@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 {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 & 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).

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.

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.

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.

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 & purification ; *Biodiversity ; Animals ; *Nematoda/classification/genetics/isolation & 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.},
}

*Eucalyptus/parasitology/microbiology
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Biodiversity
Animals
*Nematoda/classification/genetics/isolation & purification
Soil/chemistry/parasitology
RNA, Ribosomal, 16S/genetics
South Africa
Phylogeny
Rhizosphere

@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.

OBJECTIVE: We aimed to measure artificial sweeteners and emulsifier polysorbate-80 (P-80) in patients with CD and assess their associations with disease activity.

DESIGN: 1461 biosamples from 487 subjects (245 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.

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.

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 &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.

RESULTS: Using data from three independent human cohorts (n = 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.

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.

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.

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.

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.

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.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects/pharmacology
*Fecal Microbiota Transplantation/methods
Animals

@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 & 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.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Gastrointestinal Microbiome/immunology
Animals
Immunomodulation

@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.},
}

Animals
*Chickens/immunology
Female
*Animal Feed/analysis
Fermentation
*Intestines/immunology/microbiology
Diet
Dietary Supplements
Gastrointestinal Microbiome
*Oviposition
Eggs
Cytokines
Immunoglobulin A/blood

@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.

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 = 12) and environmental samples (personal devices, high-touch surfaces; n = 14), integrated with public 16S rRNA data (Qiita studies; n = 2,263 samples) for model training.

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 h in our observations), suggesting persistent microbial transfer.

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.

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.

RESULTS: System validation demonstrated <0.1% residual oxygen stability for anaerobic preservation, detection sensitivity down to five genomic copies per microliter, AUC > 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.

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.

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.

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.

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 & development ; *Sutures/microbiology/adverse effects ; Female ; Humans ; *Cerclage, Cervical/adverse effects ; Pregnancy ; *Gardnerella/physiology/growth & development ; *Gardnerella vaginalis/physiology/growth & 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.

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.

RESULTS: Sutures incubated without Gardnerella were included as controls. To compare staining of biofilm biomass between groups, one-way ANOVA was performed and Šidák 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.

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.},
}

*Biofilms/growth & development
*Sutures/microbiology/adverse effects
Female
Humans
*Cerclage, Cervical/adverse effects
Pregnancy
*Gardnerella/physiology/growth & development
*Gardnerella vaginalis/physiology/growth & development

@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.

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.

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 α- and β-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.

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.

OBJECTIVE: To construct protein-protein interaction (PPI) networks of key periodontopathogens and identify conserved as well as pathogen-specific virulence hubs.

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.

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.

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.},
}

Humans
*Cardiovascular Diseases/metabolism/pathology/etiology
*Inflammation/metabolism/pathology
*Hypoglycemic Agents/therapeutic use
Gastrointestinal Microbiome
Animals
*Diabetes Mellitus/metabolism/drug therapy

@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.},
}

Animals
*Anthozoa/physiology/microbiology
Coral Reefs
Panama
*Extreme Heat/adverse effects
*Coral Bleaching
Symbiosis
*Hot Temperature
Stress, Physiological

@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.},
}

Humans
*Chronic Pain/microbiology/physiopathology/nursing
*Gastrointestinal Microbiome/physiology
*Nurse Anesthetists/education
Dysbiosis
*Brain

@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 & 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.},
}

Humans
*Neoplasms/psychology/immunology/nursing/therapy
*Stress, Psychological/therapy/etiology/nursing
*Oncology Nursing/methods/organization & administration
Depression
Social Support
Anxiety

@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.},
}

Humans
Female
Infant
*Child Development/physiology
*Gastrointestinal Microbiome/physiology
*Food Insecurity
*Neurodevelopmental Disorders
Child
*Nutritional Status
Pregnancy
Child, Preschool
Infant, Newborn

@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.},
}

*Gastrointestinal Microbiome
Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/diagnosis
Dysbiosis/microbiology
Oxides
Calcium Compounds

@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.},
}

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

@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 & 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.},
}

Animals
Malaysia
*Microbiota/genetics
Humans
RNA, Ribosomal, 16S/genetics
Larva/microbiology
*Bacteria/genetics/classification/isolation & 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

@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.},
}

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

@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.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Pesticides/toxicity/adverse effects
Animals

@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 & 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.

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.

METHODS: We analyzed rectal swabs from 316 participants, 86 without HIV, 100 with acute (≤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).

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 (aβ -1.31, FDR p<0.001). Among participants with HIV, relative abundance of Akkermansia muciniphila was positively correlated with plasma HIV RNA levels (aβ 0.48, FDR p=0.016).

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.

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.

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.

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 & 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 & 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 & 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.},
}

Humans
*Gastrointestinal Microbiome
Infant, Premature
*Sepsis/microbiology/prevention & control
Infant, Newborn
*Nod2 Signaling Adaptor Protein/metabolism/genetics
*Endopeptidases/metabolism
*Bacteria/enzymology

@article {pmid41956066,
year = {2026},
author = {Potiron, A and Francken, JC and El Aidy, S},
title = {Rethinking microbiome health through functional dynamics.},
journal = {Cell host & 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.},
}

Humans
*Microbiota/physiology
*Host Microbial Interactions/physiology
*Gastrointestinal Microbiome
Health

@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 & 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.},
}

Humans
Female
*Microbiota/physiology
*Vagina/microbiology
Probiotics/therapeutic use
*Urogenital System/microbiology
Host Microbial Interactions

@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.},
}

*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

@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.

OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.

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.

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 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 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.

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 & 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.

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.

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.

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.

METHODS: Eight healthy male beagle dogs (8 months old; 10.70 ± 1.79 kg body weight; 3.00 ± 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 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.

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 < 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.

CONCLUSION: Overall, our findings validate that adding 1,000 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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42095-w.},
}

@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.

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.

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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00533-0.},
}

@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 & 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.},
}

Humans
*Bacteria/classification/genetics/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
Male
Adult
*Carbonated Beverages/microbiology

@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 & 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.},
}

*Rhizosphere
*Chenopodiaceae/microbiology
*Poaceae/microbiology
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
Microbiota
Phylogeny
Islands

@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, Ž 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 & purification/genetics/classification ; *Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation & 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.},
}

*Microbiota
*Fungi/isolation & purification/genetics/classification
*Air Pollution, Indoor/analysis
*Bacteria/genetics/classification/isolation & purification
*Air Microbiology
Humans
Dust/analysis
RNA, Ribosomal, 16S/genetics

@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 Próstata/ ; 2021.07634//Fundação para a Ciência e a Tecnologia/ ; 2021.07367//Fundação para a Ciência 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 & 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.

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.

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.

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.

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.

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.},
}

Humans
*Carcinogenesis/pathology
*Neoplasms/microbiology/pathology/therapy
Animals
*Bacteria/pathogenicity
*Bacterial Infections/complications/microbiology
Signal Transduction
Cytokines/metabolism
Apoptosis

@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.

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.

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 α-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.

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.

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 & 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.},
}

*High-Throughput Nucleotide Sequencing/methods/statistics & numerical data
Computer Simulation
*Models, Statistical
Humans
Single-Cell Analysis

@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.

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.

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&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.},
}

Humans
Child
*Pain Management/methods
*Autism Spectrum Disorder/complications/epidemiology
Prevalence
Adolescent
Child, Preschool
Pain Measurement
*Pain/epidemiology
*Chronic Pain/epidemiology/therapy

@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.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Humans
*Software
Phylogeny
*Computational Biology/methods
Bacteria/genetics/classification

@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 & 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 & purification/genetics ; Anal Canal/microbiology ; DNA, Bacterial/genetics/chemistry ; *Bacteria/classification/genetics/isolation & 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.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology
Female
Male
Feces/microbiology
Middle Aged
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Aged
DNA, Ribosomal/chemistry/genetics
*Fusobacterium/isolation & purification/genetics
Anal Canal/microbiology
DNA, Bacterial/genetics/chemistry
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
Adult

@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 & 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.},
}

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 & purification
Indoles/metabolism
RNA, Ribosomal, 16S/genetics
Metabolome
United Kingdom

@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.

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.

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.

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-κB pathway-mediated neuroinflammation. Moreover, oral supplementation with IAA replicated the antidepressant effects of SNS and suppressed CUMS-induced neuroinflammation via the AhR/NF-κB signaling pathway.

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-κB-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.

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.

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.

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 genome, and metabolic profiles identified acetate as a key effector of C. somerae. Acetate incubation upregulated collagen I expression in TGF-β-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.

CONCLUSION: The comprehensive results provided evidences that gut microbes regulated 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.},
}

Humans
*Microbiota
*Translational Research, Biomedical/ethics
*Translational Science, Biomedical/ethics
Research Design

@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.},
}

Humans
*Microbiota
*Biomedical Research/ethics
Global Health
Europe
North America

@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, Ż 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 & purification ; Life Style ; Streptococcus agalactiae/isolation & 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).

DESIGN: Cross-sectional observational study.

SETTING: Tertiary university hospital, Department of Obstetrics and Perinatology, Lublin, Poland.

POPULATION: One hundred pregnant women, including 47 with GD and 53 healthy controls.

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.

MAIN OUTCOME MEASURES: Prevalence of selected vaginal microorganisms (Candida albicans, Streptococcus agalactiae), body composition indices, and lifestyle factors.

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.

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.},
}

Humans
Female
Pregnancy
Cross-Sectional Studies
Adult
*Diabetes, Gestational/microbiology/epidemiology
*Vagina/microbiology
*Body Composition
*Microbiota
Candida albicans/isolation & purification
Life Style
Streptococcus agalactiae/isolation & purification
Poland/epidemiology
Young Adult