@article {pmid41993453,
year = {2026},
author = {Liber, JA and Coelho, MA and He, SY},
title = {Aimea gen. nov. defines a novel plant-associated yeast genus in Microbotryomycetes with three novel species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41993453},
issn = {2692-8205},
abstract = {Plant tissues and surfaces are among the largest microbial habitats on Earth, and commensal yeasts are common members of these communities, where they can contribute to plant-microbe interactions including the biological control of plant diseases. Here, we describe a novel genus, Aimea, of unpigmented, plant-associated basidiomycete yeasts, in the class Microbotryomycetes, and name three new species (A. erigeronia, A. cardamina, and A. sorghi) represented by four isolates from leaves and roots of multiple hosts. We characterize these taxa through analyses of metabolic requirements, tolerance to differences in osmolarity, pH, and temperature, and enzymatic activities. In parallel, we generate near-chromosome-scale hybrid genomes annotated with transcriptome data. We employ whole-genome and multilocus phylogenetic approaches to infer the placement of these species within a monophyletic clade. We use comparative genomics to examine how the gene content of these yeasts differs from that of other members of the Microbotryomycetes, including an apparent proliferation of retrotransposons. We further demonstrate the genetic transformability of these taxa using Agrobacterium tumefaciens-mediated transformation. The description of these new species, together with high-quality genome resources and a genetic transformation protocol, establishes a foundation for experimental studies of these novel plant-associated yeasts and their interactions with hosts and other microbes.},
}

@article {pmid42054893,
year = {2026},
author = {Nkoh, JN and Wu, Z and Shang, C and Zhang, Q and Wang, J and Ntie-Kang, F and Hussain, MA},
title = {Differential long-term tolerance to copper and salt stress by Bruguiera gymnorhiza and Kandelia obovata is driven by species-specific metabolic modulation and rhizobacterial recruitment.},
journal = {Plant physiology and biochemistry : PPB},
volume = {234},
number = {},
pages = {111310},
doi = {10.1016/j.plaphy.2026.111310},
pmid = {42054893},
issn = {1873-2690},
abstract = {The resilience of the plant phytobiome to environmental stress hinges on multitrophic interactions. This study reveals how Bruguiera gymnorhiza L. savigny and Kandelia obovata Sheue & al achieve differential tolerance to copper (Cu) toxicity and salt stress through distinct rhizobacterial recruitment and root metabolic modulation strategies. Using multiomics and chemical approaches, we analyzed rhizobacterial community dynamics, root/rhizosphere metabolic profiles, root/leaf antioxidant enzyme activities, and rhizosphere physicochemical properties. The results revealed that metabolic modulation was the primary stress response mechanism, especially in the less tolerant B. gymnorhiza. Based on the number of differentially abundant metabolites, lipids and lipid-like molecules dominated stress response in both the roots and rhizospheres, except in the roots of K. obovata, where phenylpropanoids and polyketides dominated. The marked differences observed in eicosanoid metabolism between the roots and rhizospheres highlight how species-specific adjustments determine stress tolerance levels. These distinct metabolic strategies influenced species-specific rhizobacterial recruitment, optimizing nutrient uptake and growth. Specifically, K. obovata exhibited more effective enrichment of stress-tolerant rhizobacteria (e.g., Bacteroidota, Firmicutes, and Proteobacteria), which was correlated with improved tolerance under all stresses and improved growth under Cu and Cu-salt stress. In contrast, B. gymnorhiza relies on the synergistic effect of Cu-salt stress to recruit beneficial consortia (Proteobacteria) for 11.5% growth promotion. Thus, tolerance to Cu/salt stress relies on species-specific microbiome-metabolite cross-talk, with the inherent adaptability of K. obovata outperforming the stress-dependent responses of B. gymnorhiza. These findings underscore microbiome-assisted restoration following species-specific management strategies.},
}

@article {pmid42054907,
year = {2026},
author = {Yang, Q and He, S and Xiang, B and Chen, Y},
title = {Hexavalent chromium exposure disrupts gut microbial structure and metabolic function in broiler chickens.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {95},
number = {},
pages = {127874},
doi = {10.1016/j.jtemb.2026.127874},
pmid = {42054907},
issn = {1878-3252},
abstract = {Hexavalent chromium (Cr(VI)) is a pervasive environmental contaminant with well-documented toxicity, yet its impact on the gut microbiome remains poorly understood. This study investigated the effects of chronic dietary Cr(VI) exposure (37 mg/kg feed for 40 days) on the gut microbiota of broiler chickens using 16S rDNA sequencing and bioinformatic analysis. While alpha diversity remained unchanged, significant shifts in beta diversity indicated substantial structural reorganization of microbial communities. Taxonomic analysis revealed a decrease in Firmicutes and an increase in Proteobacteria and Cyanobacteria at the phylum level, along with genus-level alterations including enrichment of Romboutsia and depletion of Enterococcus. Functional prediction via PICRUSt2 further indicated disruptions in key metabolic pathways, particularly the phosphotransferase system (PTS), galactose metabolism, and propanoate metabolism. These findings elucidate a novel mechanism through which chromium exposure may induce toxicity, via disruption of gut microbial structure and function, and underscore the importance of the gut microbiome in mediating chemical toxicity, providing new insights for assessing ecological and health risks of heavy metal exposure.},
}

@article {pmid42054964,
year = {2026},
author = {Autuori, M and Neyrinck, AM and Lengelé, L and Olivera, EV and Rombaux, M and Rodriguez, J and Cani, PD and Walter, J and Bindels, LB and Delzenne, NM},
title = {Breath volatilome analysis reveals new gut microbiome-related metabolites that discriminate high versus low dietary fibre intake.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106662},
doi = {10.1016/j.clnu.2026.106662},
pmid = {42054964},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Gut bacteria produce a wide variety of metabolites that are playing important roles in human health. Dietary fibres (DF) are beneficial nutrients that have been shown to modulate key intestinal functions when fermented by gut bacteria. Since most bacteria-derived metabolites are volatile, their presence in exhaled breath allows to propose new non-invasive methods to study DF-microbiome interactions in humans. We aimed to identify potential novel biomarkers of gut microbiota activity released in exhaled breath following the consumption of DF at breakfast, upon untargeted analysis in healthy volunteers.

METHODS: 14 volunteers (7 women/7 men, 21 ± 2 years old) participated to two test days at a one-month interval, where they received either a low-(2.6 g) or high-(16.1 g) fibre breakfast. Before each test days, stools were collected to evaluate the microbiota composition using Illumina sequencing (V5-V6 region of 16S rRNA gene). Throughout the test days, breath samples were analysed using selected-ion flow-tube mass spectrometry (SIFT-MS). A sparse partial least squares-discriminant analysis (sPLS-DA) identified 30 signals that best discriminated between test days, corresponding to 173 candidate breath compounds.

RESULTS: The gut microbiota of the volunteers remained stable one month apart. The composition of exhaled breath shifted starting from 5 h after the high-fibre breakfast ingestion. Ninety compounds were identified as potential metabolites of gut microbes, with 81 showing increased concentrations after the high-fibre breakfast. These included acrylic acid (positively correlated with Faecalibacterium/Ruminococcaceae/Bacillota and negatively correlated with Bifidobacterium/Bifidobacteriaceae/Actinomycetota). The high-fibre breakfast also led to increases in limonene, ethylbenzene/xylene, p-cymene, and methionol that were positively correlated with the genus Faecalibacterium. Moreover, positive correlations were observed between cyclooctane/ethylcyclohexane, methanol and the phylum Bacillota. Dimethyl disulfide was strongly negatively correlated with the genus Bacteroides and its family Bacteroidaceae.

CONCLUSION: This study shows that DF consumption at breakfast stimulates the production of exhaled bacteria-derived metabolites reflecting profound changes in the metabolic activity of the gut microbiota. We also identified new potential biomarkers of DF intake, that are not directly linked to DF fermentation. Specific bacteria known to play a role in gut barrier, immunity and host metabolism were associated with those new metabolites.},
}

@article {pmid42055251,
year = {2026},
author = {van Dijk, LLA and Rijsbergen, LC and Havelaar, AC and Hartog, YD and Koutstaal, RW and Groen, K and de Vries, RD and de Swart, RL},
title = {Innate airway responses shape permissiveness to human respiratory syncytial virus.},
journal = {Virus research},
volume = {},
number = {},
pages = {199734},
doi = {10.1016/j.virusres.2026.199734},
pmid = {42055251},
issn = {1872-7492},
abstract = {The interaction between human respiratory syncytial virus (HRSV) and the innate immune system has been demonstrated both in vitro and in vivo. Disruption of interferon (IFN) signaling pathways increases susceptibility and permissiveness to HRSV infection, whereas pretreatment of cells with IFN confers (partial) resistance. This suggests that HRSV disease severity is likely influenced by a pre-existing antiviral state of the respiratory epithelium, driven by baseline or primed expression of type I and type III IFNs. Here, we investigated whether prior exposure to respiratory bacteria or viruses alters in vitro susceptibility and permissiveness to HRSV infection by shaping an antiviral state using both immortalized cell lines and airway organoid models. In A549 cells, pre-exposure to S. aureus had the most significant impact by reducing HRSV infection and inducing robust interferon responses. However, this effect was not reproduced in airway organoids. Conversely, sequential virus infection experiments in airway organoids revealed that prior infection with human parainfluenza virus type 3 (HPIV‑3) reduced the spread of subsequent HRSV infection. In addition to interferon signaling this proved to be associated with epithelial damage mediated by HPIV-3 infection. Collectively, these findings show that HRSV susceptibility and permissiveness are influenced by the up- or downregulation of specific anti- and pro-viral factors induced by prior bacterial or viral exposure, together with the maintenance or disruption of epithelial integrity. Understanding these interactions could be crucial when identifying specific risk groups for severe HRSV-associated disease and the development of targeted HRSV interventions.},
}

@article {pmid42055298,
year = {2026},
author = {Choi, J and Shin, N and Jin, D and Xu, E and Kwon, Y and Park, S and Lee, U and Lee, J and Oh, YK},
title = {Intestinal microenvironment-modulating nanomedicines for inflammatory bowel disease.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114953},
doi = {10.1016/j.jconrel.2026.114953},
pmid = {42055298},
issn = {1873-4995},
abstract = {Inflammatory bowel diseases present a highly restrictive intestinal microenvironment for drug delivery, in which epithelial injury, chronic inflammation, and microbial dysbiosis collectively impair transport, retention, and therapeutic efficacy. Excessive reactive oxygen species (ROS), mucus barrier disruption, altered luminal acidity, hydrogen sulfide accumulation, and abnormal enzymatic activity destabilize therapeutic cargos and limit access to inflamed tissues. These pathological features have motivated the development of nanocarriers designed either to directly modulate biochemical abnormalities, such as ROS scavenging and H2S removal, or to respond to disease-associated biochemical cues including ROS, luminal pH, enzymatic activity, and mucus abnormalities. In parallel, modulation of the immunological microenvironment has been pursued through nanomedicine platforms engineered to regulate inflammatory signaling, enhance mucosal targeting, protect therapeutic payloads from premature degradation, and prolong local residence. Complementary microbiome-oriented delivery strategies, including engineered probiotics, nanoparticles that release postbiotic factors, and carriers coated with microbial membranes, leverage host microbe interactions to achieve localized and sustained therapeutic effects. Despite substantial progress, effective delivery remains constrained by patient specific variability, spatial heterogeneity of inflammatory conditions, and limited durability of mucosal retention. Integrating biochemical responsiveness, immune modulation, and microbiome informed targeting represents a promising direction for advancing precision nanomedicine in inflammatory bowel diseases.},
}

@article {pmid42055311,
year = {2026},
author = {Cao, Z and Lin, Y and Li, W and He, L and Wang, H and Sun, L and Wang, X and Chen, L and Li, E},
title = {Physiological and metabolic responses of juvenile Chinese mitten crab (Eriocheir sinensis) to dietary hydrolyzed anchovy-cottonseed protein and amino acid supplementation.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology},
volume = {285},
number = {},
pages = {111238},
doi = {10.1016/j.cbpb.2026.111238},
pmid = {42055311},
issn = {1879-1107},
abstract = {This study investigated the physiological and metabolic responses of juvenile Chinese mitten crab (Eriocheir sinensis) to dietary inclusion of coenzymatically hydrolyzed anchovy-cottonseed protein (HACP) with or without arginine and methionine supplementation. A 56-day feeding trial was conducted. Juvenile crabs were fed a control diet containing 15% fishmeal and experimental diets in which fishmeal was partially replaced by HACP at graded levels (5%, 10%, and 15%). Increasing dietary HACP levels significantly affected growth performance, feed intake, digestive enzyme activities, hepatopancreatic condition, and intestinal microbial composition. The 5% HACP inclusion maintained growth performance and protein utilization comparable to the control, whereas higher inclusion levels reduced feed intake and digestive enzyme activity, suggesting potential alterations in digestive enzyme activity and metabolic status. Arginine and methionine supplementation partially alleviated these effects by enhancing trypsin and lipase activities, reducing hepatopancreatic stress indicators, and improving antioxidant status, suggesting potential improvements in nutrient utilization and metabolic responses. Microbiota and metabolomic analyses further revealed coordinated shifts in intestinal microbial composition and metabolic pathways associated with amino acid, lipid, and energy metabolism. Overall, these findings indicate that dietary HACP influences physiological function through integrated effects on digestion, metabolism, and microbiome-metabolome interactions, and highlight the role of amino acid balance in mediating metabolic response under altered dietary protein composition.},
}

@article {pmid42055337,
year = {2026},
author = {Nitin, N and Daneshgar, P and Kniffen, D and Vicaretti, SD and Whitmore, B and Kipchumba, L and Quin, C and Gibson, DL and Bergstrom, KSB and Zandberg, WF},
title = {Longitudinal analysis of human milk oligosaccharides (HMOs) and Mucin-2-glycans in infants reveals enrichment of sulfated and glucuronic acid-bearing HMOs.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113099},
doi = {10.1016/j.jbc.2026.113099},
pmid = {42055337},
issn = {1083-351X},
abstract = {In infants, the acquisition of an adult-like gastrointestinal (GI) microbiome begins at birth, fully developing by toddlerhood. This colonization is influenced by the diet which, in breast-fed infants, contains high concentrations of soluble human milk oligosaccharides (HMOs), prebiotics bearing structural-resemblance to the glycans that decorate Mucin-2 (MUC2). MUC2 is the first line of defense between the microbiota and the underlying mucosal tissues; it also provides a nutrient-rich habitat for GI commensal microbes. The research described herein builds on two earlier findings: the ability to sample MUC2 adhering to the surface of stool samples and the discovery of a class of sulfated HMOs within human milk. Studies have shown that de-sulfation of MUC2-borne glycans is a key for their metabolism by GI microbes in vitro and, if sulfated glycans are otherwise metabolically-resistant, two hypotheses follow. First, in contrast with major prebiotic HMOs, sulfated HMOs will be enriched in the infant GI tract; second, high abundances of glyco-epitopes like sulfation in HMOs will deflect the microbiome's metabolic activity away from MUC2 leading to detectible changes in the host glycome. We show that both HMOs and MUC2 could be non-invasively sampled from the same infant stool samples. Capillary electrophoresis analyses of paired milk/stool samples demonstrated significant enrichment of sulfate-containing HMOs in stool. High-resolution mass spectrometry (HRMS) was used to detect numerous sulfated HMOs, including a new class concurrently containing glucuronic acid (GlcA) residues. Infant MUC2-derived glycans were also analyzed by HRMS; this is the first reported semi-quantitative longitudinal study and provides a benchmark for future research.},
}

@article {pmid42055352,
year = {2026},
author = {Abdessamad, H and Abdallah, D and Attieh, R and Eid, S and Nahal, J and Jamal, O and Fakih, A and Zahran, K and Khalil, A and Helmy, S and Ibrahim, A and Moghnieh, R},
title = {Revisiting Fluoroquinolone Prophylaxis in Hematological Malignancies and Hematopoietic Cell Transplantation: A Decade of Evidence and Gaps in Understanding the Impact of Gut Colonization with Fluoroquinolone-Resistant Enterobacterales.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107824},
doi = {10.1016/j.ijantimicag.2026.107824},
pmid = {42055352},
issn = {1872-7913},
abstract = {Rising antimicrobial resistance necessitates reevaluation of fluoroquinolone (FQ) prophylaxis (FQP) in patients with hematologic malignancies undergoing intensive chemotherapy or hematopoietic cell transplantation (HCT). This narrative review synthesizes recent evidence on the clinical efficacy of FQP and the modifying effect of gut colonization with fluoroquinolone-resistant Enterobacterales (FQRE). FQP consistently reduced febrile neutropenia and bloodstream infections, particularly in autologous HCT and selected chemotherapy cohorts. However, its benefit was context-dependent, with diminished or absent effects in allogeneic HCT and in settings with higher background FQ resistance (≥30%). Breakthrough infections during prophylaxis were predominantly caused by FQ-resistant organisms, reflecting strong selective pressure. Baseline colonization with FQRE further increased the risk of bloodstream infection and reduced the likelihood of benefit from prophylaxis. Mortality was not significantly affected across populations. Microbiome data suggest that FQP exerts a selective effect on Gram-negative gut colonization rather than causing broad disruption of microbial diversity. Overall, the effectiveness of FQP is strongly influenced by resistance epidemiology and colonization status. These findings support a shift toward more individualized, resistance-informed prophylaxis strategies within antimicrobial stewardship frameworks.},
}

@article {pmid42055363,
year = {2026},
author = {Zhang, K and Qiu, MT and Shao, YH and Liu, J and Tu, ZC},
title = {High-tryptophan diet mitigates parvalbumin-induced allergic responses via gut microbiome remodeling and immune modulation.},
journal = {International journal of biological macromolecules},
volume = {364},
number = {},
pages = {152245},
doi = {10.1016/j.ijbiomac.2026.152245},
pmid = {42055363},
issn = {1879-0003},
abstract = {Parvalbumin-induced food allergy model in BALB/c mice were established to investigate the intervention effect of high- tryptophan (Trp) diet on allergic responses. Trp suppressed histamine and IL-6 release from the sensitized KU812 cells, effectively mitigated parvalbumin-induced cellular sensitization. High-Trp diet alleviated allergic symptoms, reduced the organ index of the spleen and serum specific IgE, IgG, IgG1 and IgG2a levels, alongside suppressed Th2-type immune responses in mice. Meanwhile, Trp not only influenced the relative abundance of allergy-related gut microbiome, such as Faecalibaculum, Romboutsia, Lachnoclostridium unclassified_f__Lachnospiracea and norank_f__Ruminococcaceae, but also increased the production of short-chain fatty acids. Meanwhile, Trp enhanced the expression of intestinal tight junction proteins, repaired the impaired intestinal barrier in allergic mice, and also induced the phosphorylation of STAT3 and enhanced the expression of Reg3γ, then may activated the AhR/IL-22 signal pathway in murine intestinal epithelial cells. These findings demonstrated that high-Trp diet mitigated parvalbumin-induced allergic responses were responsible for gut microbiome remodeling and immune modulation.},
}

@article {pmid42056070,
year = {2026},
author = {López, I and Pineda, C and Camargo, A and Arenas, C and Torrano, A and Glorieux, G and Aguilera-Tejero, E},
title = {Supplementation with Enterococcus lactis (SF68) and its association with biochemical parameters and inflammatory biomarkers related to renal impairment in dogs with chronic kidney disease.},
journal = {The veterinary quarterly},
volume = {46},
number = {1},
pages = {2665483},
pmid = {42056070},
issn = {1875-5941},
mesh = {Animals ; Dogs ; *Probiotics/administration & dosage/therapeutic use ; *Renal Insufficiency, Chronic/veterinary/therapy/blood ; Biomarkers/blood ; *Dog Diseases/blood/therapy ; Male ; Female ; Gastrointestinal Microbiome ; *Enterococcus ; Dietary Supplements ; Animal Feed/analysis ; Inflammation/veterinary ; Arginine/analogs & derivatives/blood ; Diet/veterinary ; },
abstract = {To investigate the influence of probiotic supplementation on parameters of renal function, dogs with chronic kidney disease (CKD) received a commercial probiotic formulation containing Enterococcus lactis SF68 (n = 8) or placebo (n = 8) for 60 days. Gut microbiome was investigated by comparing with healthy dogs (n = 10). Blood biochemistry, urinalysis, inflammatory and oxidative markers, uremic toxins and blood pressure were monitored. Higher presence of Lachnospiraceae family, Blautia bacterial species and Ruminococcus gnavus group was observed in dogs with CKD when compared with healthy dogs. Adding the probiotic to the diet decreased the abundance of Ruminococcus gnavus. Probiotic treatment resulted in a significant reduction in plasma concentrations of symmetric dimethylarginine (SDMA), from 1.50 ± 0.18 to 1.35 ± 0.16 µmol/l (p = 0.008), and indoxyl sulfate (IxS), from 19.1 ± 6.8 to 12.8 ± 4.8 µmol/l (p = 0.04). Cytokine inflammatory markers did not show significant changes. An increase in urine protein-to-creatine ratio, 1.5 ± 0.6 vs 1.2 ± 0.5, and in systolic blood pressure, 163 ± 11 vs 144 ± 6 mmHg (p = 0.033), was observed in the placebo group but not in dogs receiving probiotic. In conclusion, feeding Enterococcus lactis SF68 to dogs with CKD results in changes in intestinal microbiota that are associated with a decrease in plasma concentrations of IxS and SDMA and a reduction in proteinuria and systolic blood pressure.},
}

Animals
Dogs
*Probiotics/administration & dosage/therapeutic use
*Renal Insufficiency, Chronic/veterinary/therapy/blood
Biomarkers/blood
*Dog Diseases/blood/therapy
Male
Female
Gastrointestinal Microbiome
*Enterococcus
Dietary Supplements
Animal Feed/analysis
Inflammation/veterinary
Arginine/analogs & derivatives/blood
Diet/veterinary

@article {pmid42056166,
year = {2026},
author = {Wang, M and Liu, X and Liu, S and Xin, W and Liu, H and Zhao, Z and Wei, J and Lu, X and Liu, P and Chen, Q and Yang, S},
title = {Characteristics of the rhizosphere microbial communities of different mulberry varieties in saline soil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48685-y},
pmid = {42056166},
issn = {2045-2322},
support = {2022C02065//the Project of Major Social and Public Welfare in Zhejiang Province/ ; NY202401//Coastal Characteristic Plant Innovation and Utilization Project/ ; },
abstract = {Mulberry is a common crop with different varieties of resistance. Understanding the differences in rhizosphere soil microbial community characteristics among different salt-tolerant mulberry varieties in saline soils is important for the rational development and utilization of coastal saline soils. Using high-throughput sequencing, we compared the rhizosphere microbiota of salt-tolerant variety Guoxuan3 (GX3) and the salt-sensitive variety A18 in coastal saline soils, with bare soil as a control. Bare, unplanted soil (CK) collected from the same field was used as a baseline control to distinguish plant-driven effects from background soil microbial structure. The results revealed that 1236 bacterial OTUs and 396 fungal OTUs were identified from the mulberry rhizosphere samples. The dominant bacteria in the mulberry rhizosphere were Proteobacteria and Actinobacteria, while the dominant fungi were Ascomycota and Basidiomycota. Significant differences in microbial composition were observed between varieties. The salt-tolerant GX3 specifically enriched Rozellomycota and key genera, including Nocardioides, Aspergillus, and Fusicolla in its rhizosphere. Mulberry varieties shape distinct rhizosphere microbiomes. Salt-tolerant GX3 recruits beneficial bacteria like Nocardioides, Georgenia, Azoarcus through organic acids, enhancing nutrient cycling and stress resistance. Salt-sensitive A18 inhibits beneficial fungi such as Calcarisporiella, accumulates phenolics, and enriches nitrifying Nitrospira, indicating nitrogen cycle inefficiency under salinity. Plant salt tolerance links to rhizosphere microbiome shaping, highlighting the need to consider both bacterial and fungal communities for coastal saline soil phytoremediation, aiding marginal ecosystem utilization.},
}

@article {pmid42056339,
year = {2026},
author = {Thenappan, DP and Joshi, V},
title = {Host genotype Impacts the Assembly and Functional Potential of Bacterial Communities in the Spinach Phyllosphere Within Commercial Organic Farming Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02762-x},
pmid = {42056339},
issn = {1432-184X},
support = {2022-51300-37886//USDA-NIFA-OREI/ ; 9647-1//USDA- NIFA- HATCH/ ; },
}

@article {pmid42056655,
year = {2026},
author = {Wu, K and Hu, HW and Gupta, D and Li, Y and He, ZY and Wang, F and He, JZ},
title = {Core Microbial Taxa Strengthen Root Microbial Network Stability Under Drought Stress.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70307},
pmid = {42056655},
issn = {1462-2920},
support = {IH200100023//Australian Research Council/ ; 4-H808GTH//Department of Agriculture, Fisheries and Forestry, Australian Government/ ; },
mesh = {*Plant Roots/microbiology ; *Droughts ; *Soil Microbiology ; *Microbiota ; *Triticum/microbiology/growth & development ; Rhizosphere ; Stress, Physiological ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Drought stress is intensifying globally, but its effects on plant-associated microbiome diversity and stability remain poorly understood. We grew wheat under drought stress and sampled bulk soils, rhizosphere soils and roots across three growth stages to quantify microbial diversity, co-occurrence network stability and the contributions of core taxa to network stability. Drought affected microbial diversity depending on microbial kingdoms, plant niches and growth stages. We further found that drought stress reduced the complexity and stability of microbial networks in the rhizosphere soils while enhancing those in the roots, mainly through shifts in the abundances of core taxa (i.e., taxa that are widely distributed across samples, specific to drought stress and highly connected in the network). Three types of analyses (shared operational taxonomic units, network keystone nodes and taxa with high specificity and occupancy values) were employed to identify the core taxa enriched in the roots under drought stress, including Glycomyces and Thermoactinomycetaceae, which were typical drought-tolerant taxa that are important for maintaining root microbial network stability. Environment stress usually disrupts microbial community stability, but we found drought stress enriched core taxa, enhancing drought-tolerant crop root microbiomes stability. Our findings provide a blueprint for enhancing crop stress tolerance via microbiome manipulation.},
}

*Plant Roots/microbiology
*Droughts
*Soil Microbiology
*Microbiota
*Triticum/microbiology/growth & development
Rhizosphere
Stress, Physiological
*Bacteria/classification/genetics/isolation & purification

@article {pmid42056687,
year = {2026},
author = {Wedell, E and Shen, C and Warnow, T},
title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {37-52},
pmid = {42056687},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; *Metagenomics/methods ; Algorithms ; Likelihood Functions ; *Computational Biology/methods ; },
abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.},
}

*Phylogeny
*Software
*Metagenomics/methods
Algorithms
Likelihood Functions
*Computational Biology/methods

@article {pmid42056825,
year = {2026},
author = {Rafieian-Naeini, HR and Keshavareddy, VPR and Katha, HR and Gyawali, I and Lee, DJ and Kim, Y and Kim, WK},
title = {Effect of dietary wheat on the progression of Histomonas meleagridis infection in turkey poults.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106970},
doi = {10.1016/j.psj.2026.106970},
pmid = {42056825},
issn = {1525-3171},
abstract = {Blackhead disease (Histomoniasis), caused by Histomonas meleagridis (HM), remains a major constraint to turkey production, and dietary factors that may influence disease progression are poorly defined. This study evaluated whether moderate wheat inclusion alters HM outcomes in turkey poults. A total of 432 one-day-old male turkey poults (Nicholas) were allocated to a 2 × 3 factorial arrangement with HM challenge (HM+ or HM-) and dietary wheat inclusion (0, 15, or 30%), yielding 6 treatments with 6 replicates (12 birds/replicate) for a 22-d experimental period. Diets were formulated to be isocaloric and isonitrogenous. Growth performance (BW, feed intake, BWG, FCR, and mortality) was assessed during d 0-12, d 13-16, and d 17-22. Additional parameters included infection rate and lesion severity (ceca and liver), clinical presentation, ileal digesta viscosity, intestinal histomorphology, jejunal cytokine/tight junction mRNA abundance, bone formation by calcein labeling, bone mineral density/content by DEXA, and cecal microbiota. Wheat × HM interactions were not detected for growth performance, mortality, lesion distributions, infection rate, clinical scores, or jejunal gene expression (P > 0.05). Wheat inclusion improved early performance prior to challenge. Poults fed 15% or 30% wheat had greater BW at d 12 and 16, with increased BWG and improved FCR during the pre-challenge/early infection periods (P < 0.05), whereas BW at d 22 was not influenced by wheat. In contrast, HM challenge markedly reduced BW, feed intake, and BWG, worsened FCR during d 17-22, and increased mortality (P ≤ 0.001). Dietary wheat did not mitigate HM-induced cecal and liver lesions, infection rate, or clinical presentation. HM challenge profoundly disrupted cecal microbiota, reducing alpha diversity and shifting community structure, characterized by expansion of Enterobacteriaceae and reduction of Lachnospiraceae. In conclusion, 15% wheat inclusion supported improved early growth and bone apposition under non-challenged conditions, but HM challenge overwhelmingly dictated disease severity and associated physiological and microbiome outcomes regardless of wheat level.},
}

@article {pmid42056921,
year = {2026},
author = {Li, B and Zhang, Y and Li, Z and Chen, Z and Guo, Z and Wu, W and Tan, L and Dong, L and Zhang, X and Lyu, X and Hu, M and Long, Q},
title = {A novel serum metabolite classifier for identifying Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) integrating metabolomics and machine learning.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04842-1},
pmid = {42056921},
issn = {1471-230X},
support = {No.82302586//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) presents a growing global health burden, while reliable non-invasive biomarkers for identifying affected individuals remain limited. This study aimed to characterize serum metabolomic signatures associated with steatosis and fibrosis and to develop a clinically applicable metabolite-based classifier.

METHODS: Untargeted serum metabolomics was performed in a FibroScan-characterized discovery cohort (n = 35) to identify candidate metabolic features associated with hepatic steatosis and fibrosis burden. To provide biological context for the observed metabolic alterations, 16 S rDNA sequencing was subsequently conducted in paired fecal samples from a subset of participants (n = 27). Differential metabolites were then subjected to LASSO regression for feature selection and used to construct a random forest diagnostic model in a validation cohort comprising healthy controls (n = 19) and ultrasound-confirmed MASLD patients (n = 52).

RESULTS: Metabolomic profiling revealed distinct metabolic patterns across different degrees of steatosis and fibrosis. A total of 55 and 46 metabolites were identified as differentially abundant in relation to steatosis and fibrosis burden, respectively. Microbiome analysis indicated alterations in gut microbial composition, and integrative correlation analysis suggested several potential microbe-metabolite associations, including two metabolite-genus pairs showing relatively strong correlations. LASSO regression selected a panel of ten metabolites as the most informative diagnostic features. Using these metabolites as input variables, a random forest classifier was constructed and achieved an area under the receiver operating characteristic curve (AUROC) of 0.87. Incorporation of four clinical variables (BMI, ALT, triglycerides, and HDL cholesterol) further improved model performance, yielding an AUROC of 0.94.

CONCLUSION: This study characterizes systemic metabolic alterations associated with MASLD and presents a non-invasive diagnostic model integrating serum metabolites with clinical indicators. Together, these findings highlight the potential utility of metabolomics-assisted approaches for identifying MASLD and for improving biological understanding of disease-associated metabolic changes.},
}

@article {pmid42057114,
year = {2026},
author = {Zhou, CY and Qi, YF and Li, HJ and Zhang, C and Lin, BX and Lin, JT and Wu, YL and Zheng, MM and Zhong, WZ},
title = {Current and future immunotherapies for NSCLC.},
journal = {Journal of hematology & oncology},
volume = {19},
number = {1},
pages = {},
pmid = {42057114},
issn = {1756-8722},
support = {2024ZD0529400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82573732//National Natural Science Foundation of China/ ; 82241235//National Natural Science Foundation of China Major Joint Project on Key Scientific Issues of Lung Cancer/ ; KA0120231004//National High-Level Talents Special Support Program/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/genetics/pathology ; *Lung Neoplasms/therapy/immunology/pathology/genetics ; *Immunotherapy/methods/trends ; Immune Checkpoint Inhibitors/therapeutic use ; Biomarkers, Tumor ; },
abstract = {Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide. Immune checkpoint inhibitors targeting the PD-1/PD-L1 and CTLA-4 axes have fundamentally transformed its treatment landscape. This narrative review traces the evolution of NSCLC immunotherapy, from advanced-stage monotherapy and chemoimmunotherapy to its critical expansion into early-stage disease, highlighting the paradigm shift brought by neoadjuvant, adjuvant, and perioperative strategies. We examine essential clinical challenges, including optimal treatment duration, management of brain metastases, immune-related adverse events, and mechanisms of primary and acquired resistance, with a focus on genomic alterations like KRAS co-mutations with STK11 and KEAP1. Furthermore, we critically evaluate the evolving biomarker landscape, moving beyond PD-L1 to encompass circulating tumour DNA, microbiome composition, and multiparametric approaches like T-cell receptor clonality. Finally, we provide an in-depth exploration of next-generation strategies, including bispecific antibodies, novel checkpoint targets, mRNA vaccines, antibody-drug conjugates, and advanced cellular therapies. While significant progress has been made, refining biomarker-driven selection and optimizing combination sequencing remain paramount. This thorough synthesis highlights promising future directions to overcome these hurdles and improve long-term survival in NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/immunology/genetics/pathology
*Lung Neoplasms/therapy/immunology/pathology/genetics
*Immunotherapy/methods/trends
Immune Checkpoint Inhibitors/therapeutic use
Biomarkers, Tumor

@article {pmid42057125,
year = {2026},
author = {Tan, SSL and Garg, V and Dhiman, A and Bansal, N and Conway, P},
title = {Inflammaging and the role of micronutrients as immunomodulators: a pathway to healthy aging.},
journal = {Immunity & ageing : I & A},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12979-026-00569-5},
pmid = {42057125},
issn = {1742-4933},
abstract = {BACKGROUND: Healthy aging is increasingly challenged by inflammaging, a chronic, low‑grade inflammatory state primarily exacerbated by gut microbiota dysbiosis and declining immune function. Persistent digestive and systemic inflammation, along with immunosenescence, contributes to multiple age‑related diseases. Micronutrients regulate key components of immune system and support the composition and function of the gut microbiota, underscoring their emerging role as modulators of inflammaging.

MAIN BODY: This narrative review synthesizes current evidence insights on how micronutrients regulate cellular and molecular drivers of inflammaging, with emphasis on immune function and gut microbiota imbalance. Adequate intakes of vitamins A, B‑complex, C, D, E, and K, together with trace elements (zinc, selenium, magnesium, iron, and copper), supports both innate and adaptive immune response, genomic and epigenetic stability, mitochondrial efficiency, telomere integrity, and immune regulation. Importantly, micronutrients influence gut microbial composition and inflammatory signaling pathways, thereby mitigating dysbiosis-driven digestive inflammation, a major contributor to systemic inflammaging. The review also delineates the bidirectional micronutrient-microbiome relationship, whereby microbial composition shapes nutrient bioavailability, while micronutrients influence microbial diversity, short‑chain fatty acid production, and inflammatory signaling.

CONCLUSION: Micronutrient sufficiency may help reduce digestive inflammation, restore microbial balance, and modulate immune pathways implicated in inflammaging. However, translating these benefits requires robust assessment of micronutrient status and gut microbiota. Developing standardized evaluation and microbiota‑informed nutrition strategies may enable more precise targeted interventions to support healthy aging.},
}

@article {pmid42057164,
year = {2026},
author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I},
title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00893-9},
pmid = {42057164},
issn = {2524-6372},
abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.

RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short‑term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine‑scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.

CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non‑equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long‑term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.},
}

@article {pmid42057198,
year = {2026},
author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J},
title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01660-8},
pmid = {42057198},
issn = {1756-994X},
support = {09150162410022/ZONMW_/ZonMw/Netherlands ; 2021-01637//Vetenskapsrådet/ ; 967569//Västerbotten Läns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; },
abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.

METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.

RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.

CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.},
}

@article {pmid42057229,
year = {2026},
author = {Wu, Y and Chen, K and Hu, T and Luo, Y and Zhang, Y and Yang, G and Wang, J and Zhu, Y},
title = {Lactobacillus johnsonii-derived extracellular vesicles modulate gut microbiota metabolites and macrophage-related immune responses against Salmonella Typhimurium infection.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-026-01750-w},
pmid = {42057229},
issn = {1297-9716},
support = {2023YFC3404301//National Key Research and Development Program of China/ ; },
abstract = {Salmonella Typhimurium is a significant pathogen causing diarrhea in weaned piglets, capable of triggering systemic inflammation and severe intestinal damage. As bioactive components of gut microbiota, extracellular vesicles (EVs) derived from Lactobacillus johnsonii (Lj-EVs) are likely to penetrate the intestinal mucus layer and reach host cells, potentially mediating host-microbiome interactions. Here, we found that Lj-EVs improved the intestinal barrier and attenuated intestinal injury in mice infected with S. Typhimurium. Multi-omics analysis showed that Lj-EVs intervention enriched mucin-utilizing Akkermansia. Moreover, Lj-EVs were associated with metabolic alterations, characterized by enhanced oxidative phosphorylation during homeostasis and suppression of HIF-1α-mediated glycolysis during infection. Proteomic profiling showed that Lj-EVs enriched functional proteins related to oxidative phosphorylation, indicating their potential immunomodulatory role. Notably, Lj-EVs modulated macrophage-mediated immune responses, contributing to limiting bacterial dissemination and alleviating intestinal inflammation. In conclusion, our study demonstrates that Lj-EVs alleviate Salmonella infection by reducing bacterial burden and confer metabolic and immunomodulatory benefits. These findings provide new evidence for future investigation of the protective roles of probiotic vesicles.},
}

@article {pmid42057366,
year = {2026},
author = {Murakami, K},
title = {Comprehensive management of immune-related adverse events: predictive strategies, mechanistic insights, and therapeutic approaches.},
journal = {Immunological medicine},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/25785826.2026.2664951},
pmid = {42057366},
issn = {2578-5826},
abstract = {Immune checkpoint inhibitors (ICIs) have been game changer in cancer therapy but can trigger diverse immune-related adverse events (irAEs) that impact multiple organs. This review offers a unified perspective on irAE risk assessment, underlying mechanisms, and therapeutic strategies aimed at maintaining anticancer efficacy while safeguarding patient well-being. We explore predictive tools-including baseline profiles of several cytokines, HLA genotype, and markers such as interleukin-6-for identifying high-risk individuals. Key drivers of irAEs were dysregulated T- and B-cell responses, antigenic cross-reactivity, and gut microbiome imbalances. Management follows a graduated approach: initial glucocorticoid intervention, followed by biologics (anti-TNF agents, IL-6 receptor blockers) or small-molecule inhibitors (JAK inhibitors) in refractory cases. Real-world data support cautious ICI use in pre-existing autoimmune disorders under stringent monitoring. We also discuss the emerging notion of "inverse irAEs," where immunosuppression may predispose to secondary malignancies, underscoring the importance of long-term surveillance. Finally, we highlight the urgent need for expansive, multicenter studies to refine irAE management to enhance therapeutic outcomes.},
}

@article {pmid42057740,
year = {2026},
author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM},
title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17636},
pmid = {42057740},
issn = {1520-5118},
abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.},
}

@article {pmid42057783,
year = {2026},
author = {Harshvardhan, and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S},
title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799124},
pmid = {42057783},
issn = {1664-302X},
abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.

METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.

RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.

CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.},
}

@article {pmid42057790,
year = {2026},
author = {Zhu, B and Fu, C and Fan, D and Wang, Y and Sheng, P and Feng, J and Wang, X},
title = {The impact of antibiotic exposure on obesity and metabolic phenotypes via the gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1782016},
pmid = {42057790},
issn = {1664-302X},
abstract = {Antibiotics are among the most commonly used anti-infective agents in modern medicine. However, their long-term effects on the gut microbiome have attracted increasing attention. Epidemiological studies and animal experiments in recent years suggest that antibiotic exposure can disrupt the structure and function of the gut microbiota, thereby affecting host energy metabolism, fat deposition, and immune homeostasis. Such disruptions may contribute to the development of obesity and related metabolic phenotypes. Different classes of antibiotics exert markedly distinct effects on the gut microbiota. Broad-spectrum antibiotics such as macrolides, lincosamides, and fluoroquinolones often induce more pronounced and prolonged microbial alterations, whereas the effects of certain β-lactam antibiotics appear relatively transient. Antibiotic-induced gut dysbiosis can influence host metabolism through multiple mechanisms, including reduced short-chain fatty acid production, disrupted bile acid metabolism, impaired intestinal barrier function, and chronic low-grade inflammation. These alterations may promote fat accumulation, insulin resistance, and disruption of immune homeostasis. Early-life antibiotic exposure occurs during a critical developmental window for gut microbiota maturation and may exert more profound effects on long-term metabolic health. Recent advances in multi-omics technologies have further illuminated the complex interaction network among antibiotics, the microbiome, and host metabolism. Microecological intervention strategies, such as probiotics and synbiotics, show potential for improving metabolic abnormalities associated with antibiotic-induced dysbiosis. However, their efficacy is strain-specific, and the overall effect size remains limited. This review summarizes current research progress on how antibiotic exposure influences obesity and metabolic phenotypes through the gut microbiota, outlines the underlying mechanisms, and discusses potential applications of microbiological intervention strategies. It also provides insights into antibiotic-related metabolic risks and future precision intervention approaches.},
}

@article {pmid42057793,
year = {2026},
author = {Bautista, J and López-Cortés, A},
title = {The hallmarks of host-microbiome decoupling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1801100},
pmid = {42057793},
issn = {1664-302X},
abstract = {The human host and its resident microbiome maintain continuous interactions that influence immune regulation, metabolism, neuroendocrine signaling, epithelial barrier function, and circadian organization. Although multi-omics approaches have improved mechanistic understanding of host-microbiome interactions, dominant translational models remain largely based on compositional descriptions and often do not capture persistence, systemic propagation, or temporal instability in microbiome-associated disease. Host-microbiome decoupling is defined here as a progressive reduction in functional coordination between host regulatory systems and microbial ecological behavior. The concept refers to conditions in which microbial signals, activities, or rhythmic patterns no longer remain aligned with host physiological regulation. A hallmarks-based framework is proposed to examine biological domains in which coordination between host regulation and microbial ecology deteriorates. Core hallmarks include breakdown of signaling fidelity, microbiome-driven immune miscalibration, barrier compartment failure, endocrine-microbiome uncoupling, ecological destabilization, and temporal desynchronization between host circadian programs and microbial oscillations. Additional dimensions include pathological microbial metabolite dominance with epigenetic embedding, endocrine and neuro-microbiome regulatory uncoupling, ecological destabilization of microbiome functional capacity, and temporal desynchronization between host circadian programs and microbial oscillations. Across inflammatory, metabolic, neurodegenerative, and neoplastic conditions, microbial activity may operate outside normal ecological constraints, influencing immune regulation, metabolic signaling, neuroimmune communication, and tumor-associated processes. Within this framework, resilience, signaling proportionality, host responses appropriately scaled to microbial input, and temporal coordination represent central properties of host-microbiome compatibility.},
}

@article {pmid42058119,
year = {2026},
author = {Qu, HL and Li, JN and Gao, Y and Zhang, XB and Yang, SD},
title = {From association to intervention: Semantic trajectories and knowledge frontiers in epilepsy-gut microbiota research revealed by bibliometrics and NLP.},
journal = {IBRO neuroscience reports},
volume = {20},
number = {},
pages = {609-624},
pmid = {42058119},
issn = {2667-2421},
abstract = {BACKGROUND: Research on the epilepsy-gut microbiota axis is accelerating, yet its conceptual evolution and translational signals remain difficult to track across disciplines. Here, we propose a semantic-bibliometric fusion framework that combines network-based science mapping with phrase- and topic-level natural language processing (NLP) to resolve both structural and linguistic dynamics in the field.

METHODS: Publications indexed in the Web of Science Core Collection from January 1997 to November 17, 2025 were retrieved and analyzed using CiteSpace, VOSviewer, Pajek, and Scimago Graphica, complemented by an NLP pipeline for topic modeling and temporal phrase tracking. In total, 516 records were included.

RESULTS: Annual output rose sharply after 2021 and peaked in 2024, with China and the United States leading contributions. Beyond conventional hotspots, semantic analyzes revealed a field-wide shift from early infection/safety-oriented discourse to mechanism- and intervention-driven themes dominated by the microbiota-gut-brain axis.

CONCLUSION: The most prominent and expanding intervention clusters involved the ketogenic diet, short-chain fatty acids, probiotics, and fecal microbiota transplantation, while "Mendelian randomization" emerged as a nascent frontier signaling movement from correlation to causal inference. By integrating knowledge-network topology with discourse dynamics, this study delivers an up-to-date, multi-resolution map of epilepsy-microbiome research and highlights actionable directions for future work, including causal validation, multi-omics stratification, and trial-ready microbiome-informed interventions.},
}

@article {pmid42058141,
year = {2026},
author = {Ferraz, M and Santos, J and Vieira da Silva, M},
title = {A systematic review of indoor air quality in schools settings: Focus on microbiome and their relation to particulate matter and chemical pollutants.},
journal = {Public health in practice (Oxford, England)},
volume = {11},
number = {},
pages = {100790},
pmid = {42058141},
issn = {2666-5352},
abstract = {OBJECTIVES: Indoor air quality (IAQ) in schools is a growing concern due to its impact on children's health. Continuous exposure to indoor air pollutants, such as particulate matter (PM), carbon dioxide (CO2), and microorganisms, such as bacteria and fungi, can affect school performance, increase absenteeism, and trigger respiratory problems. This systematic review aimed to analyze the potential correlation between the presence of microorganisms and PM and chemical pollutants in school indoor environments.

STUDY DESIGN: A systematic literature review was conducted using the methodology PRISMA and 25 articles were selected.

METHODS: The current systematic review follow the steps: definition of research objectives; selection of the science databases; definition of keywords; establishment of the inclusion and exclusion criteria, evaluation process and evaluation and management of selected studies.

RESULTS: The findings highlight the significant presence of airborne microorganisms, including bacteria and fungi, often associated with PM and chemical pollutants such as CO2 and volatile organic compounds (VOCs). Positive correlations between CO2 and bacteria were observed in ten studies and were statistically significant in six of them. Both positive and negative correlations between fungi and CO2 were reported. Fungal genera such as Aspergillus spp. And Cladosporium spp. Were associated with particulate matter (PM). In general, the concentrations of bacteria and fungi were often correlated with PM levels, with larger particles (PM10) favoring the adhesion and transport of microorganisms, while smaller particles (PM2.5) remain suspended in the air for longer periods, increasing exposure.

CONCLUSIONS: Despite the methodological variations among the various studies, the results reinforce the need to create effective interventions to reduce pollutant concentrations to minimize health risks for occupants.},
}

@article {pmid42058331,
year = {2026},
author = {Gupta, S and Anushree, and Doke, G and Misra, D and Shukla, AK and Honey, B},
title = {Shared Pathophysiology and Early Detection Biomarkers in Endometriosis and Polycystic Ovary Syndrome (PCOS): Opportunities for AI-Enabled Screening.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e106013},
pmid = {42058331},
issn = {2168-8184},
abstract = {Endometriosis and polycystic ovary syndrome (PCOS) are common, multifactorial gynecological disorders shaped by endocrine imbalance, immune dysfunction, metabolic disruption, genetic susceptibility, and environmental exposures. Despite their major contribution to infertility and long-term cardiometabolic morbidity, early detection remains poor because symptoms are nonspecific, phenotypes are heterogeneous, and diagnosis is still dominated by single-modality and symptom-driven pathways. This review addresses this gap by synthesizing 2015-2025 evidence on shared and disease-specific biological mechanisms and evaluating how artificial intelligence (AI) can improve scalable screening and risk stratification. A narrative and integrative methodology was applied using peer-reviewed studies retrieved from PubMed, Scopus, Web of Science, and Google Scholar, emphasizing diagnostic rigor and external validity. Key findings identify convergent pathways involving chronic low-grade inflammation, adipokine dysregulation, oxidative stress, microbiome-mediated estrogen signaling, ferroptosis-linked iron imbalance, mitochondrial dysfunction, and epigenetic regulation through microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Promising early-detection signals include age-stratified anti-Müllerian hormone (AMH) thresholds, circulating cell-free deoxyribonucleic acid (cfDNA) methylation markers, and reproductive tract microbial signatures. AI-based models, including transformer architectures and multimodal machine learning, show strong potential to integrate clinical, hormonal, imaging, omics, and digital symptom phenotyping into reproducible early screening frameworks. Clinical translation requires standardized diagnostic definitions, longitudinal multi-ethnic cohorts, explainable algorithms, and prospective validation. AI-enabled precision screening offers a practical pathway to shorten diagnostic delay and improve reproductive outcomes.},
}

@article {pmid42058649,
year = {2026},
author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A},
title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {6677609},
pmid = {42058649},
issn = {1687-918X},
abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.},
}

@article {pmid42058850,
year = {2026},
author = {Yang, M and Wan, M and Yang, L},
title = {Ecological strategies determine continuous cropping susceptibility in Panax and Achyranthes.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1791596},
pmid = {42058850},
issn = {1664-462X},
abstract = {INTRODUCTION: Medicinal plants frequently suffer from severe continuous cropping problems, yet it remains unclear whether divergent ecological strategies underlie species-specific susceptibility to this problem.

METHODS: In this study, we investigated rhizosphere assembly patterns in three continuous cropping-sensitive Panax species (P. ginseng, P. quinquefolius, P. notoginseng) and the resilient species Achyranthes bidentata by analyzing paired cultivated and uncultivated soil samples from four major production regions in China. We measured soil physicochemical properties and enzyme activities and characterized bacterial (16S) and fungal (ITS) communities via amplicon sequencing. Plant-specific effects were quantified using Log2 fold change relative to uncultivated controls.

RESULTS: The Panax species aggressively remodeled their rhizosphere, inducing significant acidification and ammonium accumulation (Log2 FC up to 1.64 in P. notoginseng) while suppressing nitrification enzymes, and assembled fungal-dominated microbiomes enriched with pathogenic Nectriaceae, including Ilyonectria (LDA = 4.2) and Neocosmospora (LDA = 5.3). Their co-occurrence networks showed reduced stability, with negative correlations as low as 3.2%, and functional prediction indicated activated terpenoid metabolism (+74.8%). In contrast, A. bidentata maintained a neutral pH while specifically increasing available phosphorus (Log2 FC = +1.74) and nitrate nitrogen (Log2 FC = +0.74), and it enriched beneficial Actinobacteria by 15-85% and Hypocreales fungi. Its networks retained structural stability, with negative correlations of 12.7-18.6%. Plant species explained 60.5% of bacterial and 46.2% of fungal community variation, overwhelmingly exceeding the effect of soil compartment.

CONCLUSION: We conclude that Panax employs a resource-acquisitive strategy that assembles unstable, pathogen-prone microbiomes, whereas A. bidentata adopts a resource-conservative strategy that fosters resilient communities. This ecological framework offers a predictive basis for developing tailored microbiome management in medicinal plant cultivation.},
}

@article {pmid42058859,
year = {2026},
author = {Zhang, Q and Gu, M and Li, G and Jing, H and Qi, M and Li, H and Li, M and Ding, L and Li, Z and Wei, P and Ji, X and Zhu, T and Zhao, H},
title = {Synergistic effects of biochar and microbial inoculants on rice productivity and soil fertility are mediated by a nitrogen-dependent microbial pathway.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1804182},
pmid = {42058859},
issn = {1664-462X},
abstract = {Excessive nitrogen (N) fertilizer application threatens soil health and sustainable rice production. We hypothesized that the combined application of biochar and microbial inoculants (B+M) could maintain rice yield under reduced N input through microbiome-mediated mechanisms, and that this effect may depend on an N threshold. To test this hypothesis, pot and field experiments were conducted using the rice cultivar Nanjing 9108 with four treatments: conventional N (CK), and three B+M treatments with 20% N reduction (N80), 40% N reduction (N60), and 0% N reduction (N100). The results indicated that compared to CK, the N100 and N80 treatments increased rice yield by 10.4-11.7% and 4.1-4.9%, and improved Nitrogen Partial Factor Productivity (NPFP) by 7.8-11.7% and 28.6-30.0%, respectively. In contrast, the N60 reduced yield by 3.9-4.6%. In pot experiments, 16S rRNA gene sequencing revealed that N100 and N80 enriched bacterial phyla (e.g., Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidota) and enhanced microbial functional genes linked to metabolism, genetic information processing, cellular processes, and environmental information processing, thereby increasing soil nutrient availability. Structural equation modeling demonstrated that the soil bacterial community was the fundamental driver of yield enhancement (model fit: χ[2]/df = 1.13, RMSEA = 0.042, CFI = 0.961). However, under 40% N reduction, the abundance of key phyla declined and microbial functional potential weakened, leading to reduced soil nutrient availability and yield. These findings reveal an N dependent microbial-mediated pathway governing the synergistic effects of biochar and microbial inoculants, identifying 20% N reduction with B+M as an optimal strategy for sustainable rice intensification.},
}

@article {pmid42058946,
year = {2026},
author = {Asadi, N and Yaslianifard, S and Hasheminejad, M and Qorbani, M and Mohammadzadeh, M},
title = {Population‑Specific Diversity of Dominant Vaginal Lactobacillus Species in Healthy Iranian Women and Those with Vaginitis: A Molecular Case‑Control Study.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {586988},
pmid = {42058946},
issn = {1179-1411},
abstract = {BACKGROUND: Lactobacillus species play a key role in maintaining vaginal microbial homeostasis and protecting against genital infections. Disruption of this microbial balance can increase susceptibility to vaginitis. Population-specific variations in the composition of vaginal Lactobacillus communities may influence disease risk and therapeutic responses. This study aimed to evaluate the distribution of major vaginal Lactobacillus species in healthy Iranian women and those with vaginitis using species-specific molecular assays.

METHODS: In this case-control study, 100 women with clinically confirmed vaginitis and 100 healthy controls were enrolled. Vaginal swabs were examined by Gram staining, followed by DNA extraction and PCR amplification using universal and species-specific 16S rRNA primers targeting L. iners, L. crispatus, L. acidophilus, L. gasseri, and L. jensenii. Associations between bacterial species and clinical status were evaluated using Odds Ratio (OR), Relative Risk (RR), Phi coefficient (Φ), and Chi-square tests.

RESULTS: Lactobacillus spp. were detected in 97% of healthy women compared with 53% of symptomatic participants. L. jensenii and L. acidophilus were significantly more prevalent in healthy individuals, demonstrating strong protective associations with vaginal health. In contrast, L. iners was more frequently detected in women with vaginitis, consistent with its proposed role as a transitional species associated with microbiome instability. Although L. crispatus is often reported as protective in other populations, it did not show a statistically significant protective association in this study population.

CONCLUSION: Our findings highlight the protective association of dominant Lactobacillus species, particularly L. jensenii and L. acidophilus, in maintaining vaginal microbial balance. The higher prevalence of L. iners among symptomatic women further supports its association with disturbed vaginal microbiota. These results suggest the presence of population-specific microbial patterns and underscore the importance of considering regional microbiome characteristics when developing diagnostic approaches and probiotic-based interventions.},
}

@article {pmid42059388,
year = {2026},
author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA},
title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0360225},
doi = {10.1128/spectrum.03602-25},
pmid = {42059388},
issn = {2165-0497},
abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.},
}

@article {pmid42059393,
year = {2026},
author = {Zhang, T and Yu, Y and Zhang, C and Zhang, M and Yuan, S and Wang, Y and Dai, K and Zhang, L and Su, Y and Zhang, M},
title = {Multi-omics analysis reveals the alterations in the tumor microbiome and metabolome associated with cervical cancer lymph node metastasis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0224725},
doi = {10.1128/spectrum.02247-25},
pmid = {42059393},
issn = {2165-0497},
abstract = {UNLABELLED: Lymph node metastasis (LNM) is the primary mode of cervical cancer (CC) metastasis and is associated with a poorer prognosis. A comprehensive understanding of the underlying mechanisms driving LNM is critical to improving CC patient outcomes. Previous studies have demonstrated that alterations in the intratumor microbiome contribute to tumor progression, with metabolic regulation as a key mechanism. This study aims to investigate the role of intratumor microbiota and tumor metabolism in CC LNM. The microbiome analysis revealed significant differences in the diversity and composition of the intratumor microbiome between CC with and without LNM. Caulobacter and Porphyromonas were the most prominent genus markers for CC with LNM and CC without LNM, respectively. Alterations in tumor metabolism were also observed through global untargeted metabolomics and high-resolution spatial metabolomics, with pathways such as breast cancer, prolactin signaling, histidine metabolism, ovarian steroidogenesis, cysteine and methionine metabolism, and estrogen signaling being significantly altered in CC with LNM. Correlation analysis identified a strong association between specific intratumor microbes (especially Porphyromonas and Virgibacillus) and tumor metabolism. Additionally, our findings suggest a potential trend of phospholipid upregulation in tumor tissues during CC LNM. In summary, our findings underscore the critical role of intratumor microbiota and tumor metabolism in CC LNM, providing valuable insights for developing novel diagnostic markers and therapeutic strategies to address this challenging aspect of cervical cancer.

IMPORTANCE: This study comprehensively characterized the intratumor microbiota and tumor metabolism associated with lymph node metastasis (LNM) of cervical cancer (CC) by performing 16S ribosomal RNA sequencing, global untargeted metabolomics, and high-resolution spatial metabolomics on surgical CC specimens. Our findings revealed distinct compositions and diversities of intratumor microbiota between CC with and without LNM. Each group exhibited specific bacterial genera that could potentially serve as diagnostic tools for CC LNM, and Caulobacter and Porphyromonas were the most prominent biomarkers for CC with and without LNM, respectively. The significantly different distribution trend of metabolites was also observed between CC with and without LNM. Correlation analysis identified a strong association between specific intratumor microbes (especially Porphyromonas and Virgibacillus) and tumor metabolism. This study not only provides valuable insights for developing novel diagnostic markers and therapeutic strategies for CC LNM but also contributes to a deeper understanding of the underlying molecular mechanisms of it.},
}

@article {pmid42059394,
year = {2026},
author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS},
title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251025},
doi = {10.1128/spectrum.02510-25},
pmid = {42059394},
issn = {2165-0497},
abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.},
}

@article {pmid42059464,
year = {2026},
author = {Yu, K and Wang, N and Huang, X and Qiu, Y and He, X and Zhu, X and Zhou, X and Yu, P and Wei, G and Pi, Y and Ni, T},
title = {Environmental Enrofloxacin Exposure as a Modifiable Driver of Mitochondria-Mediated Intestinal Aging and Barrier Dysfunction.},
journal = {Aging cell},
volume = {25},
number = {5},
pages = {e70526},
pmid = {42059464},
issn = {1474-9726},
support = {2023YFC3603300//National Key Research and Development Program of China/ ; 2023SHZDZX02//Shanghai Municipal Science and Technology Major Project/ ; },
mesh = {*Enrofloxacin/adverse effects ; *Mitochondria/drug effects/metabolism ; Animals ; Humans ; *Aging/drug effects ; Gastrointestinal Microbiome/drug effects ; *Intestinal Mucosa/drug effects/metabolism ; *Anti-Bacterial Agents/adverse effects ; Zebrafish ; *Intestines/drug effects/pathology ; Female ; *Environmental Exposure/adverse effects ; Middle Aged ; Male ; Aged ; },
abstract = {Environmental antibiotic pollution is an underexplored contributor to gut aging and chronic intestinal diseases. We provide evidence that chronic exposure to enrofloxacin (ENR), a commonly detected veterinary antibiotic, accelerates gut aging and disease progression through a mitochondria-centered mechanism. In a population-based cross-sectional analysis, recent antibiotic use was associated with increased biological age and a higher risk of diarrhea in middle-aged and older adults, supporting a link between antibiotic exposure and impaired gut health and aging processes. Using zebrafish and intestinal epithelial cell models, we demonstrate that low-dose ENR exposure impairs intestinal function, characterized by increased permeability, reduced mucus secretion, tight junction disruption, and chronic inflammation. Multi-omics profiling revealed that ENR induced gut microbial dysbiosis, reduced metabolic diversity, and intestinal hypoxia. Mitochondrial dysfunction, particularly impaired oxidative phosphorylation, was identified as the key driver of epithelial damage. Remarkably, treatment with pyrroloquinoline quinone, a mitochondrial-targeted antioxidant, reversed ENR-induced mitochondrial injury, restored intestinal integrity, reduced inflammation, and partially normalized the microbiome. Stratified analyses in the human cohort showed that higher gut microbiota-related diet quality and antioxidant capacity mitigated antibiotic-associated aging and diarrhea risk. These findings highlight mitochondrial protection and microbiota optimization as promising therapeutic strategies.},
}

*Enrofloxacin/adverse effects
*Mitochondria/drug effects/metabolism
Animals
Humans
*Aging/drug effects
Gastrointestinal Microbiome/drug effects
*Intestinal Mucosa/drug effects/metabolism
*Anti-Bacterial Agents/adverse effects
Zebrafish
*Intestines/drug effects/pathology
Female
*Environmental Exposure/adverse effects
Middle Aged
Male
Aged

@article {pmid42059507,
year = {2026},
author = {Osei-Karikari, K and Jones, K and Erickson, A and Myles, IA},
title = {Emerging microbiome-based therapies for atopic eczema: clinical insights and future development.},
journal = {Expert opinion on emerging drugs},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728214.2026.2667256},
pmid = {42059507},
issn = {1744-7623},
abstract = {INTRODUCTION: Despite growing evidence that environmental factors and microbiome dysbiosis constitute the majority of disease pathogenesis, most current therapies target inflammation, barrier dysfunction, and/or S. aureus overgrowth. However, given the emerging understanding of microbiome-mediated and environmentally driven disease mechanisms, expanding therapeutic strategies to include dysbiosis and upstream environmental contributors represents a promising direction for future research.

AREAS COVERED: This manuscript will review the strengths and limitations of the standard treatments for AD, including emollients, topical corticosteroids, calcineurin inhibitors, and systemic immunomodulators. The focus however will be on the emerging microbiome-based therapies, specifically products containing live microorganisms (biotherapeutics). The potential for, and challenges against, biotherapeutics to grow within the market of AD treatment will be discussed.

EXPERT OPINION: Immune suppressive approaches will remain limited to symptomatic control. These treatments will also be limited by tradeoffs inherent to the balance between symptom control and side effects of immune suppression. To successfully aide patients, topical biotherapeutics will need to overcome pharmaceutical-centric paradigms, academic dogma, and regulatory inertia. Limitations in current therapies, patient need, along with the potential to offer prevention against AD development, will likely propel biotherapeutics forward.},
}

@article {pmid42059556,
year = {2026},
author = {Dunham, SJB and Willkeen, GA and Darby, B and Corley, JM and Hahn, A and Klapper, I and Bean, HD and Caverly, LJ and Thornton, CS and Martin, C and Quinn, RA and Widder, S and Bailey, BA and Wagner, BD and Garg, N and Planet, PJ and Hunter, RC and LiPuma, JJ and Rohwer, F and Whiteson, KL},
title = {The Guild Model of CF Airway Microbial Ecology.},
journal = {mBio},
volume = {},
number = {},
pages = {e0366825},
doi = {10.1128/mbio.03668-25},
pmid = {42059556},
issn = {2150-7511},
abstract = {Ecological guilds are groups of organisms that utilize the same class of resources and occupy similar niches, regardless of their taxonomic identities. Here we propose the Guild Model for Cystic Fibrosis Airway Microbial Ecology, which considers the ecological function and wider role of each microbe in the ecosystem. This model consists of four functional guilds: (i) "Brewers" metabolize host-derived substrates (e.g., mucins) and produce fermentation products; (ii) "Drunkards" exploit the metabolic niche built by Brewers, consuming fermentation products and secreting exopolysaccharides to build biofilms; (iii) "Putrifiers" produce toxic compounds causing inflammation and tissue necrosis; and (iv) "Nihilists" are specialist pathogens characterized by intracellular or lytic life cycles and cytotoxin production. By focusing on microbial function and the broader community context, this model offers a refined framework for interpreting cystic fibrosis airway ecology. Although developed for CF, the Guild Model is adaptable to other diseases influenced by microbial ecology.},
}

@article {pmid42059571,
year = {2026},
author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF},
title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164025},
doi = {10.1128/msystems.01640-25},
pmid = {42059571},
issn = {2379-5077},
abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.

IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.},
}

@article {pmid42059606,
year = {2026},
author = {Yin, K and Ma, S and Yang, J and Feng, M and Zuo, Y and Wang, F},
title = {Gut microbiota composition and tumor immune features in meningioma patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0248525},
doi = {10.1128/spectrum.02485-25},
pmid = {42059606},
issn = {2165-0497},
abstract = {UNLABELLED: Meningiomas are prevalent intracranial tumors with poorly understood extraneural drivers. While the gut-brain axis influences neuro-oncogenesis, meningioma-specific gut microbiome alterations and their clinical implications remain uncharacterized. This study integrated 16S rRNA sequencing of fecal samples from 15 treatment-naïve WHO grade I meningioma patients (MPs) and 15 healthy controls (HCs) with immunohistochemical profiling of tumor immune infiltrates (MPO[+] neutrophils, CD68[+] macrophages, CD3[+] T cells). Compared with HCs, MPs exhibited significantly reduced alpha diversity (Shannon index, P = 0.026) and distinct beta diversity (permutational multivariate analysis of variance, P < 0.0009). Taxonomic analysis revealed enrichment of Proteobacteria (28.82% vs. 2.46%, P = 0.001), specifically Escherichia_Shigella at the genus level (25.95% vs. 1.61%, P = 0.008), along with depletion of Bacteroidaceae and Ruminococcaceae. LEfSe identified Escherichia_Shigella as the top meningioma-enriched biomarker. In diagnostic modeling, Escherichia_Shigella achieved an area under the receiver operating characteristic curve of 95.11% (95% CI: 86.91%-100%) for WHO grade I meningioma detection. Critically, Escherichia_Shigella abundance positively correlated with intratumoral MPO[+], CD68[+], and CD3[+] cell densities (all P < 0.05), whereas Ruminococcaceae showed inverse correlations. The 16S rRNA sequencing data are publicly available in the GSA database under accession number CRA027974. This study provides the first evidence of gut dysbiosis in grade I meningioma, characterized by Escherichia_Shigella dominance and depletion of immunomodulatory commensals. This signature correlates with increased immune infiltration and holds promise as a novel biomarker.

IMPORTANCE: Detailed exploration of host-microbe interactions can be worthwhile. Gut dysbiosis has been implicated in neuroinflammation, blood-brain barrier disruption, and oncogenesis in multiple cancer types, including gliomas. However, the gut microbiota composition and metabolic characteristics in patients with meningioma have not been previously reported. To address these critical knowledge gaps, we conducted a case-control study integrating 16S rRNA sequencing, clinical phenotyping, and immunohistochemical profiling. Our study revealed significant alterations in the gut microbiota of MPs, characterized by reduced alpha diversity, enrichment of Proteobacteria, and depletion of beneficial taxa, including Bacteroidaceae and Ruminococcaceae. Critically, we identified Escherichia_Shigella as a potential diagnostic biomarker and demonstrated strong correlations between elevated Escherichia_Shigella/Enterobacteriaceae abundance and increased intratumoral infiltration of MPO⁺ neutrophils, CD68⁺ macrophages, and CD3⁺ T cells. These findings are the first evidence that gut microbiome dysbiosis is closely associated with meningioma inflammation.},
}

@article {pmid42059625,
year = {2026},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0362625},
doi = {10.1128/spectrum.03626-25},
pmid = {42059625},
issn = {2165-0497},
abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.

IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.},
}

@article {pmid42059647,
year = {2026},
author = {Ma, X and Jiang, Z and Yang, T and Zhang, H and Lu, W and Liu, K and Fan, X and Yang, G and Wu, S},
title = {Integrated multi-omics analysis reveals gut dysbiosis and altered energy metabolism in Chinese ALS patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0060926},
doi = {10.1128/spectrum.00609-26},
pmid = {42059647},
issn = {2165-0497},
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder with a complex etiology. Emerging evidence implicates gut microbiota dysbiosis in ALS pathology via the gut-brain axis, yet the specific integrative profile of the gut microbiome, virome, and metabolome, particularly in Chinese patients, remains incompletely characterized. Although global diversity indices showed no significant differences, taxonomic analysis revealed distinct compositional shifts. The ALS microbiome was characterized by a significant depletion of beneficial anti-inflammatory genera, specifically Akkermansia and Faecalibacterium, and an expansion of opportunistic pathogens such as Escherichia and oral-associated taxa (e.g., Streptococcus). We also observed a specific alteration in the gut virome, with viral genera including Puppervirus and Donellivirus enriched in ALS patients. Functionally, the ALS microbiome exhibited a marked upregulation of pathways involved in L-ascorbate (vitamin C) degradation and fatty acid biosynthesis, suggesting a microbial contribution to systemic oxidative stress. Metabolomic analysis corroborated these findings, identifying 271 differentially expressed metabolites. ALS patients showed elevated levels of inflammatory lipids (e.g., LysoPC) and metabolic intermediates of the tricarboxylic acid (TCA) cycle, alongside a downregulation of antioxidants. Integrative analysis highlighted profound dysregulation in porphyrin metabolism, oxidative phosphorylation, and energy homeostasis. Our findings demonstrate that ALS is associated with a specific dysbiotic gut ecosystem characterized by the loss of protective commensals, unique viral signatures, and functional metabolic reprogramming that exacerbates host oxidative stress and energy deficits. These results provide new insights into gut-brain interactions and highlight microbial antioxidant depletion as a potential therapeutic target.IMPORTANCEAmyotrophic lateral sclerosis (ALS) is a devastating disease with no cure. While gut bacteria are known to influence brain health, we still do not understand exactly how they contribute to ALS progression. In this study, we used advanced DNA sequencing and chemical analysis to deeply examine the gut ecosystem of ALS patients. Beyond just cataloging which bacteria are present, we discovered what they are doing: the ALS microbiome actively breaks down vitamin C (a critical antioxidant) and disrupts energy metabolism. We also found a loss of protective bacteria that maintain the gut barrier. These findings are significant because they suggest that the gut microbiome in ALS patients may be actively fueling the disease by depleting the body's antioxidant reserves. This points to a new potential treatment strategy: targeting these specific bacterial functions or replenishing specific metabolites to protect motor neurons.},
}

@article {pmid42059891,
year = {2026},
author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G},
title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-026-06221-1},
pmid = {42059891},
issn = {1420-9071},
support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; },
}

@article {pmid42060056,
year = {2026},
author = {Böhm, D and Guchelaar, HJ and Smidt, ML and Deenen, MJ},
title = {Microbiome-Modulating Strategies in Anticancer Therapy: A Review of Current Evidence and Recommendations for Further Treatment Improvement.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42060056},
issn = {1867-1314},
}

@article {pmid42060063,
year = {2026},
author = {Lee, SY and Cho, KS},
title = {Burkholderia sp. ZF6-mediated mitigation of Cd and Zn stress in contaminated soil: effects on Chinese cabbage growth and rhizosphere microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42060063},
issn = {1614-7499},
support = {2022R1A2C2006615//National Research Foundation of Korea/ ; },
abstract = {This study investigated the effects of Burkholderia sp. ZF6, a plant growth-promoting bacterium with heavy metal resistance genes (cadA and zntA), on the growth of Chinese cabbage (Brassica rapa subsp. pekinensis) and cadmium (Cd)/zinc (Zn) removal in contaminated soils. ZF6 inoculation significantly increased root biomass (over twofold) and enhanced soil Cd and Zn removal efficiencies by approximately 2-4 times (19.9% for Cd and 11.5% for Zn). The abundance of cadA and zntA genes increased by 1.2-2.7 times, suggesting an enrichment of heavy metal-resistant microbial populations. Microbial community analysis showed that ZF6 inoculation reshaped the rhizosphere microbiome, increasing the relative abundance of genera such as Klebsiella, Agrobacterium, Burkholderia, Sphingomonas, and Pseudomonas. Notably, the abundance of Burkholderia, corresponding to ZF6, exhibited an increasing trend over time. Network analysis further indicated that microbial interactions became more complex in ZF6-treated soils (1.7-4.5-fold higher connectivity). Correlation analysis revealed that zntA abundance was associated with selected functional genes (e.g., K04565 and K01534) and inversely related to soil Cd concentration, suggesting a potential link between microbial functional potential and metal dynamics. Overall, ZF6 inoculation facilitated the restructuring of soil microbial communities to favor heavy metal-resistant bacteria. These findings highlight the potential of ZF6 as a scalable microbial-assisted phytoremediation strategy, although further validation under field conditions is required.},
}

@article {pmid42060722,
year = {2026},
author = {Rodriguez Hernandez, CJ and Cruz-Cruz, A and Shrestha, CL and Terekhova, M and Chen, P and Perpich, J and Potempa, B and Carey, K and Rohlfing, M and Peeples, ME and Grayson, MH and Potempa, J and Artyomov, M and Lamont, RJ and Bagaitkar, J},
title = {Gingipain proteases from the bacterium Porphyromonas gingivalis confer protection against airway viral infection.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2503100123},
doi = {10.1073/pnas.2503100123},
pmid = {42060722},
issn = {1091-6490},
support = {DE031756//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDR)/ ; },
mesh = {*Porphyromonas gingivalis/enzymology ; Animals ; Mice ; Humans ; Gingipain Cysteine Endopeptidases ; *Respiratory Syncytial Virus Infections/immunology/prevention & control/virology ; *Cysteine Endopeptidases/metabolism ; *Adhesins, Bacterial/metabolism ; Sendai virus/immunology ; Interferons/metabolism ; Respiratory Syncytial Viruses/immunology ; Mice, Inbred C57BL ; *Respiratory Tract Infections/virology/immunology ; },
abstract = {Physical interactions with bacterial colonizers at mucosal barrier surfaces can have beneficial or detrimental effects on viral infectivity and transmission. The oropharyngeal mucosal surface is a major portal of entry for many pathogenic respiratory viruses, such as respiratory syncytial virus (RSV), and also harbors a rich and diverse microbiome. Whether oropharyngeal bacteria directly or indirectly influence host susceptibility to respiratory viruses remains unknown. Here, we show that Porphyromonas gingivalis, an oral pathobiont, potently and uniquely suppresses airway epithelial antiviral immunity by degrading interferons (IFNs) and transcriptionally repressing multiple IFN-stimulated genes (ISGs), which are essential for providing resistance to viral infection. Despite inducing a state of IFN hyporesponsiveness, we found that P. gingivalis counterintuitively protected against severe infection by RSV and the closely related murine-specific Sendai virus (SeV) in two independent models: human airway bronchial epithelial transwell cultures and airway infection in mice. This protection was conferred by the activity of P. gingivalis cysteine proteases (gingipains) that cleaved envelope glycoproteins on RSV and SeV, thereby impairing their infectious capacity. Thus, our data show a nuanced role for P. gingivalis in modulating host susceptibility to viral infection. While P. gingivalis can significantly inhibit host IFN responses, its proteases preemptively reduce viral infectious capacity, protecting the host from severe damage associated with respiratory infections.},
}

*Porphyromonas gingivalis/enzymology
Animals
Mice
Humans
Gingipain Cysteine Endopeptidases
*Respiratory Syncytial Virus Infections/immunology/prevention & control/virology
*Cysteine Endopeptidases/metabolism
*Adhesins, Bacterial/metabolism
Sendai virus/immunology
Interferons/metabolism
Respiratory Syncytial Viruses/immunology
Mice, Inbred C57BL
*Respiratory Tract Infections/virology/immunology

@article {pmid42060821,
year = {2026},
author = {Yeasmin, F and Babu, MR and Saha, P and Biswas, S and Guha, A and Islam, T and Gupta, DR and Rahman, MM},
title = {Draft genome sequence of Bacillus cereus HS120, a probiotic candidate isolated from the gut of hilsa (Tenualosa ilisha).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0015126},
doi = {10.1128/mra.00151-26},
pmid = {42060821},
issn = {2576-098X},
abstract = {Bacillus cereus HS120 was isolated from the stomach of a healthy hilsa (Tenualosa ilisha) in Nabogonga River, Bangladesh. Here, we present a 5,673,590-bp draft genome with 35.23 % GC content, which encodes numerous biosynthetic gene clusters for secondary metabolites and lacks detectable virulence factors, supporting its potential as an aquaculture probiotic.},
}

@article {pmid42060842,
year = {2026},
author = {Arroyo-Mendoza, M and Lorenzi, H and Phillips, GJ and Hinton, DM},
title = {Escherichia coli pathobionts and Crohn's disease: varied genetic paths leading to similar phenotypes.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0001626},
doi = {10.1128/jb.00016-26},
pmid = {42060842},
issn = {1098-5530},
abstract = {Crohn's disease (CD), an inflammatory bowel disease that arises from an immune attack on the gastrointestinal tract, affects roughly 1.6 million Americans. The etiology of CD and the other major irritable bowel disease, ulcerative colitis, is not known, but host genetics and immunology, the gut microbiome, and environmental factors are all thought to be involved. In addition, adherent-invasive Escherichia coli (AIEC) strains, which are able to adhere to and invade epithelial cells and macrophages, are frequently found to be associated with CD. Besides their adherence and invasion properties, key features that distinguish AIEC from commensal E. coli include increased biofilm formation, increased antibiotic resistance, and survival/replication within macrophages. However, these pathobionts lack genetic features typical of frank pathogens. Thus, the potential role AIEC plays in CD pathogenesis is not clear. The E. coli pathobiont LF82, isolated from the ileum of a patient with CD, has been a well-studied, prototypic AIEC. Dozens of single-nucleotide polymorphisms (SNPs) distinguish LF82 and other AIEC from commensal E. coli, suggesting that some of these genetic features might account for particular LF82 phenotypes. In this review, we summarize changes in the CD gut, the association of AIEC with CD, genes and SNPs associated with AIEC, and recent work connecting a specific SNP within a bacterial RNA polymerase gene to the expression of genes associated with the LF82 lifestyle.},
}

@article {pmid42061010,
year = {2026},
author = {Garrigós, M and Jiménez-Peñuela, J and Saavedra, I and Veiga, J and García-López, MJ and Garrido, M and Ruiz-López, MJ and Figuerola, J and Moreno-Indias, I and Martínez-de la Puente, J},
title = {Corrigendum to 'Interactions between urbanization, malaria infection and avian cloacal microbiome' [Environ. Res. 297 (2026) 124073].},
journal = {Environmental research},
volume = {301},
number = {},
pages = {124397},
doi = {10.1016/j.envres.2026.124397},
pmid = {42061010},
issn = {1096-0953},
}

@article {pmid42061087,
year = {2026},
author = {Cavaleri, MP and Ardondi, L and Vitali, I and Sileo, L and Ferroni, L and Cappucci, IP and Rigon, L and Burgio, F and Franceschini, D and Degasperi, M and Pezzotti, G and Rubini, G and Rubini, A and Lovatti, L and Pinton, P and Zavan, B},
title = {Apple derived extracellular vesicles as positive modulators of glial inflammation and gut-brain axis signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158232},
doi = {10.1016/j.phymed.2026.158232},
pmid = {42061087},
issn = {1618-095X},
abstract = {Plant-derived extracellular vesicles (PDEVs) are emerging as bioactive dietary particles with the capacity to modulate mammalian physiology. Here, we characterize the structure and functional properties of apple-derived extracellular vesicles (ADEVs) and evaluate their relevance to neuroimmune and gut-brain communication. ADEVs exhibit canonical PDEV features and elicit rapid IP3-dependent Calcium (Ca[2+]) signaling in fibroblasts while preserving blood-brain barrier integrity. Neural assays reveal marked cell-type specificity: ADEVs are efficiently internalized by glial cells and activate glial Ca[2+] signaling yet display minimal neuronal uptake and no detectable Ca[2+] response in differentiated SH-SY5Y neurons. Consistent with this selectivity, ADEVs attenuate TNF-α-induced cytokine secretion in activated glia but remain inert in resting neural cells. Although capable of encapsulating L-DOPA efficiently, ADEVs fail to deliver functional neuroprotection against rotenone toxicity, indicating limited neuronal compatibility for dopaminergic cargo. In parallel, using advanced in vitro colon simulation platforms, ADEVs modulate the colonic microbiome in a dose-dependent manner, promoting carbohydrate fermentation and short-chain fatty acid production while reducing proteolytic metabolism under physiologically relevant conditions, with sustained, region-specific effects during prolonged exposure. In vivo, ADEV administration in dogs with chronic intestinal inflammation is associated with altered circulating serotonin levels, suggesting engagement of gut-brain neurochemical pathways with potential implications for mood regulation. Collectively, these findings identify ADEVs as biocompatible, glia-responsive plant vesicles with potential neuromodulatory activity, while delineating intrinsic constraints in their use as neuronal drug-delivery systems.},
}

@article {pmid42061103,
year = {2026},
author = {Aliniay-Sharafshadehi, S and Sheykhhasan, M and Sharifi, K and Ansari-Mohseni, A and Yousefi, MH and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Dental Pulp Stem Cells for the Management of Plaque Biofilm-Associated Infections : A Review.},
journal = {International dental journal},
volume = {76},
number = {4},
pages = {109559},
doi = {10.1016/j.identj.2026.109559},
pmid = {42061103},
issn = {1875-595X},
abstract = {This structured narrative review synthesises current evidence (2000-2025) on the antimicrobial, immunomodulatory, and regenerative properties of dental pulp stem cells (DPSCs) in the context of plaque-induced gingivitis and oral biofilm infections. We systematically reviewed peer-reviewed literature from PubMed, Scopus, and Web of Science via keywords related to DPSCs, oral biofilms, antimicrobial peptides (eg, β-defensins, LL-37), and immunomodulation. Unlike conventional antimicrobial therapies that solely target pathogen eradication, DPSCs offer a dual-function strategy: (1) direct microbial control through the secretion of antimicrobial peptides that disrupt Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans and (2) resolution of inflammation via macrophage M2 polarisation, suppression of IL-1β/TNF-α (Interleukin-1β and Tumor Necrosis Factor-α), and microbiome rebalancing. Additionally, DPSCs support periodontal tissue regeneration through trophic signalling and differentiation into periodontal lineage cells. Critically, no clinical trials to date have evaluated DPSCs for the management of gingivitis. This review highlights DPSCs as promising, antibiotic-sparing therapeutic candidate and outlines key knowledge gaps for future translational research.},
}

@article {pmid42061108,
year = {2026},
author = {van Kalkeren, CAJ and van Deuren, T and Huang, W and Park, SQ and Blaak, EE and Adam, TC},
title = {Neurocognition and food cue-related brain reactivity after fiber supplementation within a high-protein, plant-based diet in individuals with overweight and prediabetes: A randomized-controlled trial (the DISTAL-study).},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106668},
doi = {10.1016/j.clnu.2026.106668},
pmid = {42061108},
issn = {1532-1983},
abstract = {BACKGROUND: The increasing prevalence of obesity and related diseases, such as type 2 diabetes mellitus (T2DM) and neurocognitive dysfunction, warrants sustainable and effective strategies for treatment and prevention. A healthy diet, containing dietary fibers that are fermented by the gut microbiome, produces short-chain fatty acids, among other metabolites, known to alleviate insulin resistance. SCFA also may protect against neurocognitive decline and increase satiety through food-reward-related pathways of the gut-brain axis, thereby contributing to sustainable dietary habits and counteracting obesity and -related diseases. We therefore studied the effects of dietary fibers in the context of a high-protein, partially plant-based diet on neurocognitive functioning and food-reward related brain activity.

METHODS: This 12-week RCT compared a potato fiber and sugar beet pectin supplement to an isocaloric placebo (maltodextrin), both within a high-protein (±45% plant-based) diet. We investigated the effects on food-reward-related brain activity using functional magnetic resonance imaging (fMRI) with visual food stimuli, comprising high-calorie, low-calorie, and non-food items. Neurocognitive performance was tested with the Cambridge Neurocognitive Test Automated Battery (CANTAB). Furthermore, satiety hormones, stress, and general well-being were assessed, and associations with cardiometabolic markers were explored.

RESULTS: Overall, there was a trend towards an increased amygdala BOLD response over time in the fiber group compared to placebo, independent of visual stimuli conditions. The change in amygdala activity was positively associated with increased colonic permeability in both groups. After the intervention, both groups showed improvements in psychomotor speed, visual memory, and learning abilities, and reported less subjective hunger after 12 weeks on a high-protein, partially plant-based diet. General well-being, stress, and satiety hormone concentrations remained unchanged.

CONCLUSION: Twelve weeks of fiber supplementation did not change brain activity induced by visual food cues in reward-related brain regions. However, the high-protein, partially plant-based diet seemed to provide neurocognitive benefits, improving psychomotor speed and memory, and decrease perceived hunger.},
}

@article {pmid42061238,
year = {2026},
author = {Rahman, FA and Granados, EAF and Adhikari, Y and Naeem, M and Rochell, S and Bourassa, D and Poudel, S},
title = {Longitudinal analysis of broiler cecal microbiome: unraveling the species level dynamics across age and sex.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106911},
doi = {10.1016/j.psj.2026.106911},
pmid = {42061238},
issn = {1525-3171},
abstract = {This study investigated the longitudinal dynamics of the cecal microbiome in male and female broiler chickens from hatch (d 0) to market age (d 42) using full-length 16S rRNA gene sequencing via Oxford Nanopore Technology. Microbial composition, diversity, and differential abundance were assessed across four time points (d 0, 14, 28, and 42). Alpha diversity analyses showed no significant differences between male and female within the same age group. The longitudinal comparisons revealed significantly lower diversity on d 0 compared to later timepoints in both male and female. Beta diversity analyses using Bray-Curtis and Jaccard metrics demonstrated distinct microbial community clustering at d 0 and a major compositional shift by d 14. PERMANOVA confirmed age as a significant factor influencing microbial composition. However, both sex and age influenced the dominant bacterial species. On d 0, Enterococcus faecalis was the most abundant in both males (58.57%) and females (61.35%). Whereas on d 42, Romboutsia ilealis (14.12%) became the predominant species in female and Negativibacillus massiliensis (9.7%) in males. In addition to the variation in the dominant species, differential abundance analysis revealed that bacterial species such as Clostridium celatum, C. disporicum, C. jeddahitimonense, and C. saudiense, had significantly higher abundance at d 0 compared to later time points in both males and females. Whereas bacterial species such as Bittarella massiliensis, Turicibacter bilis,and Turicibacter sanguinis had significantly higher abundance at d 28 and 42. Furthermore, core microbiome analysis showed microbial richness plateaued at approximately 330-350 species from d 14 onward. Our results indicate that early microbial communities are more sex-specific and they gradually converge over time probably due to extrinsic environmental factors.},
}

@article {pmid42061249,
year = {2026},
author = {Biasato, I and Hassan, T and Buzzanca, D and Bagatella, S and Schiavone, A and Capucchio, MT and Gasco, L and Kenéz, Á and Ferrocino, I},
title = {Gut health in broiler chickens fed a mixture of Hermetia illucens and Tenebrio molitor meals: does it have a key role in shaping bird performance?.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106966},
doi = {10.1016/j.psj.2026.106966},
pmid = {42061249},
issn = {1525-3171},
abstract = {Insect meals are promising sustainable protein sources for poultry, but comprehensive insights into their effects on gut health and growth performance are lacking. This study is the first to elucidate relationships between gut health parameters and performance in broilers fed Hermetia illucens (HI) and Tenebrio molitor (TM) meals at 5% or 10% inclusion levels, singly or in a 1:1 combination. A 37-day trial used 420 male Ross 308 chicks randomly allocated to seven treatments: control (C), HI5 (5% HI), HI10 (10% HI), TM5 (5% TM), TM10 (10% TM), MIX5 (5% MIX), and MIX10 (10% MIX). By integrating intestinal histomorphometry, mucin histochemistry, multi-organ histopathology, and multi-omics cecal microbiome characterization, we identified key structural, microbial, and metabolic biomarkers associated with performance variations (false discovery rate [FDR]<0.05 and P < 0.05 for microbiome and histomorphology, respectively). High-performing groups (MIX5, TM5) showed microbiomes enriched in short-chain fatty acid-producing bacteria (Veillonellaceae, Butyricicoccus, Limosilactobacillus crispatus), positively correlated with ADG and ADFI (FDR<0.05) and negatively correlated with FCR (FDR<0.05). Favorable metabolomic profiles (increased dopamine, tyramine, malic and orotic acids; reduced 3-deoxyglucosone, hexanoylcarnitine [FDR<0.05]) and preserved balance between neutral (positively correlated with BW and ADFI [P < 0.05]) and acidic mucins (positively correlated with BW, ADFI and ADG, and negatively correlated with FCR [P < 0.05]) were also observed. Low-performing groups (MIX10, HI10) displayed microbiomes dominated by Ruminococcaceae, Alistipes, and l-Eubacterium (negatively correlated with FCR and associated with purine metabolism alterations [FDR<0.05]), alongside worsened morphology (tendency for reduced villus height in MIX10 [P = 0.07], positively and negatively correlated with ADG and FCR, respectively [P < 0.05], and thinner mucosal/muscular layers [P < 0.05]) and decreased neutral mucins (P < 0.05). TM10 maintained unaffected growth performance via beneficial taxa (Limosilactobacillus crispatus, Tyzzerella), and reduced Campylobacter jejuni and antimicrobial resistance genes (FDR<0.05). Jejunal inflammation, negatively correlated with ADG (P < 0.05), was not influenced by dietary treatments (P > 0.05). In conclusion, specific taxa (Butyricicoccus, Veillonellaceae, Limosilactobacillus crispatus), metabolites (dopamine, tyramine, malic and orotic acids), and mucosal features (villus height, mucin composition) were identified as biomarkers of optimal performance in insect-fed broilers.},
}

@article {pmid42061266,
year = {2026},
author = {Li, T and Wang, P and Zhi, Z and Li, Q and Guo, T and Zhou, J and Zhang, H and Zhang, J and Zhang, J},
title = {Modulation of cecal microbiota and metabolite profiles by Zanthoxylum bungeanum seeds enhances antioxidant capacity and meat quality in Pekin ducks.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {107010},
doi = {10.1016/j.psj.2026.107010},
pmid = {42061266},
issn = {1525-3171},
abstract = {Zanthoxylum bungeanum seeds (ZBS) are a bioactive-rich byproduct with potential as antibiotic alternatives, yet their systemic effects on waterfowl remain unclear. This study investigated the effects of dietary ZBS supplementation on growth performance, physiological status, meat quality, and the microbiome-metabolome profile in Pekin ducks. A total of 240 ducks (14-day-old) were assigned to four treatments containing 0% (CG), 1.5% (LG), 3.0% (MG), or 4.5% (HG) ZBS for 21 days. Trend analysis revealed a significant quadratic dose-response for growth performance (P< 0.05), identifying 1.5% as the optimal inclusion level for maximizing body weight. Physiologically, ZBS supplementation enhanced antioxidant capacity and liver function by linearly upregulating serum SOD, CAT, and GSH-Px activities while significantly reducing MDA, ALT, AST, and triglyceride levels (P< 0.05). Regarding meat quality, ZBS linearly increased breast meat redness (a*) and facilitated the linear deposition of glutamic acid and alpha-linolenic acid, mirroring the ZBS nutrient profile (P < 0.05). Consequently, this deposition optimized key nutritional indices, characterized by a linear reduction in the n-6/n-3 polyunsaturated fatty acid ratio (P< 0.01) and an improved BCAA/AAA ratio. Mechanistically, 16S rRNA sequencing indicated a beneficial filtering effect where ZBS reduced alpha diversity by suppressing inflammation-associated genera (Desulfovibrio, Fusobacterium) while enriching beneficial fermenters (Faecalibacterium, Barnesiella). Metabolomics further identified upregulated antioxidant and immunomodulatory metabolites, such as orsellinic acid and purine analogs, which correlated with improved host health. Collectively, ZBS functions as an ecological modulator that promotes liver health and meat nutritional value in a linear manner, while optimizing growth performance quadratically, with 1.5% identified as the optimal dosage.},
}

@article {pmid42061335,
year = {2026},
author = {Zhu, T and Hussain, M and Shi, C and Ruan, Y and Gao, X and Zhu, J and Wu, G},
title = {Transgenerational sublethal effects of emamectin benzoate and indoxacarb on Telenomus remus: Integrative insights from host-associated microbiome and transcriptome analyses.},
journal = {Ecotoxicology and environmental safety},
volume = {317},
number = {},
pages = {120193},
doi = {10.1016/j.ecoenv.2026.120193},
pmid = {42061335},
issn = {1090-2414},
abstract = {The extensive application of synthetic insecticides like emamectin benzoate (EB) and indoxacarb (IN), threatens ecologically beneficial parasitoids such as Telenomus remus. This study evaluated the transgenerational impacts of continuous exposure (over seven generations) to EB and IN on T. remus by integrating toxicity assays, life-history analysis, microbiome profiling, and transcriptomics. Acute risk assessment indicated EB posed a moderate risk (Risk Quotient, RQ > 50), while IN showed low acute risk (RQ < 50). After multigenerational selection, T. remus developed only minor tolerance (ratios of 1.47 for EB and 1.46 for IN) but incurred significant fitness costs; prolonged development (EB: 10.33 days vs. control: 9.00 days), reduced parasitism (EB: 82.07%; IN: 85.00% vs. control: 90.29%), and shortened female longevity. Host-associated microbiome analysis revealed disrupted community homeostasis, with a notable decline in dominant Wolbachia abundance (from 33.20% in controls). Transcriptomics identified limited differentially expressed genes (53 for EB, 52 for IN), suggesting physiological adaptation, with key changes enriched in detoxification (e.g., cytochrome P450s, UGTs) and immune pathways. Integrated correlation analyses (Mantel tests) linked microbial dysbiosis to altered host gene expression and reduced fitness. These findings highlight that even insecticides with low acute toxicity (like IN) or those inducing only minor tolerance shifts can cause severe transgenerational impairments. Correlations between microbiome alterations and transcriptomic changes suggest potential interactive mechanisms that warrant further validation. Field application rates and ecological risk assessments should be re-evaluated to account for these chronic sublethal effects to conserve T. remus in sustainable agro-ecosystems.},
}

@article {pmid41863002,
year = {2026},
author = {Wang, Y and Ling, W and Ouyang, L and Zhang, S and Zhou, H and Luo, T and Liu, S and Tang, J and Zhou, Z and Tang, L and Wang, Z and Wei, F and Huang, G},
title = {A lagging recovery: the delayed restoration of gut microbial diversity in Rhinolophus sinicus post-hibernation.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41863002},
issn = {2524-4671},
support = {32192420//National Natural Science Foundation of China/ ; 32322015//National Natural Science Foundation of China/ ; 20233ACB209001//Natural Science Foundation of Jiangxi Province/ ; 2023SSY02081//Jiangxi Provincial Key Laboratory of Conservation Biology/ ; },
abstract = {BACKGROUND: Hibernation enables animals to survive extreme environments, yet gut microbiome dynamics across the full hibernation cycle remain poorly understood, particularly in chiropterans with unique physiological traits. This study aimed to precisely characterize seasonal microbial succession in wild Rhinolophus sinicus using 16S rRNA gene sequencing across 6 physiological stages, with a focus on taxonomic and functional shifts linked to hibernation-associated fasting and post-hibernation activity.

RESULTS: Alpha diversity followed a pronounced V-shaped trajectory, declining during hibernation and recovering only gradually—remaining suppressed in the early active stage and rebounding markedly by mid–late active stages. Beta diversity revealed a clear separation between hibernation and active phases, with physiological stage explaining 34.9% of community variation. At the phylum level, Pseudomonadota was the dominant taxon during hibernation, while Bacillota became the most abundant phylum in the active period. At the genus level, Yokenella was the core genus in the hibernation stage, and Lactococcus was the dominant genus in the active period. Functional predictions showed enrichment of lipid and amino acid metabolism during hibernation, supporting energy maintenance under fasting, while active-phase microbiota were oriented toward carbohydrate metabolism, matching increased energy demands.

CONCLUSIONS: Our findings demonstrate that hibernation drives directional restructuring of the gut microbiota in R. sinicus, offering new insights into microecological strategies underlying bat survival under extreme conditions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00552-x.},
}

@article {pmid41864867,
year = {2026},
author = {Ma, W and Bai, B and Liu, M and Sheng, P and Bao, J and Song, C and Liu, J and Ma, H and Du, S and Ge, G and Jia, Y and Wang, Z},
title = {Synergistic effects of cellulase and lactic acid bacteria(Pediococcus pentosaceus and Levilactobacillus brevis) on alfalfa silage fermentation and microbial dynamics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41864867},
issn = {1471-2180},
support = {(2025YFHH0210)//Research and Demonstration of High-Quality Forage Supply and Efficient Breeding Technology System for Dairy Cows/ ; },
abstract = {UNLABELLED: This study evaluated the effects of Lactic acid bacteria and cellulase, individually and in combination, on fermentation quality and microbial community dynamics of alfalfa silage. Six treatments were tested, including control, cellulase alone and two lactic acid bacteria species (Pediococcus pentosaceus, Levilactobacillus brevis) applied individually or in combination with cellulase. The results showed that Levilactobacillus brevis in combination with cellulase, producing higher lactic acid concentrations, lower pH (< 4.2) to the other treatments. The microbiome analysis revealed that Lactiplantibacillus was dominant, while undesirable bacterium Achromobacter was suppressed. Functional prediction of microbial communities analysis indicated a higher predicted abundance of sequences associated with pyruvate metabolism, glycolysis/gluconeogenesis and starch and sucrose metabolism pathways. These findings provide insights into optimizing alfalfa silage quality through synergistic use of cellulase and lactic acid bacteria silage inoculants with high metabolic stability.

GRAPHICAL ABSTRACT: [Image: see text]},
}

@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.

METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages.

RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.

CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01646-6.},
}

@article {pmid42049742,
year = {2026},
author = {Guarino-Vignon, P and Louis, E and Pham, HP and Orianne, G and Tkacz, E and Brot, L and Mazzetti, E and Sedda, D and Ruffié, P and Rolhion, N and D'Haens, G and Hadida, B and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72375-y},
pmid = {42049742},
issn = {2041-1723},
abstract = {A marked decrease in Faecalibacterium prausnitzii is a hallmark of Crohn's disease (CD)-associated dysbiosis and predicts disease relapse. Here, we present the development and first-in-human evaluation of F. prausnitzii strain EXL01 for CD treatment. The EXL01-strain demonstrates anti-inflammatory effects in four models of colitis in rodents. A first-in-human, open-label, single-arm study of oral EXL01 was conducted in eight adult participants with mild to moderate CD, following corticosteroids-induced clinical response or remission. The primary endpoint was safety, and secondary endpoints included clinical, endoscopic, histological, molecular, and microbiome assessments. Exploratory endpoints included mucosa transcriptome and cytokine levels. EXL01 is well-tolerated with no treatment-related adverse events. Six participants completed the study; two discontinued treatment due to disease flare. While gut microbiota composition remains largely stable, transcriptomic analyses reveal distinct changes in ileal gene expression following EXL01 treatment, notably modulation of immune-related genes and upregulation of energy metabolism pathways. Compared to participants who remained in remission, those who flared show higher baseline systemic inflammation markers and innate immunity gene expression. These findings demonstrate that oral administration of EXL01 is feasible and well tolerated and establishes proof-of-concept for F. prausnitzii as a first-in-class live biotherapeutic for CD. ClinicalTrials.gov registration: NCT05542355.},
}

@article {pmid42050189,
year = {2026},
author = {Mesnage, R and Ferguson, S and Nechalioti, PM and Cercelaru, L and Hbous, MA and Docea, AO and Tsatsakis, A and Kouretas, D and Antoniou, MN},
title = {Impact of glyphosate and its mixture with 2,4-D and dicamba on gut biochemical function, intestinal barrier integrity and microbiome composition in adult rats with prenatal commencement of exposure.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
pmid = {42050189},
issn = {1432-0738},
support = {26/53/2/31.05.2022//Universitatea de Medicină şi Farmacie din Craiova/ ; },
}

@article {pmid42050215,
year = {2026},
author = {Seneff, S and Boros, LG},
title = {The essential role of hydrogen gas recycling by gut microbes in reducing deuterium load in host mitochondria: is trimethylamine oxide a deuterium sensor?.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {3},
pages = {},
pmid = {42050215},
issn = {1573-3890},
mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Deuterium/metabolism ; *Mitochondria/metabolism ; *Hydrogen/metabolism ; Mice ; },
abstract = {BACKGROUND: The human gut microbiome plays many essential roles, but an often-overlooked role is to maintain an abundant supply of deuterium depleted (deupleted) nutrients to fuel the host mitochondria. Excess deuterium (heavy hydrogen) damages mitochondrial ATP synthase nanomotors, leading to a decrease in matrix water production with increased reactive oxygen species (ROS) and inefficient ATP production. A microbial metabolite, trimethylamine N-oxide (TMAO) is a powerful signaling molecule whose plasma levels are high in association with many chronic diseases, including diabetes, fatty liver disease, and atherosclerosis, as well as cancer and dementia. Thus, TMAO is an important gut-host signaling molecule that serves as a marker for an imbalanced microbiome that is unable to fully metabolize trimethylamine (TMA), an important step in maintaining a deupleted nutrient supply.

AIM OF REVIEW: In this paper, we present a hypothesis that TMAO is a marker for deuterium overload in the methylation pathway, in addition to its role as an indicator of a disrupted gut microbiome. The original study that brought attention to TMAO involved feeding mice synthetic choline with fully deuterated methyl groups. Fully deuterated TMAO was subsequently detected in the plasma. By contrast, a diet rich in eggs, a natural source of choline (a precursor to TMAO), does not raise TMAO levels. Many of the pathologies that are linked to elevated TMAO can also be viewed as strategies to promote the supply of deupleted water to the mitochondria, systemically.

KEY SCIENTIFIC CONCEPTS: The mantra that "food is medicine" is well supported by the powerful role that gut dysbiosis plays in influencing human health and disease.},
}

*Methylamines/metabolism
*Gastrointestinal Microbiome/physiology
Humans
Animals
*Deuterium/metabolism
*Mitochondria/metabolism
*Hydrogen/metabolism
Mice

@article {pmid42050221,
year = {2026},
author = {Izah, SC and Ogwu, MC and Alum, EU},
title = {Innovative approaches to mitigating persistent toxic substances and their impacts on soil health and human well-being.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42050221},
issn = {1573-2959},
mesh = {*Soil Pollutants/analysis ; Humans ; *Environmental Monitoring/methods ; *Soil/chemistry ; *Environmental Restoration and Remediation/methods ; Agriculture ; *Hazardous Substances/analysis ; Environmental Pollution/prevention & control/statistics & numerical data ; },
abstract = {Persistent toxic substances (PTS), including heavy metals, persistent organic pollutants (POPs), and persistent, mobile, and toxic/very persistent and very mobile (PMT/vPvM) substances present an increasing menace to soil health, alimentary systems, atmospheric cleanliness as well as human health. Despite the large amount of literature on each of the individual groups of contaminants, there is still no unified model that connects the dynamics of the soil-atmosphere environment, bioaccumulation in the food chain, new detection techniques, and policy measures. This review presents an interdisciplinary synthesis of dynamics in the PTS in the agricultural environment, explicitly incorporating (i) historic contaminants and emerging PMT/vPvM chemicals, (ii) soil-crop-livestock-human transfer pathways, and (iii) the state-of-the-art remediation and monitoring technologies into a single management framework. We critically evaluated conventional remediation methods alongside next-generation methods, such as engineered consortia of microorganisms, synergistic phytotransformation of plants and microbes, biochar-assisted immobilization, nanosensor-based detection, IoT-based soil sensing, precision agriculture, machine-learning-driven risk prediction, and blockchain-based traceability. Contrary to the previous reviews, which only take into account the remediation, detection, and policy separately, this study presents a systems-based approach, which integrates technological innovation, sustainable agronomic practices, and multilayered governance tools (such as the Stockholm Convention, REACH, and national soil action plans). We highlight the fact that the combination of smart agricultural technology and regenerative land management will help reduce the accumulation of PTS and maintain productivity, especially in resource-scarcity settings. The review outlines the research gaps, including contaminant-microbiome interactions, longitudinal deterioration of ecosystem services, and socioeconomic barriers to technology adoption. We propose a transdisciplinary roadmap that aligns environmental toxicology, soil science, public health, and policy innovation to mitigate PTS and safeguard food security. This integrative approach provides a strategic framework for advancing sustainable management of persistent toxic substances in agricultural systems.},
}

*Soil Pollutants/analysis
Humans
*Environmental Monitoring/methods
*Soil/chemistry
*Environmental Restoration and Remediation/methods
Agriculture
*Hazardous Substances/analysis
Environmental Pollution/prevention & control/statistics & numerical data

@article {pmid42050297,
year = {2026},
author = {Park, SH and Park, SB and Kang, J and Shin, S and Kim, GY and Bong, Y and Gu, M and Lee, YS and Bin, G and Seo, W},
title = {Multiomics characterization of an alcohol-induced hepatocellular carcinoma mouse model.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {42050297},
issn = {1548-4475},
support = {2018R1A5A2025286//National Research Foundation of Korea (NRF)/ ; 2021R1A6C101A442//National Research Foundation of Korea (NRF)/ ; 2021R1C1C1009445//National Research Foundation of Korea (NRF)/ ; RS-2024-00404418//National Research Foundation of Korea (NRF)/ ; RS-2024-00439963//National Research Foundation of Korea (NRF)/ ; NIAAA, BG//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {Hepatocellular carcinoma (HCC) is a major global health problem, ranking as the sixth most frequently diagnosed cancer and the third leading cause of cancer-related mortality worldwide. Although the incidence of viral infection-mediated HCC has decreased in recent years, the incidence of alcohol- and metabolic dysfunction-associated HCC has increased, driven by changes in lifestyle and diet. Excessive alcohol consumption contributes to advanced liver diseases, including liver fibrosis, cirrhosis and HCC. Despite the clinical relevance of alcohol-associated HCC, there are no suitable animal models that adequately reflect the pathophysiological features of alcohol-associated HCC in humans. Here, to address this limitation, we established a mouse model of alcohol-associated HCC through the combined administration of N-diethylnitrosamine and carbon tetrachloride (CCl4), followed by administration of an alcohol-containing Lieber-DeCarli diet. The results indicated that chronic alcohol exposure in the presence of N-diethylnitrosamine and CCl4 substantially accelerated HCC development, which was characterized by increased oxidative stress, inflammation and severe fibrosis. Furthermore, we found that chronic ethanol consumption disrupted hepatic immunity, characterized by natural killer/natural killer T cell depletion, increased PD1[+]CD8[+] cells, reduced cytotoxicity and elevated inflammation. We also observed marked alterations in the gut microbiome following chronic alcohol administration. These immunological and microbiome alterations fostered an immunosuppressive microenvironment that accelerated HCC progression. Our newly developed mouse model induced liver tumorigenesis within a relatively short timeframe and recapitulated the clinical and pathological features of alcohol-associated HCC. The model therefore represents a valuable tool for studying the mechanisms underlying alcohol-associated HCC and related chronic liver diseases.},
}

@article {pmid42050317,
year = {2026},
author = {Lima, ALA and Costa, SS and do Socorro Dos Reis, R and de Souza, DC and Baião, GC and Moreira, RG and Rogez, HLG and das Graças, DA and Viana, RB and Marques, JM},
title = {Age Influences the Bacterial Composition of Samples From Buffaloes in the Marajó Archipelago, Pará, Brazilian Amazon.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70330},
pmid = {42050317},
issn = {1758-2229},
support = {88887.633228/2021-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
mesh = {Animals ; *Buffaloes/microbiology ; Brazil ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Feces/microbiology ; *Milk/microbiology ; *Microbiota ; Cattle ; Female ; Age Factors ; Soil Microbiology ; },
abstract = {Buffalo milk stands out for its nutritional qualities and is mainly produced in Brazil in the Amazon region, particularly in the Marajó Archipelago, State of Pará. In this context, the milk microbiome is an intriguing and underexplored research topic. This study tested the hypothesis that the buffalo milk microbiome could share taxa with faeces, pasture soil and calf spittle. A possible correlation between generations was also explored. Samples of milk, faeces, spittle and pasture soil were analysed using a 16S rRNA metabarcoding approach, revealing significant phylogenetic and ecological differences among matrices. Beta-diversity analysis showed clustering between milk samples from heifers and cows, as well as proximity between soil and buffalo samples (milk and faeces). Relative abundance analysis identified shared taxa between buffaloes and their calves, though no clustering was observed between generations. A total of 15 bacterial families were found across all matrices, with Staphylococcaceae, Planococcaceae and Enterobacteriaceae being the most prominent. The milk microbiota was similar among animals of different ages. The grouping pattern varied depending on the animal and matrix, but not on the maternal relationship. Despite compositional differences, the shared taxa reinforce the idea of interaction among the studied microbial communities.},
}

Animals
*Buffaloes/microbiology
Brazil
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
Feces/microbiology
*Milk/microbiology
*Microbiota
Cattle
Female
Age Factors
Soil Microbiology

@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}

@article {pmid42050578,
year = {2026},
author = {Srisanoi, K and Curado, TFF and Leles, C and Egli, A and Rooney, AM and Srinivasan, M},
title = {From culture-based to 16S sequencing approaches: oral microbiota changes in aging, frailty, and oral hypofunction - a systematic review.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08387-3},
pmid = {42050578},
issn = {1472-6831},
}

@article {pmid42050719,
year = {2026},
author = {Yang, D and Yang, L and Yang, J and Wang, G},
title = {Beyond the known: prospective research directions for the gut-brain axis in obesity and type 1 diabetes mellitus.},
journal = {Diabetology & metabolic syndrome},
volume = {18},
number = {1},
pages = {},
pmid = {42050719},
issn = {1758-5996},
abstract = {BACKGROUND: This letter engages with the seminal review by Argyrakopoulou et al. Obesity and the Gut-Brain Axis in Type 1 Diabetes Mellitus: Terra Incognita? Curr Obes Rep, https://doi.org/10.1007/s13679-025-00654-8IF:11.0Q1B1 . on the putative role of the gut-brain axis in the rising prevalence of obesity within type 1 diabetes mellitus (T1DM).

OBJECTIVE: We aim to commend the authors while proposing key future research avenues to advance the field from correlation to causation and therapeutic application. We also seek to integrate recent high-impact evidence to contextualize our perspectives.

MAIN POINTS: First, we emphasize the need for deep mechanistic studies using gnotobiotic models and targeted metabolomics to delineate the causal role of specific microbial metabolites, informed by recent concepts of host genetic regulation of the gut-liver axis (e.g., via p53/PI3K/AKT/Wnt signaling) and microbiota composition in metabolic disease pathophysiology (1, 2). Second, we highlight the imperative for longitudinal cohort studies to determine the temporal relationship between gut dysbiosis, autoimmunity, and subsequent metabolic complications. Finally, we discuss the promising intersection of microbiome science with emerging therapeutics, including next-generation probiotics and GLP-1 receptor agonists, whose efficacy may be partly mediated through the gut-brain axis.

CONCLUSION: By addressing these priorities and integrating recent knowledge, the scientific community can translate this compelling paradigm into tangible clinical benefits for patients with T1DM.},
}

@article {pmid42050755,
year = {2026},
author = {Russnak, V and Koll, R and Keuter, S and Sanders, T and Dähnke, K},
title = {The Elbe Estuary Microbiome Shifts With Salinity and Discharge and Depends on Fresh Organic Matter and Nutrient Availability.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70349},
pmid = {42050755},
issn = {1758-2229},
support = {03F0864C//Bundesministerium für Bildung und Forschung/ ; 407270017/RTG2530//Deutsche Forschungsgemeinschaft/ ; 496691966/FA 1568//Deutsche Forschungsgemeinschaft/ ; MOSES//Helmholtz Association/ ; 101000518//European Commission/ ; },
mesh = {*Estuaries ; *Salinity ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Seasons ; RNA, Ribosomal, 16S/genetics ; Germany ; Nutrients/analysis ; *Seawater/microbiology/chemistry ; Biodiversity ; Nitrogen/analysis ; },
abstract = {The Elbe Estuary (Germany) stretches 142 km from the weir in Geesthacht to the North Sea. It is classified as mesotidal, partially mixed and heavily impacted by anthropogenic activities and modifications. Despite well-documented changes in ecosystem status, little is known about the microbial community in its surface water. In this study, we used 16S rDNA sequencing to characterise bacterial communities in surface water of the Elbe Estuary. Samples were collected across three seasons (winter, spring, and summer) in 2021 and 2022, to assess the relationship between environmental factors and bacterial community structure. Our analyses revealed that bacterial community diversity and composition varied seasonally and along the estuary stretch and were closely linked to physicochemical properties. Alpha diversity was highest in winter and in oligohaline samples. Distance-based redundancy analysis showed that salinity, discharge, temperature, inorganic nitrogen (NO2), and silicate are key factors in shaping the bacterial community compositions. Although spatial differences were observed, seasonal variation was the main determinant of bacterial diversity and community structure. Overall, our results show that anthropogenic pressures and seasonal changes are reflected in a dynamic microbial community with metabolic functions strongly shaped by human activity.},
}

*Estuaries
*Salinity
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Seasons
RNA, Ribosomal, 16S/genetics
Germany
Nutrients/analysis
*Seawater/microbiology/chemistry
Biodiversity
Nitrogen/analysis

@article {pmid42050886,
year = {2026},
author = {Fatima, R and Ud Din Shah, S and Hameed, A and Ditta, A and Saleemi, MK and Gill, A and Tarique, H},
title = {Microbiome-host interactions driving the transition from non-pregnant to pregnant states in a goat model.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag144},
pmid = {42050886},
issn = {1525-3163},
abstract = {Pregnancy in goats involves complex hormonal, metabolic, and immune shifts, and growing evidence suggests that the gut microbiome plays a key regulatory role in these physiological transitions, yet its specific role in guiding the shift from non-pregnant to pregnant states is still not clearly defined. This study investigated dynamic changes in the microbial community, biochemical markers, and metabolic profile shifts that influence host physiology during the transition from non-pregnant to pregnant states. The results revealed that significant changes in the abundance of microbial genera such as Ruminococcus, Bacteroides, and Lactobacillus were observed across groups. Alpha diversity metrics (Chao1, Shannon, Sobs) indicated substantial differences between groups, while Simpson diversity remained unaffected. Beta diversity analysis (PCoA, NMDS) revealed clear group separation, and pairwise PERMANOVA tests confirmed significant differences (P < 0.05). Heatmap and box plot analyses revealed distinct clustering of microbial profiles, and showed significant differences in genus abundance, including Bacteroides, Christensenella, and Prevotella_7 (P < 0.05). Moreover, significant variations in hematological parameters (RBC, HGB, MCV, MCH, MCHC, PLT, WBC) were noted, with distinct patterns between groups (P < 0.05). Correlation analysis identified strong associations between microbiota taxa (Lachnospira, p < 0.01; Oscillibacter, P < 0.001) and hematological markers. In addition, progesterone and estrogen hormones significantly increased in G1, G2 and G3 groups in response to control group (P < 0.01). Furthermore, antioxidant markers (SOD, CAT) were significantly elevated in G3 group, with a marked decrease in TAC as compared to control group (P < 0.05). FTIR analysis of plasma biomolecules revealed distinct functional group variations across the phases, indicating alterations in key metabolic components. LEfSe analysis identified microbial biomarkers specific to each group, with distinct taxa associated with each pregnancy stage. KEGG pathway analysis showed significant functional shifts, particularly in carbohydrate, amino acid, and energy metabolism. These findings suggest that microbial shifts, metabolic changes, and hormonal fluctuations are intricately linked and play a pivotal role in the reproductive transitions of Beetal goats. The study underpins the potential of microbiome analysis as a tool for improving reproductive health management in livestock.},
}

@article {pmid42050950,
year = {2026},
author = {Jia, Q and Jin, KJ and Liu, SQ and Zhang, YM and Meng, YL and Nie, H and Hu, S and Yang, F and Zhao, XC and Ye, J},
title = {[Research Progress on the Methodological System for Decomposition Stage Classification in Forensic Medicine].},
journal = {Fa yi xue za zhi},
volume = {42},
number = {1},
pages = {34-42},
doi = {10.12116/j.issn.1004-5619.2025.450906},
pmid = {42050950},
issn = {1004-5619},
mesh = {Humans ; *Postmortem Changes ; Algorithms ; *Forensic Medicine/methods ; Machine Learning ; *Forensic Pathology/methods ; Microbiota ; Metabolomics ; },
abstract = {Accurate classification of postmortem decomposition stages is a critical step in estimating the postmortem interval (PMI) and tracing the initial decomposition environment. Research on the decomposition staging methodological system is gradually shifting from empirical observation to the establishment of systems based on multidimensional quantitative indicators. This paper focuses on two key pathways, "macroscopic morphological evolution" and "microscopic molecular succession", and systema-tically reviews the evolutionary patterns and applicability of the decomposition staging system in three typical environmental media: surface exposure, burial, and aquatic systems. It also summarizes research progress in constructing stage classification models utilizing microbiome and metabolomic features. Furthermore, it highlights the integrated application of decomposition characteristic quantification techniques, multi-omics data integration, and machine learning algorithms in decomposition analysis systems. It analyzes the prospects and challenges of applying these approaches to build a standardized and practical decomposition staging system, aiming to provide theoretical support for establishing a decomposition staging system with high accuracy and strong adaptability to different environments.},
}

Humans
*Postmortem Changes
Algorithms
*Forensic Medicine/methods
Machine Learning
*Forensic Pathology/methods
Microbiota
Metabolomics

@article {pmid42051014,
year = {2026},
author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L},
title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70280},
pmid = {42051014},
issn = {1744-7917},
support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; },
abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.},
}

@article {pmid42051097,
year = {2026},
author = {Kasthuri, S and Padmavathi, S and Jeevitha, M and Rajangam, J},
title = {Therapeutic Innovations in Parkinson's and Alzheimer's Disease: Molecular Mechanisms and Emerging Strategies.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273445849260403045802},
pmid = {42051097},
issn = {1996-3181},
abstract = {Parkinson's Disease (PD) and Alzheimer's Disease (AD) are still significant neurodegenerative disorders that have few disease-modifying therapies. In this review, recent advances are assessed based on the strength of evidence for major molecular targets and the therapeutic approaches that have been developed around those targets. Alpha-synuclein is a key target in PD, as indicated by genetic correlations, pathological distribution, and experimental evidence supporting its involvement in neuronal injury. Initial trials of alpha-synuclein antibodies and vaccines show evidence of target engagement, with yet-to-be-determined clinical outcomes. Interventions targeting gene-based dopamine synthesis restoration using AADC or multi-enzyme vectors have shown consistent biological effects, with clinical variability, and determining optimized delivery and patient selection is necessary. In AD, amyloid-beta- and tau-directed interventions have produced measurable changes in biomarkers, and some agents have demonstrated a slight deceleration of deterioration at an early stage of the disease. The experience with previous BACE inhibitors also demonstrates that excellent mechanistic rationale does not always translate into clinical efficacy in the case of interference with critical physiological processes by target modulation. Regenerative methods, such as stem-cell-based neuronal grafts in PD and neurotrophic factor gene delivery in AD, show potential to repair network function, but still pose issues regarding long-term stability, integration, and the complexity of the procedures. Lifestyle-driven interventions, control of the gut microbiome, and neuromodulation methods also remain of interest and can be included in the list of supportive strategies offered to complement molecular therapies. AI-based analytics and digital tools are helpful in the earlier detection, monitoring, and trial stratification. Taken together, existing evidence suggests that authenticated protein targets, neurotransmitter-targeted remedial strategies, and technology-enabled accuracy methods are the most promising approaches for the development of disease-modifying therapies in PD and AD.},
}

@article {pmid42051198,
year = {2026},
author = {Pan, Y and Xu, JF},
title = {Microbiome and its role in bronchiectasis.},
journal = {Therapeutic advances in respiratory disease},
volume = {20},
number = {},
pages = {17534666261444168},
doi = {10.1177/17534666261444168},
pmid = {42051198},
issn = {1753-4666},
mesh = {Humans ; *Bronchiectasis/microbiology/therapy/physiopathology/diagnosis ; *Dysbiosis/microbiology ; *Microbiota ; *Lung/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Prognosis ; Severity of Illness Index ; Animals ; Mouth/microbiology ; Disease Progression ; },
abstract = {Bronchiectasis (BE) is a chronic respiratory disease characterized by damage to the bronchial wall structure and permanent dilation of the bronchi. The symptoms include a persistent cough, excessive production of purulent sputum, and recurrent hemoptysis. Dysbiosis of the microbiome plays a crucial role in the progression of BE. An increased abundance of pathogenic bacteria, along with viral and fungal infections, is closely associated with disease severity and clinical outcomes. Next-generation sequencing technology has significantly enhanced the sensitivity and resolution of the airway microbiome, providing powerful tools for a more detailed characterization of the microecology of BE. However, certain challenges still exist in clinical applications of this technology. In addition, extra-airway microbiomes, such as the gut and oral microbiome, may participate in airway inflammation and immune regulation through the gut-lung axis and oral-lung axis. In this review, we summarize the characteristics of microbiome dysbiosis in BE and highlight the potential value of related biomarkers in disease classification, severity assessment, and prognosis. We also provide an overview of recent treatment advancements. A deeper understanding of the microbiome's role in BE may facilitate early diagnosis and the optimization of individualized treatment strategies.},
}

Humans
*Bronchiectasis/microbiology/therapy/physiopathology/diagnosis
*Dysbiosis/microbiology
*Microbiota
*Lung/microbiology/physiopathology
*Gastrointestinal Microbiome
Prognosis
Severity of Illness Index
Animals
Mouth/microbiology
Disease Progression

@article {pmid42051260,
year = {2026},
author = {Liu, YN and Jia, SY and Zhou, LS and Tang, XJ and Ming, Z and Su, Y and Lin, JY},
title = {Paeoniflorin as a candidate disease-modifying therapy for diabetic peripheral neuropathy: mechanisms, exposure challenges, and translational priorities.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1751578},
pmid = {42051260},
issn = {1663-9812},
abstract = {Diabetic peripheral neuropathy (DPN) is the most common chronic complication of diabetes and remains largely treated with symptomatic analgesics (e.g., pregabalin, duloxetine) that do not reverse nerve fiber loss or demyelination, underscoring the need for disease-modifying therapies. Paeoniflorin (PF), a plant-derived monoterpene glycoside metabolite from Paeonia spp., shows multitarget activity relevant to DPN pathophysiology in preclinical studies, including activation of Nrf2/HO-1 antioxidant signaling, suppression of TLR4/NF-κB-driven neuroinflammation, support of neurotrophic/repair pathways (e.g., BDNF/TrkB) for axonal regeneration and remyelination, and modulation of microvascular pathways (e.g., HIF-1α/VEGF) linked to endoneurial perfusion. We critically appraise this evidence and highlight key translational constraints: very low oral bioavailability and poor intestinal permeability, extensive presystemic biotransformation (microbiome-mediated hydrolysis and CYP-mediated metabolism) with unresolved "active species" (parent PF versus metabolites), and limited DPN-relevant pharmacokinetics, particularly the lack of peripheral nerve/DRG exposure measurements aligned with pharmacodynamic endpoints. Although formulation and delivery approaches may improve exposure, PF-specific validation in DPN models is currently limited and should be distinguished from platform-level concepts. Finally, because DPN patients frequently experience polypharmacy, a clinically meaningful safety narrative requires systematic assessment of CYP/transporter-mediated drug-drug interaction potential. Priority next steps include integrated PK-PD studies with nerve/DRG distribution, metabolite-resolved exposure-activity linkage, PF-specific delivery validation using disease-modifying endpoints beyond pain behavior, and standardized DDI screening to support trial design.},
}

@article {pmid42051286,
year = {2026},
author = {Zeng, Y and Yang, L and Liu, H and Liao, H and Zhou, Y and Liu, J},
title = {Gut-Brain Connection: Deciphering Causal Pathways Between Gut Microbiota and Neuroimaging Profiles Through Mendelian Randomization.},
journal = {Food science & nutrition},
volume = {14},
number = {},
pages = {e71820},
pmid = {42051286},
issn = {2048-7177},
abstract = {Recent research on the gut-brain axis (GBA) indicates that the gut microbiome can significantly influence brain structural and functional connectivity. However, the specific causal relationships between the gut microbiome and brain imaging-derived phenotypes (IDPs) of functional/structural connectivity, as well as how the gut microbiota influences mood and cognition, remain unclear. This study utilizes data from large-scale genome-wide association studies (GWAS) and employs a bidirectional Mendelian randomization (MR) approach to evaluate the causal effects between the gut microbiome and brain connectivity. We obtained data on 196 gut microbiome taxa from the MiBioGen consortium and acquired IDPs for seven resting-state networks (RSNs) from the UK Biobank (UKB). Subsequently, we conducted bidirectional MR analyses to explore their causal relationships. In the forward MR analysis, Ruminococcus torques, Eubacterium fissicatena, and Coprobacter exerted positive effects on the default mode network (DMN), whereas Terrisporobacter influenced the structural connectivity of the dorsal attention network (DAN). Conversely, Gammaproteobacteria inhibited the functional connectivity of the ventral attention network (VAN). Additionally, reverse MR analysis revealed that increased functional connectivity of the DAN was positively associated with the abundance of Alloprevotella. The enhanced functional connectivity of the VAN negatively impacted Alloprevotella, Catenibacterium, and Methanobacteria. Furthermore, the structural connectivity of the frontoparietal network (FPN) and somatomotor network (SMN) significantly reduced the abundance of Bacilli and Intestinibacter, respectively. This study utilized a bidirectional MR approach to establish causal evidence for the relationship between the gut microbiome and brain network connectivity, and support the bidirectional regulatory pattern of the GBA. These findings provide new insights into the potential roles of gut microbiota in emotional regulation, cognitive function, and neurodevelopment, and offer a theoretical basis for microbiome-based intervention strategies.},
}

@article {pmid42051335,
year = {2026},
author = {Li, B and Ren, Z and Li, H and Li, M and Zhong, H and Nie, Q and Chen, J and Wu, R and Zheng, JS and Deng, K and Cai, Y},
title = {Microbiota-metabolites interaction associated with glycemic improvement following a dietary herbal intervention in type 2 diabetes.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1793130},
pmid = {42051335},
issn = {2296-861X},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a global metabolic disorder characterized by chronic hyperglycemia and disruption of the gut microbiome. Nutritional and microbiota-targeted interventions have emerged as promising strategies for glycemic management, yet longitudinal clinical evidence integrating microbial and metabolic mechanisms remains limited. This study investigated microbiota-metabolites alterations during a standardized dietary herbal intervention (QingYun7, QY7) and explored their relationship with glycemic regulation across both animal study and clinical settings.

METHODS: The metabolic and microbial effects of QY7 were first evaluated in diabetic rats through measurements of blood glucose, and gut microbiota composition. Subsequently, a prospective cohort of 385 patients with T2D received QY7, with longitudinal monitoring of fasting, random, and 2-h postprandial glucose, gut microbiota, and serum metabolites across multiple time points. Fecal microbiota transplantation (FMT) from patients before and after intervention into antibiotic-treated mice was performed to evaluate the causal contribution of the gut microbiome to glycemic improvement. Mediation analyses were conducted to delineate potential pathways linking gut microbes, serum metabolites, and glucose outcomes.

RESULTS: In diabetic rats, QY7 administration significantly reduced blood glucose, and restored gut microbial composition. In the clinical cohort, the intervention was associated with rapid and sustained reductions in fasting, random, and postprandial glucose levels, accompanied by consistent remodeling of the gut microbiome and serum metabolite profile. FMT experiments demonstrated that microbiota derived from post-intervention patients conferred improved glycemic responses in recipient mice, supporting a causal role of gut microbiota in metabolic regulation. Serum metabolomic profiling revealed significant alterations, including enrichment of branched-chain amino acid related pathways. Mediation analyses identified key metabolites, phenyllactic acid, 3-methyl-2-oxobutanoic acid, and anandamide, as mediators linking specific bacterial taxa (Alistipes shahii and Limosilactobacillus mucosae) to fasting and postprandial glucose levels.

CONCLUSION: This study provides translational evidence that a dietary herbal intervention associated with glycemic improvement in T2D through microbiota-mediated metabolic reprogramming. Gut microbiome alterations induced by the intervention exerted causal effects on blood glucose regulation, with serum metabolites acting as potential key intermediaries. These findings highlight the mechanistic insight in nutrition-based microbiome modulation strategy in T2D.},
}

@article {pmid42051338,
year = {2026},
author = {Shahzad, M and Saidal, A and Ismail, M and Tariq, K and Melhem, AL and Iqbal, K and Khattak, MI and Ahmad, HA and Saeed, M and Ghani, M and Al Nabhani, Z and Andrews, SC},
title = {Dietary intake, nutritional status and healthcare characteristics of mothers and newborn infants in a prospective cohort study (CHAMP) from a malnutrition-endemic region of Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785862},
pmid = {42051338},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary intake, nutritional status, healthcare access, and early-life exposures play a critical role in shaping infant growth and development. Recent evidence suggests that the impact is largely mediated by gut microbiome. The Child Health, Nutrition and Microbiome in Pakistan (the CHAMP study) is a longitudinal cohort study aiming to assess the bidirectional relationship between gut microbiome and infant growth and development in a cohort of children residing in malnutrition endemic areas of Pakistan.

OBJECTIVES: The current study report the baseline sociodemographic, dietary, healthcare, and nutritional characteristics of mother-infant dyads participating in the CHAMP study.

METHODS: Baseline data were collected from 70 mothers and 72 newborn infants recruited from rural communities in District Swat, Pakistan. Information on household socioeconomic status, maternal dietary intake, antenatal, delivery and postnatal care, infant feeding practices, morbidity, and anthropometric measurements was obtained using validated tools. Descriptive and sex-stratified analyses were conducted.

RESULTS: Households were socioeconomically disadvantaged, with low parental education, large family size, and mean household income substantially below the national minimum wage. Maternal utilization and quality of antenatal and postnatal care were suboptimal, including limited completion of recommended antenatal visits. Dietary quality was also poor, and none of the mothers met the recommended minimum dietary diversity for women. Among infants, morbidity was common, with nearly half experiencing diarrheal illness or respiratory infections. Exclusive breastfeeding reported only in 43.1% of infants. Anthropometric assessment revealed evidence of early growth faltering, with 35.4% of infants were low-length-for-age with higher prevalence among females.

CONCLUSION: These baseline findings highlight substantial socioeconomic vulnerability, poor maternal diet quality, gaps in maternal and infant healthcare, and early-life undernutrition in this rural Pakistani cohort. The study finding provides foundation for longitudinal analyses examining how these factors interact with gut microbiome development and child growth, informing and cost effective and culturally relevant intervention strategies.},
}

@article {pmid42051340,
year = {2026},
author = {Lee, S and Dubrof, S and Ahmed, I and Zhao, Q and Callaway, TR and Lourenco, J and Park, HJ},
title = {Maternal docosahexaenoic acid supplementation shapes offspring gut microbiota to modulate the gut-brain axis in a sow-piglet model.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1776896},
pmid = {42051340},
issn = {2296-861X},
abstract = {INTRODUCTION: Modification of maternal nutrition during the perinatal period represents an important window that may influence offspring neurodevelopment. Docosahexaenoic acid (DHA), a key omega-3 polyunsaturated fatty acid found in the brain, is reported to have beneficial effects on cognitive outcomes of infants. However, its specific effects on the shaping of gut microbiota to influence the piglet gut-brain axis remain to be elucidated.

METHODS: Using a sow-piglet model, this study aimed to investigate changes in offspring gut microbiota, intestinal barrier integrity, and their correlations with brain resting-state functional connectivity following maternal supplementation of DHA.

RESULTS: Piglets born to DHA-supplemented sows showed significant differences in microbial alpha- and beta-diversity compared to control piglets. Jejunal claudin-1 expression was upregulated in DHA piglets, and tight junction protein levels were positively correlated with specific microbial taxa. Furthermore, gut microbial diversity and specific taxa were significantly associated with functional brain networks.

DISCUSSION: Our findings demonstrate the role of maternal DHA supplementation in shaping offspring gut microbiome and gut integrity, potentially altering offspring brain function networks. Furthermore, these results underscore the importance of gut microbiota shaping through perinatal nutritional interventions as a means of programming the gut-brain axis in the early stages of life.},
}

@article {pmid42051348,
year = {2026},
author = {Liu, B and Zhang, Y and Deng, W and Zhou, YN and Cao, Y and Xiong, L and Shen, R and Lee, SM and Bian, J and Bian, Y},
title = {Dietary restriction as a potential neuroprotective intervention: a narrative review of its impact on neuroinflammation across neurodegenerative diseases and other neurological disorders.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1731416},
pmid = {42051348},
issn = {2296-861X},
abstract = {Dietary restriction (DR) involving chronic or intermittent calorie/nutrient reduction without malnutrition, delays neurological disease progression. Decades of research across in vitro models, animal studies, and clinical trials provide preclinical evidence for a potential role of DR in modulating multiple mechanisms underlying CNS disorders. Interactions between caloric intake, meal frequency, diet composition, and the gut microbiome regulate specific metabolic pathways governing cellular, tissue, and organ homeostasis as well as inflammatory processes during neurodegenerative and neurological diseases. In this review, we synthesize evidence on the role of DR in modulating neuroinflammation and related mechanisms within a selected set of neurodegenerative and neurological disorders, aims to provide a consolidated evidence base and perspective on the potential of DR as an adjunctive strategy for the future therapeutic investigations.},
}

@article {pmid42051417,
year = {2026},
author = {Stokes, CS and Türk, T and Lammert, F and Appenrodt, B},
title = {Comparison of Mucosal and Faecal Microbiomes in Patients With Cirrhosis.},
journal = {Gastroenterology research and practice},
volume = {2026},
number = {},
pages = {6847983},
pmid = {42051417},
issn = {1687-6121},
abstract = {OBJECTIVE: The colonic sigmoid mucosal microbiome is reportedly different from the faecal microbiome in patients with cirrhosis. This exploratory study is aimed at comparing the luminal and mucosal microbiome in patients with cirrhosis, with a specific focus on the proximal intestine.

METHODS: Mucosal and faecal samples were obtained from 12 patients with cirrhosis. The microbiome was quantified with V4 16S rRNA gene sequencing. Relative abundance, alpha and beta diversity were calculated, compared between the mucosal and faecal samples and correlated with stage of cirrhosis.

RESULTS: Faecal samples displayed lower microbial diversity than mucosal samples (Shannon diversity, p = 0.025) and the microbiome profiles differed significantly: Operational taxonomic units primarily of the phyla Firmicutes and Actinobacteria were more abundant in faecal samples, whereas biopsy samples contained units spanning all six phyla. Microbial composition of faecal samples were more similar to faecal samples from other patients rather than to the individual's corresponding biopsy sample (principal coordinate analysis, p = 0.004). At the family level, Lachnospiraceae, Erysipelotrichaceae and Enterobacteriaceae were significantly more abundant in faecal samples, whereas biopsy samples contained more Streptococcaceae (p = 0.011) and Prevotellaceae (p = 0.031). Faecal samples from patients in Child-Pugh Stage C contained less Bacteroidetes but significantly more Streptococcaceae than Stage B samples (p = 0.04); however, biopsy samples did not differ significantly.

CONCLUSIONS: This exploratory study in a small sample of patients with cirrhosis observed significant differences in the microbial signature of faecal versus biopsy samples from the proximal intestine. Future studies are needed to further investigate the relationship between different gastrointestinal microbial sites and cirrhosis.},
}

@article {pmid42051455,
year = {2026},
author = {Du, X and Su, H and Huang, Y and Liu, J and Li, Q and Yang, X and Tao, X and Li, R},
title = {Gut microbiome dysbiosis in PCOS: from pathogenesis to microbiome-targeted therapies.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1747766},
pmid = {42051455},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/microbiology/therapy/etiology/pathology ; *Dysbiosis/microbiology/therapy/complications ; *Gastrointestinal Microbiome/physiology ; Female ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {(PCOS), one of the most common endocrine and metabolic disorders in women of reproductive age, has a complex pathogenesis that continues to be unraveled by ongoing research. The condition is defined by three key features: hyperandrogenemia, ovulatory dysfunction, and insulin resistance. Recent studies have highlighted the gut microbiome and its metabolites as crucial regulators in PCOS development. Evidence suggests that gut dysbiosis and intestinal barrier dysfunction play a pivotal role in the onset and progression of PCOS. This review comprehensively examines the central role of gut microbiota in PCOS pathogenesis, including shifts in microbial communities such as bacteria, fungi, and viruses, and their impact on critical metabolites like short-chain fatty acids, bile acids, and tryptophan metabolites, which modulate host metabolism and reproductive function. Furthermore, based on mechanistic insights, the review explores targeted gut microbiota interventions, systematically evaluating clinical evidence for dietary modifications, probiotic/prebiotic supplementation and fecal microbiota transplantation. These approaches provide novel perspectives for precision medicine in PCOS treatment. The findings not only deepen our understanding of PCOS pathogenesis but also establish a strong theoretical foundation for innovative microbiome-based therapeutics.},
}

Humans
*Polycystic Ovary Syndrome/microbiology/therapy/etiology/pathology
*Dysbiosis/microbiology/therapy/complications
*Gastrointestinal Microbiome/physiology
Female
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid42051461,
year = {2026},
author = {Wang, Q and Zhou, Z and Pang, L and Du, Y and Li, X and Dai, L},
title = {Gut microbiota in chronic kidney disease-mineral and bone disorder: shared mechanisms, disease-specific signatures, and therapeutic prospects.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1802845},
pmid = {42051461},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; *Chronic Kidney Disease-Mineral and Bone Disorder/microbiology/therapy/metabolism/pathology ; Fibroblast Growth Factor-23 ; Animals ; *Renal Insufficiency, Chronic/microbiology ; },
abstract = {Chronic Kidney Disease-Mineral and Bone Disorder (CKD-MBD) is a systemic syndrome characterized by mineral metabolism disorders and impaired bone homeostasis. Recent studies have indicated that gut microbiota dysbiosis is a key regulatory factor driving the development and progression of this disease. This review systematically summarizes the mechanisms by which gut microbiota acts in CKD-MBD through the "gut-kidney-bone axis": dysbiosis drives chronic low-grade inflammation by impairing the intestinal barrier and promoting endotoxin translocation; alterations in its metabolites (e.g., reduced short-chain fatty acids, accumulation of uremic toxins) and dysregulation of endocrine pathways (e.g., FGF23-Klotho axis, PTH) collectively exacerbate renal injury and abnormal bone metabolism. Additionally, in diseases such as CKD, rheumatoid arthritis (RA), osteoarthritis (OA), and osteoporosis (OP), gut microbiota exhibits the coexistence of "shared dysbiosis" and "disease-specific characteristics," which collectively contribute to chronic inflammation and metabolic disorders. Interventional strategies targeting gut microbiota have demonstrated the potential to regulate this axis and improve bone health, marking that the management of metabolic bone diseases and chronic kidney disease is entering the "era of microbiome medicine." This review aims to provide new insights into understanding the comorbidity mechanisms of the aforementioned diseases and lay a theoretical foundation for the development of microbiota-targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/microbiology
*Chronic Kidney Disease-Mineral and Bone Disorder/microbiology/therapy/metabolism/pathology
Fibroblast Growth Factor-23
Animals
*Renal Insufficiency, Chronic/microbiology

@article {pmid42051499,
year = {2026},
author = {Lee, AR and Choi, H and Lee, SY and Kang, HY and Moon, YM and Nam, SW and Lee, BI and Cho, ML},
title = {Overexpression of mitochondrial STAT3 protein improves colonic inflammation and fibrosis in inflammatory bowel disease by enhancing mitochondrial function.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1728341},
pmid = {42051499},
issn = {1664-3224},
mesh = {*STAT3 Transcription Factor/genetics/metabolism ; Animals ; *Inflammatory Bowel Diseases/metabolism/pathology/genetics ; Mice ; *Mitochondria/metabolism/genetics ; Fibrosis ; *Colon/pathology/metabolism/immunology ; Disease Models, Animal ; *Colitis/metabolism/pathology/genetics ; Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; Cytokines/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Inflammation ; },
abstract = {INTRODUCTION: The STAT3 protein is involved in mitochondrial functions such as the respiratory electron transport chain, regulation of cellular metabolism, and scavenging of reactive oxygen species. Inflammatory bowel disease (IBD) is associated with damaged intestinal cells and mitochondrial dysfunction due to the inflammatory environment of the intestine. Here, we studied the potential use of the Stat3 gene to induce STAT3 expression in mitochondria to help treat IBD.

METHODS: We transferred the Stat3 gene and examined its effects on the expression of proinflammatory cytokines and fibrosis markers, and mitochondrial function, in intestinal tissues via immunohistochemistry. The microbiomes of mice were also analyzed.

RESULTS: The gene increased the expression of mitochondrial STAT3 (mtSTAT3), which reduced the levels of iNOS and fibrosis factors (aSMA, COL1A1) as well as proinflammatory cytokines (IL-17, IL-6) in the colon. It also enhanced mitochondrial function in the colon, and in immune cells, and led to higher levels of the beneficial bacteria Lactobacillus reuteri and Akkermansia muciniphila in the intestine. Taken together, these changes helped alleviate colitis and protected against intestinal damage.

DISCUSSION: Stat3 gene transfer targeting mtSTAT3 expression ameliorates colitis, enhances mitochondrial function in the colon, and reduces inflammation via inhibition of the inflammatory response and necroptosis, offering a potential treatment for IBD.},
}

*STAT3 Transcription Factor/genetics/metabolism
Animals
*Inflammatory Bowel Diseases/metabolism/pathology/genetics
Mice
*Mitochondria/metabolism/genetics
Fibrosis
*Colon/pathology/metabolism/immunology
Disease Models, Animal
*Colitis/metabolism/pathology/genetics
Gastrointestinal Microbiome
Male
Mice, Inbred C57BL
Cytokines/metabolism
*Mitochondrial Proteins/genetics/metabolism
Inflammation

@article {pmid42051509,
year = {2026},
author = {Ali, S and Kuang, R and Abdelkarim, OF and Nawaz, AH and Rahim, MF and Wang, D and Asif, A and Zhu, M},
title = {Integrative transcriptome and microbiome analysis reveals ferroptosis-driven duodenal damage caused by Ochratoxin A in mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804647},
pmid = {42051509},
issn = {1664-3224},
mesh = {Animals ; *Ferroptosis/drug effects/genetics ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Duodenum/drug effects/pathology/metabolism/microbiology ; *Ochratoxins/toxicity ; *Transcriptome ; Male ; Gene Expression Profiling ; Intestinal Mucosa/metabolism/drug effects/pathology ; Mice, Inbred C57BL ; },
abstract = {Ochratoxin A (OTA), a prevalent mycotoxin produced by fungal contaminants, poses a significant threat to intestinal health. That can induce ferroptosis, a regulated iron-dependent cell death by disrupting duodenal epithelium and gut microbiota homeostasis. We exposed mice to OTA (2 mg/kg body weight/day) for seven days and assessed duodenal damage using histological analysis, transmission electron microscopy (TEM), transcriptomics, quantitative real-time PCR (qRT-PCR), Western blotting, immunofluorescence, biochemical assays, and 16S rRNA sequencing of cecal contents. OTA markedly reduced body weight from day 2 onwards and significantly elevated serum lipopolysaccharides (LPS) (P<0.05), duodenal malondialdehyde (MDA), and iron levels compared to the control group. OTA significantly diminished duodenal antioxidant defenses, including glutathione, SOD, CAT, and total antioxidant capacity (T-AOC), and caused villus atrophy, crypt hyperplasia, and mitochondrial shrinkage with cristae loss, which are the hallmarks of ferroptosis. Transcriptomic analysis revealed 769 differentially expressed genes (DEGs), including 134 upregulated and 635 downregulated genes, with 26 overlapping ferroptosis-regulating genes (FerroDb). Among these, four key genes SLC7A11, GSTM1, CP, and SLC40A1 were downregulated, which are major regulators of redox and iron homeostasis, and were enriched in ROS/lipid metabolism pathways. Microbiome profiling showed augmented diversification, altered Bacteroidota abundance and enrichment of pathogenic microbiota (e.g., Oscillibacter and Barnesiella), linking ferroptosis with dysbiosis. These findings demonstrate that OTA induces duodenal ferroptosis through dual microbiota-duodenum axis, where microbial dysbiosis amplifies redox imbalance and iron homeostasis. Ferroptotic inhibitors may preserve the gut health in animals and humans exposed to fungal contaminants.},
}

Animals
*Ferroptosis/drug effects/genetics
Mice
*Gastrointestinal Microbiome/drug effects
*Duodenum/drug effects/pathology/metabolism/microbiology
*Ochratoxins/toxicity
*Transcriptome
Male
Gene Expression Profiling
Intestinal Mucosa/metabolism/drug effects/pathology
Mice, Inbred C57BL

@article {pmid42051515,
year = {2026},
author = {Zheng, QX and Wang, HW and Ge, L and Lin, Y and Gao, X and Zhu, Y and Huang, L and Jiang, XM},
title = {Influences of dietary intake on Chinese women with gestational diabetes mellitus by inhibiting gut microbiome on plasma metabolome.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745459},
pmid = {42051515},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Diabetes, Gestational/microbiology/blood/metabolism ; Adult ; *Metabolome ; China ; *Diet ; Prospective Studies ; Dysbiosis ; East Asian People ; },
abstract = {BACKGROUND: Lines of evidence indicate that microbiome and its derived metabolites are implicated in gestational diabetes mellitus (GDM) etiology through the regulation of insulin resistance and inflammatory responses, and pregnant women with GDM have significant gut dysbiosis and metabolic disturbance. Although the gut microbiota and gut metabolites in pregnant women with GDM are extensively studied, the trilateral relationship between diet, gut microbiota, and plasma metabolites in patients with GDM remains unclear. Therefore, the aim of this study was to systematically analyze the associations between diet, gut microbiome, and plasma metabolome among Chinese pregnant healthy controls and patients with GDM.

METHODS: The study is a prospective cohort study conducted at two maternal and child hospitals in China from 8 October 2021 to 31 December 2022. We compared the daily dietary intake, microbial compositions, and plasma metabolic signatures of 173 patients with GDM and 47 pregnant healthy individuals. A food frequency questionnaire was used to investigate the dietary intake of pregnant healthy controls and patients with GDM. 16S rRNA sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used to sequence the gut microbiome and plasma metabolome, respectively.

RESULTS: We found that women with GDM had higher intakes of whole grains, red meat, poultry, and eggs compared with normal pregnant women. Women with GDM had lower amounts of Klebsiella, Lactiplantibacillus, and Sphingomonas, and higher amounts of Desulfovibrio; they also had higher amounts of D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid in plasma. Moreover, whole grains negatively influenced Sphingomonas, Klebsiella, and Lactiplantibacillus; red meat had a negative influence on Sphingomonas; and eggs had a positive impact on Desulfovibrio; these gut microbiota affected D-mannose, D-ribose, homo-L-arginine, and norophthalmic acid.

CONCLUSION: Overall, this study provided information about the influences of dietary intake on Chinese women with GDM by inhibiting gut microbiome on plasma metabolome, and their interactions play vital roles in GDM pathogenesis. These findings may be useful for patients with GDM in terms of dietary counseling and glucose control during pregnancy.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
*Diabetes, Gestational/microbiology/blood/metabolism
Adult
*Metabolome
China
*Diet
Prospective Studies
Dysbiosis
East Asian People

@article {pmid42051550,
year = {2026},
author = {Chakraborty, DK and Roy, T and Ngo, ST and Al-Chalabi, A and Al Khleifat, A},
title = {Gut microbiota and ALS: cause, consequence or correlation? - a systematic review.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1774417},
pmid = {42051550},
issn = {1662-4548},
abstract = {BACKGROUND: Gut microbiome disturbances have been proposed as contributors to amyotrophic lateral sclerosis (ALS), a multisystem neurodegenerative disorder characterised by motor neuron loss, extra-motor symptoms, and rapid progression. Mechanistic links between dysbiosis, epithelial and blood-brain barrier dysfunction, metabolic imbalance, and immune activation have been suggested, but causality remains unresolved. We conducted a systematic review to evaluate the evidence supporting microbiome involvement in ALS pathogenesis.

METHODS: We searched PubMed, Medline, Embase, Scopus, Semantic Scholar, and Google Scholar (Nov 23, 2025) for human and ALS-relevant animal studies assessing bacterial microbiota, gut or blood-brain barrier integrity, microbial metabolites, or immune pathways. No language or date restrictions were applied. Studies were screened according to predefined criteria, and quality was assessed using QUADAS-2. Owing to the heterogeneity of study designs and sequencing approaches, findings were synthesised narratively.

FINDINGS: 61 of 2,397 studies met inclusion criteria. Across human cohorts, ALS was consistently associated with reduced microbial diversity, shifts in key taxa, and disruption of microbial pathways regulating short-chain fatty acids, nicotinamide metabolism, and inflammatory signalling. Several mechanistic animal studies demonstrated that microbiota manipulation, through antibiotics, faecal microbiota transfer, or supplementation with protective taxa, modulated motor function, microglial activation, gut permeability, and survival, indicating that dysbiosis can influence disease trajectories. Conversely, longitudinal human data showed that dysbiosis often emerged alongside worsening physical function, gastrointestinal dysmotility, weight loss, and changes in dietary intake, suggesting secondary effects of disease progression. Integrative multi-omics studies linked microbial alterations with systemic cytokine profiles, metabolic stress pathways, and CNS immune phenotypes, reinforcing a bidirectional gut-brain axis. However, the predominance of cross-sectional designs and small sample sizes substantially limits causal inference.

INTERPRETATION: Current evidence supports a model in which gut dysbiosis interacts with ALS via barrier failure, metabolic disruption, and immune dysregulation, but does not establish dysbiosis as a primary cause of disease. Preclinical findings highlight microbiome-derived mechanisms with disease-modifying potential, yet human data largely indicate association rather than initiation. Clarifying temporal relationships will require longitudinal, multi-modal studies, integration with pre-symptomatic cohorts, and controlled interventional trials. Microbiome-targeted therapies remain a promising but unproven avenue for ALS.},
}

@article {pmid42051692,
year = {2026},
author = {Wang, LM and Chen, C and Danzheng, JC and Zhao, J},
title = {Gut microbiome in sepsis: from dysbiotic biomarker to precision and palliative decision-making.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1811304},
pmid = {42051692},
issn = {2296-858X},
abstract = {Sepsis is a major cause of mortality in critically ill patients, necessitating improved early detection, risk stratification, and individualized clinical decision-making. The gut microbiome actively regulates host immunity, metabolism, and barrier function, engaging in bidirectional interactions with sepsis progression. Evidence suggests that gut dysbiosis not only accompanies sepsis but may also accelerate it. Characteristic shifts, including reduced microbial diversity, expansion of opportunistic pathogens, and decreased short-chain fatty acid production, could offer early prognostic signals prior to clinical decline. Advances in multi-omics and computational analytics are enabling the translation of microbial signatures into actionable clinical insights, supporting phenotype-specific stratification in sepsis. Emerging microbiome-targeted interventions such as next-generation probiotics, synbiotics, metabolite supplementation, and fecal microbiota transplantation show potential for modulating host responses in a stage-specific manner. Within a precision medicine framework, microbiome-derived biomarkers may refine both critical care management and palliative decision-making. In advanced or refractory sepsis, these insights could help tailor treatment intensity, prioritize symptom control, and avoid non-beneficial therapeutic escalation. Realizing this potential will require prospective validation and standardized approaches to integrate microbiome data into personalized, goal-concordant sepsis care.},
}

@article {pmid42051745,
year = {2026},
author = {Urrutia, ÍM and Plaza, N and Moraga, F and Griffiths-Sanhueza, C and Pérez-Reytor, D and Karahanian, E and Ramírez-Araya, S and Kinkead, A and Gómez, MP and Garcia, K},
title = {High intellectual ability and the gut-brain-sex steroids axis: a perspective on cognitive and emotional diversity.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1791778},
pmid = {42051745},
issn = {1664-042X},
abstract = {The gut-brain axis is a bidirectional communication network integrating neural, endocrine, immune, and metabolic signals that regulate neurodevelopment, cognition, and emotion. It contributes to neurotransmitter production, inflammatory regulation, and the microbial metabolism of sex steroids, processes that have been shown to modulate synaptic plasticity and emotional behavior in experimental and clinical contexts, although their specific relevance to high intellectual ability remains unknown. In this perspective, we propose that high intellectual ability could be explored as a heterogeneous construct, within which some individuals identified as having HIA may exhibit responses potentially associated with differential sensitivity to gut-brain-sex hormone interactions. We discuss that microbial modulation of steroid bioavailability and neuroactive metabolites may represent one hypothetical pathway through which variations in steroid bioavailability and neuroactive metabolites could intersect with cognitive performance and emotional intensity, traits frequently described in some individuals with HIA. Integrating evidence from neuroendocrinology, microbiome science, and cognitive neuroscience, we outline a conceptual framework linking microbial, hormonal, and neural processes. This model aims to stimulate empirical research examining how physiological variation across the gut-brain-sex hormone axis may underlie cognitive and emotional diversity in gifted subpopulations. Importantly, this framework is conceptual and extrapolates from converging evidence in microbiome science and neuroendocrinology, as direct empirical studies in high intellectual ability are currently lacking.},
}

@article {pmid42051940,
year = {2026},
author = {Sandra, F and Scania, AE and Dewi, NM and Ranggaini, D and Halim, J and Pakpahan, A and Lee, KH},
title = {Coevolution of Human Diet and Gut Microbiome: Implications for Nutrigenomics and Cross-Population Health.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {5597426},
pmid = {42051940},
issn = {1687-918X},
abstract = {The coevolution of the human diet and gut microbiome has played a pivotal role in shaping metabolic, immune, and epigenetic functions across human history. Dietary transitions from high-fiber ancestral patterns to modern ultraprocessed diets have markedly influenced microbial diversity and functionality, contributing to the emergence of chronic diseases such as obesity, Type 2 diabetes, and inflammatory conditions. Recognizing the significance of gut microbial patterns in humans, this review explores the coevolution of diet and gut microbiota, especially on how gut microbiota influences human gene regulation, and the implications of these interactions for personalized nutrition and global health strategies. Comparative insights across populations in different periods reveal that geography, dietary practices, and host genetics interact to shape distinct microbiome configurations and disease susceptibility. Therefore, implementing a nutrigenomics and nutrigenetics approach might provide a molecular framework to understand these interactions and to develop personalized nutrition strategies. Though several clinical implementations utilizing genomic data have been embedded in several countries, global implementation remains challenging due to population-specific genetic variability, cultural dietary preferences, cost limitations, and ethical considerations. Integrating microbiome and genetic data into clinical practice and public health policy offers a promising path to mitigate diet-related health disparities that is tailored to individual and population-level needs.},
}

@article {pmid42052124,
year = {2026},
author = {Liao, X and Liu, J and Pang, Z and Li, X and Jiang, D and Wang, J and Sun, Y and Pang, B},
title = {Pharmacodynamic Material Basis of the Components of Four Epimedium Species with Activities Against Hepatocellular Carcinoma Based on Biological Target Networks and Multi-Omics Analysis.},
journal = {Journal of hepatocellular carcinoma},
volume = {13},
number = {},
pages = {578719},
pmid = {42052124},
issn = {2253-5969},
abstract = {AIM: Epimedium plants are used in traditional Chinese medicine due to their medicinal properties and can be clinically used for the treatment of liver cancer.Using network pharmacology and HPLC, we identified a key anti-HCC complex, CMPLX (containing icariin and kaempferol), from four Epimedium species. In vitro and in vivo studies demonstrated that CMPLX suppresses HCC proliferation by downregulating p-Akt, p-PI3K, and Bcl-2 expression. Untargeted metabolomics and gut microbiome analysis revealed significant negative correlations between serum levels of lignin/kaempferol derivatives and Escherichia coli abundance. These findings highlight CMPLX as a promising candidate for HCC drug development.

PURPOSE: Investigate the pharmacodynamic material basis of the components of four Epimedium species with activities against hepatocellular carcinoma based on biological target networks and multi-omics analysis.

MATERIALS AND METHODS: We first screened four Epimedium extracts for anti-HCC activity using HepG2 cells. Shared bioactive compounds were identified through network pharmacology and HPLC, defining core target AKT1 and key complex CMPLX (icariin and kaempferol). Molecular docking/dynamics simulations confirmed CMPLX-AKT1 binding. In vitro assays (CCK-8, wound healing, colony formation, Annexin V/PI, Western blot) demonstrated CMPLX inhibits proliferation, migration, and induces apoptosis via PI3K/AKT/Bcl-2 pathway. In vivo validation in H22 tumor-bearing mice showed tumor suppression, corroborated by histology, serum metabolomics and gut microbiota analysis.

RESULTS: CMPLX suppressed hepatocellular carcinoma proliferation in vitro and in vivo. Mechanistically, it downregulated p-Akt, p-PI3K, and Bcl-2 expression, inhibiting growth and promoting apoptosis in HepG2 cells. Integrated multi-omics revealed CMPLX treatment elevated flavonoid/kaempferol derivatives while reducing Enterobacteriaceae_A/Escherichia abundance, with Marinifilaceae dominating the gut microbiota. Crucially, lignan/kaempferol derivatives showed significant negative correlation with Escherichia levels.

CONCLUSION: CMPLX demonstrated synergistic anti-HCC efficacy in vitro and in vivo. Multi-omics analysis revealed its modulation of tumor-related pathways and gut microbiota composition, collectively contributing to tumor suppression.},
}

@article {pmid42052326,
year = {2026},
author = {Shabibi, A and Basati, G and Zarif, BR and Davari, K and Rangin, A},
title = {Laboratory Analysis of Fecal Lactobacillus Strains and pH in Tobacco Smokers: A Comparative Study From a Developing Country.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72348},
pmid = {42052326},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Tobacco smoking is a major cause of preventable mortality globally, disproportionately impacting developing countries. While its systemic health effects are well-known, the influence of tobacco on gut microbiota-especially beneficial Lactobacillus species-remains poorly explored in resource-limited settings.

METHODS: This study examined fecal Lactobacillus composition and stool pH among 200 participants from western Iran, including cigarette smokers, hookah users, combined users, and non-smoking controls. Standard microbiological methods were employed: stool pH measurement, anaerobic culture on MRS agar, Gram staining, biochemical tests, phenotypic assays (acid/bile resistance, antibiotic susceptibility), and PCR sequencing of the 16S rRNA gene for species identification.

RESULTS: Results showed significantly elevated stool pH in tobacco users, particularly hookah smokers (p = 0.001). Lactobacillus prevalence was markedly lower in all smoker groups compared to controls (p < 0.001). Dominant species identified were L. casei, L. plantarum, and L. acidophilus, with control strains exhibiting greater acid and bile tolerance (p < 0.05). Antibiotic resistance was common, notably to vancomycin (75%) and ampicillin (67%).

CONCLUSION: These findings indicate tobacco-associated gut dysbiosis characterized by increased stool pH and diminished Lactobacillus viability, potentially impairing gut barrier integrity. The study highlights the importance of clinical microbiological evaluation of smoking-related microbiota alterations, especially in populations with limited probiotic access.},
}

@article {pmid42052329,
year = {2026},
author = {Brar, GS and Sharma, A and Siddiqui, AJ and Sharma, L},
title = {Emerging Microbiome-Based Therapies for Skin Infections: From Probiotics and Prebiotics to Synthetic Microbiome Engineering.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {592685},
pmid = {42052329},
issn = {1178-6973},
abstract = {Skin infections are a major global health burden, made worse by the quick development of antimicrobial resistance (AMR) and the poor effectiveness of traditional antibiotic treatments for chronic and recurring diseases. The importance of the skin microbiome in preserving cutaneous homeostasis, pathogen exclusion, and immunological modulation is becoming more and more clear. Many infectious and inflammatory skin conditions have been linked to dysbiosis of the skin microbiota, which has led to a strategic reorientation from pathogen control to microbiome regulation. Probiotics, prebiotics, postbiotics, bacteriophages, microbiome transplants, and new methods in synthetic microbiome engineering are just a few of the recent advances in microbiome-based therapies in skin diseases that are covered in detail in this review. We go into the clinical effectiveness, safety issues, regulatory obstacles, and molecular underpinnings of various therapies. The promise of microbiome-based treatments to lower AMR, improve long-term effectiveness, and restore microbial balance is highlighted by comparison with traditional antibiotics. Lastly, future possibilities are examined that highlight the translational potential of microbiome-centred techniques in dermatology treatments, such as multi-omics integration, artificial intelligence-guided customisation, or synthetic microbial consortia.},
}

@article {pmid42052390,
year = {2026},
author = {Guo, Z and Feng, Y and Ren, Z and Wang, W and Huang, R and Zhao, J},
title = {Neurotransmitter-mediated gut-brain axis: a bibliometric analysis of research trends and knowledge structure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771169},
pmid = {42052390},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut-brain axis constitutes a bidirectional network linking the gastrointestinal tract and central nervous system through neural, endocrine, metabolic, and immune pathways. Neurotransmitters play a central role in mediating this crosstalk, serving as intermediates through which the gut microbiota influences brain function. Although important mechanistic advances have been made, research on the neurotransmitter-mediated gut-brain axis remains fragmented across disciplines. This study aimed to provide a comprehensive bibliometric overview of this field.

METHODS: We conducted a bibliometric analysis of 788 publications retrieved from Web of Science, Scopus, and PubMed between 2005 and 2025. Using VOSviewer, CiteSpace, and Pajek, we analyzed publication trends, geographic distribution, institutional and author contributions, journal co-citations, and keyword evolution to characterize the knowledge structure and emerging themes of the field.

RESULTS: The results revealed three developmental phases: an exploratory phase (2005-2016) with limited output, a developmental phase (2017-2019) with moderate growth, and a rapid expansion phase (2020-2025) marked by exponential increases in publications driven by advances in microbiome and neurotransmitter research. China led in publication volume, while the United States and Ireland served as major hubs of collaboration. University College Cork showed the highest citation impact, with 10,935 citations from 28 publications (average citations per document = 390.54). John F. Cryan, Timothy G. Dinan, and Gerard Clarke were among the leading contributors, with Cryan ranking first in both publication output and citation count. Keyword and thematic analyses identified gut microbiota, serotonin, short-chain fatty acids, depression, and inflammatory bowel disease as core topics, reflecting a shift from mechanistic studies to disease-specific and neurotransmitter-targeted research. Highly cited studies focused on microbial regulation of neurotransmitters, neuroimmune signaling, and their implications for neurodevelopmental and neurodegenerative disorders.

DISCUSSION: This study provides the first comprehensive bibliometric overview of neurotransmitter-mediated gut-brain axis research, offering a macroscopic perspective on its evolution, core knowledge base, and emerging frontiers. Future research should integrate multidisciplinary approaches, apply omics technologies, and develop precision interventions targeting neurotransmitter pathways while considering individual microbial profiles, in order to translate mechanistic insights into therapeutic strategies for neuropsychiatric disorders.},
}

@article {pmid42052395,
year = {2026},
author = {Banerjee, A and Gupta, N and Koley, A and Kumar, MS and Saha, S and Balachandran, S},
title = {Microbial contamination and microbiome composition of fresh edible mushrooms: a critical review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1757755},
pmid = {42052395},
issn = {1664-302X},
abstract = {Fresh edible mushrooms have gained popularity as valuable dietary components, with global consumption steadily increasing due to their high nutritional and functional benefits. However, their constitutional characteristics make them especially vulnerable to microbial spoilage, potentially harming the fruiting bodies during cultivation and creating major challenges in harvesting, handling, and storage after harvest. This review highlights the types, sources, and impacts of microbial contamination in fresh edible mushrooms, with a focus on spoilage organisms. It explores the emerging field of mushroom microbiome research, highlighting the composition, diversity, and functional roles of microbial communities associated with 4 edible mushroom species (Agaricus sp., Pleurotus sp., Lentinula sp., and Flammulina sp). Studies employing high-throughput sequencing technologies to explore the microbial associations of edible mushrooms are discussed, providing deeper insights into these complex microbial ecosystems and their impacts on mushroom quality, shelf life, and safety. Bibliometric studies using VOSviewer over a 10-year period have uncovered global research trends, emerging focus areas, and identified gaps in the field. This review also discusses post-harvest control strategies and microbiome-targeted interventions to enhance microbial safety and extend shelf life. Edible mushrooms also contribute to the circular bioeconomy by converting agricultural residues into nutritious food. However, microbial contamination can compromise product quality and safety within this sustainable production system. Persistent knowledge gaps in understanding microbial dynamics and mushroom-microbiota interactions must be addressed to develop innovative, sustainable approaches to mushroom preservation and food safety management.},
}

@article {pmid42052398,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ},
title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794875},
pmid = {42052398},
issn = {1664-302X},
abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.},
}

@article {pmid42052400,
year = {2026},
author = {Xie, J and Zhang, J and Zhang, L and Chen, X},
title = {Exercise prescription for mood and cognition: targeting the microbiota-gut-brain axis through short-chain fatty acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740680},
pmid = {42052400},
issn = {1664-302X},
abstract = {Scientific study has extensively corroborated the advantageous impacts of exercise on mood, cognitive function, and stress resilience. Nonetheless, the fundamental biological mechanisms underpinning these effects have yet to be thoroughly integrated. This review advocates for and substantiates an integrated model focused on the "Exercise-Gut Microbiome-Short-Chain Fatty Acids (SCFAs)-Brain Function" axis. Consistent physical exercise alters the gut microbiota, enhancing Short-Chain Fatty Acid (SCFA)-producing populations, which is associated with markedly elevated bioavailability of key metabolites (acetate, propionate, and butyrate). Rather than detailing exhaustive molecular pathways here, we emphasize that these SCFAs facilitate gut-brain communication through multiple synergistic routes, including receptor-mediated neuroendocrine signaling, epigenetic modulation of neuroplasticity, and the attenuation of systemic neuroinflammation. Current human observational and interventional data strongly support an associative link between exercise-induced SCFA fluctuations and improved mental health outcomes. Crucially, we propose the novel "Exercise × Fiber Synergy" hypothesis: exercise primes the intestinal ecological niche for efficient substrate-utilizing bacteria, while adequate fermentable dietary fiber provides the necessary raw materials. Synergistically, this combination optimizes SCFA production to maximize cognitive and emotional benefits. To transition this framework into clinical practice, future research must prioritize 2 × 2 factorial designs (Exercise × Fiber) with dynamic kinetic measurements, paving the way for microbial phenotype-oriented precision exercise and personalized nutritional interventions to enhance public mental health.},
}

@article {pmid42052590,
year = {2026},
author = {Alebouyeh, M and Aminzadeh, M and Pourmand, MR and Bahiraee, M and Mirbagheri, SZ and Bakhtiari, R},
title = {Culturable bacteria in the gastric tissue and diversity of antimicrobial resistance in adults with gastritis.},
journal = {Caspian journal of internal medicine},
volume = {17},
number = {1},
pages = {143-151},
pmid = {42052590},
issn = {2008-6164},
abstract = {BACKGROUND: Despite growing knowledge in microbiome studies data about the diversity of cultivable bacteria and their drug resistance patterns in patients with gastritis are scant.

METHODS: Two gastric biopsies of 171 symptomatic patients were collected and examined by histological and microbiological methods. Viable bacteria were characterized using conventional techniques, and antimicrobial susceptibility of the isolates was detected.

RESULTS: Acute gastritis, chronic gastritis, and peptic ulcers were detected in 3.5%, 86.5%, and 5.8% of the patients, respectively. Culturable bacteria were isolated from 71.3% of the patients, including Helicobacter pylori (H. pylori) (26.9%), Staphylococcus epidermidis (19.8%), Micrococcus (1.1%), Streptococcus viridans (S. viridans) (13.4%), Enterococcus faecalis (E. faecalis) (4.6%), Staphylococcus aureus (S. aureus) (1.7%), and Group D Streptococcus (7.1%). Single infection and coexistence of two and three types of bacteria were detected in 43.2%, 15.2%, and 5.2% of the patients, respectively. An odd ratio of 4.4 was measured for Staphylococcus spp. in patients with acute gastritis (P-value = 0.08). E-test results showed intermediate resistance to penicillin in 66.6% of the S. aureus isolates, while resistance to vancomycin was detected only in the S. viridans (30.4%). Resistance to linezolid was detected in 100%, 17.4%, and 16.7% of E. faecalis, S. viridans, and group D Streptococci isolates, respectively. A high frequency of resistance to penicillin, clindamycin, linezolid, erythromycin, and tetracycline was detected in S. epidermidis strains.

CONCLUSION: Our results highlighted the importance of Gram-positive bacteria in the etiology of gastritis. Resistance of these bacteria to different classes of antibiotics should be considered in the clinical setting.},
}