazi, A and Arora, V and Nayak, PP and Shukla, SK and Jayabalan, K}, title = {" Pharmacomicrobiomics in blood cancers: how the gut microbiome and its metabolites shape drug efficacy and toxicity ".}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {105229}, doi = {10.1016/j.critrevonc.2026.105229}, pmid = {41740635}, issn = {1879-0461}, abstract = {Clinical management of hematologic cancers is frequently complicated by marked, unpredictable inter-patient variation in both therapeutic benefit and adverse effects. Beyond host genetics, accumulating mechanistic and translational data implicate the gut microbiota and its small-molecule metabolome as active modifiers of drug chemistry, host immune tone, and clinical outcomes. In this review we synthesize three recurring, actionable findings: (1) discrete microbial enzymes, most prominently bacterial β-glucuronidases, repeatedly re-activate hepatic drug-glucuronides in the gut and amplify local gastrointestinal toxicity (e.g., irinotecan and mycophenolate), a pathway successfully targeted in preclinical and translational studies. (2) loss of anaerobic short-chain fatty acid production, especially butyrate, is a recurrent, causal mediator of mucosal injury and aggravated graft-versus-host disease after allogeneic hematopoietic cell transplantation. (3) reduced gut microbial diversity and the depletion of key functional taxa predict worse transplant outcomes (including mortality), arguing that baseline ecosystem state is a prognostic biomarker that merits routine consideration in trial design. Building on these syntheses, we propose a compact clinical framework for hematology trials and practice: (A) baseline ecosystem phenotyping (shotgun metagenome + targeted metabolite panel including butyrate and measured bacterial β-glucuronidase activity), (B) risk-stratified interventions (enzyme-targeted inhibitors, defined consortia, or metabolite replacement for high-risk patients), and (C) embedded holo-omic endpoints to confirm on-target biochemical modulation and link molecular change to clinical benefit. Together, these elements move Pharmacomicrobiomics beyond descriptive cataloging toward mechanistic stratification and testable interventions that can reduce unexplained variability in drug response and toxicity for patients with leukemia, lymphoma and myeloma.}, }
@article {pmid41740569, year = {2026}, author = {Mukhopadhyay, A and Kumar, A and Banerjee, S and Jha, S and Ghosh, S and Mohapatra, B and Bhattacharyya, P and Mukherjee, A}, title = {Fate of dissolved pharmaceutically active compounds (PhACs) in irrigation water in rice paddy: Implications to human and soil health.}, journal = {Journal of contaminant hydrology}, volume = {278}, number = {}, pages = {104898}, doi = {10.1016/j.jconhyd.2026.104898}, pmid = {41740569}, issn = {1873-6009}, abstract = {Pharmaceutically active compounds (PhACs) may enter the food chain through food crops. This study investigates the influence of dissolved PhACs in irrigation water on rice crops and soil, identifying enduring implications on human and soil health. We conducted a field-scale experiment to investigate the accumulation and impacts of two prevalent PhACs, ibuprofen (IBP) and caffeine (CAF), in irrigation water on rice paddies under realistic agronomic conditions. The experiment was carried out in designated subplots with three dosage levels. The results revealed that IBP exhibited higher persistence in the field soil, leading to ∼2 times higher plant uptake than CAF. Most of the introduced contaminants attenuated in soil,root, shoot or degraded naturally, reducing grain accumulation, which ranged from 0.13% to 0.4% and from 0.38% to 1.4% for IBP and CAF, respectively. However, toxic PhAc metabolites were identified in the grains, raising significant concerns. Owing to its higher translocation and grain accumulation, the hazard quotient (HQ) of CAF surpassed 0.1, indicating a potential risk associated with regular dietary intake. The presence of PhACs significantly altered soil microbial enzyme activities, bacterial abundance, and community composition within the soil-plant microbiome, indicating potential long-term impacts on geo-health. In conclusion, the applied PhACs undergo significant attenuation within the field-soil and plant components, lowering grain accumulation; however, the presence of toxic PhAC metabolites in grains and changes in soil bacterial composition indicate potential concerns.}, }
@article {pmid41740491, year = {2026}, author = {Yu, H and Li, J and Jin, D}, title = {Alpine grassland degradation reduced the geographic distance-decay rate of bacterial community.}, journal = {Journal of environmental management}, volume = {402}, number = {}, pages = {129065}, doi = {10.1016/j.jenvman.2026.129065}, pmid = {41740491}, issn = {1095-8630}, abstract = {The alpine grasslands of the Qinghai-Tibet Plateau, are undergoing a gradual transformation. This shift is presenting growing challenges to their capacity to maintain key ecological services and support sustainable regional development. To unravel the biogeographic consequences of degradation and guide restoration, we carried out a comprehensive study that covered 660 km and included three degradation stages (non-degraded, moderately degraded, and highly degraded) as well as the physicochemical characteristics and bacterial communities at two soil depths (0-10 cm, 10-20 cm). We systematically investigated soil bacterial community characteristics and the primary drivers of spatial distribution (dis)similarity under different degradation levels, alongside the relative roles of rich and rare species. According to our research, grassland degradation significantly altered the diversity, composition, and functional groups of bacterial communities. Furthermore, increasing degradation reduced the complexity of the molecular ecological network while concurrently enhancing its stability. Geographic distance-decay relationships (DDR) persisted across degradation gradients, and spatial turnover rates declined markedly with intensifying degradation, signaling microbial homogenization driven by environmental filtering. In the non-degraded grassland, geographic distance dominated community (dis)similarity, whereas environmental heterogeneity superseded spatial constraints post-degradation, particularly under moderate degradation. In this process, rich species emerged as keystone architects of network integrity and spatial biogeography, driving whole-community dynamics, while rare species exhibited unique responses. By bridging microbial biogeography and ecosystem stability, our work advances restoration strategies for alpine grasslands and informs microbiome management in vulnerable ecosystems globally.}, }
@article {pmid41740449, year = {2026}, author = {Yang, Y and Chen, M and Tringe, SG and Mukundan, H and Chakraborty, R}, title = {Toward an integrative framework for monitoring biodegradation of environmental contaminants across scales.}, journal = {Current opinion in biotechnology}, volume = {99}, number = {}, pages = {103471}, doi = {10.1016/j.copbio.2026.103471}, pmid = {41740449}, issn = {1879-0429}, abstract = {Organic contaminants from natural and anthropogenic sources threaten global water and food security. While bioremediation offers significant mitigation potential, tracking compound degradation in complex ecosystems remains challenging. Detection technologies span from microscale methods - biosensors, imaging, and volatile organic analysis - to landscape-scale remote sensing. Each technique provides unique information, but integrating these disparate data streams is a major bottleneck hindering ecological-scale tracking and assessment. In this review, we propose a holistic monitoring framework for detecting contaminants and tracking the progress of bioremediation, highlighting minimally invasive detection techniques and cross-scale sensor integration. We discuss emerging technologies and the generation of standardized datasets essential for machine-learning applications in predicting degradation trajectories using fabricated ecosystems. Integrating environmental sensing, microbiome science, and advanced analytics provides a new chassis for interrogating remediation efforts.}, }
@article {pmid41740355, year = {2026}, author = {Lee, J and Hong, S and Choi, J and Song, H and Han, JH and Suh, YD and Yeon, SC and Cho, S}, title = {Whole-genome shotgun metagenomics reveals environmental perturbations in the gut microbiome and resistome of wild raccoon dogs rescued at a wildlife center.}, journal = {The Science of the total environment}, volume = {1021}, number = {}, pages = {181588}, doi = {10.1016/j.scitotenv.2026.181588}, pmid = {41740355}, issn = {1879-1026}, abstract = {Raccoon dogs are potential vectors for the transmission of zoonotic pathogens and antimicrobial resistance, with their gut microbiome carrying genetic determinants of virulence and resistance. However, previous studies have primarily relied on traditional culture-based approaches, limiting our understanding of the entire dynamics and genetic potential of the gut microbiome in raccoon dogs. In this study, we employed both culture-dependent approach and whole-genome shotgun sequencing in raccoon dogs undergoing rehabilitation for eight weeks. We integratively assessed how rehabilitation-related environmental shifts influence the gut microbiome and resistome. Rehabilitation induced shifts in gut microbiome composition. Notably, within-group diversity decreased at week eight, indicating increased compositional similarity. Throughout rehabilitation, a total of 18 genera (e.g., Paeniclostridium, Psychrobacter) significantly increased, and 40 genera (e.g., Intestinimonas, Erysipelatoclostridium) decreased in abundance. Rehabilitation also induced shifts in the gut resistome, with reduced within-group diversity at weeks four and eight, indicating increased compositional similarity over time. Overall, 253 antimicrobial resistance genes (ARGs) present at week 0 disappeared, whereas 273 ARGs were acquired during rehabilitation. Additionally, the abundance of 15 ARGs significantly decreased and that of 33 increased, with beta-lactamases being the most common among the latter. Culture-dependent methods revealed a marked increase in bacteria resistant to third-generation cephalosporins, monobactams, and sulfonamides. Changes in microbiome composition during rehabilitation indirectly influenced the resistome and virulome through mobile genetic elements. Our findings suggest that rehabilitation-induced perturbations in the gut microbiome and resistome of raccoon dogs are likely driven by environmental shifts such as diet and habitat. These changes may affect their post-release fitness and raise concerns owing to the potential dissemination of zoonotic pathogens and antimicrobial resistance.}, }
@article {pmid41736164, year = {2026}, author = {Yu, L and Yang, D and Ye, Z and Wang, G}, title = {Challenges in functional validation and mechanistic interpretation of a novel LACC1 variant in familial juvenile arthritis.}, journal = {Human genomics}, volume = {20}, number = {1}, pages = {}, pmid = {41736164}, issn = {1479-7364}, support = {2023ZYQJ02//The Affiliated Traditional Chinese Medicine Hospital,Southwest Medical University/ ; 2023ZYQJ02//The Affiliated Traditional Chinese Medicine Hospital,Southwest Medical University/ ; 2023ZYQJ02//The Affiliated Traditional Chinese Medicine Hospital,Southwest Medical University/ ; 2023ZYQJ02//The Affiliated Traditional Chinese Medicine Hospital,Southwest Medical University/ ; }, mesh = {Humans ; *Arthritis, Juvenile/genetics/pathology ; *Genetic Predisposition to Disease ; Mitochondria/metabolism/genetics ; Intracellular Signaling Peptides and Proteins ; }, abstract = {In their recent publication, Alblooshi et al. report the identification and preliminary functional analysis of a novel LACC1 variant, p.Asp220Asn, associated with familial juvenile idiopathic arthritis. While their study provides a valuable genetic association, this letter offers a critical appraisal to contextualize the findings and propose essential future directions. We contend that the functional characterization, while indicative of a loss-of-function, is insufficient to distinguish it from a potential dominant-negative mechanism, a distinction with paramount implications for genetic counseling. Furthermore, the observed clinical heterogeneity within the family remains mechanistically unaddressed; we propose that integrating systems-level approaches, such as transcriptomics and microbiome analysis, is crucial to move beyond mere description. Finally, the structural and metabolic consequences of the variant are underexplored. Employing molecular dynamics simulations and profiling mitochondrial metabolism in patient-derived cells could definitively link this genetic lesion to LACC1's emerging role in immunometabolism. This critique aims to elevate the impact of the initial discovery by mapping a pathway for transforming a genetic association into a profound pathophysiological understanding.}, }
@article {pmid41735265, year = {2026}, author = {Cuesta-Marti, C and Ponce-España, E and Uhlig, F and Stoltenborg, I and Wasiewska, LA and Kareem, L and Hedayatpour, D and Olavarría-Ramírez, L and Rosell-Cardona, C and Bastiaanssen, TFS and Tofani, GSS and Valderrama, B and Vlckova, K and Dickson, SL and Lavelle, A and Stanton, C and Ross, RP and Cryan, JF and Dinan, TG and Clarke, G and O'Mahony, SM and Schellekens, H}, title = {Bifidobacterium longum and prebiotic interventions restore early-life high-fat/high-sugar diet-induced alterations in feeding behavior in adult mice.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41735265}, issn = {2041-1723}, support = {VI PPIT-US//Universidad de Sevilla (University of Seville)/ ; 22/PATH-S/10882//Science Foundation Ireland (SFI)/ ; }, mesh = {Animals ; Male ; *Diet, High-Fat/adverse effects ; Female ; Gastrointestinal Microbiome/physiology/drug effects ; *Bifidobacterium longum/physiology ; Mice ; *Prebiotics/administration &amp; dosage ; *Feeding Behavior/physiology/drug effects ; Mice, Inbred C57BL ; Hypothalamus/metabolism ; }, abstract = {An unhealthy diet disrupts feeding behavior and the gut microbiota, but whether early-life dietary effects persist, or can be restored later in life, remains unclear. We investigated whether microbiota-targeted interventions (FOS + GOS or Bifidobacterium longum APC1472) could restore early-life high-fat/high-sugar (HFHS) diet-induced feeding alterations in adult female and male mice. HFHS exposure exclusively in early-life induced persistent, sex-specific feeding alterations in adult mice, despite normalized body weight. Early-life HFHS diet reduced hypothalamic cells expressing feeding-related markers (POMC, GHSR, PNOC, NOD2) in adult mice. Females were more vulnerable, with reduced LEPR[+] cells and disrupted arginine/tryptophan metabolism, while males showed impaired peptidoglycan sensing and steroid metabolism. We show that microbiota interventions restore these effects via distinct mechanisms. FOS + GOS induced extensive microbiome compositional shifts and sex-specific restoration of gut-brain pathways, while B. longum APC1472 induced greater behavioral restoration with minimal microbiome compositional changes. These findings highlight sex-specific vulnerabilities and mechanism-dependent therapeutic potential of microbiota-based interventions after exposure to early-life unhealthy diets.}, }
@article {pmid41733927, year = {2026}, author = {Chen, J and Zhu, L and Liu, J and Chen, J and Liang, C and Liu, C and Wang, F and Zhu, Y and Yang, X}, title = {Immune cells play a mediating role in the relationship between the gut microbiota and dementia: A Mendelian randomization study.}, journal = {Innate immunity}, volume = {32}, number = {}, pages = {17534259261426829}, pmid = {41733927}, issn = {1753-4267}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Mendelian Randomization Analysis ; *Dementia/immunology/microbiology ; Genome-Wide Association Study ; *Dysbiosis/immunology ; *B-Lymphocytes/immunology ; }, abstract = {IntroductionThe gut microbiota modulates dementia pathogenesis through immune interactions. Using Mendelian randomization, we investigate immune mediated mechanisms linking microbial dysbiosis to four dementia subtypes (Alzheimer's disease, Frontotemporal dementia, Vascular dementia, Parkinson's disease dementia . Our study tests whether gut microbiome effects on dementia are transmitted via immunoregulatory pathways.MethodsGenome wide association studies data included gut microbiota, 731 immune traits, and dementia cohorts (Alzheimer's disease, Frontotemporal dementia, Vascular dementia, Parkinson's disease dementia). Two step Mendelian randomization with Inverse Variance Weighted analyses assessed mediation effects, controlled by F-statistics >10 and Steiger filtering. Sensitivity analyses addressed pleiotropy.ResultsA total of 37 gut microbiome species demonstrated potential causal effects relationships with four types of dementia, and 137 immune cell subsets exhibited potential causal effects associations with these four dementia subtypes. In the Two step Mendelian randomization analysis, CD45RA + CD28- CD8+ T cells, CD19 on IgD- CD38dim B cells, and BAFF-R on CD20- B cells were shown to exert mediating effects between class/order/family.Deltaproteobacteria and Alzheimer's disease. CD4+ CD8+ T cells were found to exert a mediating effect between genus.Roseburia and Parkinson's disease dementia . CD20- CD38- B cells, CD19 on CD20- B cells, and IgD on unswitched memory B cells were found to exert a mediating effect between class/order/family.Coriobacteriales,genus.Lactococcus and Vascular dementia.ConclusionThis Mendelian randomization study revealed that certain immune cells serve as mediators in the pathway by which the gut microbiome contributes to the onset of dementia.}, }
@article {pmid41739174, year = {2026}, author = {Sánchez-Astráin, B and Borrego-Ramos, M and Viso, R and de la Hoz, CF and Blanco, S and Juanes, JA}, title = {Unravelling Diatom-Microbiome Dynamics in the Red Alga Gelidium Corneum (Florideophyceae, Rhodophyta).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02723-4}, pmid = {41739174}, issn = {1432-184X}, }
@article {pmid41738843, year = {2026}, author = {Feng, T and Wu, Y and Xu, Y and Chen, WH}, title = {A comprehensive ruminant microbial catalog (CRMC) reveals convergent selection for key vitamin-synthesizing pathways and genes across ruminants and human.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag016}, pmid = {41738843}, issn = {2047-217X}, abstract = {BACKGROUND: The ruminant gastrointestinal tract (GIT) serves as a natural microbial reservoir in which vitamin-synthesizing microbes play key integrated roles in digestion, nutrient absorption, and metabolic balance; however, studies systematically elucidating their functional characteristics and ecological roles remain limited due to the lack of a large-scale reference genome catalog for ruminant gastrointestinal vitamin-synthesizing microbes. Here, based on 2,325 metagenomic samples from 8 ruminant hosts, we comprehensively reconstructed and analyzed the ruminant GIT microbiome and the distribution patterns of vitamin-synthesizing microbes.<br><br>RESULTS: We reconstructed a unified ruminant gastrointestinal microbiome catalog (CRMC) with 39,696 MAGs, achieving the highest mapping rate (&#x223c;83.45%) among 2,325 metagenomic datasets, surpassing GTDB, RGMGC, and other catalogs. Across the 8 ruminant hosts, we identified a total of 17,349 vitamin-synthesizing microbes spanning 9 biosynthetic pathways (thiamine, riboflavin, niacin, pantothenate, pyridoxine, biotin, folate, cobalamin, and menaquinone). These microbes exhibited unified pathway selection patterns consistent with those in the human gut microbiome. Furthermore, within the major vitamin-synthesizing pathways commonly selected across ruminants, vitamin-synthesizing microbes displayed concentrated co-selection of specific functional gene nodes, revealing that despite taxonomic differences among gastrointestinal vitamin-synthesizing communities, they share highly convergent pathway preferences and common node-level selection patterns.<br><br>CONCLUSIONS: Together, by reconstructing the ruminant GIT microbiome reference genome catalog (CRMC), we elucidated the core microbial taxa and their functional features across ruminants, as well as the pathway preferences and distribution patterns of vitamin-synthesizing microbes. These findings provide an effective reference for advancing ruminant GIT microbiome research, offering gene co-selection insights for microbial synthetic biology design, and guiding microbiome-based interventions in ruminant systems.}, }
@article {pmid41738774, year = {2026}, author = {Thomasen, M and Misiakou, MA and Li, SS and Rodriguez de Evgrafov, MC and Lynggaard, MB and Kårhus, ML and Brønden, A and Kornholt, J and Chávez-Talavera, O and Tailleux, A and Staels, B and Descat, A and Hartmann, B and Wewer Albrechtsen, NJ and Rehfeld, JF and Holst, JJ and Vilsbøll, T and Ellegaard, AM and Sommer, MOA and Sonne, DP and Knop, FK}, title = {Metabolic, enterohepatic and gut microbial effects of atorvastatin in healthy men.}, journal = {Endocrine connections}, volume = {}, number = {}, pages = {}, doi = {10.1530/EC-25-0721}, pmid = {41738774}, issn = {2049-3614}, abstract = {OBJECTIVE: Statins are low-density lipoprotein cholesterol-lowering drugs that are highly effective in the prevention of cardiovascular disease and death. Evidence that statin therapy increases the risk of type 2 diabetes is accumulating, but the mechanism behind this phenomenon remains obscure.<br><br>DESIGN: A clinical, randomised, placebo-controlled, double-blind, crossover study.<br><br>METHODS: Here, we investigated the effect of atorvastatin on fasting and postprandial circulating concentrations of glucose, gluco-regulatory hormones, bile acid profiles as well as gut microbiota composition. Fifteen healthy men came in for a mixed meal test following 14 days of treatment with atorvastatin (40 mg once-daily during week one and 80 mg once-daily during week two) or placebo.<br><br>RESULTS: Treatment with atorvastatin did not affect postprandial plasma glucose or insulin concentrations, but basal as well as postprandial concentrations of glucagon were increased compared with placebo. Postprandial plasma concentrations of the gut-derived incretin hormones glucose-dependent insulinotropic polypeptide and glucagon-like peptide 1 were increased after atorvastatin treatment compared with placebo. Also, postprandial concentrations of taurine-conjugated primary bile acids increased, whereas glycine-conjugated secondary bile acids decreased. Microbiota composition was not affected by atorvastatin treatment.<br><br>CONCLUSIONS: Atorvastatin treatment did not alter glucose or insulin concentrations, nor did it alter gut microbiota composition. However, we found that atorvastatin treatment increased fasting and postprandial glucagon concentrations, which may point to hyperglucagonaemia as a possible link between statin treatment and type 2 diabetes.<br><br>CLINICALTRIALS.GOV: NCT03018444.<br><br>SIGNIFICANCE STATEMENT: This randomised, placebo-controlled, double-blind, crossover study reveals that short-term high-dose atorvastatin treatment increases fasting and postprandial glucagon levels and alters amino acid and bile acid profiles without affecting glucose, insulin, or gut microbiota in healthy men. These findings suggest hyperglucagonaemia as a potential mechanistic contributor to the increased risk of type 2 diabetes associated with statin therapy.}, }
@article {pmid41738770, year = {2026}, author = {Yu, Q and Huang, C and Bao, P and Li, N and Wang, T and Ma, C and Deng, J and Jia, J and Yan, P}, title = {Characteristics of the gastrointestinal tract and volatile fatty acids in plateau ruminants.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0165525}, doi = {10.1128/spectrum.01655-25}, pmid = {41738770}, issn = {2165-0497}, abstract = {High-altitude ruminants face environmental stressors such as low temperature, hypoxia, and short grazing seasons, which challenge energy acquisition and nutrient absorption. The gastrointestinal tract (GIT) plays a central role in metabolic adaptation. In this study, we collected contents from the rumen, reticulum, omasum, abomasum, duodenum, jejunum, cecum, and rectum of Pamir yaks. Microbial composition and metabolic functions across GIT regions were investigated through volatile fatty acid (VFA) determination and 16S rRNA gene sequencing. The results showed that the total VFA concentrations were highest in the forestomach and lowest in the small intestine, with the hindgut showing intermediate levels. Microbial diversity was highest in the reticulum and lowest in the jejunum. At the phylum level, Firmicutes, Bacteroidota, and Proteobacteria were the dominant bacterial taxa. At the genus level, Prevotella, Rikenellaceae_RC9_gut_group, UCG-005, Muribaculaceae, and Christensenellaceae_R-7_group were the predominant genera. Functional predictions revealed that the forestomach exhibited a notable enrichment in metabolic pathways associated with carbohydrate, amino acid, and nucleotide metabolism. In contrast, the abomasum and small intestine showed significant enrichment in pathways related to nucleotide and nucleotide-sugar metabolism, protein synthesis, and DNA repair. The hindgut demonstrated enrichment in butyrate metabolism and immune-related pathways. This study highlights the spatial heterogeneity of VFAs, microbial communities, and functional potentials in the GIT, providing theoretical insights into the adaptive mechanisms of energy metabolism in high-altitude ruminants.IMPORTANCEThis study systematically characterized microbial community composition and volatile fatty acid (VFA) metabolic profiles across different segments of the gastrointestinal tract in plateau ruminants. The results revealed potential metabolic adaptation strategies to extreme conditions such as hypoxia, low temperature, and limited forage availability. The forestomach was identified as the primary site of energy acquisition and showed a marked enrichment of VFA-producing bacteria. Microbial diversity in the small intestine was relatively low, but metabolic pathways associated with nutrient absorption remained highly active. The hindgut exhibited distinct microbial colonization patterns and signs of potential metabolic compensation. Collectively, these findings provided important theoretical insights into nutritional regulation, ecological adaptation, and microecological intervention strategies in plateau ruminants. They also filled a critical gap in high-altitude animal microbiome research and offer significant scientific and practical implications.}, }
@article {pmid41738759, year = {2026}, author = {Holmes, EC}, title = {mGem: Applying microbiome therapeutic learnings to next-generation agricultural bioproducts.}, journal = {mBio}, volume = {}, number = {}, pages = {e0332325}, doi = {10.1128/mbio.03323-25}, pmid = {41738759}, issn = {2150-7511}, abstract = {Biological discoveries in plant and human systems have long advanced our understanding of how signaling, metabolism, and immunity shape cross-kingdom interactions. Building on this rich history of interdisciplinary insight, there is now a tremendous opportunity to strengthen connections between human and agricultural microbiome research. This perspective highlights key biological synergies across these systems that are essential for advancing human, agricultural, and ecosystem health. Focus is given to colonization, immune, and biosafety engineering strategies developed for microbiome therapeutics that can guide the design and development of next-generation agricultural bioproducts. Ultimately, greater knowledge exchange and collaboration across disciplines will be critical to translate microbiome discoveries into bioproducts with positive societal impact.}, }
@article {pmid41738741, year = {2026}, author = {Min, BR and Yutaka, U and Ismael, H and Abdo, H and Chaudhary, S and Hilaire, M and Kanyi, V}, title = {RETRACTED: Min et al. Malted Barley as a Potential Feed Supplementation for the Reduction of Enteric Methane Emissions, Rumen Digestibility, and Microbiome Community Changes in Laboratory Conditions. Animals 2025, 15, 664.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {5}, pages = {}, pmid = {41738741}, issn = {2076-2615}, abstract = {The journal retracts the article titled "Malted barley as a potential feed supplementation for the reduction of enteric methane emissions, rumen digestibility, and microbiome community changes in laboratory conditions" [...].}, }
@article {pmid41738266, year = {2026}, author = {Williams, KR and Fryer, AD and Jacoby, DB and Nie, Z}, title = {Heavy Moms, Wheezy Kids: How Maternal Obesity Harms Breathing in Offspring.}, journal = {American journal of respiratory cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrcmb/aanag013}, pmid = {41738266}, issn = {1535-4989}, abstract = {Offspring asthma has emerged as a significant yet underexplored consequence of maternal obesity. This review synthesizes evidence from human and animal studies linking maternal obesity to increased asthma risk in offspring. We examine potential mechanisms, including impaired fetal lung development, epigenetic modifications, microbiome alterations, and metabolic dysregulation. A dedicated section focuses on the novel role of insulin signaling in the developmental programming of airway hyperresponsiveness, as insulin resistance-and the resulting hyperinsulinemia-is common in offspring of obese mothers. By integrating current findings and identifying key research gaps, this review outlines future directions to advance understanding and mitigation of maternal obesity's impact on offspring respiratory health.}, }
@article {pmid41738242, year = {2026}, author = {Singh, S and Darawshy, F and Erlandson, K and Narayana, JK and Li, Q and Li, Y and Atandi, I and Krolikowski, K and Patel, S and Collazo, D and Mac Aogáin, M and Gilmour, A and Long, M and Chang, M and Hoque, A and Schluger, R and Kumar, S and Chung, CJ and Wong, K and Porter, G and Feng, Y and Czachor, A and McCormick, C and Clementi, E and Kyeremateng, Y and Lukovnikova, A and Harris, D and Gomez, S and Kain, T and Kocak, I and Singh, R and Rodriguez, C and Kwok, B and Barnett, C and Kugler, M and Weiden, MD and Nelson, N and Natalini, JG and Luglio, D and Desvignes, L and Gautam, S and McGuire, E and Gordon, T and Sulaiman, I and Tsay, JJ and Basavaraj, A and Wu, BG and Kamelhar, D and Addrizzo-Harris, D and Chalmers, JD and Chotirmall, SH and Segal, LN}, title = {Lower Airway Dysbiosis in NTM+ Bronchiectasis is Associated with NET-Predominant Severe Phenotypes.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag015}, pmid = {41738242}, issn = {1535-4970}, abstract = {RATIONALE: The discoveries of neutrophilic inflammation and Pseudomonas-dominant pulmonary dysbiosis have helped pave the way for host-directed therapy in bronchiectasis. Substantial knowledge gaps still remain about the interplay between neutrophilic signatures and microbes in non-tuberculous mycobacterial lung disease (NTM-LD), a phenotypically diverse lung infection that is increasingly prevalent in the United States and other parts of the world.<br><br>OBJECTIVES: Evaluate the lower airway microbiota and neutrophilic traits in NTM- and NTM+ bronchiectasis.<br><br>METHODS: 16S rRNA gene sequencing, cell counts, and neutrophil extracellular trap (NET) immunoassays were performed on bronchoscopic lower airway samples in 200 bronchiectasis subjects (108 NTM-, 92 NTM+). A preclinical model of oral commensal micro-aspiration and NTM infection was used to profile the murine lower airways with flow cytometry and a NET assay.<br><br>MEASUREMENTS AND MAIN RESULTS: Lower airways of NTM+ bronchiectasis patients were enriched with Mycobacterium and oral commensals (e.g., Veillonella, Prevotella and Streptococcus). NET levels were higher in NTM+ BAL. Mycobacterium and oral commensals co-occurred with NET and neutrophils in network studies. Distinct oral commensal taxa were associated with severe disease phenotypes such as cavitary disease and exacerbators. In a murine micro-aspiration model, the combination of oral commensals and Mycobacterium led to a sustained pro-inflammatory immune response marked by an increase in Th17, &#x3b3;&#x3b4;T cells, PD-1+ T lymphocytes as well as higher NET levels.<br><br>CONCLUSIONS: Our analyses showed that distinct microbiome features beyond the primary pathogen can contribute to neutrophilic inflammation and severe disease phenotypes in bronchiectasis/ NTM-LD.}, }
@article {pmid41737910, year = {2026}, author = {Hu, Y and Rueppell, AC and Devpura, N and Zasloff, R and Arnold, JW and Roach, J and Magness, ST and Bruno-Bárcena, JM and Azcarate-Peril, MA}, title = {Prebiotic β (1-4) Galacto-oligosaccharides Strengthen Intestinal Barrier Integrity via Mucus Production and Modulation of Tight Junction Genes.}, journal = {Food bioscience}, volume = {75}, number = {}, pages = {}, pmid = {41737910}, issn = {2212-4292}, support = {P30 DK056350/DK/NIDDK NIH HHS/United States ; }, abstract = {Preserving a functional intestinal barrier is crucial for overall host health, as increased permeability can lead to systemic pathologies, including a dysregulated immune system and increased susceptibility to infections. Pure β (1-4) galacto-oligosaccharides (GOS) and Type 2 LacNAc-enriched β (1-4) GOS (humanized GOS, hGOS) modulate the gut microbiome, increasing the abundance of beneficial microorganisms, including Bifidobacterium, Akkermansia, and Lactobacillus. In this study, we report that direct exposure of monolayers of human primary colonic cells to β(1-4) GOS and β(1-4) hGOS enhances barrier integrity by significantly upregulating MUC2 (2-5 fold) and tight junction genes (1.5-8 fold) (p<0.05). RNA sequencing revealed that β(1-4) GOS and β(1-4) hGOS activated the Aryl Hydrocarbon Receptor (AHR) pathway, with GOS specifically inducing CYP1A1 (log2FC = 3.57) and TIPARP, while hGOS enriched pathways related to apical junction integrity. This suggests that AHR activation may enhance gut barrier function, in part, by repressing IL-1β-mediated inflammation. These findings were validated in vivo in young and old C57BL/6 mice, where GOS and hGOS enhanced intestinal permeability by increasing the expression of Muc2 and promoting mucus production, resulting in a thicker mucus layer (GOS: 95% CI 0.054-0.146; hGOS: 95% CI 0.080-0.176). Tight junction integrity genes were also upregulated by the prebiotics in our study (two-way ANOVA, p < 0.05). Our findings suggest that, beyond their modulation of the gut microbiome, GOS and hGOS enhance intestinal barrier function by directly inducing the expression of mucin and tight junction genes, likely through the AHR pathway. These results highlight the potential of prebiotic supplementation in improving gut barrier function and maintaining intestinal health.}, }
@article {pmid41737876, year = {2026}, author = {Xiang, Q and Wu, Y and Li, Y and Li, S and Chang, X}, title = {Ti3C2Tx (MXene) disrupts growth and development in Daphnia magna by suppressing related genes and inducing gut microbiome dysbiosis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1748570}, pmid = {41737876}, issn = {1664-302X}, abstract = {The potential risks of Ti3C2Tx (MXene) nanomaterials to the ecological environment and human health have drawn increasing attention due to their widespread applications in the fields of biomedicine and environmental remediation. Although the aquatic ecotoxicity of Ti3C2Tx has been reported, little is known about how Ti3C2Tx disrupts the physiological processes that regulate growth and development in zooplankton. This study investigated the toxic effects and mechanisms of Ti3C2Tx exposure on the growth and development of Daphnia magna through gene expression and gut microbiome analyses. Results show that Ti3C2Tx exposure significantly reduced moulting frequency, body length, body width, and absolute growth rate in D. magna. Exposure to Ti3C2Tx led to a significant decrease in the expression of growth and development-related genes (cyp18a1, ecra, usp, hr3, and cpa1) in D. magna. Microbiome analysis revealed that exposure to Ti3C2Tx resulted in a decrease in Proteobacteria and an increase in Bacteroidota in the microbial community of D. magna. Meanwhile, Ti3C2Tx induced reduced abundances of Pseudomonas and Aeromonas, as well as increased abundances of Bacillus and Phascolarctobacterium. These microbial functions primarily contribute to energy acquisition and metabolism. This study indicated that Ti3C2Tx can inhibit the growth and development of D. magna by inhibiting the expression of growth and development-related genes and inducing intestinal microbial community dysbiosis. This study provides new insights into understanding the mechanisms of Ti3C2Tx toxicity on the growth and development of zooplankton in aquatic ecosystems.}, }
@article {pmid41737790, year = {2025}, author = {Katzenelson, RT and Izzo, P and Corrallo, BR and Crescente, CL and Alcantara, AC and de Carvalho, FG and Marques, LS and de Sousa, ET and Parisotto, TM}, title = {Microbiota evaluation in acute appendicitis: a preliminary study of appendix and childhood oral microbiota.}, journal = {Frontiers in oral health}, volume = {6}, number = {}, pages = {1690433}, pmid = {41737790}, issn = {2673-4842}, abstract = {Despite the uncertainty of the sequence of events leading to appendicitis, the microbiome is presumed to play a central role in the pathogenesis. This preliminary cross-sectional study aimed to evaluate the intestinal microbes in distinct phases of acute appendicitis compared to the oral microbiota, considering the status of dental caries. Twenty children under 12 years were assigned into two groups: non-complicated appendicitis (NCA, n = 11) and complicated appendicitis (CA, n = 9). Biological material from the oral cavity (saliva) and appendix (mucosal scrapings) was submitted to microbial analysis to quantify Bacteroidetes, Firmicutes, and Fusobacterium nucleatum by qPCR. Data were assessed using ANOVA and Pearson's correlation (α = 5%). Considering CA, significant differences were found between the mouth and appendix for Bacteroidetes, Firmicutes, and Fusobacterium nucleatum levels (p < 0.05), with increased amounts in the intestinal niche. Conversely, there was no statistical difference (p > 0.05) regarding NCA. Bacteroidetes levels in the intestinal appendix significantly correlate to all of the studied bacteria in the mouth (p < 0.05, r = 0.66-0.89), while in the NCA pattern, this happened only with Bacteroidetes. Caries conditions were similar between the two groups. In conclusion, a relationship is suggested between the intestinal appendix and oral bacteria, in a comparable caries index, in distinct phases of acute appendicitis. The severity of the children's appendix condition seems to correlate with the magnitude of microbial changes.}, }
@article {pmid41737789, year = {2025}, author = {Khan, A and Jaynes, A and Ali, F and Virkud, Y and Sun, T and O'Connell, I and Shreffler, W and Yuan, Q and Martin, V}, title = {High Rate of Positive Fecal Occult Blood Test in Healthy Infants: A Nested Case-control Study.}, journal = {Journal of translational gastroenterology}, volume = {3}, number = {4}, pages = {229-234}, pmid = {41737789}, issn = {2994-8754}, support = {K23 AI130408/AI/NIAID NIH HHS/United States ; K23 AI151556/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: Guaiac fecal occult blood test (gFOBT) is often used to evaluate evidence of food protein-induced allergic proctocolitis (FPIAP) in children in primary care and gastroenterology settings; however, it has not been validated for this diagnosis, and little is known about the positivity rates in early infancy. In this study, we used samples from healthy asymptomatic infants aged two weeks to two months to evaluate the gFOBT positivity rate compared to those diagnosed with FPIAP.<br><br>METHODS: This was a nested case-control study. Frozen stool samples from infants aged two days to five months enrolled in the Gastrointestinal Microbiome and Allergic Proctocolitis study were evaluated using gFOBT (n = 123). The results were interpreted by three blinded staff members, including a trained clinical research coordinator, a pediatric gastroenterologist, and an experienced medical assistant. Additionally, the samples were analyzed using a quantitative fecal immunochemical test (FIT) for hemoglobin to compare with gFOBT results.<br><br>RESULTS: Eight percent of samples from the 100 healthy asymptomatic infants were gFOBT positive (11% when including positive and equivocal results). Seventy-four percent of samples from infants diagnosed with FPIAP were gFOBT positive. The interrater reliability of gFOBT interpretation was 81%. Of the healthy samples that yielded a positive gFOBT result, 50% also yielded a positive FIT result. Of the 23 FPIAP samples that yielded a positive gFOBT result, 29% yielded a positive FIT result.<br><br>CONCLUSIONS: Healthy asymptomatic infants in early infancy were gFOBT positive up to 11% of the time. Caution should be used when interpreting gFOBT results in young infants in a diagnostic setting.}, }
@article {pmid41737742, year = {2026}, author = {Miller, C and Jiménez-Flores, R}, title = {Evidence for the influence of the milk fat globule membrane on bifidobacteria metabolism and cell surface properties.}, journal = {JDS communications}, volume = {7}, number = {1}, pages = {12-17}, pmid = {41737742}, issn = {2666-9102}, abstract = {Bifidobacterium, a genus commonly found in the microbiome of healthy infants, has been demonstrated to exert various beneficial effects on the gastrointestinal tract, contributing to overall health. Notably, these bacteria possess the ability to use complex glycoconjugates as nutrients, which holds importance for breast-fed infants, as human milk contains substantial quantities of these glycoconjugates. However, the underlying mechanisms of action of these beneficial properties remain largely unexplored. This study presents an alternative perspective on the nutrients in the diet that could potentially support the maintenance of a healthy Bifidobacterium population. We present evidence suggesting that the presence of milk fat globule membrane (MFGM), a component shared by all mammalian milk, significantly alters the metabolism of these bacteria. This alteration is reflected in the production of exopolysaccharides on the surface and secretome of the bacteria fed MFGM, whereas the absence of this component does not result in such changes. To substantiate this hypothesis, we employed proteomic and physicochemical methods, culminating in the evidence of the MFGM layer through electron microscopy.}, }
@article {pmid41737716, year = {2026}, author = {Kaur, S and Abhisheka, NS and Singh, L}, title = {Programmable probiotics in functional foods: adaptive responses, nutrient delivery, and food matrix interactions.}, journal = {Journal of food science and technology}, volume = {63}, number = {2}, pages = {201-213}, pmid = {41737716}, issn = {0022-1155}, abstract = {Programmable probiotics represent a transformative advance in functional food science, shifting from static supplementation toward context-responsive bioactive systems. This review critically examines the adaptive responses, nutrient biosynthesis, and food matrix interactions that define probiotic programmability. Key natural regulatory traits, including acid and bile resistance, quorum sensing, biofilm formation, sporulation, and oxygen response, are discussed for their role in enabling microbial survival and resilience during food processing and gastrointestinal transit. Programmable probiotics can biosynthesize essential micronutrients such as B-complex vitamins and γ-aminobutyric acid and generate health-relevant metabolites like short-chain fatty acids in situ, influenced by specific matrix compositions. Host-microbe-food interactions further shape microbial gene expression and metabolite output, particularly in the colon, where cross-feeding and immunomodulatory effects emerge. Non-genetic enhancement strategies, including adaptive evolution, selective fermentation, and targeted prebiotic incorporation, are also highlighted for their potential to augment functional specificity without regulatory concerns. The review highlights the need for standardized definitions and advanced tools, including metabolomics, transcriptomics, and biosensing platforms, to reliably quantify programmability. Finally, applications across dairy, plant-based, and emerging food matrices are examined, with special focus on their roles in gut health, anti-aging, and precision nutrition. By consolidating mechanistic insights with practical applications, this review positions programmable probiotics as a foundation for next-generation functional food innovation and personalized dietary interventions.}, }
@article {pmid41737675, year = {2026}, author = {Bouchali, R and Sentenac, H and Schmeller, DS and Bernardo-Cravo, A and Loyau, A}, title = {The fungal pathogen Batrachochytrium dendrobatidis drives the relationship between environmental and amphibian skin microbiota.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag016}, pmid = {41737675}, issn = {2730-6151}, abstract = {Microbial coalescence is a key process driving the assembly of communities when diverse compartments of ecosystems meet. Coalescence is likely involved in structuring amphibian skin microbiota, which play a crucial role in host immunity, but whose environmental microbial sources remain unknown. Here, we investigated the microbial sources (water and biofilm microbiota, i.e. adherent microbial community embedded collectively on submerged rocks) and coalescence processes of the skin microbiota of three amphibian species (Alytes obstetricans, Rana temporaria, and Bufo spinosus), in 20 mountain lakes of the French Pyrenees, infected or not with the fungal pathogen Batrachochytrium dendrobatidis (Bd). We used 16S ribosomal ribonucleic acid gene metabarcoding coupled with a Bayesian SourceTracker analysis and a phylogenetic null model. We found that the amphibian skin microbiome originated mainly from environmental water (9%-23%), less from biofilm (3%-6%), and not from horizontal transfer. Host exposure to Bd strongly influenced microbial engraftment. The presence of the pathogen probably did not affect the number of bacterial taxa shared between environmental and skin microbiotas, but enriched some of them, including protective ones, from the water only. Stochastic processes dominated the structuration of the resulting communities, but some deterministic selection probably occurred, maybe via microbiome dysbiosis that favor higher abundance of anti-Bd genera, which often are environmental opportunists. Our study provides first insights into the importance of microbial coalescence in shaping the amphibian skin microbiome, and the role of environmental microbial communities in mounting disease resistance.}, }
@article {pmid41737563, year = {2026}, author = {Marques, GN and Lourenço, M and Leal, M and Urbani, N and Peleteiro, MC}, title = {Pityriasis Versicolor in a Southern Ground Hornbill (Bucorvus leadbeateri).}, journal = {Case reports in veterinary medicine}, volume = {2026}, number = {}, pages = {5261490}, pmid = {41737563}, issn = {2090-701X}, abstract = {A 20-year-old southern ground hornbill (Bucorvus leadbeateri) developed hyperpigmented macules on its gular pouch, resembling the lesions typically seen in humans with pityriasis versicolor. Cytologic examination revealed over 100 budding yeasts per oil immersion field. Fungal culture showed rare growth of smooth, cream-colored yeast colonies, identified by PCR as Malassezia slooffiae. Histopathological analysis showed lymphocytic perivascular dermatitis. Periodic acid-Schiff staining revealed rare forms of yeasts between the layers of the stratum corneum. This clinical report provides further insights into the role of Malassezia spp. in the avian skin microbiome. To the authors' knowledge, this is the first report of Malassezia sp. as an agent of pityriasis versicolor in birds.}, }
@article {pmid41737395, year = {2026}, author = {Wen, D and Liu, S and Wu, Y and Zhang, H and Zhang, K}, title = {Fecal microbiota transplantation improves functional constipation through the gut microbiome-bile acid-receptor axis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1751593}, pmid = {41737395}, issn = {2296-858X}, abstract = {Functional Constipation (FC) is a prevalent gastrointestinal motility disorder worldwide that markedly impairs patients' quality of life, yet the currently available treatment options often show limited efficacy. In recent years, research has gradually revealed the critical role of the gut microbiota and bile acid metabolism in the pathogenesis of FC. Fecal Microbiota Transplantation (FMT), which restores the intestinal microecological balance by transferring gut microbiota from healthy donors, has demonstrated clinical efficacy in promoting bowel movements, improving stool consistency, and enhancing patients' quality of life. However, its underlying mechanisms remain incompletely understood. Current evidence indicates that FMT restores microbial diversity, increases beneficial taxa, and partially reconstructs the bile acids (BAs) profile, thereby modulating Farnesoid X Receptor (FXR) and Takeda G Protein-Coupled Receptor 5 (TGR5) mediated signaling pathways to enhance intestinal secretion and alleviate constipation-related symptoms. The resulting microbiota-bile acid-receptor pathway elucidates the mechanistic link between microbial remodeling and host gastrointestinal motility, thereby offering theoretical support for the therapeutic application of FMT in functional constipation.}, }
@article {pmid41737350, year = {2026}, author = {Barbazza, S and Weber, AM and Fauzi, MD and Rachmadewi, A and Zuhrina, R and Putri, F and Campos Ponce, M and van der Hoeven, M and Fortin, S and Rimbawan, R and Nasution, Z and Giriwono, PE and Wieringa, FT and Soekarjo, DD and Ryan, EP}, title = {Inclusion of stabilised rice bran in ready-to-use therapeutic food supports growth in Indonesian children with severe and moderate acute malnutrition: solutions to enhance health with alternative treatments (SEHAT), a double-blinded, randomised clinical trial.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e13}, pmid = {41737350}, issn = {2048-6790}, mesh = {Humans ; Double-Blind Method ; *Oryza/chemistry ; Infant ; Indonesia ; Male ; Female ; Child, Preschool ; *Severe Acute Malnutrition/diet therapy ; *Fast Foods ; *Dietary Fiber/administration &amp; dosage ; Prebiotics ; Body Weight ; }, abstract = {Ready-to-use therapeutic foods (RUTFs) are widely used to treat severe acute malnutrition (SAM) by improving key anthropometric outcomes; however, optimisation of RUTF formulations remains important to support sustained recovery. Rice bran, a novel nutrient-dense, prebiotic food ingredient, can support healthy growth. This two-arm, double-blinded, randomised controlled trial, compared the effectiveness of a locally produced RUTF with rice bran to the same RUTF without rice bran for the treatment of uncomplicated acute malnutrition in Jember, Indonesia. 200 children aged 6-59 months with SAM (WHZ < -3.0 and/or mid-upper arm circumference (MUAC) < 115 mm or having bilateral pitting oedema +/++) or approaching SAM (WHZ < -2.5) were enrolled in the study. Primary outcomes were weight, MUAC, and anthropometric z-scores. Linear mixed models were applied across all ages, and split by age groups (6-23 months and 24-59 months) at weeks 0, 4, 8, 12, and 16 for intention-to-treat (ITT) and per protocol analysis (PP). Children in two age groups were expected to respond differently to treatment based on their microbiome maturity. At week 4, the PP analysis revealed RUTF+rice bran treatment had significantly greater weight gain velocity (p = 0.02; p = 0.008) and MUAC velocity (p = 0.004, p = 0.03) when compared to RUTF at all ages and in the 24-59 months age group, respectively. There were no significant differences between treatment groups at time points in the other anthropometric outcomes. This investigation shows promising impact of stabilised rice bran as a prebiotic and nutrient-dense ingredient for inclusion into RUTFs that can improve child growth outcomes.}, }
@article {pmid41737300, year = {2026}, author = {Shi, W and Wang, M and Jin, Z and Chen, X and Li, J and Lai, H and Li, X and Zhong, Q and Chen, Y and Chen, S}, title = {Metabolomics Analysis Reveals Gut Microbiota-Associated Sakuranin Modulates Endometrial Stem Cell Differentiation and Inflammation to Alleviate Pain in Endometriosis.}, journal = {Journal of pain research}, volume = {19}, number = {}, pages = {557430}, pmid = {41737300}, issn = {1178-7090}, abstract = {BACKGROUND: Endometriosis (EMS) is characterized by pain symptoms that seriously affect patients' quality of life. Gut microbiome-related metabolites (GMRM) play an important role in the process of EMS. However, the role of GMRM in endometrial stem cells and EMS-related pain remains unclear.<br><br>METHODS: An untargeted metabolomics approach was employed to analyze the fecal samples of 10&#xa0;healthy individuals (heal), 11 EMS patients without dysmenorrhea (pless), and 14 EMS patients with dysmenorrhea (pain). The impact of potential key metabolite sakuranin on EMS-related pain was further investigated in vitro and in vivo.<br><br>RESULTS: We identified 33 metabolites that were commonly changed in the painful group compared to the health and pless groups, and these metabolites were associated with differential microorganisms. Among them, sakuranin was downregulated in the painful group and exhibited a notably inverse correlation with the degree of pain. ROC curve revealed that sakuranin had a relatively high predictive value for EMS-related pain (AUC=0.8027). Functionally, sakuranin inhibited differentiation, migration, and inflammatory cytokine production, and decreased the expression of VEGF and ALCAM in SUSD2-positive primary endometrial cells. In EMS mice, sakuranin suppressed ectopic lesion growth, reduced inflammation, modulated angiogenesis and proliferation markers (VEGF, ALCAM, Ki-67), and regulated sympathetic and sensory nerve markers, resulting in alleviated pain behaviors.<br><br>CONCLUSION: We delineated the metabolic landscape related to EMS-related pain and uncovered that sakuranin has the potential to inhibit the growth of EMS and alleviate EMS-related pain. This finding offers therapeutic strategies of sakuranin in alleviating the pain symptoms associated with EMS.}, }
@article {pmid41737112, year = {2026}, author = {Mistry, LN and Mulla, SA and Patil, A and Shah, S and Pulaskar, SP}, title = {A Narrative Review on Oral Microbiome Dysbiosis in Benign and Malignant Oral Lesions: Mechanistic Insights and Clinical Implications.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e102131}, pmid = {41737112}, issn = {2168-8184}, abstract = {Maintaining oral and systemic health depends heavily on the dynamic and varied microbial environment found in the human mouth cavity. There is growing evidence that the oral microbiota plays a role in the pathophysiology of both benign and malignant oral cancers by producing carcinogenic chemicals, modifying host immune responses, and causing chronic inflammation. Malignant tumors like oral squamous cell carcinoma (OSCC) show profound dysbiosis marked by enrichment of pathogenic taxa such as Porphyromonas gingivalis, Prevotella intermedia, and Fusobacterium nucleatum, whereas benign lesions like papillomas, fibromas, and odontogenic tumors show localized microbial alterations. This review examines the molecular processes connecting microbial dysbiosis to carcinogenesis, summarizes current understanding of the oral microbiome across several oral cancers, and emphasizes potential diagnostic, prognostic, and therapeutic applications.}, }
@article {pmid41736989, year = {2026}, author = {Priandhika, FH and Hidayat, W and Fitriasari, N}, title = {Oral Necrotizing Ulcerations in Acute Leukemia Patients: Clinical Characteristics, Integrated Management, and Favorable Outcomes - A Case Series.}, journal = {International medical case reports journal}, volume = {19}, number = {}, pages = {570294}, pmid = {41736989}, issn = {1179-142X}, abstract = {INTRODUCTION: Leukemia often presents with diverse oral manifestations like ulceration, bleeding, and gingival enlargement due to immunosuppression and chemotherapy. The altered oral microbiome in leukemic patients increases infection risks, including bloodstream infections. Early diagnosis and targeted treatment of oral complications are vital to improve patient outcomes and quality of life.<br><br>PURPOSE: This case series aims to explore the clinical presentation, underlying systemic conditions, and treatment response of oral necrotizing ulcerations including necrotizing ulcerative gingivitis (NUG) and necrotizing stomatitis in patients with acute leukemia.<br><br>PATIENTS AND METHODS: Three female patients aged 18 to 21 years were diagnosed with necrotizing ulcerative oral lesions associated with acute leukemia: two with Acute Lymphoblastic Leukemia (ALL) and one with Acute Myeloid Leukemia (AML). Detailed intraoral examinations were performed, alongside hematologic and biochemical laboratory analyses. Treatment protocols included gingival debridement with hydrogen peroxide 1,5%-3%, chlorine dioxide zinc antiseptic mouthwashes (chlorine dioxide zinc), topical hyaluronic acid, and Vaseline application. Suggestions of prescribing Metronidazole also been given to the referring departments. Patients were monitored through serial follow-ups for clinical progress.<br><br>RESULTS: All three patients presented with crater-like ulcerations, greyish pseudomembranes, and gingival inflammation, with varying degrees of systemic hematologic compromise. The first patient (ALL) showed marked improvement by the third follow-up, with near-complete healing by the final visit. The second patient (AML) demonstrated reduction in gingival necrosis and inflammation, although gingival hyperplasia persisted. The third patient (ALL, pre-chemotherapy) initially presented with necrotizing stomatitis and NUG; significant clinical improvement and complete lesion resolution were observed over successive follow-ups. Systemic findings, including leukopenia, anemia, and elevated inflammatory markers, were consistent with hematologic malignancies and contributed to lesion severity. Our incapability to perform additional diagnostic test such as oral lesion biopsy or microbiology test was the limitations of this case report.<br><br>CONCLUSION: Oral Necrotizing Ulcerations, including NUG, NUP, and NUS, represent significant clinical manifestations of acute leukemia, reflecting the underlying immunosuppression, hematologic abnormalities, and oral microbial dysbiosis inherent to the disease. Early recognition of characteristic clinical features, followed by integrated local oral management and close coordination with systemic medical care, can lead to favorable healing outcomes despite profound hematologic compromise.}, }
@article {pmid41736978, year = {2026}, author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH}, title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).}, journal = {Ecology and evolution}, volume = {16}, number = {2}, pages = {e73137}, pmid = {41736978}, issn = {2045-7758}, abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.}, }
@article {pmid41736871, year = {2026}, author = {Begnel, ER and Maqsood, R and Holland, LA and Ojee, E and Owiti, P and Adhiambo, J and Mabele, E and Gantt, S and Chohan, BH and Kinuthia, J and Wamalwa, D and Lim, ES and Lehman, DA and Slyker, J}, title = {Comparison of gut virome in Kenyan infants born to women with and without HIV.}, journal = {iScience}, volume = {29}, number = {3}, pages = {114900}, pmid = {41736871}, issn = {2589-0042}, abstract = {The gut virome develops in infancy, seeded from numerous sources including the maternal virome. Altered infant virome development from exposure to maternal HIV infection could contribute to the higher observed morbidity among children who are HIV-exposed, uninfected (CHEU) versus HIV-unexposed (CHUU). To assess whether infant HIV exposure affects gut virome development, we sequenced the DNA virome in stool samples collected between birth-2 years from 37 CHUU and 32 CHEU whose mothers received optimized antiretroviral therapy (ART). Richness and Shannon diversity increased with age and introduction of foods other than breastmilk, and Bray-Curtis distances varied by age. Virome richness was lower among CHEU than CHUU, but Shannon diversity and Bray-Curtis distances did not differ by HIV exposure. These findings suggest that HIV exposure is not a major determinant of the infant virome when mothers receive optimized ART.}, }
@article {pmid41736795, year = {2026}, author = {Pan, H and Wu, L and Sheng, S}, title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771312}, pmid = {41736795}, issn = {2235-2988}, mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; *Wound Healing ; }, abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.<br><br>METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.<br><br>RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.<br><br>DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.}, }
@article {pmid41736436, year = {2026}, author = {Menghua, Y and Jianbin, S and Yawei, Y and Yan, Z and Xingang, HU}, title = {Combined acupuncture and herb treatment improves intestinal flora inabdominally obese subjects based on 16s rRNA sequencing: a randomized controlled trial.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {46}, number = {1}, pages = {205-210}, pmid = {41736436}, issn = {2589-451X}, support = {2019YFC1710102//National Key R&amp;D Program of China: Clinical Evaluation Research on Intervention Technologies for Abdominal Obesity the Role of Gut Microbiota in the Effects of Combined Acupuncture and Medication on Abdominal Obesity: an Exploration with 16S rRNA Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Acupuncture Therapy ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Drugs, Chinese Herbal/administration &amp; dosage ; Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Obesity, Abdominal/microbiology/therapy/drug therapy ; Combined Modality Therapy ; }, abstract = {OBJECTIVE: To investigate Acupuncture-herb therapy modulates gut microbiota in abdominal obesity.<br><br>METHODS: A randomized controlled trial was designed in accordance with standard protocols. Abdominally obese subjects were randomized into four groups: A2 (Control): double placebo, A1 (Needle): press needle + placebo herb, A3 (herb): herbal medicine (Huatan Lishi Fang) + placebo needle, A4 (Combination): press needle + herbal medicine. After 12 weeks of treatment, groups were relabeled B1-B4. Weight, waist circumference, and body mass index were measured monthly. Gut microbiota was analyzed via 16S rRNA sequencing for diversity and abundance.<br><br>RESULTS: Combined needle-herb therapy significantly reduced waist circumference (P < 0.05). All treatments altered gut microbiota composition. The combination group showed significant changes in diversity (Chao1, Shannon, Simpson; P < 0.05). Needle therapy increased Bacteroidia; herbs reduced Lachnospiraceae and Megamonas. All results were significant (P < 0.05).<br><br>CONCLUSION: Combined needle-herb treatment modulated 25 key gut flora across multiple taxonomic levels in abdominal obesity. It reduced Firmicutes and Bacteroidota. Bacteroidota, Actinobacteriota, and Prevo-tellaceae may suppress obesity, whereas Proteobacteria, Lachnospiraceae, and Megamonas may promote it. The combination specifically altered Bacteroidaceae, Lachno-spiraceae, Bacteroidia, and Megamonas.}, }
@article {pmid41736316, year = {2026}, author = {Woo, YR and Kim, HS}, title = {Obesity, skin disorders, and the microbiota: Unraveling a complex web.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {64}, number = {1}, pages = {e2508007}, doi = {10.71150/jm.2508007}, pmid = {41736316}, issn = {1976-3794}, support = {2023R1A2C1007759//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; //Incheon St. Mary's Hospital/ ; //The Catholic University of Korea/ ; }, mesh = {Humans ; *Obesity/microbiology/complications/immunology ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Psoriasis/microbiology/immunology ; Animals ; *Hidradenitis Suppurativa/microbiology/immunology ; *Microbiota ; *Skin Diseases/microbiology ; Skin/microbiology/immunology ; Interleukin-22 ; }, abstract = {Obesity is increasingly recognized as a systemic pro-inflammatory condition that influences not only metabolic and cardiovascular health but also the development and exacerbation of cutaneous inflammatory diseases. This review examines the interplay between obesity, microbial dysbiosis, and two archetypal inflammatory skin disorders-hidradenitis suppurativa (HS) and psoriasis. We highlight how obesity-induced changes in immune signaling, gut permeability, and microbiota composition-both in the gut and the skin-contribute to cutaneous inflammation. Special emphasis is placed on shared pathways such as the Th17/IL-23 and IL-22 signaling axes, adipokine imbalance, and microbial metabolites like short-chain fatty acids and lipopolysaccharides. The review critically evaluates the current literature, distinguishing preclinical insights from clinical evidence, and underscores the potential of microbiota-targeted therapies and metabolic interventions as adjunctive treatment strategies. By integrating metabolic, immunologic, and microbiome data, we synthesize emerging evidence to better understand the gut-skin-obesity interplay and guide future therapeutic innovations.}, }
@article {pmid41736231, year = {2026}, author = {Rogalidou, M and Papadopoulou, A}, title = {Balancing therapeutic benefits and hidden risks of proton pump inhibitors in pediatric practice: a narrative review and update.}, journal = {Clinical and experimental pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.3345/cep.2025.02761}, pmid = {41736231}, issn = {2713-4148}, abstract = {Proton pump inhibitors (PPIs) are drugs whose main effect is catalytic and long-lasting suppression of gastric acid secretion, with an anti-inflammatory effect. The main indications for PPIs use include the treatment of gastroesophageal reflux disease, peptic ulcer disease, functional dyspepsia, Barrett esophagus, eosinophilic esophagitis, and hypersecretory diseases such as gastrinoma and Zollinger-Ellison syndrome. Their contribution to eradication therapy for Helicobacter pylori is also important. However, the long-term use of PPIs has been associated with various adverse drug reactions and complications, such as the development of fundic gland polyposis, atrophic gastritis, gastric cancer, vitamin B12 deficiency, hypomagnesemia, osteoporosis/ fractures, changes in the microbiome, increased risk of infection, necrotizing enterocolitis, renal injury, and other conditions. Thus, administration of PPIs should be based on scientific evidence of their efficacy and safety. Their long-term administration should be cautious, and continuation reassessed frequently. Caution should be exercised when administering PPIs to neonates and infants. This narrative review and update aims to summarize and critically evaluate the current evidence, based on the most recent clinical guidelines, regarding the use of PPIs in children, with a focus on their indications, efficacy, safety, and limitations.}, }
@article {pmid41736136, year = {2026}, author = {Song, Y and Chen, Q and Luo, S and Li, S and He, R and Yang, X and Shen, D and Long, C and Liu, S and Zhong, G and An, Y and Lu, Y}, title = {Ecology-guided Bacillus SynCom from a rice-duckweed core reveals division of labor for concurrent growth promotion and sheath blight suppression.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02360-6}, pmid = {41736136}, issn = {2049-2618}, support = {2020B1111530002//Guangdong Foundation for Program of Science and Technology Research/ ; 3022180002//Special Funds Program of Guangdong Academy of Sciences/ ; }, abstract = {BACKGROUND: Ecologically derived synthetic communities can provide robust plant benefits, yet generalizable rules for assembling multifunctional consortia remain limited. We hypothesized that a "top-down" community assembled from an ecological core would yield complementary functions and resilience superior to reductionist mixes.<br><br>RESULTS: We distilled an eight-member, Bacillus-dominated synthetic community (hereafter referred to as SynCom) from a rice-duckweed agroecosystem by targeting taxa consistently shared across soil, root and shoot niches. Under greenhouse conditions, the SynCom concurrently promoted rice growth and suppressed sheath blight caused by Rhizoctonia solani, reducing the final disease index by 70% without detectable phytotoxicity. Leave-one-member perturbations (-Dx), combined with untargeted LC-MS profiling and qRT-PCR of biosynthetic genes, revealed a division-of-labor architecture: individual strains specialized in auxin production, siderophore-linked iron mobilization, or lipopeptide/polyketide-based antagonism. These complementary yet partially redundant contributions mapped members, metabolite pools, plant outcomes and rendered community performance resilient to single-member loss. Across&#x2009;-Dx contrasts, the complete SynCom uniquely recovered the full suite of plant-growth metabolites (e.g., indole-3-acetic acid, acetoin/2,3-butanediol) together with antimicrobial chemistries (e.g., surfactin, bacillomycin, fengycin, difficidin). We formalize an assembly heuristic, ecological core, complementary functions, redundancy check, that links ecological origin to predictable, multi-trait performance.<br><br>CONCLUSIONS: A top-down, ecology-guided route can generate a multifunction SynCom with demonstrated greenhouse efficacy and mechanistic transparency. By coupling-member perturbations with multi-omics readouts, our study provides a transferable rule for building resilient plant-associated consortia and a tractable framework for future genetic and in-plant chemical confirmations. Video Abstract.}, }
@article {pmid41736135, year = {2026}, author = {Huang, H and Peng, S and Liu, Y and Chen, L and Wu, F}, title = {Fecal microbiota transplantation for advanced non-small cell lung cancer with secondary PD-1 resistance efficacy prognostic factors and microbiome diversity analysis.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07885-w}, pmid = {41736135}, issn = {1479-5876}, support = {2025YLCE0054//Talent Program of Ganzhou Sci-Tech and Medical Joint Program/ ; 82560474//Regional Programs of the National Natural Science Foundation of China/ ; 82560461//Regional Programs of the National Natural Science Foundation of China/ ; 82360507//Regional Programs of the National Natural Science Foundation of China/ ; }, }
@article {pmid41736110, year = {2026}, author = {Pirolo, M and Sherwani, MK and Espinosa-Gongora, C and Eriksen, E&#xd8; and Tassinato, C and Alberdi, A and Guardabassi, L}, title = {Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00522-3}, pmid = {41736110}, issn = {2524-4671}, }
@article {pmid41736017, year = {2026}, author = {Junaid, M and Ahmad, A and Hu, Z and Xu, M and Shi, X and Qu, N and Du, T and Ding, H and Zhu, Y}, title = {The maternal and infant gut microbiome: implications for pregnancy outcomes, immune development, and health in the first 1000 days.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-07846-3}, pmid = {41736017}, issn = {1479-5876}, support = {2024Z034, 2024Z204//Science and Technology Innovation 2035 Major Project of Ningbo/ ; K. C. Wong Magna Fund in Ningbo University//K. C. Wong Magna Fund in Ningbo University/ ; }, }
@article {pmid41735946, year = {2026}, author = {Udari, A and Arambepola, C and Thoradeniya, T and Jayasena, S and de Silva, R and Thoradeniya, D and Wickramasinghe, VP}, title = {Traditional diyabath (fermented cooked rice) as a pre-breakfast meal versus none (breakfast only) in improving gut microbiome and nutritional, health and immune parameters of young women in Sri Lanka: study protocol for a controlled trial.}, journal = {BMC complementary medicine and therapies}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12906-026-05301-w}, pmid = {41735946}, issn = {2662-7671}, support = {NSF/SCH/2025/05//National Science Foundation of Sri Lanka/ ; }, }
@article {pmid41735773, year = {2026}, author = {Liu, H and Zhang, Z and Xu, Y and Wen, J}, title = {Soybean roots recruit plant-beneficial Pseudomonas via secreting 3,4-dihydroxybenzaldehyde.}, journal = {Plant physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/plphys/kiag075}, pmid = {41735773}, issn = {1532-2548}, abstract = {Rhizosphere microbiota mediate plant defense against soil-borne diseases, yet the mechanisms by which resistant soybean cultivars assemble protective microbiomes remain poorly understood. Using metagenomics, metabolomics, in vitro assays, and genetic approaches, we compared near-isogenic lines (Williams82, resistant; Williams, susceptible) to dissect plant-metabolite-microbe interactions mediating Phytophthora root rot (PRR) resistance. Transplanting rhizosphere soil from the resistant cultivar to susceptible plants significantly reduced PRR severity, correlating with Pseudomonas enrichment and accumulation of the key rhizosphere metabolite 3,4-dihydroxybenzaldehyde. We isolated a core beneficial strain, Pseudomonas parafulva ZY6, from the resistant rhizosphere. In vitro, 3,4-dihydroxybenzaldehyde treatment promoted ZY6's biofilm formation, motility, and growth, while inhibiting Phytophthora sojae at higher concentrations. Knockout and overexpression of GmTL29 via hairy root transformation altered rhizosphere levels of 3,4-dihydroxybenzaldehyde, which in turn modulated the colonization of ZY6, the abundance of P. sojae, and the relative abundance of beneficial taxa such as Pseudomonas. Exogenous 3,4-dihydroxybenzaldehyde (0.1 μmol·g-1 soil) significantly reduced PRR disease index, increased rhizosphere bacterial diversity, and enriched Bacillus and Pseudomonas. Our study demonstrates that resistant soybeans shape a disease-suppressive rhizosphere, in which 3,4-dihydroxybenzaldehyde contributes as a prebiotic by selectively enriching beneficial microbes. These findings offer a metabolite-based strategy to engineer rhizosphere communities for sustainable soil-borne disease management.}, }
@article {pmid41735400, year = {2026}, author = {Yang, L and Yang, W and Zhang, H and Li, L and Liu, J and Li, M and Xu, R and Xiang, H and Li, Y and Yang, Y}, title = {Fusarium wilt disease induced changes in the composition and function of the rhizosphere metabolome and microbiome in tobacco plants.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40653-w}, pmid = {41735400}, issn = {2045-2322}, support = {027Y2022-023//Hubei Provincial Tobacco Corporation Key Technology Project/ ; 027Y2022-023//Hubei Provincial Tobacco Corporation Key Technology Project/ ; 110202401013 (LS-03), 110202101047 (LS-07), 110202201019 (LS-03)//the China National Tobacco Corporation Key Technology Projects/ ; 110202401013 (LS-03), 110202101047 (LS-07), 110202201019 (LS-03)//the China National Tobacco Corporation Key Technology Projects/ ; JCZRYB202500821//Natural Science Foundation of Hubei Province/ ; }, }
@article {pmid41735336, year = {2026}, author = {Stabbins, A and Goffredi, S and Gasbarro, R and Dawson, K and Magyar, J and Glazier, A and Meinert, K and Orphan, V and Cordes, E}, title = {Microbially mediated carbon utilization by a cold-water coral inhabiting methane seeps.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-32153-0}, pmid = {41735336}, issn = {2045-2322}, }
@article {pmid41735324, year = {2026}, author = {Sadeghi, Z and Jazayeri, SM and Pirkooh, AA and Foroushani, AR and Yarandi, F and Alebouyeh, M and Bakhtiari, R}, title = {Cell cycle gene expression and microbial profiles associated with HPV related cervical neoplasia and cervical microbiome shifts.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36885-5}, pmid = {41735324}, issn = {2045-2322}, support = {70494//Tehran University of Medical Sciences and Health Services/ ; }, }
@article {pmid41735321, year = {2026}, author = {Han, Z and Sun, Z and Liu, X and Zhen, D and Guo, Q and Zheng, L and Jiang, S and Zhang, Z and Shen, S and Zhang, J}, title = {Harnessing a germ‑free mouse gut bioreactor for directed evolution of probiotics to combat non-alcoholic fatty liver disease.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69823-0}, pmid = {41735321}, issn = {2041-1723}, support = {32525049//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Directed evolution has transformed biomolecular engineering but remains largely untapped for probiotic optimization, despite its immense promise for human health maintenance and disease therapy. Here, we present an in vivo, host-mediated directed-evolution platform that harnesses the gut's endogenous selective pressures to drive functional enhancement of probiotics. Using Bifidobacterium animalis subsp. lactis as a model, we expose germ-free male mice to stepwise increases in bile-acid stress via a high-fat, high-cholesterol diet. Compared to in vitro evolution, which fails to produce any functional gains, our host-mediated approach yields a variant exhibiting a 77% increase in bile acid metabolism. Multi-omics analysis identifies two critical single-nucleotide variants (SNVs) simultaneously: one in the upstream region of cbh, encoding bile salt hydrolase, and a non-synonymous mutation in mdr, a bile-acid efflux transporter. Functional validation assays confirm that these mutations drive increased corresponding gene expression and enhance substrate binding efficiency. Moreover, to demonstrate its translational potential, we administer the parental and adapted strains daily in a male diet-induced mouse model of non-alcoholic fatty liver disease (NAFLD). We find that the adapted strain significantly improves bile-acid homeostasis, reduces hepatic steatosis, lowers inflammatory and lipid biomarkers, and enhances histological liver health compared to the parental strain. Our work establishes the host gut as a living evolutionary bioreactor for precision engineering of probiotics, enabling targeted phenotypic enhancement in vivo through natural selection. This framework paves the way for personalized, functionally tailored microbiome therapeutics and sets a foundation for next-generation live biotherapeutic agents.}, }
@article {pmid41735080, year = {2026}, author = {Yu, Y and Lu, L and Ji, G and Xu, H}, title = {Ecological battle of gut microbiota under drug intervention.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.01.002}, pmid = {41735080}, issn = {1878-4380}, abstract = {Ecological consequences of drug exposure in the gut microbiota remain difficult to predict. In a recent Cell study, Shi et al. have demonstrated that nutrient competition and interspecies antagonism drive drug-induced microbiome restructuring. Their predictive framework advances mechanistic understanding of drug-microbiome interactions and fecal microbiota transplantation.}, }
@article {pmid41734872, year = {2026}, author = {van Kalkeren, CAJ and Adam, TC and Blaak, EE}, title = {Gut microbiome-associated effects of plant-based diets on glucose homeostasis, body composition, and cognitive function: a scoping review.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100610}, doi = {10.1016/j.advnut.2026.100610}, pmid = {41734872}, issn = {2156-5376}, abstract = {The worldwide prevalence of non-communicable diseases, including obesity, type 2 diabetes and neurocognitive decline, has increased rapidly over the last decades, warranting healthy and sustainable strategies to counteract these conditions. The gut microbiome is increasingly recognized as an important factor in the development of these metabolic diseases. Current nutritional guidelines advise towards more plant-based diets for health and sustainability reasons. These diets contain relatively high quantities of dietary fibers that can be fermented by the gut microbiota in the colon. This produces short-chain fatty acids (SCFA), recognized for their beneficial effects on insulin resistance, inflammation, and satiety. In the absence of fermentable fibers, however, colonic proteolytic fermentation increases, producing metabolites that are potentially harmful to host health. Moreover, plant-based proteins are less digestible compared to animal-based proteins, potentially increasing proteolytic fermentation. However, the extent to which plant-based diets affect the microbiome, and thereby host health, is still unknown. We, therefore, conducted a scoping review investigating the effects of plant-based dietary interventions on the microbiome in relation to the effects on body composition, glucose metabolism, and neurocognition. Overall, (healthy) plant-based diets, either as a whole dietary pattern, whole-grain consumption, or plant-protein-rich products, can contribute to lower body (fat) mass, fasting glucose, improve insulin resistance and episodic memory, and reduce psychological distress and anxiety. Notably, no adverse effects of plant-based diets were reported in any of the studies. The studies that reported alterations to microbial composition after plant-based interventions generally show increased microbial diversity and abundance of SCFA-producing species such as Prevotella, Lachnospiraceae, and Bifidobacteria. However, measures on microbial functionality, based on microbial metabolites such as SCFA and branched-chain fatty acids, were often lacking or remained mostly unaffected. Further research on the long-term and individual effects of both healthy and unhealthy plant-based diets on host health and the microbiome is required. Statement of Significance This review is the first to assess the effects of plant-based diets on body composition, glucose homeostasis, and neurocognition, in light of changes within the gut microbiome, showing convincing benefits for both metabolism and the microbiome.}, }
@article {pmid41734860, year = {2026}, author = {Wu, QL and Zhou, YR and Chen, ZR and Liu, MX and Liu, MX and Liu, YF and Li, ZS and Zhao, QR and Zhang, YQ and Zhang, GQ and Zhang, Z and Gong, YT and Tang, C and Yang, T and Du, ZC}, title = {Roles of the gut microbiota in cancer immunotherapy: Mechanistic foundations and therapeutic opportunities.}, journal = {Critical reviews in oncology/hematology}, volume = {221}, number = {}, pages = {105230}, doi = {10.1016/j.critrevonc.2026.105230}, pmid = {41734860}, issn = {1879-0461}, abstract = {Cancer immunotherapy has revolutionized oncological treatment through diverse modalities including immune checkpoint blockade, adoptive cell therapy, therapeutic vaccines, and cytokine-based approaches. Despite these advances, clinical responses remain heterogeneous, with sustained benefit limited to a minority of patients. Emerging evidence now implicates gut microbiota as a critical systemic regulator of immunotherapy efficacy across multiple treatment platforms, mechanistically linking intestinal dysbiosis to antitumor immunity through the gut-immune-tumor axis. Specific commensal taxa and their metabolites, including short-chain fatty acids and tryptophan derivatives, regulate anti-tumor immunity through effector T cell enhancement, dendritic cell activation, and regulatory T cell suppression. This review systematically examines the microbial-metabolite-immune axis, elucidating mechanisms whereby intestinal microbes and metabolites mediate immunotherapy responses. We comprehensively evaluate microbiota-targeting strategies including dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation, providing mechanistic insights and translational frameworks. We further discuss current challenges in transitioning from associative microbiome studies to mechanistic causality, standardizing intervention protocols, and integrating multi-modal microecological data, proposing future directions for engineered probiotics and precision microbial therapeutics to optimize outcomes under current immunotherapy.}, }
@article {pmid41734761, year = {2026}, author = {Lin, F and Li, L and He, Y and Xu, S and Mo, Q and Cao, W and Fu, A and Li, W}, title = {Commensal enteric virome regulates intestinal carbohydrate digestion and absorption.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.01.019}, pmid = {41734761}, issn = {1934-6069}, abstract = {The enteric microbiome and nutrient sensing within the small intestine play critical roles in maintaining host metabolic homeostasis. Although various bacteria and some fungi have established functions in nutrient metabolism, the role of the enteric virome remains poorly understood. Here, we demonstrate that the enteric virome significantly influences carbohydrate digestion and absorption independently of the bacteriome. Furthermore, the virome elicits distinct responses across different intestinal cell types. Specifically, it activates programs for carbohydrate digestion and absorption in intestinal epithelial cells while simultaneously stimulating antigen-presenting cells-Th17 cells-to produce interleukin-22, a cytokine that curbs excessive carbohydrate uptake. The virome's effect on carbohydrate digestion and absorption-whether suppressive or stimulatory-depends on the presence or absence of immune surveillance. This intricate interplay between metabolic and immune pathways establishes the enteric virome as a pivotal regulator of metabolism and reveals the virome's intrinsic capacity to autonomously modulate vertebrate intestinal physiology.}, }
@article {pmid41734518, year = {2026}, author = {Dhillon, A and Yadav, P and Gupta, S and Singh, SV and Sohal, JS and Rawat, KD}, title = {Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective.}, journal = {Veterinary microbiology}, volume = {315}, number = {}, pages = {110940}, doi = {10.1016/j.vetmic.2026.110940}, pmid = {41734518}, issn = {1873-2542}, abstract = {Paratuberculosis is a chronic ruminal-enteric infection caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has significant economic, trade, and public health implications. In addition to evading host immunity, MAP modulates the gut microbiome, resulting in dysbiosis that exacerbates disease progression. A conceptual framework is proposed in which Johne's disease (JD) can serve as the paradigm of chronic infection, based on dysbiosis in microbial imbalance, immune escape, and pathogen survival in a self-sustaining loop, as in human tuberculosis and Crohn's disease. This review evaluates the evidence on MAP-induced microbiome alterations and their impact on host-pathogen relations, immune responses, and metabolic processes in cattle, sheep, goats, and other ruminants. JD-associated dysbiosis is characterized by reduced microbial diversity, depletion of butyrate-producing taxa (e.g., Ruminococcaceae and Lachnospiraceae), enrichment of pro-inflammatory Enterobacteriaceae, and disruption of short-chain fatty acid (SCFA) metabolic pathways. Recent studies suggest that such alterations in microbes can be the initial signs of diagnosis and pre-treatment components, such as probiotics, prebiotics, dietary modifications, and microbiome-based vaccinations. This summary bridges the research on the veterinary and human microbiome, revealing that MAP-Microbiome interactions reflect immunological evasion and microbial persistence schemes observed with other intracellular pathogens. Evidence across species and disciplines highlights the interdependence between host microbiome stability, pathogen persistence, and disease progression. However, variances between studies show the need to adopt standardized methodologies, longitudinal studies, and multi-omics designs to establish whether dysbiosis precedes or follows MAP infection. The review is the first to combine molecular, immunological, and microbiome-level data into the One Health concept of MAP persistence. Moreover, this review takes a One Health approach where the investigation of MAP-induced dysbiosis offers an understanding of chronic inflammation, microbial ecology, and persistence strategies applicable to veterinary as well as human health. This way, we can emphasize the diagnostic, therapeutic, and translational opportunities of microbiome-based interventions in JD using a One Health model that connects ruminant disease to human inflammatory bowel diseases, including Crohn's disease.}, }
@article {pmid41734379, year = {2026}, author = {Sester, LS and Galeeva, I and de Castilhos, J and Borisov, V and Gambihler, A and Kilian, M and Vonhören, D and Friedrich, MJ and Poschet, G and Steiger, S and Chechenina, A and Lettau, K and Kohlberger, CP and Prokoph, N and Frenking, JH and John, L and Huhn, S and Reichert, P and Mai, EK and Rippe, K and Sauer, S and Müller-Tidow, C and Weinhold, N and Platten, M and Goldschmidt, H and Raab, MS and Stein-Thoeringer, CK}, title = {Fiber intake associates with increased treatment response in multiple myeloma patients along changes in gut microbiome.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2025018598}, pmid = {41734379}, issn = {2473-9537}, }
@article {pmid41734222, year = {2026}, author = {Jiang, J and Jia, F and Jiang, W and Zhang, S and Wu, H and Yang, L and Chen, Y and Cai, W and Guo, J and Yao, H}, title = {Spatial Organization of Microbiome Stability and Nitrogen Removal Resilience in a Full-Scale Plug-Flow PN/A System.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15228}, pmid = {41734222}, issn = {1520-5851}, abstract = {Partial nitritation/anammox (PN/A) enables energy-efficient nitrogen removal, yet the ecological drivers of stability and resilience in full-scale systems remain insufficiently characterized. Here, this study integrated 13-month performance monitoring with multiomics analyses to characterize spatial heterogeneity and recovery patterns following a dissolved oxygen (DO) shock in a full-scale plug-flow PN/A system. During stable operation, the system achieved a total nitrogen removal efficiency of 84.5 ± 4.8%, with the upstream zone accounting for 61.3 ± 10.1% of total removal. Along the decreasing nutrient gradient, community composition shifted markedly, and metatranscriptomes indicated spatially differentiated nitrogen-cycling transcription, with anammox-related transcripts enriched upstream. A 3-day DO shock (>0.5 mg/L) reduced the nitrogen removal rate (NRR) from 0.16 ± 0.03 to 0.07 ± 0.04 kg N/(m[3]·d). Although NRR recovered to baseline within three months, community structure and total bacterial 16S rRNA gene copies did not return to preshock levels, indicating a decoupling between microbiome and functional recovery. Across zones, higher bacterial diversity and nitrogen cycling functional redundancy were positively associated with faster recovery trends, and upstream microbiome stability was most representable of whole-system resilience. These findings provide measurable ecological indicators and an upstream-focused control target to strengthen full-scale PN/A operation under dynamic aeration disturbances.}, }
@article {pmid41734043, year = {2026}, author = {Thakur, M and Dolker, S and Wangmo, LK and Sharma, LK and Acharya, S and Mohapatra, P}, title = {Illumina-Based Metagenomic Insights into the Gut Microbiome of Amblyomma helvolum (Koch, 1844) Parasitizing Xenochrophis trianguligerus from Great Nicobar Island, India.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {15303667261423035}, doi = {10.1177/15303667261423035}, pmid = {41734043}, issn = {1557-7759}, abstract = {During a faunal survey in Great Nicobar Island, we collected four Amblyomma helvolum ticks infesting the snake Xenochrophis trianguligerus and processed for gut-metagenomic analysis using Illumina paired-end sequencing. A total of 8.7 million high-quality reads were generated, revealing that the gut microbiome was dominated by Bacteria (∼99.9%), primarily represented by Proteobacteria (∼95.7%), followed by minor fractions of Firmicutes, Actinobacteria, and Bacteroidetes. The predominant bacterial families were Alcaligenaceae, Bradyrhizobiaceae, Boseaceae, and Rickettsiaceae, with Achromobacter xylosoxidans emerging as the most abundant species (∼30% of total reads). Species-level analyses revealed a complex microbial community dominated by Achromobacter, Brevibacillus, Stutzerimonas, and Aeromicrobium. Several putative opportunistic pathogens were detected, including Myroides sp., Sphingobacterium sp., Stutzerimonas stutzeri, Cutibacterium acnes, Mycobacterium abscessus, Staphylococcus hominis, Achromobacter xylosoxidans, and Pseudomonas otitidis. This study represents the first metagenomic characterization of A. helvolum from India and provides baseline data on reptile-tick-associated microbial diversity from Great Nicobar Island. The findings underscore the importance of molecular surveillance in remote ecosystems and highlight the potential of reptile ticks as reservoirs of opportunistic and zoonotic bacteria.}, }
@article {pmid41733955, year = {2026}, author = {Millick, DD and Ghosh, S and Wu, G and Krzyzanowska, AK and Osorio, L and Zhao, L and Strair, R and Sant'Angelo, DB}, title = {Dietary animal fat disrupts gut microbiota and aggravates Scl-cGVHD after allogeneic hematopoietic stem cell transfer.}, journal = {Blood advances}, volume = {10}, number = {4}, pages = {1204-1216}, doi = {10.1182/bloodadvances.2024014831}, pmid = {41733955}, issn = {2473-9537}, mesh = {Animals ; *Graft vs Host Disease/etiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Mice ; Transplantation, Homologous ; *Dietary Fats/adverse effects ; Disease Models, Animal ; Cytokines/blood ; Female ; Humans ; }, abstract = {Allogeneic hematopoietic stem cell transplant (allo-HSCT) is an effective treatment for high-risk or relapsed acute leukemia. However, the frequent occurrence of graft-versus-host disease (GVHD) poses significant complications. Modifiable factors such as the gut microbiome and dietary regimen have the potential to influence the frequency and severity of GVHD. Previous studies in mouse models have shown a direct link between obesity and increased severity of GVHD; however, analysis of human data has not suggested a causal relationship. We hypothesized that dietary fat content before transplantation, rather than obesity itself, might affect outcomes, given that increased dietary fat is associated with reduced gut microbiome diversity. In our study, we evaluated the effects of an animal fat-based diet (AFD) and a plant fat-based diet (PFD) in a mouse model of sclerodermatous chronic GVHD (Scl-cGVHD). Mice initially fed normal chow (∼10% kcal from fat) were switched to either an AFD or a PFD (each with ∼25% kcal from fat) 2 weeks before allo-HSCT. Mice on the AFD had an elevated serum cytokine response, more severe skin inflammation, and greater intestinal immune dysregulation than mice on the PFD. Although both diets reduced gut microbial diversity, the fat source led to distinct microbiota compositions that included 2 coabundance guilds that differentiated between the AFD and PFD groups. Our findings demonstrate that even short-term consumption of diets with equivalent macronutrient content, but different fat sources, can modulate the gut microbiome, disrupt intestinal homeostasis, and influence Scl-cGVHD outcomes.}, }
@article {pmid41733908, year = {2026}, author = {Ma, C and Ye, X and Guo, W and Zhao, R and Zhou, S and Li, H and Hong, Y and Wang, L and Xie, Z}, title = {Gut Microbial Secondary Metabolites of Bile Acids and Amino Acids Regulate Th1/Th2 Immune Modulation in Unexplained Infertility: A Multiomics and Cohort Analysis Approach.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {4}, pages = {e71573}, doi = {10.1096/fj.202504204R}, pmid = {41733908}, issn = {1530-6860}, support = {82174104//the National Natural Science Foundation of China/ ; 22104158//Natural Science Foundation for Young Scientists of Shanxi Province (Young Scientists Fund of the National Natural Science Foundation of China)/ ; 2023A1515011346//guangdong basic and applied basic research foundation/ ; 2023A1515012418//guangdong basic and applied basic research foundation/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; 2024YG009//Medicine Plus Program of Shenzhen University/ ; JCYJ2023080711510801//the Science and Technology Innovation Committee of Shenzhen/ ; 20213357010//Clinical research project of Shenzhen Second People's Hospital/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/physiology ; Female ; *Bile Acids and Salts/metabolism ; *Th1 Cells/immunology ; Adult ; *Th2 Cells/immunology ; *Amino Acids/metabolism ; Cohort Studies ; Metabolomics/methods ; Male ; *Infertility, Female/immunology/metabolism/microbiology ; Cross-Sectional Studies ; Cytokines/metabolism ; Dysbiosis/immunology ; Multiomics ; }, abstract = {Unexplained Infertility (UI) is a complex condition of elusive etiology, where the interplay between immune dysregulation and metabolic disturbances remains poorly understood. We hypothesized that gut microbiota-derived metabolites act as central modulators of the systemic immune and metabolic balance in UI patients. We employed an integrated multiomics approach, combining metabolomics, gut microbiome analysis, and immune profiling, in a cross sectional discovery cohort (47 UI patients and 53 healthy controls), and validated key findings in an independent cohort (37 UI patients and 39 healthy controls). Our findings demonstrated that UI patients exhibited a proinflammatory Th1-dominant immune profile, marked by elevated proinflammatory cytokines and reduced anti-inflammatory IL-10. This immune imbalance was accompanied by a deficiency in protective gut-derived secondary metabolites, notably secondary bile acids and phenylpropanoic acid. Furthermore, gut microbiota analysis revealed significant dysbiosis (increased pathogenic taxa and decreased beneficial microbes) and a functional deficiency in the aromatic amino acid metabolism gene cluster, explaining the observed metabolite scarcity. Mechanistically, in vitro assays and network pharmacology indicated that these metabolites directly modulate the Th1/Th2 immune balance by regulating a core host network centered on TNF, PPARG, and PTGS2. In summary, our data reveal the role of a novel gut microbiota-metabolite-immune axis in UI pathophysiology, where a deficiency in protective gut-derived secondary metabolites contributes directly to systemic immune dysregulation and a proinflammatory state. These metabolites serve as potential candidates for future evaluation and represent promising therapeutic targets for interventions to restore immune homeostasis in UI patients.}, }
@article {pmid41733768, year = {2026}, author = {Zhou, S and Yao, Y and Yuan, R and Chu, W}, title = {Comparative Microbiome Analysis of Rhodiola fastigiata Rhizosphere Versus Bulk Soil in Xizang with Targeted Isolation of Rhizosphere-Derived Functional Strains.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41733768}, issn = {1559-0305}, support = {PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Rhodiola fastigiata, a critically endangered medicinal plant of the Qinghai-Xizang Plateau, faces severe threats from habitat degradation. This study aimed to support its microbial-assisted conservation by characterizing the rhizosphere microbiome and isolating functional plant growth-promoting (PGP) bacteria. Using high-throughput sequencing of the 16S rRNA gene and ITS region, we found the rhizosphere community to be distinct and enriched in key taxa (e.g., Sphingomonas, Mortierella). Metabolic predictions suggested upregulated stress-adaptive pathways. Crucially, from 126 isolates, we obtained four Bacillus strains that concurrently produce protease, amylase, and cellulase and solubilize phosphate-quantifying a multifunctional PGP profile critical for nutrient-poor soils. These culturable, spore-forming strains provide direct resources for developing synthetic inoculants. Our work bridges microbial ecology with applied biotechnology, delivering both a foundational microbial map and candidate strains to enable the cultivation and conservation of this endangered species in extreme environments.}, }
@article {pmid41733674, year = {2026}, author = {Kulakovskaya, EV and Kulakovskaya, TV}, title = {Inorganic Polyphosphate and Human Diseases.}, journal = {Progress in molecular and subcellular biology}, volume = {63}, number = {}, pages = {83-114}, pmid = {41733674}, issn = {0079-6484}, mesh = {Humans ; *Polyphosphates/metabolism/chemistry ; Animals ; Neurodegenerative Diseases/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Inorganic polyphosphate (polyP), a linear polymer of orthophosphoric acid residues, is essential for living cells from bacteria to humans. It forms complexes with metal ions, DNA, and polyhydroxybutyrate. The interaction of polyP with proteins includes polyphosphorylation at lysine and histidine residues, as well as participation in amyloid formation. The enzymes of polyP metabolism are polyfunctional, and their substrates include second messenger compounds and nucleoside phosphates. PolyP is a universal regulatory compound and plays an important role in bone tissue development, thrombosis and inflammation, signal transmission in nerve cells, carcinogenesis, and amyloid formation. PolyP participates in biofilm formation and other processes occurring during the interaction of pathogenic microorganisms with the host. PolyP of the gut microbiome is involved in maintaining intestinal functions. PolyP and the enzymes of its metabolism are promising targets for developing drugs against infections and novel approaches to treat bone, cardiovascular, and neurodegenerative diseases.}, }
@article {pmid41733363, year = {2026}, author = {Ziegert, ZA and Troester, A and Frebault, J and Goffredo, P and Gaertner, WB and Jahansouz, C and Staley, C}, title = {SparCC co-occurrence networking reveals intracommunity dynamics of the microbiome following colorectal surgery.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0397325}, doi = {10.1128/spectrum.03973-25}, pmid = {41733363}, issn = {2165-0497}, abstract = {The intestinal microbiota plays a critical role in post-surgical wound healing following bowel resection; however, perioperative, prophylactic antibiotic administration may deleteriously affect it. We previously used 16S rRNA amplicon sequencing of stool samples to assess perioperative and longitudinal changes in the microbiome through 6 months in patients undergoing (i) colonoscopy after mechanical bowel prep (MBP) alone, (ii) non-resectional colorectal surgery after MBP with oral antibiotics and prophylactic intravenous antibiotics no longer than 24 h post-operative (surgical bowel prep [SBP]), and (iii) resectional colorectal surgery with SBP. Our objective in this study was to investigate the translational utility of SparCC co-occurrence networking to uncover biologically relevant patterns. Network topological parameters and hub species were calculated using NetCoMi, and permutational statistical tests were used to compare parameters. Network similarity among cohorts and time points generally matched changes in beta diversity, except in the resectional cohort, where all networks could not be differentiated statistically. Similarity in centrality measures among hub species was frequently significantly less similar than expected by chance and corresponded to an increased edge density and modularity, suggesting the latter parameters may reflect re-stabilization of the microbiome following surgery. We further noted the infrequently reported genera Enterocloster and Ruthenibacter were hub species during time points associated with surgical recovery, suggesting potentially novel roles for these genera in wound healing. Streptococcus, frequently implicated in surgical site infections at our center, was also frequently positively associated with Blautia throughout all networks, suggesting an increasing abundance of commensal bacteria serves as a prophylactic strategy.IMPORTANCEThis study employs the emerging approach of co-occurrence networking to assess ecological dynamics in the microbiome following colonoscopy and colorectal surgery. We expand upon applications of this approach to determine hub species and investigate clinically translational interpretations of network topological parameters in the context of recovery across three different trajectories of perturbation. Our results provide a context in which to interpret these network parameters biologically and represent a foundational step in beginning to quantitatively leverage network-based approaches to study microbial ecology. Furthermore, we identify network hub taxa that may play previously unexplored roles in wound healing.}, }
@article {pmid41733360, year = {2026}, author = {Cao, H and Yang, X and Hu, L and Zou, Q and Li, G and Gou, W and Su, H}, title = {Geographical diet variations and microbial diversity: insights into François' langur's adaptive strategies.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0059425}, doi = {10.1128/msphere.00594-25}, pmid = {41733360}, issn = {2379-5042}, abstract = {The diversity in foraging behavior observed among species is indicative of their ability to adapt to specific environmental conditions, with dietary differences playing a crucial role in shaping the composition of gut microbiota. However, there are limited reports on the dietary habits and gut microbiota of François' langur (Trachypithecus francoisi) across different wild geographical populations. To address this, our study employed DNA metabarcoding and 16S rRNA sequencing to investigate variations in dietary composition and their influence on gut microbiota among distinct wild populations of François' langur, as well as among different groups within the same region. The dietary analysis revealed a broad diet, identifying 134 families and 336 genera of plants. The habitat quadrat survey results indicate significant differences in the habitats of François' langurs across different geographic populations. However, the dietary composition analysis reveals that while the food composition of different groups within the same region is relatively similar, there are notable differences across geographically distinct regions. The microbial community analysis demonstrated distinct compositional and structural divergence in gut microbiota between these populations, whereas no significant microbial differences were detected among groups within the same region. Further correlation analysis between diet and microbiota indicated that dominant plant taxa in the diet exhibited significant associations with Firmicutes, Proteobacteria, and other microbial phyla, displaying varying degrees of positive or negative correlations. This study elucidates how dietary variations among geographically distinct populations of François' langur drive changes in gut microbiota, reflecting their adaptive responses to local habitats. These findings provide valuable insights for the conservation management of François' langur populations and potential applications in health status monitoring.IMPORTANCEUnderstanding the mechanisms by which animals adapt to their environment is essential for effective conservation efforts. This study examines the endangered François' langur, focusing on the largely unexplored relationship between its dietary habits and gut microbiota across various wild populations. Our research indicates that although habitat vegetation varies significantly even among groups within the same region, their diets remain similar. Conversely, langur populations from distinct geographic areas exhibit notable dietary differences. These dietary variations, in turn, lead to distinct compositional differences in their gut bacterial communities. This diet-microbiome interaction serves as a crucial physiological indicator of how these primates adapt to their local forest environments. By illustrating that gut microbiota composition reflects an animal's ecological response to its environment, this study offers a powerful and non-invasive tool for conservation. These findings are critical for developing targeted strategies, such as habitat restoration, and for monitoring the health of these rare primates through gut microbiome analysis.}, }
@article {pmid41733349, year = {2026}, author = {van den Broek, S and Nybom, I and Feola Conz, R and Sun, Y and Bucheli, TD and Doetterl, S and Hartmann, M and Garland, G}, title = {Soil microbial and plant responses to increasing antibiotic concentration: a case study of five antibiotics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0158125}, doi = {10.1128/aem.01581-25}, pmid = {41733349}, issn = {1098-5336}, abstract = {UNLABELLED: Antibiotic contamination from biogenic waste in agricultural soils poses a significant threat to soil health and crop productivity. We investigated the effect of antibiotics on the soil microbial community, antibiotic resistance genes, and mobile genetic elements (MGEs) and plant productivity in a 6-week greenhouse trial. Here, Spinacia oleracea (spinach) and Raphanus sativus (radish) were grown from seeds, and a mix of five antibiotics, namely sulfamethoxazole, trimethoprim, enrofloxacin, clarithromycin, and chlortetracycline, was added to the soil at concentrations of 0, 0.1, 1, and 10 mg kg[-1] soil dry weight (c0, c0.1, c1, and c10, respectively). Overall, we found that the antibiotic treatments significantly impacted prokaryotic α-diversity and prokaryotic and fungal β-diversity. The relative abundance of human and plant pathogens did not increase under antibiotic exposure, but there was a significant reduction in plant growth-promoting bacteria. Moreover, the c10 treatment significantly increased the abundance of MGE intI1, indicative of horizontal gene transfer and sulfonamide resistance gene sul1, and significantly lowered radish biomass and nitrogen uptake, while spinach biomass and nitrogen uptake were unaffected. In summary, our study showed that antibiotic exposure significantly changed prokaryotic community diversity, while fungi remained largely unaffected. The reduction of plant growth-promoting bacteria may have a significant impact on soil nutrient cycling and crop productivity, but more research is needed to understand the long-term impact of these co-applied antibiotics on food production. Additionally, more studies are needed to understand the effect of antibiotics on realistic, field-scale conditions to fully understand the impact on environmental and human health.<br><br>IMPORTANCE: Agricultural soils are frequently contaminated with complex mixtures of antibiotics from various biogenic sources, yet we lack a clear understanding of their specific ecological impact. While many studies investigate antibiotics, they are often studied in pollution sources like manure, which contain confounding factors like heavy metals. To provide a mechanistic understanding of antibiotic-specific responses, we investigated the effects of a complex, five-antibiotic mixture on the soil-plant system, independent of other contaminants. As expected, antibiotics reduced prokaryotic diversity and increased the abundance of some genes related to antibiotic resistance. Additionally, antibiotic exposure reduced plant growth-promoting bacteria, which may have subsequent detrimental effects on plant and soil health. Moreover, we found that antibiotic exposure can reduce plant biomass and nitrogen uptake, but this is highly plant dependent. This research highlights the critical need to monitor antibiotic pollution due to its potential detrimental effect on plant health and alterations to the soil microbiome.}, }
@article {pmid41733313, year = {2026}, author = {Lu, Y and Yu, J}, title = {Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2025.0762}, pmid = {41733313}, issn = {2095-3941}, support = {2023ZD0500200//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 3133344//Strategic Seed Funding Collaboration Research Scheme CUHK/ ; 3135509//Strategic Impact Enhancement Fund CUHK/ ; 3134277//Impact Case for RAE CUHK/ ; }, abstract = {Colorectal cancer (CRC) remains a major global health burden with the gut microbiome emerging as a critical contributor to tumor initiation and progression. Advances in high-throughput sequencing have deepened our understanding of host-microbe interactions across genomic, transcriptomic, epigenomic, and metabolomic levels. This review synthesizes current knowledge on how microbial communities shape colorectal carcinogenesis, including induction of genomic instability, remodeling of host transcriptional and epigenetic landscapes, and reprogramming of metabolic pathways within the tumor microenvironment. Integrative multi-omics strategies and advanced computational tools are powerful means for dissecting these complex biological systems. However, analytical challenges, such as data compositionality, sparsity, and high dimensionality, still hinder meaningful interpretation. Emerging technologies, like long-read sequencing and bacterial single-cell spatial transcriptomics, are enhancing the resolution and accuracy of microbiota profiling. Finally, the convergence of advanced experimental models, artificial intelligence-driven computational integration, and precision microbiome medicine are highlighted as key avenues for translating microbiome insights into preventive, diagnostic, and therapeutic innovations in CRC.}, }
@article {pmid41733159, year = {2026}, author = {Diab, E and Du, C and Tigani, W and Elsayed, SS and van Wezel, GP}, title = {Plant Coumarins Modulate Natural Product Biosynthesis in a Streptomyces Root Endophyte.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.5c01626}, pmid = {41733159}, issn = {1520-6025}, abstract = {The plant microbiome plays a central role in regulating plant health and resilience, providing eco-friendly alternatives to agrochemicals. Plant-associated Streptomyces species are prolific producers of structurally diverse natural products with a demonstrated role in promoting plant growth. Coumarins are prevalent plant metabolites that shape the root microbiome, but their impact on microbial natural product biosynthesis is poorly understood. Here, we demonstrate that the coumarins scopoletin and its glucoside scopolin remodel specialized metabolism in the Arabidopsis root endophyte Streptomyces sp. ATMOS53. Multiomics analyses revealed that the coumarins activate the biosynthesis of the pyrrolizidine alkaloids bohemamines and alter the balance in anthracycline biosynthesis, with reduced production of late-stage anthracycline congeners and accumulation of shunt metabolites earlier in the pathway. These metabolic shifts resulted in a marked reduction of the antimicrobial activity of ATMOS53 against plant-associated Bacillus and Paenibacillus species. Notably, coumarin-mediated repression of anthracycline production was also observed in the established producers Streptomyces peucetius and Streptomyces galilaeus, indicating that the regulatory effect on anthracycline biosynthesis is conserved in streptomycetes. Our findings highlight coumarins as modulators of specialized metabolism of Streptomyces and show the significance of plant-derived chemicals for the control of the biosynthetic capacity of plant-associated microbes.}, }
@article {pmid41733121, year = {2026}, author = {Emmanouil, C and Anezaki, M and Simistiras, A and Glentis, S and Scarmeas, N and Hatzis, P and Rouskas, K and Dimas, AS}, title = {Rapid Remodeling of the Human Gut Microbiome in Response to Short-Term Animal Product Restriction and Associations with Host Molecular Phenotypes.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e15575}, doi = {10.1002/advs.202515575}, pmid = {41733121}, issn = {2198-3844}, support = {716998//ERC/ ; }, abstract = {Diet strongly influences the gut microbiome, which in turn influences health, yet the effects of dietary patterns on microbiome composition and function in humans remain underexplored. A unique group of apparently healthy individuals from Greece, who alternate between omnivory and restriction of animal products for religious reasons (periodically restricted group, n = 200), has been profiled. Using 16S rRNA sequencing, plasma metabolomics, and proteomics, the impact of three-to-four weeks of dietary restriction on gut microbiome composition and function is assessed and associations with host plasma biology are explored. Findings are compared to a continuously omnivorous group profiled in parallel (non-restricted group, n = 211). Animal product restriction reduced microbial diversity, primarily affecting rare taxa, and altered the abundance of nearly one-third of bacterial genera. Inferred functional shifts included downregulation of pathways contributing to cholesterol biosynthesis and purine degradation, alongside upregulation of vitamin B2 and tryptophan biosynthesis, suggesting compensatory microbial responses to dietary nutrient depletion. Multi-omics integration revealed four microbial-metabolite-protein clusters, including a diet-responsive module associating Negativibacillus with metabolic regulator FGF21 and intermediate-density lipoproteins. This findings demonstrate rapid adaptive plasticity of the human gut microbiome in response to short-term dietary restriction and highlight candidate microbial and molecular pathways associated with animal product restriction and host biology.}, }
@article {pmid41732881, year = {2026}, author = {Li, Y and Fillebeen, C and Li, S and Chen, J and Sweeney, G and Pantopoulos, K}, title = {High Dietary Carbonyl Iron Reshapes the Gut Microbiome and Impairs Hepatic Insulin Sensitivity in a Time-Dependent Manner.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {4}, pages = {e71626}, pmid = {41732881}, issn = {1530-6860}, support = {PJT-186193//Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism/drug effects ; Mice ; *Insulin Resistance ; Mice, Inbred C57BL ; Male ; *Iron, Dietary/adverse effects ; Muscle, Skeletal/metabolism ; *Iron ; }, abstract = {The gut microbiome is widely viewed as an important regulator of host metabolism and immunity. Loss of microbial diversity can lead to gut dysbiosis, which has been linked to cardiometabolic and inflammatory disorders. Iron is an important micronutrient for both host and microbes, but its excess is toxic. To investigate the impact of dietary iron on the intestinal microbiome and host metabolism, wild type mice on standard chow were switched at baseline to a high-iron diet, containing 2% carbonyl iron for 3 weeks. Other groups of mice were switched to the high-iron diet only during the final 3 or 7 days of the 3-week period; control animals remained on standard chow. Fecal samples were collected at baseline (t = 0) and at the endpoint (t = 1) for microbiome analysis, while liver and skeletal muscle samples were analyzed for Akt phosphorylation as a marker of insulin sensitivity. Feeding with high carbonyl iron significantly altered the intestinal microbiome and increased overall alpha and beta diversity in a time-dependent manner. Differential abundance and network analyses revealed extensive taxonomic and structural reorganization, with notable increases in Akkermansiaceae, Rikenellaceae, Bilophila, Ruminiclostridium, and Lactobacillus, and decreases in Bifidobacteriaceae and Clostridiaceae_1. Iron overload was accompanied by reduced Akt phosphorylation, evident in the liver but not skeletal muscles at the 3-week endpoint. Together, these results demonstrate that feeding of mice with a high carbonyl iron diet reshapes gut microbial composition, increases diversity, and reorganizes microbial community networks. However, iron overload mitigates insulin responsiveness in the liver.}, }
@article {pmid41732740, year = {2026}, author = {Yang, Z and Chen, X and Li, Y and Feng, Y and Lin, L and Hou, X}, title = {Autism and the gut metabolome: Evidence for altered short-chain fatty acid profiles from a systematic review and meta-analysis.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {53}, number = {}, pages = {101189}, pmid = {41732740}, issn = {2666-3546}, abstract = {UNLABELLED: Growing evidence implicates gut microbiome dysbiosis and its metabolites, particularly short-chain fatty acids (SCFAs), in the pathophysiology of autism spectrum disorder (ASD). However, individual study findings are inconsistent.<br><br>OBJECTIVE: This systematic review and meta-analysis synthesized evidence comparing SCFA profiles between individuals with ASD and neurotypical controls.<br><br>METHODS: We comprehensively searched PubMed, EMBASE, Cochrane Library, Web of Science, and CNKI databases from inception to December 1, 2024. Observational studies reporting quantitative SCFA measurements were included. Standardized mean differences (SMDs) with 95% confidence intervals (CIs) were calculated using random-effects models.<br><br>RESULTS: Sixteen studies (473 ASD cases, 514 controls) were included. Meta-analysis revealed substantial heterogeneity across studies for most SCFAs. Despite this, levels of valeric acid (SMD&#xa0;=&#xa0;0.76, 95% CI: 0.23 to 1.29) and hexanoic acid (SMD&#xa0;=&#xa0;0.60, 95% CI: 0.05 to 1.16) were significantly elevated in individuals with ASD. Isobutyric acid also showed a positive association (SMD&#xa0;=&#xa0;0.21, 95% CI: 0.03 to 0.46) with lower heterogeneity. No significant overall differences were found for acetic, propionic, or butyric acids, but subgroup analyses indicated crucial variations based on sample source (e.g., fecal, plasma, urine).<br><br>CONCLUSION: This meta-analysis provides evidence for altered SCFA profiles in ASD, specifically elevated valeric and hexanoic acids and a consistent signal for isobutyric acid, suggesting gut microbial dysbiosis involving distinct metabolic pathways. The significant heterogeneity and sample-source-dependent effects highlight the complexity of the gut-brain axis in ASD and underscore the need for future research with standardized protocols and longitudinal designs to clarify the role of SCFAs.}, }
@article {pmid41732730, year = {2026}, author = {Koester, DC and Plocek, MR and Dierenfeld, ES and Amato, KR and Dunham, NT}, title = {Variation in zoo diets, offerings of leafy browse, and body condition scores in Matschie's tree kangaroos (Dendrolagus matschiei) and their associations with gut microbiome composition.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20875}, pmid = {41732730}, issn = {2167-8359}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Animals, Zoo/microbiology ; *Diet/veterinary ; *Animal Feed/analysis ; Female ; Male ; Feces/microbiology ; *Macropodidae/microbiology/physiology ; }, abstract = {Recommended zoo diets for the arboreal folivore, the Matschie's tree kangaroo (Dendrolagus matschiei; TK) were recently found to be much lower in fiber and higher in starch than wild diet items for this species. In contrast to wild animals, zoo-housed TKs are ~30-40% higher in body mass, known to suffer from infections indicating immune dysfunction, and exhibit various reproductive issues. These problems may have ties to gut microbiome dysbiosis related to differences in diet between captive and wild individuals, but to date, the microbiome of TKs has not been explored. This study aimed to (1) quantify the macronutrient intake of zoo-housed TKs and compare the intake of over-conditioned animals to those at ideal body condition, and (2) examine gut microbial communities for any differences associated with TK macronutrient intake, leafy browse offerings, or body condition. Detailed diet intake information (n = 31 individuals at 16 facilities accredited by the Association of Zoos and Aquariums) was collected for approximately 1 week at two different time points (i.e., July-September and January-March). Body condition scores were recorded by primary caregivers or veterinary staff no more than one month from each diet intake week. Fecal samples (n = 57) were collected concurrently during the diet recording weeks. We used 16S rRNA gene amplicon sequencing to examine TK gut microbiota. We found that animals assigned over-conditioned body scores consumed significantly more kilocalories compared to animals assigned an ideal body condition score. These differences were driven primarily by significantly greater crude protein and starch intake in over-conditioned TKs. TKs offered high and intermediate amounts of leafy browse exhibited substantially different fecal microbial communities compared to animals offered low or no browse. Our results indicate that formulation of diets for zoo-housed TKs, similar to other folivores, should closely resemble the macronutrient and caloric values of wild counterparts to encourage ideal body condition and promote gastrointestinal health. Future research should examine the gut microbiota of free-ranging TKs and assess how different species of leafy browse impact TK gut microbiota.}, }
@article {pmid41732696, year = {2026}, author = {Zakari, A and Peng, SW and Han, CL and Wang, SY and Lan, SC and Shih, YY and Liao, ZA and Hsiao, TC and Yang, FM and Wang, YH and Ho, SC and Lee, KY and Chadeau-Hyam, M and Chung, KF and Ho, KF and Chuang, KJ and Chang, JH and Chuang, HC}, title = {Extreme temperature exposure induces lung-gut dysbiosis in healthy mice.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100564}, pmid = {41732696}, issn = {2666-5174}, abstract = {Climate change has a strong effect on respiratory health, the effects of extreme temperatures on the lung-gut axis remains unclear. This study investigates the impact of extreme temperatures on the lung-gut microbiome and its associated biological pathways in mice. B6.Sftpc[CreERT2/+] ROSA26Sor[CAG-tdTomato] mice were exposed to normal (22 °C), low (10 °C), high (40 °C), or fluctuating (40 °C 2 hrs to 10 °C 2 hrs; 40-10 °C) temperatures at 65 % relative humidity, 4hrs/day for 7days. Lung and gut microbiota were analyzed by 16S rDNA sequencing, short-chain fatty acids (SCFAs) were quantified using gas chromatography-mass spectrometry. Intestinal LDH, IL-6, and KC levels were measured. Liquid chromatography-tandem mass spectrometry was used to characterized proteins. Significant beta diversity was observed among groups in the both lung and gut microbiomes. In the lung, Deferribacterota and Desulfobacterota increased at 10 °C and 40-10 °C, while Firmicutes and Verrucomicrobiota decreased under the same conditions. Desulfobacterota and Patescibacteria were enriched at 40-10 °C, whereas Verrucomicrobiota and Firmicutes increased at 40 °C and 10 °C in mice stool, respectively. 40 °C elevated intestinal KC levels, while 10 °C reduced serum butyric and pentanoic acids in mice serum. Significant correlations between lung and stool microbiota, SCFAs, inflammatory markers, and LDH were observed. Proteomic profiling makes available unique temperature-dependent expression patterns, involving: metabolic regulation, immune response, cellular stress, and injury pathways. Extreme temperature exposure induced lung-gut dysbiosis, intestinal inflammation, Serum SCFAs imbalance, and proteomic alterations in mice. These findings revealed the adverse effects of extreme temperature events in disrupting the host-microbiome homeostasis, which potentially increase the susceptibility to temperature-sensitive adverse health outcomes.}, }
@article {pmid41732695, year = {2026}, author = {Biscarrat, P and Pepke, F and Defois-Fraysse, C and Jeaidi, A and Hennequet-Antier, C and Rué, O and Castelli, F and Chollet, C and Bedu-Ferrari, C and Berthon, JY and Chaudemanche, C and Dreux-Zigha, A and Langella, P and Cherbuy, C}, title = {Interactions between gut commensal bacteria and polysaccharides derived from algae and legumes: identification of metabolites produced and pathways involved.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100567}, pmid = {41732695}, issn = {2666-5174}, abstract = {UNLABELLED: Diet is a key driver of gut microbiome functions, largely via microbial fermentation of dietary fibers. We investigated how 15 human gut commensals from Bacteroidota, Bacillota, and Actinomycetota metabolize structurally distinct poly-/oligosaccharides from algae (Ulva lactuca, Saccharina latissima, Undaria pinnatifida) and chickpeas (Cicer arietinum). In low-nutrient, carbon-defined cultures, we quantified growth (ΔOD), acidification (ΔpH), and short-chain fatty acids (SCFAs). Then, we conducted untargeted liquid chromatography-high-resolution mass spectrometry (LC-HRMS) metabolomics and RNA sequencing on eight representative strains. Chickpea raffinose-family oligosaccharides (RFOs) broadly stimulated growth, fermentation, and SCFA production across phyla, whereas algal polysaccharide use was restricted to specific Bacteroidota species. Metabolomics revealed phylum- and strain-resolved signatures and bioactive molecules beyond SCFAs, including tryptophan derivatives (for example, indolelactic acid), γ-aminobutyric acid (GABA), and micronutrient-related compounds (for example, riboflavin), whose abundance depended on both taxon and substrate. Transcriptomic analysis in the presence of raffinose indicated coordinated activation of carbohydrate-active enzymes (CAZymes), specialized transport systems (SusC/D, TonB, or ATP-binding cassette [ABC] transporters), and transcriptional regulators (for example, LacI), consistent with substrate-responsive carbohydrate gene clusters. Bacteroidota exhibited the largest CAZyme mobilization and transcriptional remodeling, while Bacillota and Actinomycetota showed targeted responses consistent with narrower substrate scopes.<br><br>CONCLUSIONS: Fiber structure mechanistically links to selective microbial functions. Pulses-derived RFOs elicit broad, phylum-specific metabolic programs, and algae polysaccharides engage a limited set of Bacteroidota specialists. This integrative framework (growth, SCFAs, metabolomics, transcriptomics) refines how discrete fiber types can be matched to microbial capacities, informing precision-nutrition strategies that leverage sustainable fibers (pulses, algae) to promote health-relevant metabolites and targeted microbiome modulation.}, }
@article {pmid41732646, year = {2026}, author = {Patel, R and Mangold, M and Mandala, AR}, title = {Beyond the Gut: A Case Report of Antibiotic-Induced Dysbiosis as a Hidden Cause of Chronic Insomnia.}, journal = {Cureus}, volume = {18}, number = {1}, pages = {e102143}, pmid = {41732646}, issn = {2168-8184}, abstract = {Insomnia is a common sleep disorder that affects many adults on a long-term or intermittent basis. While conventional management includes pharmacotherapy and cognitive behavioral therapy, emerging evidence highlights the gut microbiome as a critical regulator of sleep via the microbiome-gut-brain axis. Prolonged antibiotic exposure can lead to an alteration or imbalance in the structure, composition, and function of the gut microbial community, known as gut dysbiosis. Gut dysbiosis may disrupt neurotransmitter synthesis and circadian rhythm, contributing to refractory insomnia. We report a 40-year-old man with early T-cell precursor acute lymphoblastic leukemia who underwent induction chemotherapy and allogeneic stem cell transplantation. Over two years, he received multiple prolonged antibiotic courses for infectious complications, resulting in significant cumulative exposure. Several months later, he developed severe insomnia, unresponsive to melatonin, mirtazapine, CBT-I, and multiple hypnotics, including zolpidem and lemborexant. Actigraphy revealed sleep latency of 90 minutes, total sleep time <4 hours, and sleep efficiency of 50-55%. Integrative evaluation demonstrated marked gut dysbiosis (low Firmicutes/Bacteroidetes ratio, overgrowth of Streptococcus, Klebsiella, Fusobacterium) and multiple micronutrient deficiencies. Targeted interventions, multistrain probiotics, fermented foods, high-fiber diet, and amino acid/vitamin supplementation, led to progressive improvement. At six months, the patient achieved restorative sleep without pharmacologic support, alongside improved mood, appetite, and functional status. This case underscores the potential role of antibiotic-induced dysbiosis in chronic insomnia through disruption of microbial metabolites (short-chain fatty acids) and neurotransmitter pathways. Restoration of gut health may modulate circadian rhythm and sleep architecture, offering a novel adjunctive strategy for refractory insomnia. Clinicians should consider gut microbiome assessment in persistent insomnia, particularly in patients with extensive antibiotic exposure. Further research is warranted to elucidate mechanisms and validate microbiome-targeted therapies.}, }
@article {pmid41732506, year = {2026}, author = {Ayub, H and Ahmad, H and Zehra, SH and Ramzan, K and Arif, MA and Tariq, N and Capucchio, MT and Mugabi, R and Sharma, A and Nayik, GA}, title = {Anthocyanins from fruit and vegetable waste: biosynthesis, extraction, and gut health benefits.}, journal = {Food chemistry: X}, volume = {34}, number = {}, pages = {103614}, pmid = {41732506}, issn = {2590-1575}, abstract = {Anthocyanins (ANCs), naturally abundant in fruit and vegetable waste, represent a promising class of sustainable functional ingredients with notable gut-related health benefits. This review uniquely focuses on waste-derived anthocyanins and their microbiome-modulating effects, including enhancement of intestinal barrier integrity, prebiotic-like activity, and short-chain fatty acid production. Advances in green extraction and purification techniques such as ultrasound-, microwave-, enzyme-assisted, pulsed electric field, and deep eutectic solvent-based methods have improved recovery efficiency while promoting environmental sustainability. Furthermore, stabilization strategies including acylation, protein/polysaccharide complexation, co-pigmentation, and nano/microencapsulation enhance anthocyanin bioavailability and industrial applicability. By integrating technological innovation with gut health insights, this review highlights emerging opportunities to valorize agro-industrial waste and develop next-generation nutraceutical and functional food systems.}, }
@article {pmid41732369, year = {2026}, author = {Fu, R and Li, J and Wang, M and Xiao, D and Li, F and Zhu, X}, title = {Microscopic-scale gut microbiota dataset of Kunming mice revealed by 16S rRNA gene high-throughput sequencing.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112572}, pmid = {41732369}, issn = {2352-3409}, abstract = {Gut microbiota profoundly influence host physiology, yet most studies rely on bulk-scale intestinal samples, overlooking microbial heterogeneity at the micro-scale. Here, we present a dataset generated from 378 colonic micro-scale grains (20-40 µm) and 20 bulk samples collected from four Kunming mice. Using Illumina NovaSeq 6000 sequencing of the 16S rRNA V4 region, we obtained over 8.0 million raw reads, processed into 1506 amplicon sequence variants (ASVs) spanning 19 phyla and 203 genera. Firmicutes and Bacteroidetes were the dominant phyla across scales, while marked differences were observed in ASV richness (p < 0.001, Wilcoxon test) and network complexity (number of edges, p = 0.03, Wilcoxon test) between bulk samples and micro-scale grains. The dataset, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1249752, provides a high-resolution view of gut microbial spatial organization at the sub-100 µm scale. These data advance current understanding of microbial assembly processes, interspecies interactions, and scale-dependent community structure, thereby serving as a valuable resource for microbiome ecology and future mechanistic studies.}, }
@article {pmid41732362, year = {2026}, author = {Tanja, Z and Maja, R}, title = {Gut microbiomes of wild and domesticated mammals and birds in Slovenia, Europe: 16S rRNA sequencing data.}, journal = {Data in brief}, volume = {65}, number = {}, pages = {112564}, pmid = {41732362}, issn = {2352-3409}, abstract = {From a One Health perspective, the gut microbiota of animals acts as a major driver of microbial exchange between animals and the environment. Animals continuously release gut microbes into their surroundings, shaping environmental and human microbial communities and potentially dispersing pathogens. Characterizing gut microbiota across diverse animal hosts is therefore critical for understanding the patterns of microbial spread through ecosystems and their impact on animal, human and environmental health. Here, we introduce a large, taxonomically diverse dataset of fecal microbiomes from 715 individual animals representing over 50 mammalian and avian species. We collected samples from both wild and domestic animals with an emphasis on capturing microbial diversity across a wide range of taxa and ecological contexts. The samples were subjected to 16S rRNA gene sequencing, targeting the V3-V4 hypervariable region. Bioinformatic analysis was performed using Usearch to generate zero-radius operational taxonomic units (ZOTUs). This dataset was generated primarily for the development of microbial source tracking (MST) assays used for identifying the sources of fecal pollution in contaminated water. However, it provides a valuable resource for broader microbiome research. It enables comparative studies across host species, trophic guilds, and environmental contexts such as domestication.}, }
@article {pmid41732311, year = {2026}, author = {Makkieh, Y and Shah, HH and Imran, SB and Pathan, SMK and Saju, AC and Majooju, M and Garg, A and Naag, T and Islam, R and Fahima, C and Ali, R}, title = {The gut-heart axis: Exploring the role of the gut microbiome in cardiovascular health - A focused systematic review.}, journal = {American heart journal plus : cardiology research and practice}, volume = {61}, number = {}, pages = {100687}, pmid = {41732311}, issn = {2666-6022}, abstract = {This focused systematic review examines the role of the gut microbiota in cardiovascular disease (CVD). The review explores mechanisms linking gut dysbiosis with CVD via microbial metabolites such as trimethylamine-N-oxide (TMAO) and short-chain fatty acids (SCFAs), which affect inflammation, endothelial function, and lipid metabolism. Interventions including dietary modifications, probiotics, prebiotics, fecal microbiota transplantation, and pharmacological agents such as statins, rifaximin, and empagliflozin are evaluated for their impact on microbial composition and cardiovascular outcomes. Probiotic strains and fiber-rich diets demonstrated modest improvements in blood pressure, lipid profiles, and inflammatory markers. Studies revealed that gut microbiome alterations influence drug metabolism and bleeding risk in patients taking oral anticoagulants. Limited evidence suggests that modulation of the microbiota may reduce chemotherapy-induced cardiotoxicity. However, only nine eligible studies met the inclusion criteria, reflecting the early and heterogeneous nature of this research area. Consequently, these findings should be interpreted as exploratory and hypothesis-generating. The focused review emphasizes the need for large-scale trials to validate microbiome-targeted strategies in CVD prevention and management. This focused systematic review is registered with PROSPERO (ID: CRD420251022190).}, }
@article {pmid41732151, year = {2026}, author = {Liu, X and Han, H and Zhang, X and Kong, F and Dai, D and Hao, Y and Wang, W and Li, S}, title = {Potassium carbonate improves milk quality by enhancing rumen metabolism in Holstein cows.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {24}, number = {}, pages = {534-548}, pmid = {41732151}, issn = {2405-6383}, abstract = {Mid-lactation is a key stage in dairy production characterized by high milk yields and metabolic stress in cows. Dietary potassium carbonate may enhance milk quality, but its response mechanisms, particularly the link between rumen microbiome changes and production performance, remain poorly understood. To address this knowledge gap, a total of 60 multiparous Holstein cows (parity = 2.47 ± 1.06, body weight = 601 ± 25 kg, and days in milk = 127.83 ± 31.91) were divided into four groups (n = 15 cows per group) using a randomized complete block design and fed the corresponding diets for 84 days. The feed treatments were as follows: a control group (CON, basal diet), a low dose group (LD, basal diet + 250 g/d K2CO3·1.5H2O per head), a medium dose group (MD, basal diet + 500 g/d K2CO3·1.5H2O per head), and a high dose group (HD, basal diet + 750 g/d K2CO3·1.5H2O per head). The results showed that potassium carbonate supplementation significantly influenced rumen fermentation patterns, particularly by increasing acetate (P = 0.008) and isovalerate concentrations (P < 0.001). Milk fat (P = 0.004) and protein percentage (P = 0.006) exhibited the most pronounced effects in the MD group. The rumen microbiota and metabolome revealed significant alterations in microbial community structure and function. Notably, the results indicated that in the MD group, there was an increase in the abundance of Kyoto Encyclopedia of Genes and Genomes (KEGG) genes associated with crucial metabolic pathways: amino acid biosynthesis, long-chain fatty acid biosynthesis and fatty acid elongation pathways. These findings suggest that dietary supplementation with 500 g/d of potassium carbonate optimizes milk composition by modulating the rumen microbiota and associated metabolic pathways, supporting the potential for targeted nutritional strategies in dairy management.}, }
@article {pmid41731760, year = {2026}, author = {Zhou, J and Wu, P and Luo, Z and Huang, Z and Ma, H and Fang, H and Yin, X and Yang, C and Sun, N and Li, Y}, title = {Causal relationship between gut microbiome and childhood allergy: A bidirectional Mendelian randomization analysis.}, journal = {Medicine}, volume = {105}, number = {8}, pages = {e47793}, pmid = {41731760}, issn = {1536-5964}, support = {CYXZPT2025-36//the Cuiying Scientific Training Program for Undergraduates of Lanzhou University Second Hospital/ ; 20240050147&#xef;&#xbc;&#x152;20250050021//Student Entrepreneurship and Innovation Action Plan of Lanzhou University/ ; 2025-TSXM0017//Taishun County Science and Technology Plan Project/ ; 2025-zdx-2//Guided Science and Technology Plan Project of Chengguan District, Lanzhou : Social Development Program./ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Mendelian Randomization Analysis ; *Hypersensitivity/microbiology/genetics/epidemiology ; Child ; Risk Factors ; Metabolic Networks and Pathways ; }, abstract = {This study aims to investigate the potential causal relationship between gut microbiome pathways and childhood allergy risk using a bidirectional Mendelian randomization (MR) approach. We conducted a bidirectional MR analysis using inverse variance weighting methods to assess the suggestive causal relationship between gut microbiome pathways and childhood allergy. The reverse MR analysis revealed that childhood allergy showed suggestive causal associations with several microbial features. For metabolic pathways, a higher risk of childhood allergy was associated with Lipid IV~A~ biosynthesis (odds ratio [OR] 1.11, 95% confidence interval [CI]: 1.00-1.22, P = .044) and NAD salvage pathway I (OR 1.14, 95% CI: 1.01-1.28, P = .030). At the taxonomic level, a lower risk of childhood allergy was associated with Bacteroidaceae (OR 0.90, 95% CI: 0.81-0.99, P = .031), Adlercreutzia (OR 0.79, 95% CI: 0.67-0.92, P = .003), Bacteroidales (OR 0.90, 95% CI: 0.81-0.99, P = .031), Roseburia (OR 0.89, 95% CI: 0.80-0.99,P = .032), Adlercreutzia equolifaciens (OR 0.79, 95% CI: 0.67-0.92, P = .003),Holdemania (unclassified) (OR 0.79, 95% CI: 0.64-0.98, P = .028), and Bacteroides vulgatus (OR 0.86, 95% CI: 0.78-0.95, P = .004). This study provides evidence for the potential causal relationship between specific gut microbiome pathways and childhood allergy. Several gut microbial features demonstrated suggestive causal associations with childhood allergy risk. For metabolic pathways, inverse associations (suggesting protective effects) were observed for creatinine.degradation I (OR 0.86, 95% CI: 0.76-0.98, P = .021) and superpathway of pyrimidine ribonucleosides degradation (OR 0.75, 95% CI: 0.62-0.91, P = .004). Conversely, positive associations with allergy risk were identified for isoleucine biosynthesis I from.threonine(OR 1.22, 95% CI: 1.00-1.48, P = .049), glutamate degradation V via hydroxyglutarate (OR 1.15, 95% CI: 1.01-1.32, P = .040), superpathway of polyamine biosynthesis II (OR 1.15, 95% CI: 1.01-1.32, P = .035), allantoin degradation to glyoxylate III (OR 1.17, 95% CI: 1.02-1.33, P = .024), and UDP N acetyl D glucosamine biosynthesis I (OR 1.50, 95% CI: 1.11-2.02, P = .008). At the taxonomic level, inverse associations were found for Odoribacter splanchnicus (OR 0.73, 95% CI: 0.58-0.91, P = .005) and Coprococcussp.ART55/1 (OR 0.84, 95% CI: 0.73-0.97, P = .014). Positive associations with allergy risk were observed for Betaproteobacteria (OR 1.29, 95% CI: 1.06-1.58, P = .013), Lactobacillaceae (OR 1.16, 95% CI: 1.04-1.30, P = .010), Clostridiaceae (OR 1.14, 95% CI: 1.01-1.29, P = .033), Clostridium (OR 1.15, 95% CI: 1.00-1.31, P = .046), Burkholderiales (OR 1.29, 95% CI: 1.06-1.58, P = .013), and Eubacterium hallii (OR 1.24, 95% CI: 1.08-1.41, P = .002).This study provides evidence for the potential causal relationship between specific gut microbiome pathways and childhood allergy.}, }
@article {pmid41731601, year = {2026}, author = {Zhang, J and Ma, R and Duan, X and Ma, L and Gu, J and Bu, D}, title = {Enhancing the fiber degradation efficiency in dairy cattle rumen through engineered bacterial communities.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02331-3}, pmid = {41731601}, issn = {2049-2618}, support = {No. 2022YFD1301002//National Key Research and Development Program of China/ ; ASTIP-IAS-17//Agriculture Science and Technology Innovation Program/ ; BAIC05-202//Beijing Innovation Consortium of Livestock Research System/ ; }, abstract = {BACKGROUND: The rumen functions as an anaerobic fermentation chamber, housing microorganisms with cellulolytic and proteolytic capabilities that facilitate feed utilization. Fiber-degrading bacteria possess the capability to enhance the productivity of cellulolytic feed. The application of omics technologies has greatly improved our understanding of the rumen microbiome. Determining microbial composition and functional patterns in the rumen does not equate to a comprehensive exploration of rumen microbial resources and their mechanisms of action. This study seeks to integrate high throughput 16S rRNA data with information on culturomics, cellulolytic activities, nutrition, and synthetic microbial communities (SynCom) engineering. The objective is to evaluate the relationship between rumen microbial activity and fiber utilization efficiency in cattle, ultimately aiming to develop a more powerful intervention strategy for the ruminant industry.<br><br>RESULTS: The enrichment culture with various carbon sources led to significant alterations in the composition and structure of rumen microbiota, particularly enhancing those associated with carbohydrate metabolism. Employing the culturomics methodology, 896 strains from 78 species (including 8 novel species) were isolated, resulting in a 10.1% isolation rate relative to the rumen bacterial community. Among them, 35 strains demonstrated boosted cellulose-degrading capability on plates, while 25 exhibited the ability to degrade hemicellulose as well. SynComs of these candidates were prepared based on the ratio observed in rumen microbiota exhibiting high cellulolytic performance. SynCom&#xa0;3 improved the neutral detergent fiber degradation (NDFD) by 20.39%&#xa0;averagely. Additionally, both in vitro and in situ assessments indicated that the optimization of dose/strain in SynCom&#xa0;3 significantly improved the in vitro NDFD by 20.56% and increased the in situ NDFD by 7.81%, along with the acidic detergent fiber (ADF,&#xa0;+&#x2009;11.47%). Genomic analysis revealed that the SynCom&#xa0;3 functioned well in fiber degradation through the synergistic action of key carbohydrate-active enzymes.<br><br>CONCLUSIONS: This study strengthens rumen microbiome research by integrating omics and SynCom engineering within a microbiota-bacteria-enzymes-genes framework, revealing the significance of enzymatic synergy in carbohydrate metabolism. The findings establish a framework for utilizing low-abundance microbes and engineering functional consortia, which are crucial for improving ruminant feed utilization and biomass conversion. Future research should investigate the transcriptomic profiles and the metabolic cross-feeding mechanisms of fiber-degrading strains in the rumen. Video Abstract.}, }
@article {pmid41731555, year = {2026}, author = {Yasuda, S and Palomo, A and Smets, BF and Terada, A}, title = {Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02351-7}, pmid = {41731555}, issn = {2049-2618}, abstract = {BACKGROUND: In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill.<br><br>RESULTS: A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment.<br><br>CONCLUSIONS: The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.}, }
@article {pmid41731095, year = {2026}, author = {York, A}, title = {Gut microbiome control of HIV immunodeficiency.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41731095}, issn = {1740-1534}, }
@article {pmid41730922, year = {2026}, author = {Mandell, J and Wang, T and Mathad, JS and Shafiq, M and Naik, S and Alexander, M and Kulkarni, V and Deshpande, P and Humphrys, MS and Ma, B and Holm, JB and Bhosale, R and Ghanem, KG and Kinikar, A and Ravel, J and Gupta, A and Wang, S and Shivakoti, R}, title = {Impact of maternal HIV infection on the gut microbiome and metabolome of mothers and infants: the PRACHITi cohort in Pune, India.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69912-0}, pmid = {41730922}, issn = {2041-1723}, support = {R00HD089753; R01HD081929//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; K23AI129854; UM1AI069465//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01NR015495//U.S. Department of Health &amp; Human Services | NIH | National Institute of Nursing Research (NINR)/ ; }, abstract = {Human immunodeficiency virus (HIV) affects millions of reproductive-age women globally, and during pregnancy is associated with adverse birth and infant health outcomes. Research on how maternal HIV shapes the gut microbiota, a potentially modifiable factor, during pregnancy, postpartum, and in infancy remains limited. The PRACHITi cohort study was conducted in India among 244 pregnant women with and without HIV, who were followed along with their children through 1 year postpartum. Our study focuses on secondary objectives of the PRACHITi study related to gut microbiota, with longitudinal samples being collected in the full cohort and more frequent sampling in a sub-study. Here, our findings reveal gut dysbiosis (based on 16S rRNA sequencing) and distinct plasma metabolomic profiles across pregnancy, postpartum, and their infants among women with HIV compared with seronegative women. We show that specific taxa and metabolites are differentially abundant by HIV status, some of which are linked to adverse outcomes, including preterm birth, low birth weight, and inflammation, conditions that are more common among populations with HIV. These results suggest potential biological pathways through which HIV affects maternal and infant health.}, }
@article {pmid41730770, year = {2026}, author = {Tartar, JL and Valls, A and Totev, M and Mendoza, MB and Lopez, JV and Smith, RP}, title = {Extending Sleep Improves Sleep and Stress Measures With Limited Microbiome Shift.}, journal = {Journal of sleep research}, volume = {}, number = {}, pages = {e70321}, doi = {10.1111/jsr.70321}, pmid = {41730770}, issn = {1365-2869}, support = {//Nova Southeastern University/ ; //College of Psychology Faculty Fellowship/ ; }, abstract = {Poor sleep quality and duration are associated with adverse health. However, these can be remediated by experimental sleep extension. While the physiological mechanisms underlying the benefits of experimental sleep extension are unknown, recent evidence has highlighted the role of the gut microbiome in sleep physiology, potentially via the gut microbiome and inflammatory pathways. This pilot study examined whether extending sleep for 2 weeks would improve sleep, reduce stress and inflammation, and alter gut microbiome composition. Healthy female adults underwent a 2-week baseline assessment, followed by a 2-week sleep extension intervention. Pre- and post-intervention assessments included actigraphy, subjective sleep quality, perceived stress, salivary cortisol, interleukin-6 (IL-6), and gut microbiome profiling. Sleep extension increased total sleep time and time in bed without compromising sleep efficiency. Participants reported reductions in perceived stress and improved sleep quality, with large effect sizes. Skeletal muscle mass increased significantly, though no statistically significant changes were observed in cortisol or IL-6. While microbial diversity remained unchanged, linear discriminant analysis effect size analysis revealed a significant increase in the relative abundance of Peptostreptococcus, a genus implicated in producing indoleacrylic acid, a tryptophan-derived metabolite with anti-inflammatory and gut barrier-enhancing properties. Our findings suggest that increases in sleep duration can yield psychological, physiological, and microbiome-related benefits, supporting sleep extension as an intervention to improve stress-related health outcomes.}, }
@article {pmid41730718, year = {2026}, author = {Todd, IMF and Pedersen, LH and Miller, JE and Burgner, DP and Magnus, MC}, title = {Joint Effects of Prenatal Antibiotics, Mode of Birth and Breastfeeding Duration on Childhood Infections: The Norwegian MoBa Cohort Study.}, journal = {Paediatric and perinatal epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ppe.70120}, pmid = {41730718}, issn = {1365-3016}, support = {//Australian Government Research Training Program Scholarship/ ; 262700//Research Council of Norway/ ; GTN1175744//National Health and Medical Research Council/ ; //Victorian Government Operational Infrastructure Support Program/ ; }, abstract = {BACKGROUND: Prenatal antibiotic exposure and caesarean births are associated with an increased risk of hospitalised infection in children, but few studies have evaluated their impact on less severe infections and possible joint effects. Conversely, longer breastfeeding duration is protective against infections, but whether this effect varies according to previous perinatal exposures has not been explored. These three exposures are all hypothesised to influence the infant microbiome.<br><br>OBJECTIVES: To examine the individual and joint effects of prenatal antibiotic exposure, caesarean birth, and breastfeeding duration for both the incidence of infections and for hospitalisation for infection up to age three.<br><br>METHODS: Participants were from the Norwegian Mother, Father, and Child Cohort Study (MoBa). The three exposures were prenatal antibiotic exposure, caesarean birth, and breastfeeding duration. Using quasi-Poisson regression, we analysed the number of infections and hospitalisation for infections according to: (1) each exposure individually, (2) combined exposure to prenatal antibiotics and caesarean birth and (3) breastfeeding duration across the strata of prenatal antibiotics and birth mode.<br><br>RESULTS: Among 45,485 children followed from birth to age three, there was weak evidence for an increased number of infections according to the exposures of interest (incidence rate ratio for prenatal antibiotics 1.04, 95% CI 1.02, 1.05; caesarean birth 1.02, 95% CI 1.00, 1.03; breastfeeding <&#x2009;6&#x2009;months 1.04, 95% CI 1.02, 1.05), while there was an increased risk of hospitalised infection (risk ratio for prenatal antibiotics 1.11, 95% CI 1.05, 1.17; caesarean birth 1.20, 95% CI 1.14, 1.27; breastfeeding <&#x2009;6&#x2009;months 1.16, 95% CI 1.10, 1.22). Analyses of combined effects showed&#xa0;a 1.55-fold (95% CI 1.24, 1.93) increased risk of hospitalisation for infection with all three exposures compared to none.<br><br>CONCLUSIONS: Prenatal antibiotic exposure, caesarean birth and shorter breastfeeding duration were each associated with an increased risk of hospitalisation for infection in early childhood, with higher magnitude when multiple exposures occurred.}, }
@article {pmid41730403, year = {2026}, author = {Liu, W and Zhang, Z and Wu, W and Yan, X and Huang, Y and Feng, H and Mou, Q and Wan, J and Yan, M and Tang, H and Liang, J and Zhang, Y and Peng, C and Pan, X}, title = {Ligilactobacillus murinus Confers a Dual Benefit: Counteracting Crotonis Fructus-induced Intestinal Toxicity and Synergizing with Its Processed Form against Ulcerative Colitis.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {121420}, doi = {10.1016/j.jep.2026.121420}, pmid = {41730403}, issn = {1872-7573}, abstract = {Ulcerative colitis (UC) poses a major clinical challenge. Classical Chinese medical texts record the use of Crotonis Fructus (CF), the seeds of Croton tiglium L., for treating conditions like "chronic dysentery" presenting symptoms similar to UC. However, the clinical application of both raw and processed CF is limited due to intestinal toxicity.<br><br>AIM OF THE STUDY: This study investigates the role of gut microbiota in mitigating the intestinal toxicity induced by CF and in enhancing the anti-UC efficacy of its processed form.<br><br>METHODS: Metagenomic analysis investigated CF-induced intestinal toxicity. The benefits of probiotics combined with CF or processed CF cream were evaluated in Caenorhabditis elegans (C. elegans) and a dextran sulfate sodium (DSS)-induced mouse model. Their combined effect was further assessed in DSS-exposed C. elegans, with qRT-PCR measuring intestinal barrier integrity.<br><br>RESULTS: Metagenomic analysis revealed that CF-induced intestinal toxicity was associated with gut microbiota dysbiosis characterized by a pronounced reduction in Ligilactobacillus murinus (L. murinus). Supplementation with L. murinus alleviated CF-induced damage in C. elegans. In DSS-induced UC mice, both L. murinus and processed CF cream ameliorated colitis and suppressed TNF-&#x3b1;, IL-6, and IL-1&#x3b2;. When co-administered in DSS-exposed C. elegans, two agents acted synergistically, leading to greater restoration of intestinal barrier integrity and more pronounced upregulation of barrier-function genes.<br><br>CONCLUSION: This study demonstrates that L. murinus plays a dual role: it mitigates CF-induced intestinal toxicity and acts synergistically with processed CF cream to enhance UC treatment, providing a microbiome-based strategy for safer clinical application.}, }
@article {pmid41729946, year = {2026}, author = {Thomson, AM and Drost, DC and Johannsen, NM and Silvestri, C and Sénéchal, M}, title = {Understanding the gut microbiome through a fitness intervention of aerobic and resistance training for individuals with type 2 diabetes mellitus (GUTFIT: A Study Protocol).}, journal = {PloS one}, volume = {21}, number = {2}, pages = {e0343294}, pmid = {41729946}, issn = {1932-6203}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Resistance Training/methods ; Female ; Male ; *Exercise/physiology ; Blood Glucose ; Middle Aged ; Adult ; Single-Blind Method ; }, abstract = {INTRODUCTION: Exercise is a cornerstone of type 2 diabetes (T2DM) management, yet individuals exhibit vast inter-individual variability in glycemic response to interventions. Gut microbial diversity and exercise intensity may be factors influencing this response variability. However, the interplay between exercise intensity, microbial adaptations, and glycemic outcomes in individuals living with T2DM remains unclear.<br><br>OBJECTIVES: The purpose of this protocol is to describe the GUTFIT study, which aims to test whether performing vigorous-intensity combined aerobic and resistance training produces greater changes in glycemia and gut microbial diversity than moderate-intensity training in individuals living with T2DM. A secondary objective is to explore whether decreases in glycemia after exercise are associated with alterations in gut microbial community architecture and diversity.<br><br>METHODS: The GUTFIT Study (NCT06268743) is a parallel-group, single-blinded, randomized trial involving 40 adult participants (n&#x2009;=&#x2009;20 female) living with T2DM. Participants will be randomized to 16 weeks of: 1) vigorous-intensity exercise (aerobic training at 70-80% heart rate reserve and resistance training at 8-10 repetitions of 75-80% maximal strength) or 2) moderate-intensity exercise (aerobic training at 45-55% heart rate reserve and resistance training at 12-15 repetitions of 65-70% maximal strength). Glycemia will be measured via glycated hemoglobin (HbA1c), and gut microbial composition will be determined in participant fecal samples using next-generation sequencing (Illumina MiSeq) of 16S ribosomal DNA genes. All outcome measures will be tested pre- and post-intervention.<br><br>DISCUSSION: Results of this study will provide further insight into the role of exercise intensity in changes in glycemia and the gut microbiome, and whether there is an intensity-dependent association between exercise-induced changes in glycemia and gut microbial diversity in individuals living with T2DM.}, }
@article {pmid41729814, year = {2026}, author = {Lin, Z and Yang, L and Han, Y and Qi, C and Chen, L and Luo, Y and Lin, Y and Sweren, E and Chen, P and Alphonse, MP and Garza, LA and Wang, G}, title = {Microbiota-fibroblast crosstalk represents the missing link in skin barrier dysfunction and fibrosis.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljag068}, pmid = {41729814}, issn = {1365-2133}, abstract = {Dermal fibroblasts are key cellular components of the skin stroma, primarily responsible for extracellular matrix synthesis and maintenance of tissue structure and function. Beyond this canonical role, these cells also possess immune regulatory functions, enabling them to sense and integrate microbial cues to orchestrate cutaneous inflammatory responses, wound repair, and fibrogenesis. The skin microbiome is a critical regulator of fibroblast homeostasis; its dysbiosis disrupts fibroblast-microbe crosstalk, leading to aberrant fibroblast activation and contributing to the pathogenesis of various dermatological conditions. Clinically, the burden of these disorders is substantial, and current therapeutic strategies targeting fibroblast dysfunction often yield limited efficacy. Fortunately, recent advances in deciphering the pathophysiological mechanisms underlying fibroblast-microbe interactions have highlighted critical molecular regulatory networks, opening new therapeutic avenues. Among these emerging approaches, interventions targeting the microbiota-fibroblast axis-such as probiotics, postbiotics, and fibroblast-directed agents-hold considerable promise. Deciphering the nuances of this crosstalk is pivotal for advancing precision, regenerative therapies, with potential implications for both cutaneous and systemic fibrotic disorders.}, }
@article {pmid41729372, year = {2026}, author = {de Louweren, B and Nieuwdorp, M and Gerdes, VEA}, title = {Abdominal Pain After Bariatric Surgery and the Role of the Gut: A Review.}, journal = {Diabetes therapy : research, treatment and education of diabetes and related disorders}, volume = {}, number = {}, pages = {}, pmid = {41729372}, issn = {1869-6953}, abstract = {Obesity is a major health concern, affecting over 1 in 8 people worldwide. Bariatric surgery (BS) is currently the most effective long-term treatment for morbid obesity. In addition to sustained weight loss, BS is beneficial in treating obesity related comorbidities including dyslipidemia and type 2 diabetes (T2DM). The beneficial effects of BS are a result of weight loss and surgery-induced shifts in the gut microbiota and its metabolites. At the same time, BS may also lead to complications and side effects. Abdominal pain is one of the most frequently reported complaints after BS with a prevalence of 33.8-54.4% within this patient group. However, in many patients the abdominal pain remains unexplained beyond gallstones, internal herniation, and ulcers. This raises the question whether the gut microbiota itself may play a direct role in the pathophysiology of unexplained abdominal pain. Over the years several studies have shown changes in the gut microbiota and related metabolites after BS. These include increased gut microbial diversity and altered microbial composition after BS. Higher abundances of Proteobacteria and Fusobacteria are reported, while a decrease in butyrate-producing Firmicutes is reported. Along with these changes in microbiota, BS causes higher plasma bile acid levels and altered short-chain fatty acid (SCFA) profiles. These metabolic shifts are believed to support weight control, glucose regulation, and lipid metabolism. More recently, specific microbial taxa and metabolite profiles were linked to abdominal complaints following BS. This suggests that dysbiosis and metabolites may play a role in unexplained abdominal pain after BS.}, }
@article {pmid41729340, year = {2026}, author = {Rout, M and Prusty, SK and Singh, V and Kispotta, S and Sarangi, P and Kar, DM}, title = {Targeting the Microbiota-Gut-Brain Axis: Bacillus coagulans Protects Against Rotenone-Induced Parkinson's Disease in Rats.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41729340}, issn = {1573-6903}, mesh = {Animals ; *Rotenone/toxicity ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Rats ; *Probiotics/therapeutic use/pharmacology ; *Bacillus coagulans ; *Brain/metabolism/drug effects ; *Neuroprotective Agents/pharmacology/therapeutic use ; *Brain-Gut Axis/drug effects/physiology ; Rats, Wistar ; alpha-Synuclein/metabolism ; }, abstract = {Gut microbiota and its derived metabolites affect brain physiology through several pathways. Dysfunction of gut-microbiota is involved in the pathogenesis of Parkinson's disease (PD). Introduced the pleiotropic effect of probiotics (PBT) in the function of the central nervous system, can delay the disease progression through microbiota-gut-brain axis (MGBA). PD is characterized by aggregated alpha-synuclein (α-syn), oxidative stress and neuroinflammation leading to depletion of dopaminergic neurons in the midbrain region. Our study designed to assess the neuroprotective effect of PBT Bacillus coagulans (B. coagulans) against rotenone (ROT) induced PD rats. To eliminate hormone-based errors associated with estrous cycle, we only used male rats in this experiment. ROT (50 mg/kg/day) caused perturbation of intestinal barrier leading to gut microbiome disturbances along with accumulation of α-syn in intestine and brain with motor deficits. qPCR of gut homogenate interpreted that treatment with B. coagulans alter the gut microbial composition in experimental PD through MGBA. This formulation claims as a supportive agent to restore the progression and aid in the therapeutic management of PD.}, }
@article {pmid41729185, year = {2026}, author = {Fitzgerald, MJ}, title = {Reciprocal Accord: Seeing Microbiomes as Parts of Ourselves.}, journal = {The Journal of medicine and philosophy}, volume = {}, number = {}, pages = {}, doi = {10.1093/jmp/jhaf040}, pmid = {41729185}, issn = {1744-5019}, abstract = {Human beings and their microbiomes are interrelated. Now what is the nature of their relation? In this paper, I claim that human beings have microbiomes as parts of themselves. In other words, rather than merely being casually associated with human beings, those microbiomes that reside in/on/around people are constituent parts of human beings. I argue this by reference to organismal homeostasis as understood as a systems-level phenomenon. To support my argument, I provide a survey of contemporary scientific literature surrounding the composition, location, structure, and function of the human microbiome(s). Finally, I cash out this finding by developing the idea of the "constitutive publicity" of the human organism. By this I mean that the human organism is not a "private" entity that then finds itself in the world, but rather that it is constantly created, suffused by, and contributing to the "public" world.}, }
@article {pmid41729077, year = {2026}, author = {Tesfaigzi, Y and Yildirim, A&#xd6; and Polverino, F and Conlon, TM and Sidhaye, V and Sauler, M and Raju, SV and Jurkowska, RZ and Chandra, D and Cho, MH and Silverman, EK and Sun, RC and Castaldi, P and Tata, PR and Benam, KH and Antony, L and Lehmann, M and Kosmider, B and Bahmed, K and Negasi, ZH and Bankoti, K and Swaby, C and Lagowala, DA and Vural, Y and Bayram, H and Faner, R and Washko, G and Bui, DS and Celli, B and Wasnick, RM and Neptune, E}, title = {New approaches to uncover COPD pathobiology and develop therapies.}, journal = {JCI insight}, volume = {11}, number = {4}, pages = {}, doi = {10.1172/jci.insight.199693}, pmid = {41729077}, issn = {2379-3708}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/therapy/genetics/etiology/pathology/diagnosis ; Biomarkers ; Risk Factors ; Microbiota ; Animals ; Proteomics ; Metabolomics ; Disease Progression ; }, abstract = {Chronic obstructive pulmonary disease (COPD) was the third leading cause of global mortality in 2011 but receives limited attention and research funding. This Review describes the current knowledge on COPD risk factors, including genetic and epigenetic determinants and their interactions with the microbiome and environmental exposures. Preclinical models are being refined and single-cell transcriptomic, metabolomic, and proteomic technologies are being implemented to investigate the molecular mechanisms of disease progression. Patient cohorts to define biomarkers of early disease and the latest approaches to diagnose pre-COPD are essential to accelerate the development of novel and effective therapeutic interventions and translate new findings into clinical trials. This Review is a summary of topics covered by a symposium organized by the COPD-iNET consortium, an international network of researchers who have established a platform that facilitates collaboration of this multidisciplinary group of preclinical, translational, and clinical researchers.}, }
@article {pmid41729001, year = {2026}, author = {Kithan-Lundquist, R and McMillan, HM and Gdanetz, K and Liber, J and He, S-Y and Sundin, GW}, title = {Microbial community succession and dynamics during the season-long development of apple fruit (Malus × domestica).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0283625}, doi = {10.1128/spectrum.02836-25}, pmid = {41729001}, issn = {2165-0497}, abstract = {Microorganisms colonize every external and internal surface of plants, including fruits. Relatively little is known about the fruit microbiome and its role in disease resistance and fruit quality during fruit development and storage. The fruit tissue, the carposphere, is a carbohydrate-rich habitat. Amplicon sequencing of fungal and bacterial communities identified distinct microbial community composition and diversity across tissue types such as the exocarp and mesocarp. We determined microbial richness was highest during bloom and in mature fruits. Endophytic microbes were shared across many fruit development stages, while epiphytic microbes were transient. However, we identified a pattern of succession with increasing diversity of the epiphytic microbiota across the growing season. Notably, we also show that fungal and bacterial taxa with carbohydrate-degrading potential have different abundance patterns across apple developmental stages, which could indicate that host plants have distinct regulation for microbial subgroups or that microbes interact with different elements of host regulatory mechanisms. The identification of a stable microbiota associated with tree fruit, and understanding how those microbes establish and function, will provide fundamental insights regarding the engineering of a consortium of microbes that could thrive under storage and possibly reduce food waste.IMPORTANCEPlant-associated microbes are not well-characterized in specialty crop systems. We describe the fungal and bacterial microbial communities colonizing the surface and interior of apple flowers and fruits over the course of one growing season. This work provides a foundational understanding of microbes present, how the populations change over time, and provides insight into the origins of endophytic microbes. These findings will be used in future apple disease-related research, particularly on the development of organic or biologically based pesticides.}, }
@article {pmid41728982, year = {2026}, author = {Woo, AYM and Sandoval-Espinola, WJ and Bollenbach, M and Wong, A and Sakanaka-Yokoyama, M and Zhang, Q and Nieto, V and Rey, FE and Balskus, EP}, title = {Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism.}, journal = {mBio}, volume = {}, number = {}, pages = {e0117225}, doi = {10.1128/mbio.01172-25}, pmid = {41728982}, issn = {2150-7511}, abstract = {Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host's impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline trimethylamine-lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levels in vivo. These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities.IMPORTANCEGut microbial metabolic activities play important roles in human health, prompting interest in the discovery of gut microbiome-targeted small molecule inhibitors as potential therapeutics. Anaerobic choline metabolism by the gut microbiome generates trimethylamine and its downstream metabolite trimethylamine-N-oxide (TMAO), which cause trimethylaminuria and are correlated with cardiometabolic diseases, respectively. Current strategies for modulating microbial metabolism with small molecule inhibitors typically require having a target enzyme. Here, we show that a growth-based phenotypic screen can identify inhibitors of choline metabolism with chemical scaffolds that are structurally distinct from choline and existing inhibitors. The resulting optimized compounds lower serum TMAO in gnotobiotic mice without significantly perturbing gut microbiome composition. This work highlights the potential of using phenotypic screening to rapidly discover additional inhibitors of microbial metabolic activities, which would accelerate mechanistic studies of the microbiome and deepen our understanding of disease biology from correlation to causation.}, }
@article {pmid41728964, year = {2026}, author = {Dieser, M and Smith, HJ and Caruso, K and Foreman, CM}, title = {Seven genome sequences of bacterial environmental isolates from the western coast of the Greenland Ice Sheet.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0119225}, doi = {10.1128/mra.01192-25}, pmid = {41728964}, issn = {2576-098X}, abstract = {We report the genomic sequences of seven bacterial isolates from the western coast of the Greenland Ice Sheet. The surface ice along the margins of the ice sheet is dominated by microbes. As the ice sheet melts, it is important to understand the ecological role and biotechnological potential of this novel extremophile microbiome.}, }
@article {pmid41728751, year = {2026}, author = {Bigdeli, Z and Molaei, A and Rahmani, N and Mazhary, Z and Fard, NA}, title = {An In Silico Omics Investigation of the Lactobacillus Genus Complex for Allergenicity Mitigation.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {2}, pages = {e70365}, pmid = {41728751}, issn = {2050-4527}, support = {021015-I-858//National Institute of Genetic Engineering and Biotechnology/ ; }, mesh = {*Allergens/immunology ; *Lactobacillus/immunology/genetics ; Humans ; Proteomics/methods ; *Probiotics ; Computer Simulation ; *Food Hypersensitivity/immunology/prevention &amp; control ; Genome, Bacterial ; Computational Biology/methods ; Proteome ; Bacterial Proteins/immunology/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Among the useful methods of immune response modulation, probiotics can be included. A delicate balance in the microbiome is of extreme importance for immune homeostasis, the composition of which is influenced by lifestyle and dietary habits. The aim of this study was to identify Lactobacillus strains with potential allergenicity-mitigating properties through comprehensive in silico analysis of their genomes and proteomes. Abrogation in such a balance may lead to the development of food allergy. So far, certain components in probiotics, including immunosuppressive motifs or metabolites like 17,18-epoxy eicosatetraenoic acid (17,18 EpETE), seem to have the potential to reduce prevalence. However, some bacterial proteins may be allergenic or may induce cross-reactivity.<br><br>METHODS: We performed an in silico study over the 161 reference genomes and proteomes of Lactobacillus. We analyzed the presence of Nucleotide immunosuppressive motifs (NISM)s, calculated the per million frequency of bases, and checked for the presence of the CYP450 enzymes/stable allergen epitopes. This was evaluated using various bioinformatics tools like Uniprot proteomes, NCBI genomes, AlgPred, PeptideCutter, EMBOSS, and MAST.<br><br>RESULTS: Our analysis identified Latilactobacillus sakei as a promising candidate, based on its genomic and proteomic features, for mitigating allergenicity.<br><br>CONCLUSIONS: Latilactobacillus sakei might be a useful candidate for nutritional allergy management and related conditions. However, this potential requires verification through further experimental studies.}, }
@article {pmid41618331, year = {2026}, author = {Frias-Toral, E and Reytor-González, C and Annunziata, G and Verde, L and Jimenez-Flores, E and Sen, K and Galasso, M and Muscogiuri, G and Simancas-Racines, D and Dalamaga, M and Barrea, L}, title = {Nutrition and longevity - diet in centenarians.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41618331}, issn = {1479-5876}, abstract = {BACKGROUND: Nutrition plays a central role in the biological mechanisms that shape aging, health span, and longevity. Micronutrients—including vitamins, trace elements, and polyphenols—support genomic stability, mitochondrial integrity, and antioxidant defense, while dietary patterns rich in plant-based foods modulate inflammation, metabolic regulation, and epigenetic processes. Centenarian populations consuming Mediterranean, Okinawan, Nordic, and Nicoyan diets offer a natural model for understanding how nutrient-rich, minimally processed foods, moderate caloric intake, and balanced lifestyles interact with molecular pathways to extend functional life.<br><br>MAIN BODY: This review synthesizes current evidence on how micronutrients influence DNA repair, oxidative stress reduction, and mitochondrial protection, particularly through the actions of vitamins C and E, niacin-dependent PARP activity, folate-mediated methylation, and metal cofactors involved in antioxidant enzymes. Plant-based diets rich in fiber and polyphenols enhance microbial diversity and promote beneficial taxa such as Akkermansia and Bifidobacterium, supporting gut barrier integrity and immune balance. Caloric restriction and intermittent fasting activate nutrient-sensing pathways, including AMPK and sirtuins, reduce mTOR activity, and stimulate autophagy, collectively improving cellular resilience. Findings from centenarian regions highlight the convergence of lifestyle, nutrition, and cultural practices that reduce systemic inflammation, maintain metabolic flexibility, and support healthy aging trajectories.<br><br>CONCLUSIONS: Diet emerges as a decisive modifiable determinant of lifespan and health span. The convergence of molecular nutrition, microbiome composition, and traditional dietary habits underlies the exceptional longevity observed in centenarian populations. Future research should integrate nutrigenomics, metabolomics, and microbiome profiling to clarify causal mechanisms and guide precision nutrition strategies for aging societies.}, }
@article {pmid41736911, year = {2025}, author = {Medeiros, MJ and Burger, AD and Price, DK and Yew, JY}, title = {Microbiome composition of Drosophila suzukii varies across geographical regions.}, journal = {Frontiers in ecology and evolution}, volume = {13}, number = {}, pages = {}, pmid = {41736911}, issn = {2296-701X}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; P20 GM139753/GM/NIGMS NIH HHS/United States ; }, abstract = {Drosophila suzukii is a common agricultural pest in numerous parts of the world, costing more than $500 million annually in crop loss in the United States alone. Understanding the genetic and physiological mechanisms underlying its remarkable adaptability has been a major focus for the agricultural industry as well as evolutionary biologists. The microbiome, the community of microbes associated with host organisms, can play a pivotal role in local adaptation by improving host resilience to environmental stress and providing access to new sources of nutrition. Here, we test the hypothesis that the colonization of nonnative regions is associated with the incorporation of regionally-specific microbial taxa. We compare the microbiome profiles of wild-caught D. suzukii across five global sites, Asia, Europe, the United Kingdom, North America, and Hawai'i. We also compare microbial communities of D. suzukii found in Hawai'i to another local invasive species, D. immigrans, and native Hawaiian drosophilids. Our results reveal that wild-caught D. suzukii from Asia, Europe, the United Kingdom, North America, and the Hawaiian Islands exhibit distinct microbial compositions indicating that the environment is a stronger driver of microbiome composition than species identity. Seven bacterial families were conserved between all wild D. suzukii populations. Within Hawai'i, non-native D. suzukii bacterial communities differed from those of native Hawaiian Drosophila species as well as non-native D. immigrans. By contrast, fungal microbiome profiles between the Hawaiian Drosophila and two invasive species closely resemble each other. In sum, all populations of D. suzukii in this study contain a subset of conserved bacterial families but also incorporate local bacterial taxa. This strategy may contribute to the rapid range expansion of D. suzukii and enhance its ability to exploit new dietary sources.}, }
@article {pmid41742931, year = {2024}, author = {El-Derby, AM and Schaaf, CR and Shelkey, E and Cook, KL and Votanopoulos, KI and Soker, S}, title = {Immune-reactive tumor organoids system to determine the effects of microbial metabolites on cancer immunity and immunotherapies.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {}, pmid = {41742931}, issn = {2813-4338}, abstract = {Immunotherapies are a revolutionary approach to treating cancer by utilizing the body's immune system to target and combat cancer cells. This approach offers promising alternatives to traditional chemotherapies. Its potential to induce long-lasting remissions and specificity for cancer cells, which minimizes side effects, makes it a cutting-edge treatment with tremendous potential. With the increase of the clinical usage of immunotherapy, evidence emerges of the microbiome's impact on both tumor growth and response to immunotherapy. The proposed involvement of the microbiome can change treatment efficacy by altering drug metabolism and reshaping the immune system response. Understanding the specific interactions between tumor cells, immune cells, and the microbiome is a critical step in the advancement of immunotherapy. To study the complex interaction between cancer immunity and the microbiome, various preclinical in vivo and in vitro models have been developed. We have recently described the use of an ex vivo preclinical model for anti-cancer treatment outcome prediction -tumor tissue equivalents (organoids). Specifically, immune-reactive tumor organoids are proposed as a novel tool for understanding how the microbiome influences cancer immunity and immunotherapy. More importantly, this platform can utilize patient samples to dissect patient-specific elements regulating cancer immune response and microbiome influence. This review presents the rationale for using the immune-reactive tumor organoids model to study the interactions between the microbiome and cancer immunotherapy. It will discuss available components of the model and analyze their interplay, summarize relevant experimental data, and assess their validity. Additionally, it explores the potential of immune-reactive organoids for personalized treatment approaches. Understanding the microbiome's role in immunotherapy outcomes will lead to transformative cancer treatment via a simple change of diet or other microbiome manipulations. Ongoing research on microbiome-cancer interactions utilizing the described model systems will lead to innovative treatment strategies and improved patient outcomes.}, }
@article {pmid41728621, year = {2026}, author = {Wu, M and Ding, J and Zhang, X}, title = {Neutrophil extracellular traps in gynecological disease: pathogenic mechanisms and therapeutic opportunities.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1710628}, pmid = {41728621}, issn = {2296-858X}, abstract = {Gynecologic disorders, including infections, sterile inflammatory diseases, endocrine abnormalities, and malignancies, share a common signature of dysregulated immunity within a uniquely hormone-responsive reproductive tract. Neutrophil extracellular traps (NETs) are increasingly recognized as central effectors at this interface of innate immunity, endocrine signaling, tissue remodeling, and thrombosis. In this review, we first outline the mechanistic basis of NET formation and emphasize how the cyclical anatomy, fluctuating sex hormones, and regional microbiota of the female reproductive tract shape NET induction, localization, and clearance. We then synthesize evidence across disease spectra. In infectious conditions such as pelvic inflammatory disease, genital tuberculosis, and vaginal dysbiosis, NETs confine pathogens but also drive epithelial injury, fibrosis, and infertility. In sterile inflammatory and endocrine-related disorders, including endometriosis, polycystic ovary syndrome, premature ovarian insufficiency, and primary dysmenorrhea, NET-associated oxidative stress, inflammasome activation, and profibrotic signaling link hormonal and metabolic imbalance to chronic pain and organ dysfunction. In gynecologic cancers, NETs promote tumor cell adhesion, invasion, immune escape, and thromboembolic complications within hormone-conditioned microenvironments, while circulating and tissue NET markers, as well as NET-related gene and lncRNA signatures, hold diagnostic and prognostic value. Finally, we discuss how biomaterial-based strategies in vaginal reconstruction exploit antimicrobial NET functions yet risk excessive fibrosis if NETs are not tightly controlled. Across these contexts, we highlight an emerging NET-sex hormone axis and propose endocrine-aware, biomarker-guided strategies that combine NET-targeting agents with hormonal and microbiome-based interventions to achieve more precise diagnosis, risk stratification, and therapy for gynecologic diseases.}, }
@article {pmid41728192, year = {2025}, author = {Kumar, N and Khatibi, SMH and Sharma, D and Azeem, F and Koutu, GK and Ali, J}, title = {Decrypting molecular mechanism of heat stress tolerance in rice to tackle climate change challenges through recent approaches.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1722694}, pmid = {41728192}, issn = {1664-462X}, abstract = {Rice (Oryza sativa) is one of the world's most important cereal crops, contributing to food and financial security, particularly in developing countries. High temperature due to climate change seriously threatens sustainable rice production. Rice crops are adversely affected by heat stress at the morphological, physiological, and molecular levels, resulting in reduced yield and poor grain quality. Rice is highly sensitive to heat during the reproductive phase, causing pollen sterility, impaired pollen dehiscence, pollen germination, and tube growth, ultimately drastically reducing spikelet sterility and yield. High temperature also promotes the accumulation of reactive oxygen species in plant cells, resulting in multiple adverse effects, including damage to chloroplasts and cell membranes, inactivation of photosystems, reduced Rubisco activity, and impaired production of photoassimilates. In this review, we have synthesized the current knowledge on the effects of heat stress on rice and summarized QTLs, genes, and regulatory pathways underlying thermotolerance. We further evaluate conventional breeding, transgenics, and diverse omics-based strategies to breed high-yielding, heat-tolerant rice varieties. The precise molecular insights gained through various omics approaches are expected to advance our understanding of the intricate nature of heat stress tolerance in rice. Additionally, we highlight the emerging roles of microbiome, high-throughput phenotyping technologies, and artificial intelligence as promising tools for accelerating the development of heat-resilient rice.}, }
@article {pmid41728113, year = {2026}, author = {Das, S and Clayton, JB and Sarkar, S}, title = {Editorial: Impact of oral and gut microbiome on health and diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1792511}, doi = {10.3389/fcimb.2026.1792511}, pmid = {41728113}, issn = {2235-2988}, }
@article {pmid41728109, year = {2026}, author = {Eom, JH and Cho, MY and Kim, JW and Kim, Y and Yang, SJ and Hwang, J and Lee, D and Kim, HS and Baek, H and Kim, YY}, title = {Peri-implantitis biofilm from explanted implants in Korean patients: microbial and functional profiling.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1768841}, pmid = {41728109}, issn = {2235-2988}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Peri-Implantitis/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Middle Aged ; *Dental Implants/microbiology ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Republic of Korea ; Microbiota ; Aged ; Adult ; DNA, Bacterial/genetics ; Dental Plaque/microbiology ; }, abstract = {Peri-implantitis is an inflammatory disease affecting tissues surrounding dental implants, with microbial biofilms recognized as the primary etiological factor. However, most previous studies analyzed samples from peri-implant pockets, and research on biofilms directly attached to explanted implant surfaces remains limited. This study compared the microbial composition and functional characteristics of biofilms from explanted implant surfaces in peri-implantitis cases with subgingival plaque from healthy controls. A total of 41 samples (peri-implantitis n=19, healthy controls n=22) were obtained from the Apple Tree Oral Biobank. The V3-V4 region of 16S rRNA gene was sequenced using Illumina MiSeq, ASVs were generated using DADA2, and taxonomic assignment was performed using SILVA database (v138.1). Alpha and beta diversity analyses were conducted, and functional potential was predicted using PICRUSt2. The peri-implantitis group showed significantly higher Simpson index (p=0.0086) and phylogenetic diversity (p<0.0001), with distinct clustering separation between groups. Beyond well-known periodontal pathogens (Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Filifactor alocis), the peri-implantitis group exhibited significant increases in sulfate-reducing bacteria (Desulfobulbus, Desulfovibrio) and emerging pathogens ([Eubacterium] nodatum group, [Eubacterium] saphenum group, Phocaeicola abscessus, Pseudoramibacter alactolyticus, Pyramidobacter). Health-associated bacteria (Corynebacterium, Neisseria, Capnocytophaga, Lautropia) were decreased. Functional analysis revealed enrichment in LPS biosynthesis, sulfur metabolism, iron acquisition, and amino acid degradation pathways, while carbohydrate metabolism was decreased. This study demonstrates that diverse emerging pathogens, including sulfate-reducing bacteria, are associated with peri-implantitis biofilms in explanted implant surface biofilms, contributing to expanded understanding of peri-implantitis etiology and development of candidate biomarkers.}, }
@article {pmid41728002, year = {2026}, author = {Canavera, G and Bellotti, G and Tiwari, H and Frioni, T and Puglisi, E}, title = {Drought-tolerant rhizobacterial consortia enhance grapevine growth and tolerance to water deficit.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1735733}, pmid = {41728002}, issn = {1664-462X}, abstract = {In both natural ecosystems and in agroecosystems, Plant Growth-Promoting Rhizobacteria (PGPR) significantly contribute to plant development and stress mitigation through diverse mechanisms. In recent times, their application as microbial biostimulants (MBs) has gained attention, particularly for alleviating drought stress, which increasingly threatens grapevine productivity in both modern and traditional wine-growing regions. Despite this interest, functionally validated and biosafe PGPR consortia specifically tailored for grapevine remain limited. This study isolated drought-tolerant PGPRs from grapevine rhizosphere cultivated under contrasting environmental conditions and experiencing midday leaf water potentials between -1.3 and -1.4 MPa. The isolates were ranked according to their Plant Growth-Promoting Traits (PGPTs), and whole-genome sequencing was performed on the nine most promising strains to evaluate their functional potential and biosafety. Such functional traits are known to influence plant performance, providing a conceptual basis for evaluating their effects on grapevine growth. Based on their complementary PGPT profiles and demonstrated compatibility, these strains were assembled into four bacterial consortia (BC1-BC4). The consortia were applied by root dipping and soil inoculation to one-year-old grapevines subjected to progressive drought stress, in order to assess their potential synergistic effects on plant growth. Treated vines were compared to a non-inoculated control (NI). Results indicate that while BC1 and BC2 did not significantly impact shoot growth, BC3 and partially also BC4 increased shoot length by 35.5% and 26.5%, respectively, compared to NI. Notably, BC3 enhanced shoot elongation during the early phase under well-watered conditions, whereas BC4 conferred greater benefits under water deficit. After five days of suspended irrigation, BC4-treated vines maintained higher photosynthetic activity and stomatal conductance compared to all other treatments, which, displayed almost complete stomatal closure. This response may be linked to the enrichment of indole-3-acetic acid-producing and exopolysaccharide-forming strains, which are known to modulate plant growth and water status. Finally, both BC3 and BC4 promoted greater root biomass by the end of the pot trial. Overall, the results highlight the potential of rationally tailored PGPR consortia to enhance grapevine growth under both optimal and drought conditions, supporting their application as context-specific MBs for sustainable viticulture.}, }
@article {pmid41728000, year = {2026}, author = {Yang, Y and Bian, Q and Feng, Y and Wang, Z and Fu, Y and Wei, Y and Zhu, J}, title = {Micro-nanobubble oxygenation irrigation ameliorates saline-alkali soil properties, cotton physiology, and yield under different salt stress levels.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1727907}, pmid = {41728000}, issn = {1664-462X}, abstract = {BACKGROUND: Addressing soil saline-alkalization is crucial for sustaining cotton production in the arid regions of Xinjiang. This study investigates the efficacy of Micro-Nanobubble oxygenated irrigation (MNBs) compared with conventional flooding (CF) in ameliorating saline-alkali soil and enhancing cotton growth.<br><br>METHODS: A field microplot experiment was conducted across four soil salinity levels (0, 3%, 6%, and 9%, with sulfate as the dominant salt).<br><br>RESULTS: The results demonstrated that MNBs effectively reduced topsoil (0~20 cm) salinity and mitigated its associated alkalinity stress by facilitating salt leaching into deeper soil layers (20~60 cm). This irrigation method also significantly improved soil enzyme activities and altered ionic dynamics toward a more favorable balance. Moreover, MNBs enhanced soil bacterial diversity, enriched beneficial phyla such as Proteobacteria and Actinobacteria, and modulated fungal genera including Alternaria and Fusarium, suggesting an improved rhizospheric microbiome. In terms of cotton physiology, Micro-nanobubble oxygenation irrigation significantly enhanced the activities of superoxide dismutase (SOD) and peroxidase (POD) in cotton leaves by 15.84% to 40.69% and 10.11% to 33.63%, respectively, while reducing malondialdehyde (MDA) content by 28.22% to 42.11%, thereby alleviating saline-alkali stress-induced oxidative damage. Additionally, MNBs promoted root growth by 0.96% to 29.90%, increased the leaf area index by 18.68% to 25.50%, and enhanced dry matter accumulation by 6.82% to 33.29%. Ultimately, these improvements led to a higher seed cotton yield. Compared with conventional flooding (CF), the MNBs treatment increased seed cotton yield by 33.78%, 35.93%, 47.11%, and 52.31% across the four salinity levels, respectively.<br><br>CONCLUSION: In conclusion, micro-nanobubble oxygenation irrigation represents an effective strategy for rehabilitating saline-alkali soils and promoting sustainable agricultural development in arid areas.}, }
@article {pmid41727994, year = {2026}, author = {Zhang, C and Wan, R and Nong, S and Huang, W and Al-Rejaie, SS and Wang, F and Yang, Z and Zhu, Z and Mohany, M}, title = {Deciphering the interplay between fruit-associated metabolites and bacterial communities across four distinct mango cultivars.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1754579}, pmid = {41727994}, issn = {1664-462X}, abstract = {Mango (Mangifera indica L.) fruit characteristics and health are strongly determined by their biochemical profiles and fruit-associated microbiome composition. However, the cultivar-specific interplay between the mango fruit metabolome and microbiome remains elusive. Here, we tracked differential changes in fruit metabolites and bacterial community composition in four economically important mango cultivars in China: Qingmang (QM), Yumang (YM), Tainong (TN), and Aomang (AM). Using untargeted metabolomics with liquid chromatography-mass spectrometry and high-throughput amplicon sequencing of bacterial 16S rRNA, we identified distinct metabolic profiles and the enrichment of a specific subset of microbiota unique to each cultivar. Different metabolites associated with nitrogen and carbon metabolism, biosynthesis of amino acids, secondary metabolites, and flavonoids were differentially abundant in the four mango cultivars. These classes of metabolites have been previously linked to fruit development, color, antioxidant capacity, and stress resistance. Importantly, significant positive correlations were found between specific bacterial taxa, such as Alcanivorax, Alistipes, Curtobacterium, Rikenella, Thiopseudomonas, Rikenella, and Vogesella and the accumulation of the metabolites ornithine, L-arginine, tricetin, casoxin D, mhppa sulfate, sorbitan palmitate, meconic acid and rengyoside B. These results indicate the critical role of mango cultivars in shaping the fruit-specific microbiomes and metabolites. Our findings provide a foundational understanding of mango fruit holobionts and offer novel insights into metabolic and microbial networks for developing strategies to enhance fruit quality and postharvest management.}, }
@article {pmid41727967, year = {2026}, author = {Duan, Y and Gu, Z and Liu, T and Song, C and Wang, Y and Wang, W and Jin, R and Wang, X and Zhang, Y and Huang, K}, title = {Effects of T2-high asthma heterogeneity and inhaled corticosteroid on airway and metabolic profiles: A multi-omic approach.}, journal = {Journal of translational internal medicine}, volume = {14}, number = {1}, pages = {79-95}, pmid = {41727967}, issn = {2450-131X}, abstract = {BACKGROUND AND OBJECTIVES: Asthma represents a heterogeneous chronic respiratory condition. Type 2 (T2) inflammation is the most crucial pathological event in asthma. In terms of whether T2 inflammation is dominant or not, asthma can be classified into T2-high and T2-low asthma. Currently, there exists a significant gap in our understanding of the heterogeneity of treatment-naive T2-high asthma patients. Moreover, no studies have examined the impacts of inhaled corticosteroids (ICS) on the airway microenvironment and metabolism of T2-high asthma during the early stage of treatment. This study, by employing multi-omic techniques, investigated the pathophysiological features and heterogeneity of untreated T2-high asthma, as well as the effects of ICS treatment. This study provided more in-depth insights into the pathophysiological mechanisms underlying T2-high asthma heterogeneity.<br><br>METHODS: Thirty-one treatment-naive T2-high asthma patients and fourteen healthy individuals were enrolled in this study. On the basis of hierarchical clustering analysis of T2 inflammation markers, fractional exhaled nitric oxide (FeNO) level and blood eosinophil count (BEC), the T2-high asthma patients were divided into three subgroups in terms of FeNO levels (&#x2264; 25 ppb, 26-50 ppb, and > 50 ppb). All asthma patients underwent asthma control scoring, pulmonary function tests, and FeNO measurement at baseline and during a regular 3-month follow-up. Induced sputum and plasma were collected. Other tests included 16S rRNA microbiome profiling of the induced sputum, Luminex xMAP immunoassays of cytokines, and plasma metabolomic analysis using Q-Exactive liquid chromatography-mass spectrometry (LC-MS/MS). Meanwhile, data from the healthy population were also harvested.<br><br>RESULTS: T2-high asthma patients differed significantly from healthy controls in terms of airway inflammatory cytokines, airway microbial community structure, and plasma metabolic profiles. At baseline, T2-high asthma patients with different FeNO levels exhibited remarkable similarities in clinical symptoms, pulmonary function indices, airway cytokines, airway microbial diversity, and metabolites. After treatment with ICS, symptoms improved in T2-high asthma patients. The levels of FeNO, blood eosinophils, and total immunoglobulin E (tIgE) decreased significantly, while pulmonary function did not show substantial improvement. Some indices of airway cytokines underwent changes. No differences were found in airway microbial diversity; however, the abundance of Actinomyces increased. Moreover, the levels of glycerophospholipids and arachidonic acid metabolites decreased. Differentially expressed metabolites were enriched in arachidonic acid metabolism. The effect of ICS treatment varied among different T2-high asthma subgroups.<br><br>CONCLUSIONS: The airway local microenvironment and systemic metabolic profiles of treatment-naive T2-high asthma patients were distinctly different from those of healthy individuals. Limited heterogeneity was observed among patients stratified in terms of T2-inflammatory burden. ICS altered the airway microenvironment and rectified the lipid/arachidonic acid metabolic dysregulation. However, ICS effects varied across various T2-high subgroups.}, }
@article {pmid41727680, year = {2026}, author = {Su, B and Cao, Y and Ma, L and Huang, J}, title = {BMI-stratified phenotypes of polycystic ovary syndrome: advances in gut microbiota research and personalized management strategies.}, journal = {Frontiers in endocrinology}, volume = {17}, number = {}, pages = {1734041}, pmid = {41727680}, issn = {1664-2392}, mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/therapy/pathology ; *Gastrointestinal Microbiome/physiology ; Female ; *Body Mass Index ; *Precision Medicine/methods ; *Obesity/complications/microbiology ; Phenotype ; Dysbiosis ; }, abstract = {Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine-metabolic disorder affecting 11%-13% of women of reproductive age. Based on body mass index (BMI), patients can be phenotypically classified into obese and non-obese subgroups: the obese PCOS is characterized by insulin resistance, hyperandrogenemia, and metabolic syndrome, with more pronounced metabolic risks; non-obese PCOS primarily manifests as reproductive endocrine dysfunction. In recent years, studies have shown that the Gut microbiota plays a key role in the pathogenesis of PCOS, and dysbiosis in the obese subgroup is generally more pronounced, potentially amplifying metabolic abnormalities through pathways such as short-chain fatty acids, bile acid disturbances, and endotoxin-related low-grade inflammation. This review systematically summarizes the clinically heterogeneous features of BMI-stratified PCOS and its gut microbiota characteristics, with a focus on elucidating the mechanistic differences between obese and non-obese individuals in terms of inflammation, metabolites, and endocrine regulatory pathways. Based on current evidence, individualized intervention strategies targeting different BMI subtypes are proposed, including dietary and lifestyle modifications, interventions with probiotics/prebiotics/synbiotics, and exploration of emerging precision microbiome therapies such as fecal microbiota transplantation. The interaction between BMI and gut microbiota provides new directions for stratified management and personalized treatment of PCOS; however, high-quality longitudinal and interventional studies are still needed to clarify causal relationships and optimize microbiota-targeted strategies.}, }
@article {pmid41727556, year = {2026}, author = {Millar, BC and Cates, MJ and Torrisi, MS and Round, AJ and Warde, A and Lowery, CJ and Moore, JE}, title = {Antimicrobial Resistance: The Answers.}, journal = {British journal of biomedical science}, volume = {83}, number = {}, pages = {15559}, pmid = {41727556}, issn = {2474-0896}, mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial ; COVID-19/epidemiology ; SARS-CoV-2 ; }, abstract = {Antimicrobial resistance (AMR) has caused a global public health crisis, contributing to approximately five million deaths in 2019 and predicted deaths of approximately ten million annually by 2050. This equates to approximately 1.4-fold more deaths annually from AMR in 2050 than the entire COVID-19 pandemic to date. To tackle this AMR pandemic, regulatory and policy frameworks have been prepared at local, national and international levels with multi-faceted proposals and advances encompassing surveillance, diagnostics, infection prevention, antibiotic prescribing and variation of existing and novel treatment approaches. This narrative review primarily focuses on research and development which have been documented over the last five years in relation to therapeutic approaches at various stages in clinical development and the potential role that vaccines can play in the fight against AMR. This review provides an overview on antibacterial drugs, including novel classes of antibiotics, which have been recently approved, as well as combination antibiotic therapy and the potential of repurposed drugs. The potential role of novel antimicrobial, antibiofilm and quorum sensing inhibitors, such as antimicrobial peptides, nanomaterials and compounds from the extreme and natural environments, as well as ethnopharmacology including the antimicrobial effects of plants, spices, honey and venoms are explored. Novel therapeutic approaches are critically discussed in terms of their realistic clinical potential, detailing recent and ongoing trials to highlight the current interest of these approaches, including immunotherapy, bacteriophage therapy, antimicrobial photodynamic therapy (aPDT), antimicrobial sonodynamic therapy (aSDT), nitric oxide therapy and microbiome manipulation including faecal microbiota transplantation (FMT). The potential of predatory bacteria as living antimicrobial agents is also discussed. Importantly, there have been many technological developments which have enhanced bioprospecting and research and development of novel antimicrobials which this review draws attention to, including artificial intelligence, machine learning and Organ-on-a-Chip devices. Finally, key messages from the recent World Health Organization report into the role of vaccines against AMR provides an interesting perspective relating to prevention which can be of significance in tackling the AMR burden.}, }
@article {pmid41727526, year = {2026}, author = {Kurucz, K and Philippe, C and Ábrahám, &#xc1; and Kratou, M and Piloto-Sardiñas, E and Obregon, D and Abuin-Denis, L and Kovács-Valasek, A and Cabezas-Cruz, A}, title = {Characterizing the Bacterial Microbiome of the Invasive Vector Aedes albopictus in Hungary: A Pilot Study Using Oxford Nanopore Sequencing.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {1956331}, pmid = {41727526}, issn = {1687-918X}, abstract = {Aedes albopictus has recently established self-sustaining populations in Hungary, but its microbiota-which may influence vector competence-remains poorly understood. We used Oxford Nanopore long-read sequencing for full-length 16S rRNA gene profiling of adult Ae. albopictus from two urban sites, Pécs and Barcs. Each location contributed 10 specimens, with contamination controls rigorously applied. Diversity metrics and co-occurrence network analyses were performed using QIIME2, SparCC, and NetCoMi, with robustness assessed via simulated node removal and addition. Sequencing depth was sufficient to saturate rarefaction curves. Although alpha and beta diversity did not differ significantly between sites, the Pécs population exhibited greater taxonomic richness (100 unique taxa vs. 61 in Barcs) and denser, more clustered networks. Only 15 genera were shared, with Wolbachia dominating both communities. Networks differed in central taxa and structural properties: Pécs retained higher connectivity and shorter paths under perturbation, suggesting greater resilience. Removal of conserved taxa revealed location-specific impacts on network stability, with Pécs more vulnerable to the loss of key genera. Negative interactions and compensatory taxa emerged post-removal, indicating distinct reconfiguration strategies. Our findings highlight marked local variation in microbiome structure and robustness, even across a 65-km gradient. These results establish a high-resolution baseline for assessing how microbiota shape Ae. albopictus vector potential, informing microbiome-based control strategies tailored to regional contexts.}, }
@article {pmid41727500, year = {2026}, author = {Han, CS}, title = {The microbial peace-signal hypothesis: distributed immune "peace hubs" across the human body.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1738273}, pmid = {41727500}, issn = {1664-3224}, mesh = {Humans ; *Fatty Acids, Volatile/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; *Microbiota/immunology ; *Immune System/immunology ; Skin/immunology/microbiology ; Homeostasis/immunology ; Animals ; Hypersensitivity/immunology ; }, abstract = {The human immune system depends on microbial partners to maintain restraint. Short-chain fatty acids (SCFAs), produced by anaerobic fermenters in the gut, mouth, and skin, act as biochemical "peace signals" that calm immune activation and promote tolerance. In this hypothesis, "peace signals" refer primarily to microbially derived SCFAs; additional microbial metabolites are discussed as possible but more speculative contributors to immune restraint. This Microbial Peace-Signal Hypothesis proposes that immune homeostasis is not a static legacy of early-life microbial exposure, but a continuous partnership with these commensal fermenters. Modern lifestyle factors-including excessive hygiene, antibiotics, and low-fiber diets-have collapsed the ecological niches that support SCFA-producing guilds. Their loss silences microbial peace signals and drives the epidemic rise of allergies and autoimmune diseases. Unlike the "hygiene" or "old friends" hypotheses, this framework positions microbial peacekeeping as a lifelong metabolic function. It predicts that restoring SCFA producers across all major surfaces-gut, oral, and skin-will reduce immune overactivation systemically. This hypothesis unites clinical, ecological, and evolutionary evidence, suggesting that maintaining distributed SCFA-producing microbiomes is the foundation of long-term immune peace.}, }
@article {pmid41727485, year = {2026}, author = {Lin, BS and Yin, MY and Xie, SA and Li, P and Li, X}, title = {Pleiotropic immunoregulation by bile acids in pathophysiology.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1719092}, pmid = {41727485}, issn = {1664-3224}, mesh = {Humans ; Animals ; *Bile Acids and Salts/metabolism/immunology ; Signal Transduction/immunology ; Adaptive Immunity ; Immunity, Innate ; *Immunomodulation ; Gastrointestinal Microbiome/immunology ; }, abstract = {Bile acids (BAs) have evolved from their classical role in lipid digestion to become central signaling molecules that integrate host metabolism, gut microbiota, and immune function. This review examines how diverse BAs regulate both innate and adaptive immunity through specific receptors-including farnesoid X receptor, Takeda G-protein-coupled receptor 5, vitamin D receptor, and retinoid orphan receptors-modulating the activity of macrophages, dendritic cells, T cells, natural killer cells, and natural killer T cells. Tissue-specific BA signaling influences immune homeostasis in the intestine, liver, central nervous system, and tumor microenvironment. Furthermore, we discuss the pathogenic role of dysregulated BA signaling in inflammatory, autoimmune, metabolic, and malignant diseases, and evaluate emerging therapeutic strategies that target BA pathways via synthetic ligands, engineered microbes, and dietary modulation. Leveraging BA-immune crosstalk to advance research on precision immunotherapy and microbiome-based interventions is a promising area of research.}, }
@article {pmid41727451, year = {2026}, author = {Yang, Y and Wang, G and Song, Y and Ma, J and Liu, A}, title = {Immunomodulatory effects of oral microbiota in the pathogenesis of rheumatoid arthritis.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1707949}, pmid = {41727451}, issn = {1664-3224}, mesh = {Humans ; *Arthritis, Rheumatoid/immunology/microbiology/etiology/therapy ; *Mouth/microbiology/immunology ; *Microbiota/immunology ; Dysbiosis/immunology ; Animals ; *Immunomodulation ; Periodontitis/immunology/microbiology ; }, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by persistent synovial inflammation, progressive cartilage and bone destruction, and resulting functional disability. Its pathogenesis is multifactorial, involving both genetic predisposition and environmental influences. In recent years, the interaction between the oral microbiota and RA has emerged as a prominent research focus. Dysbiosis of the oral microbiome, defined as an imbalance in microbial composition relative to a healthy state, accompanies disease onset and may further act as a trigger of systemic autoimmune responses. Specific virulence factors, including the peptidylarginine deiminase from Porphyromonas gingivalis and leukotoxin A from Aggregatibacter actinomycetemcomitans, promote excessive protein citrullination and anti-citrullinated protein antibody generation, thereby contributing to the loss of immune tolerance, particularly in genetically susceptible individuals. Moreover, the bidirectional relationship between RA and periodontitis highlights shared inflammatory pathways that contribute to both periodontal and joint tissue destruction. Potential mechanisms include bacteremia induced by routine oral activities, systemic dissemination of bacterial products, and colonization of oral microbiota in the gastrointestinal tract. Current evidence suggests that periodontal therapy may reduce systemic inflammatory markers and occasionally improve RA activity, although results remain inconsistent. In this review, we explored the potential mechanisms underlying the imbalance of the oral microbiota and its contribution to the onset and progression of RA, focusing on microbially induced citrullination, host genetic susceptibility, and common inflammatory pathways, while also discussing the impact of comprehensive periodontal management and lifestyle interventions on RA outcomes. Overall, these insights underscore the role of the oral microbiome in RA pathogenesis and suggest that addressing microbial dysbiosis through integrated therapeutic strategies may complement conventional care.}, }
@article {pmid41727385, year = {2026}, author = {Li, D and Zhao, T and Gong, X and Ahemaiti, Y and Wei, L and Huang, Y and Hu, S}, title = {Alterations in gut microbiota and plasma metabolites in pulmonary arterial hypertension secondary to congenital left-to-right shunt heart disease: potential mechanisms and biomarkers.}, journal = {Frontiers in genetics}, volume = {17}, number = {}, pages = {1699787}, pmid = {41727385}, issn = {1664-8021}, abstract = {INTRODUCTION: Pulmonary arterial hypertension (PAH) secondary to congenital left-to-right shunt heart disease (CL-RSHD) is a life-threatening complication with unclear microbial and metabolic mechanisms. This study investigated gut microbiota and plasma metabolic alterations in CL-RSHD-associated PAH to identify biomarkers and mechanistic pathways.<br><br>METHODS: This cross-sectional study included 86 participants: healthy controls (HC, n = 13), CL-RSHD (n = 46), and CL-RSHD + PAH (n = 27). Gut microbiota was analyzed using 16S rRNA gene sequencing of the V3-V4 region on 41 fecal samples (HC, n = 9; CL-RSHD, n = 15; and CL-RSHD + PAH, n = 17). Untargeted plasma metabolomics was analyzed on all 86 plasma samples. Microbial diversity, differential taxa (DESeq2), metabolic pathways (OPLS-DA, KEGG), and biomarker potential (ROC curves) were assessed. Dynamic correlations linked microbiota-metabolite interactions.<br><br>RESULTS: CL-RSHD + PAH patients showed preserved &#x3b1;/&#x3b2;-diversity but distinct taxonomic shifts: enriched Lachnoclostridium phocaeense (Firmicutes) and reduced SCFA-producing Anaerostipes. Metabolomics revealed dysregulated steroid biosynthesis, cortisol metabolism, and oxidative stress pathways. Key metabolites, including elevated 5-hydroxymethylcytidine (5-hmC) and &#x3b3;-L-glutamyl-L-cysteine, and reduced histidine intermediate D-E1IG3P, correlated with PAH severity. Strong microbiota-metabolite interactions (e.g., Lactonifactor-D-E1IG3P, r = 0.82, P < 0.01) suggested a disrupted vascular remodeling axis. Metabolites like ADP-glucose (AUC = 0.94) and 3-phenylpropyl glucosinolate (AUC = 0.92) showed high diagnostic accuracy.<br><br>CONCLUSION: CL-RSHD-associated PAH involves gut microbial restructuring and metabolic reprogramming linked to immune-inflammatory activation and oxidative stress. The Firmicutes-histidine metabolism axis emerges as a therapeutic target. Despite limitations, this study provides foundational insights into microbial-metabolic drivers of PAH, highlighting novel biomarkers for early diagnosis and intervention.}, }
@article {pmid41727357, year = {2026}, author = {He, JL and Ran, L and Xiao, X and Su, Y and Lin, H and Lu, C and Tang, B and Yang, S}, title = {Saccharomyces boulardii in patients with severe acute pancreatitis: a single center, open-label randomized controlled trial.}, journal = {Burns &amp; trauma}, volume = {14}, number = {}, pages = {tkag006}, pmid = {41727357}, issn = {2321-3868}, abstract = {BACKGROUND: Nosocomial infections in patients with severe acute pancreatitis (SAP) are frequently driven by impaired intestinal barrier function, which facilitates bacterial translocation and contributes to adverse clinical outcomes. Saccharomyces boulardii (S. boulardii) can reconstitute gut microbiota composition. We investigated whether S. boulardii combined with enteral nutrition (EN) affects the microbiome and nosocomial infections in SAP.<br><br>METHODS: This study is a single centre, open-label randomized controlled trial. We included 50 patients with SAP in a Chinese gastroenterology intensive care unit (ICU), randomized to Probiotic group (S. boulardii and EN) or the Control group (EN). Throat/oropharyngeal and rectal swabs were collected from patients with SAP on days 0, 1, 3, 6, 9, 12, and 15 of ICU admission. The primary endpoints were nosocomial infection and fungemia, whereas the secondary endpoints were ICU mortality, 28-day mortality, ICU stay, and length of hospital stay. All samples were subjected to full-length 16&#xa0;s rRNA and internal transcribed spacer (ITS) sequencing. Multivariate analysis was performed using normalized microbial and corresponding clinical data.<br><br>RESULTS: After data processing, 213 16S rRNA and 120 ITS samples were analysed. S. boulardii prevented nosocomial infections (0/27 in the Probiotic group vs 5/23 in the Control group; P&#xa0;<&#x2009;0.05). Intestinal fungi were closely associated with nosocomial infections. Bioinformatic analysis showed that S. boulardii prevented nosocomial infections by reducing intestinal bacterial perturbation and inhibiting the proliferation of Enterococcus in the intestine, and Candida in the respiratory tract and intestines.<br><br>CONCLUSIONS: S. boulardii in patients with SAP may positively alter the respiratory and intestinal microbiome and decrease the incidence of nosocomial infections.<br><br>TRIAL REGISTRATION: This study was approved by the Ethics Committee of Xinqiao Hospital, Army Medical University, Chongqing China (2021-yd030-01), which was retrospectively registered at the Chinese Clinical Trial Registry (ChiCTR2200056011, Date of Registration: 30/01/2022 https://www.chictr.org.cn/showproj.html?proj=151215).}, }
@article {pmid41727208, year = {2026}, author = {Zhao, Y and Li, R and Zhu, T and Hu, H and An, G and Ren, Z and Cui, J and Jiang, J}, title = {Latilactobacillus sakei strains protect crucian carp against Aeromonas hydrophila-induced intestinal injury in an oral challenge model.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1768111}, pmid = {41727208}, issn = {2296-861X}, abstract = {In aquaculture, the overuse of antibiotic could lead to antimicrobial resistance and destabilize host-microbiota homeostasis. Latilactobacillus sakei, belonging to the genus Latilactobacillus, was included in the list of bacteria that could be used in food in China in 2014. Increasing evidence demonstrated that its antagonistic capacity against a broad spectrum of pathogenic bacteria, indicating its promising potential for application in aquaculture. In this study, the protective effect of three L. sakei (JO12, JO26, JO35), isolated from the intestine of fish and shrimp, on mucosal injury caused by Aeromonas hydrophila in crucian carp under an oral challenge model was investigated. The result showed that compared with LGG, all three L. sakei strains alleviated A. hydrophila induced intestinal barrier damage and inflammation (downregulated intestinal TNF-α/IL-1β, upregulated IL-10, and reduced MyD88) in crucian carp. L. sakei JO35 delivered the greatest improvement in growth and feed efficiency. Compared with the model group, L. sakei JO26 and JO35 significantly decreased the levels of serum acid phosphatase (ACP) and increased intestinal lysozyme, whereas L. sakei JO12 lowerd serum ACP but exacerbated the elevation of intestinal AKP. Microbiome and transcriptome analysis revealed that the protective effect of L. sakei may be associated with the strain's intestinal colonization capacity and its regulation of phagolysosomal competence (lysosome/phagosome, LAMP) and IgA barrier via pIgR (prominent with JO35).}, }
@article {pmid41727154, year = {2026}, author = {Hoza-Frederick, E and Martínez-Campos, S and Barber, PH and Vasquez, MI and Fotopoulos, V and Antoniou, C and Drakou, K and Godoy-Vitorino, F and Chiquillo, KL}, title = {Better together: Microbial diversity might facilitate the invasion success of the seagrass Halophila stipulacea in mixed Mediterranean seagrass communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.09.704841}, pmid = {41727154}, issn = {2692-8205}, abstract = {Microorganisms are increasingly recognized as key facilitators of invasion success for introduced species into new environments. The globally invasive seagrass Halophila stipulacea flourishes in mixed environments with native seagrasses, where it exhibits enhanced growth, while, in contrast, native seagrasses in mixed environments experience reduced growth. Here, we hypothesize that microbes may support the success of invasive seagrass in mixed Mediterranean environments. We analyzed 16S rRNA genes to characterize the microbial diversity on the phyllosphere alongside biochemical, morphological, and sediment nutrient measurements of the Mediterranean-native seagrass Cymodocea nodosa and the invasive H. stipulacea from a controlled mesocosm experiment. Overall, C. nodosa in monoculture harbored a microbiome exhibiting higher ASV richness and a distinct community composition than H. stipulacea . Variation in bacterial diversity associated with hydrogen peroxide (H 2 O 2) and internode length suggests that microbial communities of the native seagrass might be shaped by its stress. Conversely, H. stipulacea's microbiome was most abundant in mixed environments, with bacteria significantly reduced in monoculture, and bacterial diversity loosely associated with growth, suggesting that microbes are critical to assisting and possibly facilitating H. stipulacea in mixed environments. Overall, our findings suggest that invasive H. stipulacea in the Mediterranean Sea are capable of recruiting beneficial bacteria, creating microbial interactions that support its success, and undermining the resilience of native seagrasses in mixed beds. Future work should center on the mechanisms driving H. stipulacea bacterial communities and investigating whether H. stipulacea actively determines its own microbiome, or whether its microbiome is passively determined by environmental variables.}, }
@article {pmid41727025, year = {2026}, author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YP}, title = {Alamandine/MrgD Pathway Modulates Gut-Bone Marrow Axis in Aging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.12.705187}, pmid = {41727025}, issn = {2692-8205}, abstract = {Aging is associated with colon epithelial barrier integrity and upregulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in aging via modulating gut-BM axis. Mice of age 2-3 (Young) or 22-24 months (Old) were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated by using FITC-dextran. Lgr5 [+] Olfm4 [+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Fecal microbiome was analyzed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Cecal or serum bacterial metabolites were analyzed. The pro-myelopoietic potential of cecal supernatants (CS) was tested in the Young-BM cells. MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in aging was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels that were antagonized by the NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the aging microbiome and decreased Bacillota / Bacteroidota . Ala decreased the CD80 [+] and increased CX3CR [+] cells in the Old colons. Old-CS induced myelopoiesis in vitro in BM cells with higher number of monocytes and pro-inflammatory macrophages which was not observed in the CS derived from Ala-treated Old mice. Ala is a promising pharmacological agent for reversing the leaky gut of aging by restoring homeostasis in the gut-BM axis.}, }
@article {pmid41727000, year = {2026}, author = {Gasperini, C and Holton, KM and Limone, F and Juttu, M and DeMeo, CC and Kekrtova, K and Patankar, S and Wells, KM and Giadone, RM and Driss, LB and Wei, G and Kiem, A and Xu, Q and Lee, RT and Friedlander, M and Scadden, DT and Rubin, LL}, title = {Microbiome depletion rejuvenates the aging brain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.13.705770}, pmid = {41727000}, issn = {2692-8205}, abstract = {Aging is associated with cognitive decline and increased vulnerability to neurodegeneration driven by an array of molecular and cellular changes like impaired vascular integrity, demyelination, reduced neurogenesis, and chronic inflammation. Recent studies implicate the gut microbiome as a modulator of brain aging, but the underlying mechanisms remain elusive. Here, we show that depleting the gut microbiome by administering antibiotics to aged mice induces widespread molecular and structural rejuvenation in the brain. Our transcriptomic analyses by single-nucleus RNA sequencing revealed pronounced transcriptional shifts across multiple brain cell types. We confirmed that antibiotic treatment improves vascular density, promotes myelination, enhances neurogenesis, and reduces microglial reactivity. Functionally, microbiome-depleted mice showed improved hippocampal memory performance. Analyses of brain and plasma cytokine levels showed a decrease in several pro-inflammatory factors post-treatment and identified candidate factors, including the chemokine eotaxin-1. Inhibiting eotaxin-1 alone can reverse several aspects of brain aging. Our findings demonstrate that age-associated microbial inflammation contributes to brain aging and that its attenuation can restore youthful features at the molecular, cellular, and functional levels. Targeting the gut microbiome or its circulating mediators may therefore represent a non-invasive approach to promote brain health and cognitive resilience in aging.}, }
@article {pmid41726932, year = {2026}, author = {Montes, A and Klopmanbaerselman, D and Lee, B and Quiñones, B and Shim, H}, title = {Temporal dynamics of microbiome communities within urban compost piles undergoing the heat process.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.10.705224}, pmid = {41726932}, issn = {2692-8205}, abstract = {Urban composting supports soil health but also intersects with food safety, where compost is produced near farms and communities. Here, we profiled temporal microbiome dynamics across a 6-week heat compost cycle from the urban compost piles using paired physicochemical panels and long-read metagenomics. Nutrient composition and pH shifted with compost age, coinciding with stage-structured microbial succession, including temperature-linked turnover of compost communities from mesophilic to thermotolerant taxa. Bacterial profiles included the presence of antimicrobial resistance genes and foodborne-associated genera early in the cycle, with reduced representation during the thermophilic phase. Analysis of previously unclassified long reads reveals an extensive repertoire of putative bacteriophages, including several complete genomes and candidates linked to foodborne bacteria, and their abundance is coupled to the host abundance. Together, these results support thermophilic composting as a key mitigation step for microbiological hazards in urban-adjacent systems and identify compost piles as a promising reservoir for discovering candidate lytic phages for downstream isolation and host-range testing.}, }
@article {pmid41726906, year = {2026}, author = {Nicola, T and Madhvacharyula, T and Ashok, A and Mandot, A and Abdelgawad, I and Singh, R and Siedman, K and Yang, Y and Ambalavanan, N and Lal, CV}, title = {Functional Equivalence of Heat-Inactivated (HI) and Live Probiotic RSB11 in Suppressing Inflammation: Expanding Formulation and Application Potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.11.705228}, pmid = {41726906}, issn = {2692-8205}, abstract = {UNLABELLED: The clinical potential of probiotics has been widely recognized, but their translation into reliable therapeutic products has been hindered by major limitations such as undesirable immunogenic responses, the need to maintain viability, instability during storage and transport, and concerns regarding safety in vulnerable populations. Postbiotics, defined as inanimate microbial cells or their components with pro-health activities, overcome many of these limitations by offering enhanced stability, reproducibility, and safety. However, it is very vital to understand if the heat inactivation (conversion of a probiotic to its postbiotic inert form) compromise its functional efficacy. Here, we systematically compared a novel probiotic-derived candidate, Lactiplantibacillus plantarum RSB11 strain, in its live (RSB11 Life, probiotic) and heat-inactivated (RSB11-HI, postbiotic) forms across multiple human epithelial and non-epithelial models relevant to inflammation driven pathologies. To investigate the gut-tissue(s)-axis concept we used gut (Caco-2), lung (HBE), ovary (BG1), bone (osteoblasts, MG-63), kidney (A-498) and liver (HepG2) cells exposed to E-coli or lipopolysaccharide (LPS), and quantified matrix metalloproteinase-9 (MMP-9), an inflammatory mediator, by qPCR and pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α), IL-6, and IL-1β by ELISA. In addition, we assessed β-glucuronidase activity and estrogen modulation to explore gut-ovarian axis signaling. Across all models, both RSB11 Life and RSB11-HI robustly suppressed MMP-9, TNF-α, IL-6 and IL-1β induction, with equivalent magnitude of effect. The inactivated form retained full cytokine-suppressive capacity and, notably, enhanced β-glucuronidase activity, suggesting additional benefits in microbiome hormone cross-talk. Our findings demonstrate that heat inactivation does not compromise, and may even expand, the functional range of RSB11. By maintaining bioactivity while eliminating the drawbacks of live biotics, heat inactivated RSB11 emerges as a robust, scalable, and versatile postbiotic with potential applications in systemic inflammatory disorders.<br><br>Heat-inactivated postbiotic RSB11-HI retains the anti-inflammatory efficacy of its live counterpart (RSB11Life) across diverse organ-relevant cell models. Upon LPS or E-coli stimulation, epithelial, immune, and tissue-specific cells (gut, lung, ovary, bone, kidney, liver) upregulate pro-inflammatory mediators including MMP-9, TNF-&#x3b1;, IL-6, and IL-1&#x3b2;. Both RSB11Life and RSB11-HI effectively suppress these inflammatory responses, with RSB11-HI exhibiting more consistent and robust reductions of inflammatory markers across models. Additionally, RSB11-HI uniquely enhances &#x3b2;-glucuronidase activity, facilitating estrogen metabolism and signaling through the gut-ovary axis. Together, these findings highlight RSB11-HI as a stable, safe, and multifunctional postbiotic candidate suitable for therapeutic formulation. Image was designed using ChatGPT .}, }
@article {pmid41726584, year = {2026}, author = {Xie, G and Zhou, Q and Liao, J and Zheng, Y and Wang, W and Shen, K}, title = {The ketogenic diet alters microbiome-metabolome profiles to improve West syndrome therapy.}, journal = {Pediatric investigation}, volume = {10}, number = {1}, pages = {10-24}, pmid = {41726584}, issn = {2574-2272}, abstract = {IMPORTANCE: The ketogenic diet (KD) is effective in managing epilepsy, particularly West syndrome (WS); however, the role of gut microbiome (GM) and metabolome in its efficacy remains unclear. Understanding these mechanisms could optimize the KD for WS treatment.<br><br>OBJECTIVE: To identify microbiome-metabolome signatures associated with KD efficacy in WS by analyzing changes in GM composition and metabolic pathways.<br><br>METHODS: Fecal samples were collected from WS patients (n = 16) and healthy children (n = 24). Metagenome and metabolome analyses were performed to assess GM composition and metabolic profiles.<br><br>RESULTS: WS patients showed GM imbalances compared to healthy children. Disease status contributed sufficiently to the GM. The abundance of Bacteroides, Parabacteroides, and Faecalibacterium was lower in WS (3.30% vs. 39.86%, P-adj = 0.140; 0.14% vs. 0.73%, P-adj = 0.023; 0.04% vs. 1.35%, P-adj = 0.018), whereas Bifidobacterium and Escherichia were higher (6.08% vs. 2.23%, P-adj = 0.140; 7.57% vs. 0.15%, P-adj < 0.001). After KD, Parabacteroides (particularly P. distasonis) and Bacteroides (particularly B. fragilis) increased (0.14% vs. 0.35%, P-adj = 0.034; 3.30% vs. 21.18%, P-adj = 0.380); Bifidobacterium (particularly B. breve) and Escherichia (particularly E. coli) decreased from 6.08% and 7.57% to 1.24% and 2.52%, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that ATP-binding cassette (ABC) transporters, fatty acid biosynthesis, tyrosine metabolism, and other pathways were significantly altered in patients with WS, and these alterations were reversed following ketogenic diet (KD) consumption. The KD also altered intestinal metabolites. Integrative analysis of microbial features, gene functions, and metabolites revealed that Bacteroides species and P. distasonis were significantly associated with ABC transporters, alanine aspartate and glutamate metabolism, and negatively correlated with 3-sulfinoalanine, suggesting potential regulatory roles in metabolic pathways.<br><br>INTERPRETATION: KD induces significant shifts in GM composition and metabolic pathways, which may contribute to its therapeutic efficacy in WS. The restoration of Bacteroides and Parabacteroides dominance, alongside alterations in gene functions and neurotransmitter-related metabolites, suggests a potential mechanism for the antiepileptic effects of KD.}, }
@article {pmid41726575, year = {2026}, author = {Mahoney, DE and Chalise, P and Pei, D and Griffard-Smith, R and Home, T and Pathak, HB and Umar, S and Godwin, AK}, title = {Distinguishing the significance of blood microbes in epithelial ovarian cancer.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {}, pmid = {41726575}, issn = {2993-3935}, support = {P20 GM130423/GM/NIGMS NIH HHS/United States ; R01 CA260132/CA/NCI NIH HHS/United States ; }, abstract = {The human microbiome has generated growing interest in epithelial ovarian cancer (EOC) research, yet investigations of the blood microbiome remain sparse. This study explored plasma microbial signatures unique to EOC. We accessed 180 age/race/ethnicity-matched archival plasma samples from women with (1) EOC; (2) commonly diagnosed non-EOC solid tumors in women; (3) benign gynecologic conditions; and (4) age/race/ethnicity-matched controls. The microbial profiles of the plasma specimens were assessed using an amplicon-based sequencing method that targets the 16S rRNA gene in the bacterial genome. A stringent bioinformatic pipeline was applied to filter out suspicious bacterial contaminants at the genus level. Bioinformatic decontamination analysis removed 225 high-risk bacterial contaminants. The remaining 339 high-confidence bacteria were included in the final analysis for differential abundances in the plasma between the study groups. Women with EOC, which were primarily of the high-grade serous ovarian carcinoma histologic subtype, had significantly distinct differential abundances of the genera Brevibacterium (p < 0.001), Chloronema (p < 0.001), Facklamia (p < 0.001), Sutterella (p < 0.001), and Zymomonas (p < 0.001) when compared to the other study groups. These results suggest that plasma EOC-associated bacteria could be further exploited in follow-up studies to validate clinical applicability in disease screening, diagnostics, and risk stratification.}, }
@article {pmid41726000, year = {2025}, author = {Huang, N and Guan, Y}, title = {Pre-treatment endocrine-nutritional signatures predict clinical benefit from PD-1/PD-L1 blockade in hematologic malignancies.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1753660}, pmid = {41726000}, issn = {2296-861X}, abstract = {Hematologic malignancies pose significant global health burdens, with programmed cell death protein-1 (PD-1)/programmed cell death ligand 1 (PD-L1) inhibitors revolutionizing treatment in subtypes like classical Hodgkin lymphoma (cHL) and primary mediastinal large B-cell lymphoma (PMBCL), achieving high objective response rates (ORR). However, efficacy varies widely, with limited success in multiple myeloma (< 10% ORR) and leukemias, underscoring the need for better predictors beyond tumor-intrinsic biomarkers. This review highlights pre-treatment endocrine-nutritional signatures as key host factors influencing immunotherapy outcomes. Dysregulated hormones (cortisol, thyroid, sex steroids, insulin/insulin-like growth factor-1, adipokines) and nutritional status (vitamin D, zinc, protein-energy malnutrition, iron metabolism) modulate T-cell exhaustion, myeloid suppression, and tumor microenvironment dynamics, often leading to resistance. Evidence from cohorts shows hypercortisolism, hypothyroidism, insulin resistance, vitamin D deficiency, and hypoalbuminemia correlate with inferior ORR, progression-free survival, and overall survival, while thyroid immune-related adverse events and moderate obesity predict benefit. In hematologic contexts, marrow infiltration exacerbates these imbalances, explaining heterogeneous responses. Integrated signatures (e.g., Glasgow Prognostic Score, Prognostic Nutritional Index) offer superior prognostic value, enabling targeted interventions like vitamin D supplementation, metformin, or nutritional support to enhance immune checkpoint inhibitor efficacy. Mechanistic insights reveal convergence on mTOR/IFN-γ pathways and microbiome modulation. Translating these to clinical panels could personalize immunotherapy, addressing gaps in hematologic malignancies literature and improving outcomes in relapsed/refractory settings.}, }
@article {pmid41725847, year = {2026}, author = {Liu, G and Chen, L and Guan, M and Xiao, N}, title = {Global trends and future perspectives in autism spectrum disorder and gut microbiota research: a comprehensive bibliometric analysis.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1607951}, pmid = {41725847}, issn = {1662-4548}, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition. Increasing studies examine whether gut microbiota alterations and the gut-brain axis are linked to ASD-relevant phenotypes. As the literature expands rapidly, a quantitative mapping is needed to clarify influential work and evolving themes.<br><br>OBJECTIVE: To map global research on ASD and the gut microbiota, identify major contributors and knowledge bases, and characterize thematic evolution and emerging fronts.<br><br>METHODS: We analyzed 1,391 English-language articles and reviews indexed in the Web of Science Core Collection (1999-2024). CiteSpace, VOSviewer, and R were used to evaluate publication trends, collaboration networks, co-citation structure, keyword clustering, and burst detection.<br><br>RESULTS: Publication output increased slowly before 2010 and accelerated after 2018. The United States and China were leading contributors and key collaboration hubs. The co-citation core was anchored by landmark experimental and translational studies, including work on microbiome-to-behavior links and microbiome-targeted interventions. Keyword clustering and timeline views highlighted three prominent thematic directions: fecal microbiota transplantation, Rett syndrome, and maternal immune activation. Recurrent and burst keywords emphasized the gut-brain axis, short-chain fatty acids, gastrointestinal symptoms, and oxidative stress. Recent burst terms, including obesity, major depressive disorder, and glutamate, suggest increasing connections to metabolic and broader psychiatric dimensions.<br><br>CONCLUSION: ASD-microbiome research has shifted from descriptive comparisons toward mechanism-oriented and intervention-relevant questions. Future progress will benefit from standardized protocols, longitudinal designs, and multi-omics integration, together with rigorously designed trials to evaluate microbiome-targeted strategies.}, }
@article {pmid41725807, year = {2026}, author = {Guan, X and Bai, J and Yuan, XZ and Guo, JW and Liu, X}, title = {Synergistic remediation of Pb contamination in rice field soil with FeMg-LDH@Bentonite and compost: impacts on Pb bioavailability and soil environment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1756444}, pmid = {41725807}, issn = {1664-302X}, abstract = {INTRODUCTION: Lead (Pb) contamination in paddy soils can degrade soil quality, increase plant Pb uptake, and disrupt soil microbial communities. This study evaluated integrated remediation using FeMg-LDH@Bentonite (FMLB) and compost, focusing on Pb bioavailability, plant uptake, and microbial community structure.<br><br>METHODS: A pot-based remediation experiment was conducted using Pb-contaminated paddy soil. FMLB and compost were applied at different mixing ratios. Pb bioavailability and soil Pb levels were assessed alongside plant uptake indicators. Soil microbial community structure and alpha-diversity were characterized (e.g., by 16S rRNA gene amplicon sequencing), and soil enzyme activities were measured to reflect soil biological functioning.<br><br>RESULTS: Pb contamination significantly altered soil properties, reduced soil quality, and impacted microbial diversity. Amendment application reduced Pb bioavailability across treatments, with the greatest reduction observed for the combined treatment of FMLB:compost = 3:7. This optimal combination not only decreased Pb concentrations and plant uptake potential, but also improved microbial indicators: bacterial community composition and &#x3b1;-diversity metrics shifted toward the original soil (OS) reference under identical pot conditions, and enzyme activities were enhanced.<br><br>DISCUSSION: Overall, combined application of FMLB and compost represents an environmentally sound and potentially cost-effective strategy for remediating Pb-contaminated paddy soils while improving soil fertility and microbial function. Importantly, microbiome responses and selected enzyme endpoints are interpreted as indicators associated with Pb stabilization and improved soil condition, rather than direct evidence of microbially mediated Pb transformation.}, }
@article {pmid41725587, year = {2026}, author = {Cui, C and Zhang, B and Tang, J and Hou, J and Qiu, Y and Gao, K and Wang, L and Jiang, Z and Yang, X}, title = {Glucuronolactone Promotes Mucin Sulfation to Alleviate Deoxynivalenol-Induced Intestinal Injury via Microbiota-Dependent and -Independent AHR Activation.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e22912}, doi = {10.1002/advs.202522912}, pmid = {41725587}, issn = {2198-3844}, support = {2021YFD1300402//National Key R&amp;D Program of China/ ; 2025A1515012362//Guangdong Basic and Applied Basic Research Foundation/ ; 2024CXTD14 2024CXTD22//Modern Agricultural Industrial Technology System Innovation Team of Guangdong Province/ ; R2023PY-JG013 R2020PY-JX007//Special Fund for Scientific Innovation Strategy-construction of High-Level Academy of Agriculture Science/ ; CARS-35//Earmarked Fund for China Agriculture Research System/ ; }, abstract = {Deoxynivalenol (DON), a prevalent trichothecene mycotoxin, poses a global threat to the gut health of both humans and livestock. This study investigates the protective effects and underlying mechanisms of glucuronolactone (GLU) against DON-induced intestinal injury. In a piglet model, GLU effectively alleviated DON-induced intestinal injury and inflammation. Transcriptomic analysis revealed that GLU promotes mucin sulfation, a critical process for fortifying the intestinal mucus barrier. On the one hand, integrated microbiome and metabolomics analyses uncovered that GLU increased probiotic Lactobacillus amylovorus abundance and luminal indole-3-acetic acid level, thereby facilitating mucin sulfation. On the other hand, GLU itself directly boosted mucin sulfation in a microbiota-independent manner. Mechanistically, both the microbiota-dependent and -independent pathways through which GLU promoted mucin sulfation converged on the activation of aryl hydrocarbon receptor (AHR). Activated AHR transcriptionally up-regulated the expression of the sulfotransferase GAL3ST3, which drove mucin sulfation. This study identifies GLU as a promising nutritional intervention against DON-induced intestinal injury and reveals AHR-mediated mucin sulfation as a vital mechanism for maintaining intestinal barrier homeostasis.}, }
@article {pmid41725434, year = {2026}, author = {Rashid, H}, title = {Commentary on Gut Microbiome-Metabolome Alterations in Advanced Parkinson's Disease With Motor Complications.}, journal = {CNS neuroscience &amp; therapeutics}, volume = {32}, number = {2}, pages = {e70789}, doi = {10.1002/cns.70789}, pmid = {41725434}, issn = {1755-5949}, }
@article {pmid41725112, year = {2026}, author = {Maaskant, A and van Geijlswijk, IM and Devreese, M and Cherlet, M and van Geest, LF and Wagenaar, JA and Langermans, JAM and Zomer, AL and Bakker, J and Gehring, R}, title = {Pharmacokinetics of Long-Acting Ampicillin and Its Impact on the Gut Microbiome and Resistome in Rhesus Macaques (Macaca mulatta).}, journal = {Journal of veterinary pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/jvp.70055}, pmid = {41725112}, issn = {1365-2885}, abstract = {Injectable antimicrobials with documented prolonged dosing intervals (> 48 h) for use in rhesus macaques are sparse. The objective of our study was to assess the pharmacokinetics, urine excretion, and effects on gut microbiome and resistome of intramuscular administered long-acting formulation of ampicillin (Albipen LA) in macaques. Four female rhesus macaques (Macaca mulatta) were administered intramuscularly 25 mg/kg anhydrous ampicillin (AMP-LA). Serial plasma samples were collected over a 72 h period and urine samples were collected over a 150 h period. Rectal swabs were collected over a 180-day period for microbiome and resistome analysis. Both plasma and urine samples were analyzed with ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The pharmacokinetic parameters for AMP-LA ranged as follows: Cmax 1.3-10.3 μg/mL, T1/2 5.5-10.6 h, AUC0-∞ 52.5-135.4 μg h/mL. Post-administration, alpha diversity significantly decreased on Day 2 and maintained reduced up till Day 14. Sequence depth of beta-lactam resistance genes significantly increased on Day 2 after administration and then declined until Day 90. A dose of 25 mg/kg AMP-LA administered intramuscularly maintains a plasma concentration ≥ 0.25 μg/mL for up to 48 h. Therefore, administration of AMP-LA could be an effective treatment with a prolonged treatment interval for relevant organisms with short lasting effects on the intestinal microbiome and resistome.}, }
@article {pmid41725055, year = {2026}, author = {Ganamurali, N and Sabarathinam, S}, title = {Prostaglandin E2-EP4 Signaling at the Gut-Immune-Metabolic Interface: A Lipid Mediator Perspective on Obesity and Insulin Resistance.}, journal = {Comprehensive Physiology}, volume = {16}, number = {1}, pages = {e70099}, doi = {10.1002/cph4.70099}, pmid = {41725055}, issn = {2040-4603}, mesh = {Humans ; *Obesity/metabolism/immunology ; *Insulin Resistance/physiology ; Animals ; *Receptors, Prostaglandin E, EP4 Subtype/metabolism ; Signal Transduction/physiology ; Gastrointestinal Microbiome/physiology ; *Dinoprostone/metabolism ; }, abstract = {Despite advances in dietary and pharmacologic therapies, obesity rates continue to escalate globally. Emerging evidence implicates the gut-immune interface as a key determinant of metabolic dysfunction. This review highlights the prostaglandin E2 (PGE2) EP4 signaling axis as a pivotal mediator linking gut dysbiosis to systemic insulin resistance. In obesity, elevated COX-2-derived PGE2 reprograms the gut microbiota, depleting short-chain fatty acid (SCFA)-producing taxa and reducing regulatory T cell (Treg) homeostasis. The ensuing loss of intestinal integrity promotes metabolic endotoxemia and chronic low-grade inflammation, culminating in insulin resistance. Targeting the PGE2-EP4 microbiota Treg network through EP4 antagonists or microbiome restoration offers a promising therapeutic strategy to restore metabolic balance and prevent obesity associated complications.}, }
@article {pmid41725015, year = {2026}, author = {Wang, R and Wang, Z and Liao, W and Wang, T and Su, Y}, title = {Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02334-8}, pmid = {41725015}, issn = {2049-2618}, support = {31872670//National Natural Science Foundation of China/ ; 2021A1515010911//Guangdong Basic and Applied Basic Research Foundation/ ; 202206010107//Science and Technology Projects in Guangzhou/ ; JCYJ20210324141000001//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; }, abstract = {BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses.<br><br>RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH&#x2084;&#x207a; into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation.<br><br>CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.}, }
@article {pmid41725012, year = {2026}, author = {Ramírez, AL and Páez, L and Vega, L and Aya, V and Hernández, C and Luna, N and Muñoz, M and Patiño, LH and Ramírez, JD}, title = {Metagenomic analysis of the human gut virome reveals functional signatures and viral stability across hospitalized and non-hospitalized diarrheal and non-diarrheal individuals.}, journal = {Gut pathogens}, volume = {18}, number = {1}, pages = {}, pmid = {41725012}, issn = {1757-4749}, abstract = {BACKGROUND: The human gut virome is a fundamental yet understudied component of the intestinal microbiome. However, its taxonomic composition and functional potential in Latin American populations remain poorly understood, particularly under clinical stressors such as hospitalization and diarrhea conditions often linked to microbial dysbiosis.<br><br>METHODS: We conducted a hybrid metagenomic analysis of the human gut virome from 37 fecal samples: 10 from patients admitted to intensive care units (ICU), 13 from hospitalized patients outside the ICU (Non-ICU), and 14 from non-diarrheic individuals, including taxonomic and functional profiling of viruses and detection of viral auxiliary metabolic genes (vAMGs).<br><br>RESULTS: We identified 494 high-quality viral vOTUs, from which 37,619 ORFs were predicted. Taxonomically, Caudoviricetes and Intestiviridae were consistently present across all groups, supporting their role as part of a conserved core virome. Functionally, we identified 309 putative vAMGs spanning 90 functional categories, primarily related to metabolism and environmental information processing. Non-diarrheic individuals harbored a higher number and diversity of vAMGs compared to hospitalized groups (Kruskal-Wallis, p&#x2009;<&#x2009;0.01), whereas ICU and Non-ICU patients showed reduced and more variable functional profiles. Beta diversity analysis revealed that diarrhea status, rather than hospitalization per se, was associated with modest but significant shifts in functional composition (PERMANOVA, R&#xb2; = 0.047, p&#x2009;=&#x2009;0.025), driven by quantitative changes in shared AMGs rather than the presence of unique functions. Notably, resistance-related vAMGs, including bacitracin transporters and Zinc D-Ala-D-Ala carboxypeptidase, were detected across samples, highlighting the potential of phages as mobile reservoirs of antibiotic resistance.<br><br>CONCLUSION: Together, our findings indicate that hospitalization and diarrhea do not markedly alter the taxonomic structure of the gut virome but are associated with modest shifts in viral functional potential. The maintenance of a stable viral community alongside variable AMG repertoires suggests that phages may modulate host-microbiome interactions primarily through functional fine-tuning rather than large-scale community restructuring. Our study provides evidence for the ecological resilience of the human gut virome and underscores the need to integrate viral communities into resistome research.}, }
@article {pmid41724983, year = {2026}, author = {Yang, K and Li, J and Li, L and Fu, L and Liu, W and Jia, Z and Wang, Z and Wei, Z and Zhang, F}, title = {Soil antibiotic resistome in farmland exhibits higher diversity and horizontal transfer potential than adjacent pastureland in agro-pastoral ecotone.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00871-1}, pmid = {41724983}, issn = {2524-6372}, support = {CCPTZX2024QN03//National Center of Pratacultural Technology Innovation Special fund for innovation platform construction/ ; 42407171//National Natural Science Foundation of China/ ; 2025T180072, GZB20240311//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND: Soil antibiotic resistant genes (ARGs) and mobile genetic elements (MGEs) are associated with agricultural land-use differences. However, assessing the soil antibiotic resistome differences between farmland and pastureland is often limited due to geographically unbalanced sample collection. Leveraging a typical agro-pastoral ecotone in northern China as the study model, we compared the soil microbiome and resistome between 15 adjacent farmland and pastureland pairs using metagenomic sequencing.<br><br>RESULTS: Results showed that farmland soils harbored higher soil ARG diversity (+&#x2009;2.75%), MGE diversity (+&#x2009;1.62%) and multidrug resistance-related gene abundance (+&#x2009;19.5%) than pastureland. Among them, genes conferring multidrug resistances were dominant in farmland, mainly carried by Pseudomonadota. While, vancomycin-resistant ARGs were dominant in pastureland, mainly carried by Actinomycetota. Metagenome-assembled genomes revealed that sul2 conferring sulfonamide resistance was shared by both Pseudomonadota and Acidobacteriota in farmland together with insertion sequence ISVsa3. Structural equation model analysis integrating with soil geography, pedology and microbiome data showed microbial community and soil properties were identified as major driving factors shaping soil antibiotic resistome diversity in both land-use contexts. MGE diversity showed a clear positive effect on ARG diversity in farmland soils but a minor effect in pastureland.<br><br>CONCLUSIONS: Together, this study elucidates the shared and distinguished soil antibiotic resistome pattern between farmland and pastureland, extending our understanding of driving factors in agricultural soil ARG contamination.}, }
@article {pmid41724893, year = {2026}, author = {Yaseen, R}, title = {Immobilization of a biostimulator microbial consortium on bacterial cellulose and its effect on onion growth, soil nutrient status and the microbial community.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {3}, pages = {}, pmid = {41724893}, issn = {1573-0972}, mesh = {*Onions/growth &amp; development/microbiology ; *Cellulose/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Microbial Consortia/physiology ; Rhizosphere ; Bacteria/metabolism/classification ; Nutrients/analysis/metabolism ; Egypt ; Microbiota ; Cells, Immobilized ; Plant Roots/microbiology/growth &amp; development ; }, abstract = {The immobilization of plant growth-promoting rhizobacteria (PGPR) in biodegradable polymeric networks is a promising strategy for protecting them from environmental stresses and optimizing their plant-beneficial functions. In this study, a microbial consortium of Pseudomonas stutzeri and Beijerinckia mobilis was immobilized in bacterial cellulose (BC) produced by Komagataeibacter xylinus. Its efficacy was evaluated in onion (Allium cepa) under three treatments: uninoculated control, free cells, and immobilized cells, during a field trial conducted in the 2025 winter cropping season at El-Kharga Oasis, New Valley Governorate, Egypt. Both inoculation forms significantly (P < 0.05) enhanced plant growth, nutrient uptake, and soil fertility, with immobilized cells increasing bulb yield by 44.9% over the control and outperforming free cells. Treatments elevated N, P, K levels in bulbs and soil, with immobilized cells showing superior nutrient mobilization. The microbial diversity in the onion rhizosphere was assessed at harvest. Ecological diversity indices revealed that bacterial treatments, especially in immobilized form, were associated with a short-term reduction in overall microbial diversity, reflecting selective enrichment of plant-beneficial taxa while suppressing non-beneficial competitors. This functional shift enhanced rhizosphere efficiency without long-term detriment to soil health, as confirmed by post-harvest observations. The novelty of this work lies in the field-scale validation of BC as a biodegradable, highly porous carrier that protects PGPR under arid conditions while simultaneously modulating rhizosphere communities. This study highlights microbial immobilization in BC as a robust, eco-friendly approach to enhance crop yield and soil nutrient dynamics, offering a scalable strategy for sustainable agriculture. Photo 1 Graphical illustration showing PGPR immobilization in biocellulose and its effect on onion growth and nutrient uptake through microbiome modulation.}, }
@article {pmid41724803, year = {2026}, author = {Ding, N and Zhu, S and Yue, L and Zhang, L and Liu, L and Wang, Q and Wang, C and Gao, Y and Yan, J and Tong, S and Chen, F and Sun, J and Zhang, J}, title = {Methamphetamine induces long-lasting dysbiosis of the gut microbiota.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {41724803}, issn = {1476-5578}, support = {31401172//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371780//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81401867//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204645//National Natural Science Foundation of China (National Science Foundation of China)/ ; U2202211//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {As a highly addictive and neurotoxic stimulant, methamphetamine poses a severe threat to public psychological well-being and social se