@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04699-6},
pmid = {41540332},
issn = {1471-2180},
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

@article {pmid41540252,
year = {2026},
author = {Jo, Y and Joshi, NR and Chellappa, K},
title = {The microbiome at the centre of NAD[+] supplementation.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41540252},
issn = {2522-5812},
}

@article {pmid41540124,
year = {2026},
author = {Nickols, WA and Kuntz, T and Shen, J and Maharjan, S and Mallick, H and Franzosa, EA and Thompson, KN and Nearing, JT and Huttenhower, C},
title = {MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41540124},
issn = {1548-7105},
support = {U19AI110820//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32GM135117//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Microbial community analysis typically involves determining which microbial features are associated with properties such as environmental or health phenotypes. This task is impeded by data characteristics, including sparsity (technical or biological) and compositionality. Here we introduce MaAsLin 3 (microbiome multivariable associations with linear models) to simultaneously identify both abundance and prevalence relationships in microbiome studies with modern, potentially complex designs. MaAsLin 3 can newly account for compositionality either experimentally (for example, quantitative PCR or spike-ins) or computationally, and it expands the range of testable biological hypotheses and covariate types. On a variety of synthetic and real datasets, MaAsLin 3 outperformed state-of-the-art differential abundance methods, and when applied to the Inflammatory Bowel Disease Multi-omics Database, MaAsLin 3 corroborated previously reported associations, identifying 77% with feature prevalence rather than abundance. In summary, MaAsLin 3 enables researchers to identify microbiome associations more accurately and specifically, especially in complex datasets.},
}

@article {pmid41539935,
year = {2026},
author = {Vizon, C and Hochart, C and Galand, PE and Nugues, MM},
title = {Impacts of Nearby Algae on Recruitment Success and Early Microbiome Development of the Coral Acropora cytherea.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70241},
doi = {10.1111/1462-2920.70241},
pmid = {41539935},
issn = {1462-2920},
support = {ANR-18-CE02-0009-01//Agence Nationale de la Recherche/ ; },
mesh = {*Anthozoa/microbiology/growth & development ; Animals ; *Microbiota ; Coral Reefs ; *Bacteria/classification/genetics/isolation & purification ; Larva/microbiology/growth & development ; Symbiosis ; *Dinoflagellida/physiology ; Ecosystem ; },
abstract = {The persistence of coral reefs is dependent on the arrival and settlement of coral larvae followed by their post-settlement growth and survival. Despite evidence showing that benthic algae have variable effects on corals, it is still unclear how benthic communities of the coral nursery habitat impact the early development of the coral microbiome and if these impacts relate to the survival and growth of newly settled corals. Here, we tested whether the survival and growth of Acropora cytherea recruits are impacted by surrounding algae, and whether specific algae influence their associated bacterial and Symbiodiniaceae communities. A 6-month survey of coral larvae experimentally settled near different algae showed that crustose coralline algae enhanced recruit survival. However, despite variation in their microbiome, the presence of different algae did not impact the coral microbial community composition. The recruit microbiome was colonised by bacteria shared among all benthic substrates rather than bacteria unique to specific algae. Furthermore, the microbiome of coral larvae was different from that of the recruits. We conclude that the microbiome of corals in their early life stages is structured by host ontogeny rather than by their surrounding benthos, but that the surrounding benthos contributes to the transfer of opportunistic bacteria.},
}

*Anthozoa/microbiology/growth & development
Animals
*Microbiota
Coral Reefs
*Bacteria/classification/genetics/isolation & purification
Larva/microbiology/growth & development
Symbiosis
*Dinoflagellida/physiology
Ecosystem

@article {pmid41539801,
year = {2026},
author = {Zhang, X and Zang, X and Zhuang, J and Cheng, Y and Qin, Y and Jiang, J and Liang, Y and Song, Y and Liu, Y},
title = {Construction of a synthetic microbial community model for the predicting of characteristic aromas in Penglai Cabernet Sauvignon wines.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118162},
doi = {10.1016/j.foodres.2025.118162},
pmid = {41539801},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; Fermentation ; Saccharomyces cerevisiae/metabolism/genetics ; *Odorants/analysis ; *Vitis/microbiology ; *Microbiota ; Food Microbiology ; *Microbial Consortia ; Volatile Organic Compounds/analysis ; },
abstract = {To address the challenge of achieving targeted flavor formation in traditional fermented foods by overcoming the unpredictability of spontaneous fermentation, this study introduces a novel approach using Chinese Penglai Cabernet Sauvignon wines as a model system. First, the study identified and selected a collection of core functional microbial strains, including key Saccharomyces cerevisiae genotypes and non-Saccharomyces, from the indigenous spontaneous fermentation microbiome. By reconstituting them into a defined synthetic microbial community, we successfully developed a mathematical model that quantitatively correlates microbial community structure with characteristic aroma compounds. This model enables the accurate prediction and targeted shaping of desired aroma profiles through the rational design of starter cultures. This work provides a methodological framework that moves beyond the descriptive analysis of spontaneous fermentations towards the engineering of synthetic microbial consortia for targeted wine style. The core microbial resources and the predictive model presented here offer a concrete strategy for enhancing regional typicity and quality consistency in Penglai Cabernet Sauvignon production.},
}

*Wine/analysis/microbiology
Fermentation
Saccharomyces cerevisiae/metabolism/genetics
*Odorants/analysis
*Vitis/microbiology
*Microbiota
Food Microbiology
*Microbial Consortia
Volatile Organic Compounds/analysis

@article {pmid41539791,
year = {2026},
author = {Liu, P and Gao, C and Li, S and Wu, D and Zhang, Z and Chen, W and Li, W and Shao, F and Wang, HD and Yang, Y},
title = {A novel Fucose-specific lectin from Morchella esculenta modulates gut-liver Axis to alleviate non-alcoholic fatty liver disease.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118106},
doi = {10.1016/j.foodres.2025.118106},
pmid = {41539791},
issn = {1873-7145},
mesh = {*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Diet, High-Fat/adverse effects ; *Lectins/pharmacology/chemistry/isolation & purification ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; *Fucose/metabolism ; Lipid Metabolism/drug effects ; Disease Models, Animal ; },
abstract = {Morchella esculenta is an underexplored source of lectins with diverse bioactivities. In this study, a novel fucose-specific lectin (MEP5) was isolated from M. esculenta, with a molecular weight of 33.12 kDa and a characteristic carbohydrate-recognition domain. Structural analysis revealed that MEP5 predominantly consists of random coils and extended strands, with α-helix as a minor component. In a high-fat diet (HFD)-induced non-alcoholic fatty liver disease (NAFLD) mouse model, MEP5 treatment significantly ameliorated NAFLD by normalizing lipid profiles (TG, TC, LDL-C, HDLC), repairing adipose tissue morphology, and reducing hepatic lipid accumulation. Mechanistically, MEP5 exerted hepatoprotective effects through transcriptional modulation of key lipid metabolic regulators (PPARα, SREBP-1, Fasn, Hmgcr, G6pc1, UCP-1, CD36, ABCA1, PRDM16). Network pharmacology and experimental validation indicated that MEP5 alleviated hepatic steatosis by inhibiting the MAPK signaling pathway. Additionally, integrated metabolomic and 16S rRNA sequencing analyses identified alterations in the gut microbiome, with enrichment of Duncaniella, CAG-485, and UBA3282, and depletion of Desulfovibrio-R, which were linked to MEP5's protective effects. This study highlights the potential of M. esculenta lectins as a therapeutic tool, advancing our understanding of gut-liver interactions and metabolic regulation.},
}

*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism
Animals
*Gastrointestinal Microbiome/drug effects
Mice
Diet, High-Fat/adverse effects
*Lectins/pharmacology/chemistry/isolation & purification
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Male
*Fucose/metabolism
Lipid Metabolism/drug effects
Disease Models, Animal

@article {pmid41539761,
year = {2026},
author = {Long, M and Wang, H and Zhang, F and Ran, Y and Li, Y and Luo, J and Chen, Z and Tian, Z and Tan, S and Liu, X},
title = {Nanogel-encapsulated Rosa roxburghii Tratt fruit polyphenols ameliorated ulcerative colitis by regulating gut microbiota and PI3K/Akt and NF-κB pathways.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118149},
doi = {10.1016/j.foodres.2025.118149},
pmid = {41539761},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; *Polyphenols/pharmacology/chemistry ; Proto-Oncogene Proteins c-akt/metabolism ; *Fruit/chemistry ; Signal Transduction/drug effects ; *Rosa/chemistry ; Phosphatidylinositol 3-Kinases/metabolism ; Nanogels/chemistry ; Male ; Mice ; Anti-Inflammatory Agents/pharmacology ; Oxidative Stress/drug effects ; Mice, Inbred C57BL ; Antioxidants/pharmacology ; },
abstract = {Rosa roxburghii Tratt fruit polyphenols (RP) possess antioxidant, anti-inflammatory, and immunomodulatory properties, showing potential for ulcerative colitis (UC) treatment. However, their efficacy is limited by bioavailability and targeting efficiency. To address this, RP were encapsulated into acylated chitosan-crosslinked carboxymethyl konjac glucomannan (ACs-CKGM) nanogel (RPNG). Experimental results demonstrated that RPNG significantly enhanced intestinal barrier function by upregulating tight junction proteins (ZO-1, Occludin and Claudin-3) and mucus secretion (MUC2). It effectively mitigated oxidative stress by restoring antioxidant enzymes (SOD, GSH-Px and CAT) while reducing MPO, COX-2 and iNOS activation. Through integrated ELISA, western blot, and transcriptomic analyses, we emonstrated that RPNG specifically inhibited PI3K/Akt/mTOR and NF-κB signaling pathways, decreasing inflammatory cytokines (e.g., TNF-α, IL-6) while increasing anti-inflammatory mediators (e.g., IL-10). Gut microbiome analysis showed RPNG reversed DSS-induced dysbiosis by enriching beneficial bacteria (e.g., Muribaculum sp.) and suppressing pathogens (e.g., Escherichia coli). These findings highlight RPNG as a novel targeted strategy for UC management, supported by multi-omics mechanistic insights.},
}

*Gastrointestinal Microbiome/drug effects
*Colitis, Ulcerative/drug therapy/microbiology
Animals
NF-kappa B/metabolism
*Polyphenols/pharmacology/chemistry
Proto-Oncogene Proteins c-akt/metabolism
*Fruit/chemistry
Signal Transduction/drug effects
*Rosa/chemistry
Phosphatidylinositol 3-Kinases/metabolism
Nanogels/chemistry
Male
Mice
Anti-Inflammatory Agents/pharmacology
Oxidative Stress/drug effects
Mice, Inbred C57BL
Antioxidants/pharmacology

@article {pmid41539751,
year = {2026},
author = {Zhou, M and Xia, C and Jing, B and Duan, J and Li, H and Che, H},
title = {Sepia pharaonis ink derived melanin ameliorated high-fat diet induced lipid dysmetabolism: Insights from microbiome and hepatic transcription.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118086},
doi = {10.1016/j.foodres.2025.118086},
pmid = {41539751},
issn = {1873-7145},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism/drug effects ; *Melanins/pharmacology ; *Lipid Metabolism/drug effects ; Male ; *Sepia/chemistry ; Mice ; Mice, Inbred C57BL ; },
abstract = {Sepia pharaonis ink melanin (MSI) is a natural eumelanin-rich compound with anti-inflammatory activities and gut microbiota-regulating effects. However, its impact on lipid dysmetabolism triggered by high-fat diet (HFD) remains unclear. This study sought to investigate the improvement and the underlying mechanisms of MSI on lipid metabolism through biochemical indicators, liver transcriptomics, and intestinal microbiota analyses. The results demonstrated that MSI administration obviously reduced weight gain and fat accumulation, and reduced anomalous lipid levels in liver and serum. Liver transcriptome analysis suggested that MSI mainly affected PPARα signaling pathway and fatty acid degradation to enhance lipid metabolism. Furthermore, MSI lowered hepatic and intestinal inflammation, and boosted the levels of ZO-1 and occludin in a dose-dependent manner. Concurrently, 16S rRNA sequencing of gut microbiota showed that MSI treatment decreased the Firmicutes/Bacteroidetes ratio and increased dominant bacterial of Muribaculum, Alistipes and Odoribacter. Collectively, these findings suggested that MSI alleviated HFD-induced lipid accumulation by modulating inflammation, intestinal barrier function and gut microbiota. This comprehensive study offered a basis for the development and utilization of MSI in tackling lipid dysmetabolism.},
}

Animals
*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/drug effects
*Liver/metabolism/drug effects
*Melanins/pharmacology
*Lipid Metabolism/drug effects
Male
*Sepia/chemistry
Mice
Mice, Inbred C57BL

@article {pmid41539628,
year = {2026},
author = {Peng, Y and Liu, H and Xing, T and Zhen, F and Wu, D and Sun, Y},
title = {Instability mechanisms of overloaded anaerobic digestion: Insights from volatile fatty acid metabolism.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134006},
doi = {10.1016/j.biortech.2026.134006},
pmid = {41539628},
issn = {1873-2976},
abstract = {To clarify the mechanisms driving process instability under overload stress, a long-term semi-continuous overload instability simulation experiment was conducted. High-throughput sequencing and metagenomics were used to determine the response of the process parameters, community composition, and volatile fatty acid (VFA)-related metabolic functional genes to the organic loading rate (OLR). When the OLR increased to 12.5 kg VS/m[3]/d, the methane yield remained low at 226.40 ± 10.78 mL CH4/g VS. Further increasing the OLR to 20 kg VS/m[3]/d completely destabilized the reactor, resulting in a final methane yield as low as 0.29 mL CH4/g VS, a hydrogen partial pressure as high as 357.37 Pa, and concentrations of butyrate, propionate, and acetate of 4328.49 ± 538.18, 1036.13 ± 75.48, and 9939.67 ± 427.68 mg/L, respectively. Organic overload stress caused reactor instability mainly by blocking VFA metabolism. When the OLR was ≥ 11 kg VS/m[3]/d, the relative abundances of key genes (aceE, buk, ptb, atoD) in the butyrate and propionate metabolic pathways decreased, resulting in the accumulation of butyrate and propionate. Despite a shift in syntrophic acetate oxidation metabolism from the methyl to the carbonyl branch under overload, the latter's recovery was insufficient to compensate for the severe impairment of the methyl branch, ultimately leading to acetate accumulation. VFA accumulation caused severe inhibition of acetogens and some methanogens, while hydrolytic and acidogenic bacteria dominated the microbiome (relative abundance: 94.18 %). As a result, the microbial metabolic balance was broken. Our results provide new insights into the mechanisms driving process instability under overload stress.},
}

@article {pmid41539609,
year = {2026},
author = {Yang, D and Ren, D and Zhang, Y and Hao, Y and Yue, Y and Li, Q and Fan, Q and Sun, C and Cui, M and Zhang, M},
title = {The Gut Microbiota Dysbiosis in Geriatric Multimorbidity: Pharmacotherapeutic Implications, Pathophysiological Mechanisms, and Precision Modulation Strategies.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103023},
doi = {10.1016/j.arr.2026.103023},
pmid = {41539609},
issn = {1872-9649},
abstract = {Aging around the world is accelerating. With that comes the intersection of geriatric multimorbidity and polypharmacy, creating a large uncertainty about the pharmacological efficacy and therapeutic consequences of medications used when multiple concurrent health issues exist. The gut microbiota coordinates the way drugs work through multiple pathways: through the way drugs are metabolised, the way they maintain immune homeostasis, and the way they regulate the epithelial barrier. For these reasons, the gut microbiota is becoming an important therapeutic target for optimizing precision medicine strategies in treating patients with geriatric multimorbidities. In this narrative review, we systematically synthesize the evidence regarding how gut dysbiosis leads to decreased efficacy of multi-drug regimens through the interplay between metabolism, immune response, and barrier function in aging patients with multimorbidities, and we evaluate targeted interventions. Furthermore, we demonstrate that current interventions (e.g., probiotics, prebiotics, fecal microbiota transplants (FMT), phage therapy, and dietary modulation) have unique benefits but are limited by inter-individual variability, safety concerns, and a lack of proven long-term efficacy. Thus, many areas of microbiota-drug interactions in older adults with multimorbidity should be explored through future research. Key areas to address are: the establishment of large, multicenter longitudinal cohorts of older adults with multimorbidity that would allow for repeated collection of microbiota profiles, medication use, and health outcomes to identify the evolving interaction between multimorbidity, microbiota, and polypharmacy; the urgent need for standardized and integrated databases of microbiome-drug interactions that harmonize data formats, provide metabolic annotations and medication identifiers in order to support reproducible cross-study validation; and the further validation and application of artificial intelligence (AI) and machine learning (ML) in clinical trials. High-dimensional data collected from cohorts and databases will enable the development of predictive algorithms to identify individual drug responses and how effective microbiota-targeted interventions will be; these algorithms must then be prospectively validated. Ultimately, these initiatives are necessary to move toward the personalized management of microbiota-drug interactions in older adults with multimorbidity, providing greater safety of polypharmacy and promoting healthy aging.},
}

@article {pmid41539598,
year = {2026},
author = {Wei, S and Li, W and Ran, S and Zhang, J and Zhang, Z and Yang, Z and Tian, F and Chen, L and Hu, P and Yuan, J and Lin, H},
title = {Multi-organ metabolic dysregulation and cecal microbiota alterations following black carbon exposure.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.027},
pmid = {41539598},
issn = {2090-1224},
abstract = {BACKGROUND: Black carbon (BC) has been linked to adverse health outcomes, yet underlying mechanisms remain unclear. Integrating metabolomic and metagenomic data across tissues may clarify BC-induced biological pathways.

METHODS: We performed human epidemiology and mice experimental approaches. We included 248,288 participants with annual BC exposure estimates and plasma metabolomic profiles. Elastic net regression identified BC-associated metabolites. Male C57BL/6J mice were exposed to filtered air or BC (1 mg/m[3], 1 h/day, 5 days/week, 12 weeks). Multi-tissue metabolomics and cecal contents microbiota sequencing were conducted, with histology and gene expression measurements.

RESULTS: In humans, long-term BC exposure significantly altered plasma metabolites, notably increasing saturated fatty acids (β = 0.048), while decreasing docosahexaenoic acid (β = -0.002). Amino acid metabolism was broadly disrupted, involving elevated valine (β = 0.011) and reduced glutamine (β = -0.006). In mice, metabolomic profiling showed organ-specific shifts, including increased glutathione and cortisol in the liver (2.88-fold and 2.06-fold), increased PC(16:0/18:1(9Z)) in the heart (3.22-fold), elevated anandamide and arachidonic acid in the kidney (2.35-fold and 1.48-fold), and decreased multiple fatty acids and lysophospholipids across organs. Cecal microbiota exhibited reduced alpha-diversity (Shannon: 3.67 vs. 4.50, P < 0.05) and taxonomic shifts, including an increased abundance of g_Akkermansia and decrease in g_Bacteroides. Multi-omics integration revealed significant microbiota-metabolome correlations in the cecum and plasma (Mantel r = 0.276, P = 0.012). Histological examination confirmed organ injuries, notably lung inflammation, cardiac edema, and neuronal condensation. Gene expression analysis showed increased Il-6 in the lung (5.35-fold, P = 0.047), increased Mb in the heart (5.18-fold, P = 0.010), and increased Igfbp7 in the kidney (3.03-fold, P = 0.001), while Tjp1 expression in cecum was reduced (0.42-fold, P = 0.004).

CONCLUSIONS: Our findings suggest that BC exposure may alter systemic metabolism and gut microbiota, potentially contributing to tissue injury and inflammation. The gut-organ axis could be a target for mitigating BC-related health effects.},
}

@article {pmid41539591,
year = {2026},
author = {Pravin, V and Vellapandian, C and Naveen Kumar, V},
title = {The oral-gut-brain axis in periodontitis: microbial signaling in systemic and neuroinflammatory disease.},
journal = {Brain research},
volume = {},
number = {},
pages = {150168},
doi = {10.1016/j.brainres.2026.150168},
pmid = {41539591},
issn = {1872-6240},
abstract = {Periodontitis, a chronic inflammatory disease of the oral cavity, has been identified as a modifiable risk factor of the development of systemic and neurological disorders via a complicated interplay of microbiological, immunological, and neural interactions. Periodontal pathogens breach local immune homeostasis, are translocated to the gut and brain, and trigger a cascade of immune deregulation, leaky gut, and blood-brain barrier, thereby forming a tri-directional communication network that links local oral inflammation to systemic and neurovascular conditions. This review synthesizes existing evidence on how oral dysbiosis, can spread to the gut and trigger systemic inflammation, leading to neuroinflammation and neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. Mechanistically, the OGB axis acts through various processes, such as hematogenous spread, retrograde axonal transport, immune cell trafficking (Trojan horse mechanism), and extracellular vesicle-based signaling corresponding to the causes of neuroinflammation, microglial activation, and the pathology of tau and amyloid. The diagnostic and therapeutic implications of the OGB axis provide new pathways toward early intervention with precision medicine, microbiome remodeling, immune-based therapy, and neuroprotective approaches. Emerging technologies, including AI-based diagnostics and biosensing technologies, offers noninvasive tools to track host-microbial interactions and inflammatory biomarkers. This integrative view underscores the central importance of oral health in systemic homeostasis and the development of neurodegenerative conditions, necessitating collaborative approaches between dentistry, neurology, and immunology to cooperate to deliver efficacy in disease elimination and mitigation.},
}

@article {pmid41539578,
year = {2026},
author = {Chehadeh, C and Nakatsuji, T and Gallo, RL},
title = {Staphylococcus aureus in Atopic Dermatitis: How a common bacterium exploits and drives disease.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.12.1009},
pmid = {41539578},
issn = {1097-6825},
abstract = {The role of Staphylococcus aureus (S. aureus) in atopic dermatitis (AD) has been extensively studied. Although its role in the pathophysiology of AD was previously controversial, current evidence now shows that it is a major factor promoting the disease and is responsible for significant morbidity. Its influence in AD stems from widespread exposure since S. aureus is common on healthy skin and is frequently part of the normal human skin microbiome. In AD, S. aureus and the closely related S. epidermidis gain a selective growth advantage over most other members of the skin microbiome due to a complex relationship involving the skin's innate immune system, other members of the microbiome, and skin barrier properties. Disruption in the functioning of those components or changes in their interactions leads to dysbiosis, skin barrier damage, and the progression of skin disease. This review summarizes research findings on these relationships and highlights the interactions and factors that promote S. aureus survival on skin and its participation in the pathogenesis of AD.},
}

@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial Taxonomic and Functional Responses to Heavy Metal Gradients in Mining-Impacted Stream Sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1%, 12.4%, and 12.9% of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4%) and Acidithiobacillus (5.0%), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8%) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}

@article {pmid41539436,
year = {2026},
author = {Berube, LT and Wang, C and Curran, M and Pompeii, ML and Hu, L and Barua, S and Li, H and St-Jules, DE and Schoenthaler, A and Segal, E and Bergman, M and Popp, CJ},
title = {Personalized dietary feedback mediates the association of dietary self-monitoring adherence and weight loss: a post-hoc analysis of the Personal Diet Study.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101364},
doi = {10.1016/j.tjnut.2026.101364},
pmid = {41539436},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary self-monitoring is central to effective personalized nutrition, providing critical data to inform tailored feedback and support behavior change.

OBJECTIVE: To examine the impact of dietary self-monitoring adherence and the indirect effect of personalized scores to predict postprandial glycemic response (PPGR) on weight loss.

METHODS: Post-hoc analysis of the Personal Diet Study that investigated the impact of a machine algorithm-based diet that integrates clinical and microbiome features (Personalized) compared to a standard, low-fat diet (Standardized) on weight loss. All participants received behavioral counseling and were encouraged to self-monitor dietary intake via a smartphone app. Personalized received algorithm-based scores (1 to 5) on predicted PPGR to foods logged (PPGR score; 1-2 indicating optimal; 3-5 suboptimal). Dietary self-monitoring adherence was the percentage of days logging ≥50% of target calories, classified as high or low. PPGR score quality was calculated by the proportion of optimal predicted PPGR scores per day; defined as "high-PPGR quality" days when this exceeded the group average. Mediation analysis assessed whether PPGR quality mediated the relationship between dietary self-monitoring adherence and weight loss.

RESULTS: Participants with high self-monitoring adherence lost an average of 4.2% of their baseline weight, compared to 1.9% among those with low adherence (p=0.016). High self-monitoring adherence was associated with a greater likelihood of achieving ≥5% weight loss (aOR=3.67, 95% CI: 1.63-8.50). Within Personalized, high PPGR quality mediated 53.4% of the total effect of self-monitoring adherence on weight loss (p<0.001).

CONCLUSION: Consistent self-monitoring coupled with personalized feedback may significantly enhance weight loss in a precision nutrition approach.

CLINICAL TRIAL REGISTRATION: NCT03336411.},
}

@article {pmid41539328,
year = {2026},
author = {Meduri, GU and Lannini, S and Smit, JM},
title = {Limitations in the Design of Critical Care Studies and Suggestions for Future Research Directions.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2762-8278},
pmid = {41539328},
issn = {1098-9048},
abstract = {Glucocorticoid (GC) therapy has been a cornerstone of critical care; however, its full potential has been constrained by fixed-dose regimens and trial designs that predate current insights into the dynamic, phase-specific functions of glucocorticoid receptor α (GRα). This study shifts focus from mechanistic pathways to the clinical implications of phase-adaptive care, emphasizing how GC therapy can be optimized through individualized, response-guided strategies tailored to illness trajectory and biological variability. Rather than reiterating GRα's mechanistic role, which is discussed in Chapter 3, this work highlights its practical relevance in therapeutic decision-making across the three sequential phases of critical illness: priming, modulatory, and restorative. In this clinically oriented framework, phase-specific treatment adjustments are informed by real-time changes in systemic stress markers, immune dynamics, and metabolic indicators. Earlier randomized controlled trials were instrumental in establishing safety but often failed to account for evolving physiological demands or receptor variability, contributing to inconsistent outcomes. To bridge this translational gap, this study proposes the integration of response-guided protocols utilizing accessible clinical biomarkers-such as C-reactive protein, interleukin-6, D-dimer, and lactate-allowing for adaptive dosing and tapering strategies aligned with patient-specific recovery patterns. Moving beyond pharmacologic dosing, the study outlines adjunctive clinical strategies-including targeted micronutrient supplementation and microbiome-supportive therapies-not as theoretical possibilities but as practical co-interventions that can be incorporated into intensive care unit protocols. Furthermore, it explores how artificial intelligence-enabled clinical decision systems and adaptive trial designs can operationalize precision care by dynamically stratifying patients and tailoring interventions to shifting biological profiles. Together, these applied strategies support a transition from static treatment paradigms to a precision medicine model in critical care-one that aligns GC therapy with individualized recovery trajectories, maximizes therapeutic responsiveness, and reduces treatment-related risks through multimodal, phase-responsive interventions.},
}

@article {pmid41539295,
year = {2026},
author = {Zhang, H and Liao, C},
title = {Illuminating the functional dark matter of the gut microbiome.},
journal = {Cell host & microbe},
volume = {34},
number = {1},
pages = {12-14},
doi = {10.1016/j.chom.2025.12.004},
pmid = {41539295},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/genetics/enzymology ; Bacterial Proteins/metabolism/chemistry ; Bacteriophages ; Host Microbial Interactions ; },
abstract = {In this issue of Cell Host & Microbe, Liu et al. provide a roadmap for decoding the gut microbiome's functional dark matter through a structural atlas of gut phage and bacterial proteins, validating structure-guided functions from endolysins to microbial-host isozymes, and developing an alignment-free method for detecting bacteria-human remote homologs.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Bacteria/genetics/enzymology
Bacterial Proteins/metabolism/chemistry
Bacteriophages
Host Microbial Interactions

@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
doi = {10.1016/j.psj.2026.106371},
pmid = {41539238},
issn = {1525-3171},
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}

@article {pmid41539110,
year = {2026},
author = {Shrivastav, K and Pandey, M and Gor, H and Nema, V},
title = {Gut virome plays an extended role with bacteriome in neurological health and disease.},
journal = {Journal of the neurological sciences},
volume = {481},
number = {},
pages = {125754},
doi = {10.1016/j.jns.2026.125754},
pmid = {41539110},
issn = {1878-5883},
abstract = {The gut-brain axis (GBA) is a complex two-way communication system that links the gastrointestinal tract and the central nervous system (CNS) through neural, immune, hormonal, and microbial pathways. The microbiota-gut-brain axis (MGBA), a more specific concept, focuses on how gut microorganisms, including bacteria, viruses, and other microbes, modulate this communication and influence neurological health. This comprehensive review examines the intricate mechanisms through which gut microorganisms modulate neural function and contribute to neurological health and disease pathogenesis. The gut microbiota, comprising bacteria, viruses, fungi, and bacteriophages, produces essential neuroactive compounds including neurotransmitters- Gamma-Aminobutyric Acid (GABA), serotonin (5-HT), dopamine (DA), short-chain fatty acids (SCFAs), and metabolites that directly influence brain physiology through vagal, hormonal, and immunological pathways. Dysbiosis of the gut microbiota has been implicated in various neurological disorders, including Alzheimer's disease, Parkinson's disease, autism spectrum disorders, and schizophrenia. In healthy conditions, beneficial bacterial strains such as Lactobacillus species synthesize GABA and regulate mood, while SCFA-producing bacteria like Fecalibacterium prausnitzii maintain blood-brain barrier integrity and exert neuroprotective effects. Conversely, pathological states demonstrate altered microbial compositions, reduced bacterial diversity, and compromised production of beneficial metabolites. Emerging evidence highlights the previously underexplored role of the gut virome, particularly bacteriophages, in regulating bacterial populations and influencing neurodevelopment. Viral dysbiosis correlates with cognitive impairment and neurodegenerative processes through modulation of bacterial metabolism and inflammatory responses. Understanding these complex host-microbiome-virome interactions provides novel therapeutic opportunities for neurological disorders through targeted interventions including probiotics, fecal microbiota transplantation, and phage-based therapies, representing a paradigm shift toward microbiome-centered approaches in neurological medicine.},
}

@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.

PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.

METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.

RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.

CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}

@article {pmid41537815,
year = {2025},
author = {Aoki, LR and Graham, OJ and Yoshioka, RM and Maher, R and Alma, L and Hofmann, EE and Burge, CA and Harvell, D and Groner, ML},
title = {Wasting disease of a marine foundation species links community interactions to disease dynamics.},
journal = {Biology letters},
volume = {21},
number = {12},
pages = {},
doi = {10.1098/rsbl.2025.0579},
pmid = {41537815},
issn = {1744-957X},
support = {//National Science Foundation/ ; //William Calver Postdoctoral Fellowship/ ; },
mesh = {*Zosteraceae/microbiology/parasitology/physiology ; *Ecosystem ; Animals ; Climate Change ; Microbiota ; *Plant Diseases/parasitology ; },
abstract = {Infectious disease plays a key role in shaping marine communities, including in seagrass meadows, which form biodiverse coastal habitats. Eelgrass (Zostera marina) is the most widespread seagrass species and is susceptible to seagrass wasting disease, caused by the protist Labyrinthula zosterae. As a foundation species, eelgrass strongly influences ecosystem structure, function and services; recent work has begun to explore the links between critical community interactions and seagrass wasting disease. Here, we highlight recent advances about how the eelgrass community regulates and responds to seagrass wasting disease, from the microbiome to herbivores and filter feeders. We further show how efforts to model seagrass wasting disease progression can build on prior efforts to predict eelgrass growth and productivity and can inform our understanding of ecosystem health, resilience and vulnerability. As climate change alters environmental conditions, potentially favouring the wasting disease pathogen, efforts to integrate community interactions with disease ecology will be critical to forecast ecosystem dynamics and to develop effective coastal management strategies. We offer guidance on addressing major knowledge gaps in the study of eelgrass wasting disease in order to deepen both ecological theory and applied practices and identify how an integrated marine-disease-community ecology can inform a broader, cross-cutting understanding of disease.},
}

*Zosteraceae/microbiology/parasitology/physiology
*Ecosystem
Animals
Climate Change
Microbiota
*Plant Diseases/parasitology

@article {pmid41538371,
year = {2026},
author = {Alves, G and Hamaneh, MB and Ogurtsov, AY and Yu, YK},
title = {Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.},
journal = {Journal of the American Society for Mass Spectrometry},
volume = {},
number = {},
pages = {},
doi = {10.1021/jasms.5c00332},
pmid = {41538371},
issn = {1879-1123},
abstract = {Microbiome communities are found across diverse environments and play critical roles in both ecosystem function and human health. Mass-spectrometry-based metaproteomics provides a powerful means for directly identifying and quantifying microbial proteins. However, its application is hindered by the shared peptide problem, where peptides map to multiple proteins across taxa, complicating taxon-protein quantification. To address this challenge, we extend a previously published modified expectation-maximization algorithm that incorporates taxonomic biomass constraints into the Microorganism Classification and Identification (MiCId) workflow. This enhanced expectation-maximization algorithm is used to quantify taxon-protein pairs derived from clusters of identified taxon-protein pairs, thereby enabling more accurate quantification and representation of taxonomic-level proteomes. The performance of the approach is evaluated using synthetic datasets consisting of simple mixtures with known relative species abundances, a more complex 24-species synthetic dataset, and a clinical human stool microbiome dataset. It is shown that, in simple synthetic datasets, fold changes computed for species-protein pairs closely match the expected values and are consistent with those obtained from MaxQuant. Using the 24-species synthetic dataset, we show that the algorithm accurately redistributes peptide extracted ion count among taxon-protein pairs that share peptides. Finally, analyzing the clinical stool microbiome dataset, we demonstrate that MiCId's results are accurate and consistent with previously reported findings. These results demonstrate the robustness of MiCId's algorithm for quantifying taxon-protein pairs in complex microbial communities. By resolving the shared peptide problem, the method enables accurate representation of taxonomic-level proteomes, thereby advancing the application of metaproteomics in microbiome research.},
}

@article {pmid41538368,
year = {2026},
author = {Dame-Teixeira, N and Melo, JLMA and Parolo, CCF},
title = {Caries Microbiome: time to move from blame to balance.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000550472},
pmid = {41538368},
issn = {1421-976X},
abstract = {BACKGROUND: Advances in next-generation sequencing(NGS) and multi-omics approaches reinforced the concept of functional diversity within biofilm communities, revealing roles beyond bacterial taxonomy and highlighting metabolic and ecological mechanisms operating at the individual level rather than within isolated caries lesions. Moving toward new clinical solutions will require broader perspectives; to this end, we propose key directions to advance the translational potential of caries microbiome research. We present a perspective that connects ecological theory, molecular evidence, and clinical implications through three central topics: (I)microbial composition, (II)microbial function, and (III)individual-level characteristics.

SUMMARY: From a compositional perspective, caries microbiome research should move beyond the search for bacterial culprits and instead consider the broader microbial ecosystem, including low-abundance and non-bacterial members (such as archaea). Within this framework, microbial taxa and functions should not be viewed as inherently "good" or "bad," but rather as context-dependent components of a dynamic ecosystem shaped by sustained environmental pressures. Functionally, the recurrent enrichment of pathways related to carbohydrate metabolism, sugar transport, and acid production likely reflects microbial adaptation to persistent sugar exposure rather than intrinsic virulence traits. This perspective suggests that progress in caries research depends on moving beyond disease-centered models toward understanding how microbial stability preserves oral health. At the individual level, individuals with previous caries experience may retain disease-associated microbial or functional signatures during remission, a phenomenon referred to here as a microbiological dysbiosis scar. This ecological memory may help explain why past caries experience remains one of the strongest predictors of future lesions and highlights the importance of incorporating individual history into the design and interpretation of caries microbiome studies. Integrating detailed clinical metadata with advanced bioinformatic approaches, including artificial intelligence, will be essential for establishing meaningful biological links.

KEY MESSAGES: Progress in caries microbiome research depends on refining study design across microbial composition, functional, and individual levels. Strengthening the resilience of the oral microbiome rather than eliminating specific pathogens or the microbiome should be the central goal of caries microbiology. Moving from blame to balance is not merely semantic; it represents a fundamental shift in how we study, prevent, and manage dental caries.},
}

@article {pmid41537975,
year = {2026},
author = {Sless, T and Chau, K and Nguyen, P and Rehan, S},
title = {Microbial communities of wild bees and comparative phylogenetics of key bacterial taxa across the bee tree of life.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2062},
pages = {},
doi = {10.1098/rspb.2025.1823},
pmid = {41537975},
issn = {1471-2954},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Bees/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; },
abstract = {Recent years have seen a rapidly growing interest in the study of microbiomes to understand the health and well-being of host animals. Within bees, much of this work has focused on managed species of agricultural importance, such as honeybees and bumblebees. However, unmanaged wild bees are also vital to both agricultural and natural systems, and studying their microbial associates is essential to understanding the impacts of microbiomes on bee health. We used metabarcoding based on 16S rRNA and internal transcribed spacer region (ITS1) loci to identify bacterial and fungal associates of adult bees from 16 species, 10 genera and 5 families, representing a diverse sampling of wild bees common to eastern North America. Overall, Apilactobacillus was the largest component of bacterial communities, while fungal communities were dominated by Cladosporium. Alpha diversity of both bacteria and fungi differed significantly across genera and species, while beta diversity varied at all taxonomic levels. Additionally, we conducted a broad phylogenetic comparison of bacterial communities across bees using previously published 16S rRNA datasets and contrasted these findings with functional traits across the bee tree of life. Several bacterial taxa showed evidence of strong phylogenetic signal in prevalence, while the presence of corbiculae was more strongly associated with bacterial community composition than sociality or nesting habit. This study provides expanded insights into the microbial associates of wild bees, as well as the broadest investigation to date into patterns of phylogenetic conservation in bacterial communities across a total of 42 species representing the five most diverse bee families.},
}

Animals
Bees/microbiology
Phylogeny
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics/analysis
*Microbiota
*Fungi/classification/genetics/isolation & purification
DNA Barcoding, Taxonomic

@article {pmid41537600,
year = {2026},
author = {Li, Y and Stieh, DJ and Droit, L and Kim, AH and Rodgers, R and Mihindukulasuriya, KA and Wang, L and Pau, MG and Yuan, O and Virgin, HW and Barouch, DH and Baldridge, MT and Handley, SA},
title = {Associations between the microbiome and immune responses to an adenovirus-based HIV-1 candidate vaccine are distinct between African and US cohorts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143525},
doi = {10.1128/msystems.01435-25},
pmid = {41537600},
issn = {2379-5077},
abstract = {Optimization of prophylactic vaccine regimens to elicit strong, long-lasting immunity is an urgent need highlighted by the COVID-19 pandemic. Stronger vaccine immunogenicity is frequently reported in individuals living in high-income countries compared to individuals living in low- and middle-income countries. While numerous host genetic and immune factors may influence vaccine responses, geographic restrictions to vaccine effectiveness may also be influenced by the intestinal microbiota, which modulates host immune systems. However, the potential role of the gut microbiota on responses to HIV-1 vaccines has not yet been explored. We analyzed the bacteriome by targeted 16S sequencing and the virome by virus-like particle sequencing of 154 fecal samples collected from healthy individuals in Uganda, Rwanda, and the United States early (week 2) and late (week 26) after vaccination with multivalent adenovirus serotype 26 (Ad26)-vectored mosaic HIV-1 vaccines. Vaccination did not affect the enteric bacteriome or virome regardless of geographic location. However, geography was the major driver of microbiota differences within this cohort. Differences in overall bacterial and viral diversity and in specific microbial taxa, including Bacteroidota and Bacillota, between participants from the United States and East African countries correlated with differential immune responses, including specific antibody titers, antibody functionality, and cellular immune responses to vaccination regimens. These findings support the microbiota as a putative modifier of vaccine immunogenicity.IMPORTANCEOur research examined how gut bacteria might influence vaccine effectiveness in different parts of the world. We studied adults from the United States, Rwanda, and Uganda who received an experimental HIV vaccine. We found that participants from East Africa had more diverse gut bacteria than those from the United States, but their immune responses to the vaccine were weaker. This is the first study to directly show this relationship between higher gut bacterial diversity and reduced vaccine effectiveness in the same group of people. We also identified specific types of bacteria that were linked to either stronger or weaker immune responses. These findings are particularly relevant now as we use vaccines globally to fight diseases like COVID-19, as they suggest that regional differences in gut bacteria Bacteroidota and Bacillota might help explain why vaccines work better in some places than others. This could inform how we design and test future vaccines.},
}

@article {pmid41537573,
year = {2025},
author = {Roos, NDB},
title = {The microbiome in mind: Reflections on antibiotic prescription in primary care.},
journal = {South African family practice : official journal of the South African Academy of Family Practice/Primary Care},
volume = {67},
number = {1},
pages = {e1-e4},
doi = {10.4102/safp.v67i1.6238},
pmid = {41537573},
issn = {2078-6204},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use ; *Primary Health Care ; *Antimicrobial Stewardship ; Child ; *Microbiota ; *Practice Patterns, Physicians' ; },
abstract = {In this opinion piece, the author critically reflects on his own antimicrobial stewardship practices in primary care and the complex factors influencing antibiotic prescription, specifically in children.Contribution: In light of emerging evidence of the role of the microbiome in both health and disease, this piece raises a key question: Are we doing more harm than good?},
}

Humans
*Anti-Bacterial Agents/therapeutic use
*Primary Health Care
*Antimicrobial Stewardship
Child
*Microbiota
*Practice Patterns, Physicians'

@article {pmid41537554,
year = {2026},
author = {Deyett, E and DiSalvo, B and Massonnet, M and Ashworth, V and Cantu, D and Lindow, S and Rolshausen, PE and Roper, MC},
title = {Grapevines Pre-Treated with Biocontrol Bacteria Have an Altered Transcriptional Response to Xylella fastidiosa and a Reduction in Pierce's Disease Severity.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-12-25-0166-R},
pmid = {41537554},
issn = {0894-0282},
abstract = {In a previous DNA-based microbiome study of grapevines in areas of Pierce's Disease (PD) pressure, we determined that taxa belonging to the Pseudomonas and Achromobacter genera negatively associated with PD severity and titer of the causal agent, Xylella fastidiosa, leading us to hypothesize that these taxa suppress PD and could be deployed as biocontrols. Here we tested this hypothesis using two bacterial isolates from the grapevine endosphere, Pseudomonas viridiflava and Achromobacter vitis. We demonstrate that pre-treatment with these two isolates significantly reduced PD symptoms and X. fastidiosa titer, comparable to that of a known PD biocontrol agent, Paraburkholderia phytofirmans PsJN. We monitored early spatial transcriptional responses using genome-wide transcriptional profiling in vines that were pre-treated with the biocontrol strains and then inoculated with X. fastidiosa. We coupled this with phenotyping of internal tylose development and external disease symptoms and bacterial titer and determined that grapevines pre-treated with the biocontrols A. vitis and PsJN developed fewer tyloses and PD symptoms and underwent major transcriptional reprogramming in response to X. fastidiosa. These included up-regulation of genes in auxin- and ethylene-signaling pathways linked to tylose development. In contrast, P. viridiflava pre-treatment also resulted in a reduction of tyloses and PD symptoms but did not induce major transcriptional changes in vines, suggesting it likely has a direct inhibitory effect to X. fastidiosa through antibiosis. Using this data, we propose a model that incorporates timely and effective deployment of tyloses driven by induction of ethylene and auxin pathways as a key factor in PD resistance.},
}

@article {pmid41537461,
year = {2026},
author = {Choi, KY and Kang, S and Cook, S and Li, D and Choi, YY and Seo, EH and Han, X and Park, JE and Lee, S and Lee, S and Chung, JY and Chong, A and Choi, SM and Ha, JM and Song, MK and Lee, JS and Choo, IH and Kim, JH and Song, HC and Kim, BC and Kim, H and Farrer, LA and Gim, J and Jun, GR and Lee, KH},
title = {The Gwangju Alzheimer's & Related Dementias (GARD) cohort: Over a decade of Asia's largest longitudinal multimodal study.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e70981},
pmid = {41537461},
issn = {1552-5279},
support = {25-BR-03-05//the KBRI Basic Research Program through the Korea Brain Research Institute, funded by the Ministry of Science and ICT/ ; NRF-2014M3C7A1046041//the Original Technology Research Program for Brain Science of the National Research Foundation funded by the Korean government, MSIT/ ; RS-2024-00407198//Brain Pool program funded by the Ministry of Science and ICT through the National Research Foundation of Korea/ ; 2023-ER1007-01//Korea National Institute of Health research project/ ; //by the Technology Innovation Program (20022810, Development and Demonstration of a Digital System for the evaluation of geriatric Cognitive impairment) funded By the Ministry of Trade, Industry & Energy (MOTIE, Korea)/ ; RS-2024-00433283//the Technology Innovation Program funded by the Ministry of Trade, Industry & Energy, Republic of Korea/ ; HR22C141105//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
mesh = {Humans ; Longitudinal Studies ; Male ; *Alzheimer Disease/epidemiology/diagnostic imaging/genetics/diagnosis ; Female ; Aged ; *Cognitive Dysfunction/epidemiology/diagnostic imaging ; Disease Progression ; Republic of Korea/epidemiology ; Cohort Studies ; Middle Aged ; Biomarkers ; Magnetic Resonance Imaging ; Aged, 80 and over ; Neuroimaging ; Proteomics ; Genomics ; },
abstract = {INTRODUCTION: Alzheimer's disease (AD) is a major public health concern in Korea, with a high prevalence among older adults. A community-based longitudinal study is essential for tracking disease progression, identifying biomarkers, and developing targeted prevention and treatment strategies. The Gwangju Alzheimer's & Related Dementias (GARD) cohort was established to address these needs through a multimodal approach.

METHODS: Participants aged ≥60 years undergo comprehensive clinical evaluations, neuroimaging, and biospecimen collection for multi-omics analyses (genomics, transcriptomics, proteomics, and metagenomics) at baseline and systematic follow-up visits.

RESULTS: From over 17,000 screened individuals, 12,877 were enrolled. Baseline diagnoses include 5,123 cognitively unimpaired (CU), 3,250 mild cognitive impairment (MCI), and 2,125 AD dementia. The resource includes magnetic resonance imaging scans (n = 10,843) and extensive multi-omics data: genomic (n = 10,775), proteomic (n = 116), and microbiome (n = 595).

DISCUSSION: The integrated GARD dataset provides a powerful and scalable resource for identifying novel biomarkers, understanding disease heterogeneity, and advancing precision medicine for AD.

HIGHLIGHTS: Gwangju Alzheimer's & Related Dementias (GARD) is a large-scale, longitudinal, community-based cohort study in South Korea. The study focuses on early detection and monitoring of dementia progression. GARD includes cognitive testing, imaging, biospecimens, and multi-omics data. We aim to identify Korean-specific biomarkers predictive of cognitive decline. Supports East Asian insights and fills gaps in global Alzheimer's research.},
}

Humans
Longitudinal Studies
Male
*Alzheimer Disease/epidemiology/diagnostic imaging/genetics/diagnosis
Female
Aged
*Cognitive Dysfunction/epidemiology/diagnostic imaging
Disease Progression
Republic of Korea/epidemiology
Cohort Studies
Middle Aged
Biomarkers
Magnetic Resonance Imaging
Aged, 80 and over
Neuroimaging
Proteomics
Genomics

@article {pmid41537394,
year = {2026},
author = {Zhang, L and Li, B and Ye, F and Li, LZ and Xiong, S and Lei, SS},
title = {Effect of Puerarin on Chronic Alcoholic Encephalopathy by Modulating the "Microbiota-Gut-Brain Axis" Lipopolysaccharides/Toll-Like Receptors 4/Nuclear Factor Kappa-B Inflammatory Pathway.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70197},
pmid = {41537394},
issn = {1099-1573},
support = {LKLY25H270003//Joint Fund of Zhejiang Provincial Natural Science Foundation of China/ ; KJTYSZX2025//Zhejiang Provincial Department of Science and Technology Research Institute Support Program/ ; WJ2023M173//the General project of the Health Commission of Hubei Province/ ; 2023YFZD043//Key science and technology project of Jingmen/ ; 2024-XK-59//Key Discipline Construction Plan for Traditional Chinese Medicine/ ; },
abstract = {Chronic alcoholic encephalopathy (CAE) is a condition induced by alcohol consumption, with a huge demand for research on its prevention and treatment drugs. Puerarin, the principal active compound found in Pueraria lobata, has been traditionally utilized in ethnopharmacology to mitigate alcoholic brain injury and rectify imbalances in intestinal flora. The study was aimed to investigate the mechanism by which puerarin exerts its anti-CAE effect. The CAE mice model induced by alcohol were treated with oral administration of puerarin. First, the effects of puerarin on cognitive function, motor ability, and hippocampal tissue pathology along with the expression of TLR4, Myd88, NF-κB, IL-1β, and IL-6 of brain and fecal LPS were investigated. Finally, the composition of the gut microbiome of fecal and TJs (Claudin-1 and Occludin) in the intestine and colon, focusing on the production and transporter of LPS, were measured. The findings revealed that puerarin administration significantly ameliorated motor deficits, anxiety-like behaviors, and cognitive impairments in CAE mice. Histopathological analysis revealed puerarin reduced hippocampal damage and decreased Iba1 immunoreactivity, indicating attenuated neuroinflammation. Puerarin treatment downregulated the protein expression of IL-1β, IL-6, TLR4, Myd88, and NF-κB in brain. Notably, puerarin restored intestinal barrier integrity by upregulating Claudin-1 and Occludin expression. Intestinal flora analysis demonstrated that puerarin treatment increased the abundance of beneficial bacteria (e.g., norank_f_Eubacterium_coprostanoligenes_group) while reducing pathogenic bacteria (e.g., Escherichia-Shigella). The study showed that puerarin exerts a treatment CAE effect, which may be related to modulation of the "microbiota-gut-brain axis" LPS/TLR4/NF-κB inflammatory pathway.},
}

@article {pmid41537224,
year = {2026},
author = {Liang, D and Wang, Y and Li, Y and Chen, Z and Zeng, Q and Ha, S and Zhou, X and Wu, D},
title = {Elevated Prevalence of Oral HPV Infection Among Females with Periodontitis: A Cross-Sectional Study.},
journal = {Oral health & preventive dentistry},
volume = {24},
number = {},
pages = {1-11},
doi = {10.3290/j.ohpd.c_2446},
pmid = {41537224},
issn = {1757-9996},
mesh = {Humans ; Female ; Cross-Sectional Studies ; *Papillomavirus Infections/epidemiology/complications ; *Periodontitis/epidemiology/microbiology/virology/complications ; Adult ; Middle Aged ; Prevalence ; Male ; Microbiota ; Risk Factors ; Nutrition Surveys ; Young Adult ; Aged ; United States/epidemiology ; },
abstract = {PURPOSE: This study investigated the association between periodontitis and oral HPV infection, while exploring the role of oral bacterial microbiota diversity.

METHODS AND MATERIALS: Data from 4,685 adults in the NHANES 2009-2012 cycles were analysed. Periodontitis was defined based on clinical examination, and oral HPV infection was identified using PCR from oral rinse samples. Multivariable logistic regression models were employed to assess the relationship, adjusting for body mass index (BMI), age, sex, ethnicity, education, smoking, alcohol consumption, daily dental flossing, and history of systemic diseases. Subgroup analyses were stratified by age, sex, and education. Mediation analysis was performed to evaluate whether the oral microbiome acts as a mediator in the relationship between periodontitis and oral HPV infection.

RESULTS: No statistically significant overall association was found between periodontitis and oral HPV infection (P > 0.05). However, females with moderate to severe periodontitis exhibited increased odds of oral HPV infection (P 0.05). Oral HPV infection was associated with greater microbial diversity (higher operational taxonomic units [OTUs]). No significant mediating effect of the oral microbiome was observed.

CONCLUSION: Moderate to severe periodontitis appears to be associated with higher odds of oral HPV infection in females. These findings highlight the potential relationship between oral health, microbial diversity, and oral HPV infection.

CLINICAL IMPLICATION: In the general population, periodontitis does not appear to be a major risk factor for oral HPV; however, female with moderate to severe periodontitis and individuals with higher educati-on showed increased odds of oral HPV infection, suggesting that maintaining periodontal health may be particularly important for HPV related risk management in these subgroups.},
}

Humans
Female
Cross-Sectional Studies
*Papillomavirus Infections/epidemiology/complications
*Periodontitis/epidemiology/microbiology/virology/complications
Adult
Middle Aged
Prevalence
Male
Microbiota
Risk Factors
Nutrition Surveys
Young Adult
Aged
United States/epidemiology

@article {pmid41537047,
year = {2026},
author = {Locher, JA and Wise, A and Strehlau, R},
title = {Intimate hygiene practices during pregnancy with demographic and preterm birth associations: a large cohort study.},
journal = {AJOG global reports},
volume = {6},
number = {1},
pages = {100592},
pmid = {41537047},
issn = {2666-5778},
abstract = {BACKGROUND: Intimate hygiene practices during pregnancy can influence maternal and neonatal health outcomes. Limited data exist on these practices among South African women. This study aimed to characterize intimate hygiene practices among pregnant women in Johannesburg and examine associations with demographic factors and preterm birth.

METHODS: A secondary analysis was conducted on data from 18,076 pregnant women enrolled in the Group B Streptococcus Correlates of Protection Cohort Study in Johannesburg, South Africa. Participants completed questionnaires detailing their intimate hygiene practices, including frequency, methods, and products used. Statistical analyses assessed the prevalence of these practices, their association with demographic characteristics (age, race, education, occupation, dwelling type, parity, and HIV status), and preterm birth outcomes.

RESULTS: The mean age was 28.4 years (range 18-49). Most participants were Black (93.0%), single (80.4%), unemployed (64.7%), and resided in urban areas (70.7%). They reported a median intimate cleaning frequency of 14 times per week (IQR 8-14). Over half (53.3%) practiced douching, and 48.4% added products to their bathwater.Race was significantly associated with adding bathwater products (P<.00001). White women (44.3%) had the highest proportion adding products. Tertiary-educated mothers were more likely to add products (27.0%, P=.0041). Students had the highest rate of product use (28.7%, P=.0018). Urban participants were more likely to add products (25.2%) than semi-urban women (23.2%, P=.025).Douching was also significantly associated with race (P<.00001), with the "Other" category (65.1%) reporting the highest rate. Women with no schooling had the highest douching rate (53.2%, P=.0006). Semi-urban mothers douched the most frequently (53.4%, P<.00001). Marital status was significantly associated with douching (P<.00001), with the highest prevalence among single women (45.8%). Occupation was also significantly associated with douching (P=.016), with students having the highest douching prevalence (28.7%).A significant association was observed between gestational age and the addition of products to bathwater for deliveries between 34 and <37 weeks compared to term deliveries (P=.045). Women who did not add products were more likely to deliver at term, while those who added products had a higher likelihood of delivering preterm. For deliveries <34 weeks compared to 34-<37 weeks, women who did not add products were more likely to deliver at 34-<37 weeks (P=.02).For deliveries at <34 weeks compared to 34-<37 weeks, women who douched were less likely to deliver at <34 weeks, while those who did not douche had lower proportions of deliveries at 34-<37 weeks (P=.035).In the combined preterm category (<37 weeks) compared to term deliveries, a statistically significant association was observed (P=.035), with women who douched being more likely to deliver preterm. Although some early preterm categories were more frequent among those who douched, overall no consistent statistically significant associations were found between hygiene practices and preterm birth outcomes.

CONCLUSION: Intimate hygiene practices are prevalent among pregnant women in Johannesburg and are significantly associated with various demographic factors. While some associations with preterm birth were identified, no consistent significant association was established, warranting further studies.},
}

@article {pmid41536683,
year = {2025},
author = {Wu, F and Lu, W and Wu, D and Zhou, Y and Lu, H and Ying, L and Wu, G},
title = {[Effects and Mechanisms of Yangyin Yiqi Huoxue Formula on the Oral Microecology in Sjögren's Syndrome Model Mice].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {6},
pages = {1556-1565},
pmid = {41536683},
issn = {1672-173X},
mesh = {Animals ; *Sjogren's Syndrome/microbiology/drug therapy ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Mice, Inbred NOD ; Disease Models, Animal ; *Microbiota/drug effects ; Female ; Saliva/microbiology ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Hydroxychloroquine/pharmacology ; },
abstract = {OBJECTIVE: To investigate the effect of the Yangyin Yiqi Huoxue formula on the oral microecology in a mouse model of Sjögren's syndrome (SS), and to explore the underlying mechanisms.

METHODS: A total of 12 8-week-old non-obese diabetic (NOD) mice were randomly assigned to a model group, a traditional Chinese medicine (TCM) group, and a hydroxychloroquine (HCQ) group, with 4 mice in each group. In addition, 4 BALB/c mice were used as the normal control group. The TCM group was administered Yangyin Yiqi Huoxue formula (15 g/[kg·d]) via gavage and the HCQ group received HCQ (0.08 g/[kg·d]) via gavage. The normal control and model groups were maintained under standard feeding conditions without intervention. After 8 weeks of treatment, saliva samples were collected for 16S rRNA gene sequencing to analyze the oral microbiota. Alpha diversity, beta diversity, and functional prediction analyses were performed.

RESULTS: Alpha diversity analysis showed that the Yangyin Yiqi Huoxue formula significantly increased oral microbiome diversity in NOD mice (P < 0.05). Species composition analysis indicated that the formula increased the abundance of the phylum Proteobacteria and decreased the abundance of the phylum Firmicutes (P < 0.01), while HCQ led to an abnormal decrease in the abundance of the phylum Firmicutes. Beta diversity analysis revealed distinct microbial clustering in the treatment groups and the model group, with the TCM group showing clustering in the phylum Proteobacteria and exhibiting lower intragroup dispersion than the HCQ group did. According to the functional prediction analysis, both the TCM and HCQ groups demonstrated regulatory potential in terms of amino acid transport and metabolism, transcription, and other related functions. KEGG analysis found greater microbial enrichment in cellular processes, environmental information processing, and disease-related pathways in the TCM group compared to the HCQ group (P < 0.05).

CONCLUSION: The Yangyin Yiqi Huoxue formula can restore oral microbiome diversity and improve the colony structure in in a mouse model of SS, providing experimental evidence for the advantages of TCM in regulating oral microecological functions.},
}

Animals
*Sjogren's Syndrome/microbiology/drug therapy
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Mice
Mice, Inbred BALB C
Mice, Inbred NOD
Disease Models, Animal
*Microbiota/drug effects
Female
Saliva/microbiology
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Hydroxychloroquine/pharmacology

@article {pmid41536544,
year = {2026},
author = {Stø, K and Skagen, KR and Holm, K and Ueland, T and Vestad, B and Bjerkeli, V and Halvorsen, B and Trøseid, M and Hov, JR and Skjelland, M},
title = {Oral Eikenella as a potential new biomarker of symptomatic carotid atherosclerosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2613521},
pmid = {41536544},
issn = {2000-2297},
abstract = {INTRODUCTION: Oral microbiota dysbiosis is linked to cardiovascular disease, and oral pathogens have been detected in atherosclerotic plaques. We aimed to investigate the relationship between the oral microbiota and carotid atherosclerosis, and the occurrence of oral pathogens in plaques.

PATIENTS AND METHODS: Oral swab and saliva samples from patients with severe carotid atherosclerosis (≥50% stenosis) were compared with those from controls. The oral microbiome was analyzed by 16S rRNA amplicon sequencing targeting the V3‒V4 region. Carotid plaques were investigated for five oral bacterial species by qRT-PCR.

RESULTS: Compared with controls, patients exhibited different inter-individual (beta) diversity (r = 0.02, p = 0.002), reduced intra-individual (alpha) diversity (p = 0.026) and 22 bacterial genera differed in relative abundance. Furthermore, abundances of five bacterial genera, including Eikenella, were increased in patients with recent cerebrovascular symptoms compared to asymptomatic patients. Eikenella corrodens was detected in all 30 carotid plaques.

CONCLUSION: Oral microbiota diversity and composition differ between patients with carotid atherosclerosis and controls. A higher relative abundance of the genus Eikenella in symptomatic versus asymptomatic patients and the detection of the species Eikenella corrodens in all carotid plaques, might suggest that Eikenella is important in atherogenesis and plaque instability. Oral Eikenella could possibly serve as a potential new biomarker.},
}

@article {pmid41536244,
year = {2026},
author = {Girdhar, K and Dedrick, S and Rhodes, L and Kim, D and Powis, A and Mahon, C and Chapdelaine, H and Obaid, L and McNamara, M and Altindis, E},
title = {Diet, gut microbiome, and type 1 diabetes: from risk to translational opportunity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2614039},
doi = {10.1080/19490976.2026.2614039},
pmid = {41536244},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/microbiology/therapy/etiology/immunology ; Animals ; *Diet ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Fecal Microbiota Transplantation ; },
abstract = {The incidence of type 1 diabetes (T1D) has risen sharply in recent decades, implicating the role of environmental factors in disease pathogenesis. Diet, a primary driver of gut microbiome development and composition, along with other environmental exposures, has emerged as a potential modulator of T1D risk and progression. While nutrients, such as certain vitamins, may exert protective effects, the roles of other dietary factors (e.g., early exposure to dietary antigens) remain unclear. Importantly, diet shapes the gut microbiome, which produces immunomodulatory metabolites, including secondary bile acids, short-chain fatty acids (SCFAs), and others that directly influence immune responses. This review presents evidence on how specific dietary factors, including macronutrients (fats, carbohydrates, proteins, such as gluten and milk proteins), fibers, and breastfeeding, affect the gut microbiome and T1D. We also discuss the effects of microbiome-targeted interventions, including probiotics, prebiotics, and fecal microbiota transplantation, on T1D and their potential as future therapeutic strategies. Although animal studies provide compelling mechanistic insights, the results from human trials remain inconsistent, underscoring the urgent need for longitudinal and interventional studies to establish causality. Understanding the complex interplay between diet, the gut microbiome, and immune homeostasis is essential for developing personalized strategies to prevent and treat T1D and delay-related complications.},
}

Humans
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 1/microbiology/therapy/etiology/immunology
Animals
*Diet
Prebiotics/administration & dosage
Probiotics/administration & dosage
Fecal Microbiota Transplantation

@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
doi = {10.1080/19490976.2025.2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}

Humans
*Milk, Human/chemistry
Female
*Oligosaccharides/analysis/metabolism
*Gastrointestinal Microbiome
Infant, Newborn
Feces/microbiology
Longitudinal Studies
Adult
Pregnancy
*Bacteria/classification/genetics/isolation & purification/metabolism
*Pregnancy in Obesity/microbiology/metabolism
Infant
Male
Body Mass Index
Mexico

@article {pmid41536172,
year = {2026},
author = {Carboni, S and Asangba, AE and Melin, AD},
title = {Microbial Contributions to Primate Reproduction.},
journal = {Evolutionary anthropology},
volume = {35},
number = {1},
pages = {e70023},
pmid = {41536172},
issn = {1520-6505},
mesh = {Animals ; *Primates/microbiology/physiology ; Female ; *Reproduction/physiology ; *Microbiota/physiology ; Male ; Humans ; Pregnancy ; Anthropology, Physical ; Sexual Behavior, Animal ; Biological Evolution ; Copulation/physiology ; },
abstract = {Reproduction is a complex process, and microbes play a far greater role than previously imagined. This review explores the ways that microbiomes influence the rich tapestry of reproductive processes and outcomes within the primate lineage, including pre-copulatory and post-copulatory mechanisms. We discuss microbiomes in a sexual selection framework, specifically how they might influence mate choice and sexual competition across multiple sensory modalities. We then consider how copulatory behavior and mating systems may in turn shape reproductive microbiomes. Moving to post-copulatory processes, we discuss the potential impact of microbes on cryptic choice and sperm competition and call for additional research in this area. Finally, we explore the influence of microbes on pregnancy outcomes, emphasizing evolutionary perspectives often overlooked in clinical research. Importantly, we compare human studies to those on nonhuman primates, bridging the two areas of inquiry and outlining future research directions. Our aim is to highlight the vast potential for microbes to contribute to all stages of reproduction, and to inspire creative, synthetic future research that moves forward this fascinating area of inquiry.},
}

Animals
*Primates/microbiology/physiology
Female
*Reproduction/physiology
*Microbiota/physiology
Male
Humans
Pregnancy
Anthropology, Physical
Sexual Behavior, Animal
Biological Evolution
Copulation/physiology

@article {pmid41536169,
year = {2026},
author = {Abdulkareem, AA and Gul, SS and Abdulbaqi, HR and Sha, AM and Preshaw, PM},
title = {Assessing Evidence to Include Filifactor alocis as a Novel Candidate in Socransky's Complexes.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {e70018},
doi = {10.1111/omi.70018},
pmid = {41536169},
issn = {2041-1014},
abstract = {Socransky's complexes have identified a range of bacteria as key contributors to the onset and progression of periodontal disease. However, advancements in microbiological detection methods have allowed for exploration of the microbiome in periodontal health/disease in greater detail. In recent years, Filifactor alocis has emerged as a potential periodontal pathogen. Therefore, the aim of this review was to investigate whether this bacterium could be included in Socransky's model by summarizing the available evidence. A comprehensive literature search performed using PubMed, ScienceDirect, and Scopus databases was undertaken. The retrieved articles were filtered according to defined eligibility criteria, which yielded 24 studies. Data were extracted from these observational and clinical studies to synthesize findings. Findings regarding the host immune response were derived from in vitro and experimental animal models and narratively summarized. Observational studies and clinical trials showed heterogeneity and a lack of standardized outcomes. However, the general trend indicated a higher prevalence of F. alocis at diseased sites than at healthy sites. In addition, periodontal treatment was found to significantly reduce F. alocis levels and was associated with improvements in clinical periodontal parameters. Experimental models and in vitro studies showed that F. alocis exhibits a range of virulence attributes and pathogenic behavior similar to that of putative pathogenic periodontal bacteria. The evidence is not sufficient to include F. alocis as a new member of Socransky's model. However, this review suggests that this bacterium has the potential to be included in Socransky's complexes in the future after further research which would require to be highly standardized to enhance comparability and generalizability of findings.},
}

@article {pmid41536161,
year = {2026},
author = {Turnlund, AC and O'Brien, PA and Rix, L and Ferguson, S and Boulotte, N and Jeong, SY and Webster, NS and Diaz-Pulido, G and Wahab, MA and Lurgi, M and Vanwonterghem, I},
title = {Bacterial Communities Associated With Crustose Coralline Algae Are Host-Specific.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70213},
pmid = {41536161},
issn = {2045-8827},
support = {//Australian Government Research Training Programme/ ; //UQ Graduate school/ ; //the Reef Restoration and Adaptation Programme/ ; },
mesh = {*Rhodophyta/microbiology/classification ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; *Microbiota ; Symbiosis ; Coral Reefs ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; *Anthozoa/microbiology ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {Crustose coralline algae (CCA) comprise hundreds of different species and are critical to coral reef growth, structural stability and coral recruitment. Despite their integral role in reef functioning, little is known about the diversity and structure of bacterial communities associated with CCA. We address this knowledge gap by characterising the surface microbial communities of 15 Indo-Pacific CCA species across eight different families from the Great Barrier Reef, using 16S rRNA amplicon sequencing. CCA microbial community composition was distinct and found to primarily differentiate by algal host species. When looking at the core bacterial communities, divergence across CCA microbiomes was additionally correlated to host phylogeny. CCA from similar light environments and depths also had more similar microbial communities, suggesting the potential role of environmental parameters in influencing microbial community organisation. The fundamental descriptions of CCA bacterial communities for a wide range of Indo-Pacific species presented here provide essential baseline information to further inform CCA microbial symbiosis research.},
}

*Rhodophyta/microbiology/classification
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Phylogeny
*Microbiota
Symbiosis
Coral Reefs
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA
*Anthozoa/microbiology
DNA, Ribosomal/genetics/chemistry

@article {pmid41536159,
year = {2026},
author = {Morgan, L and Tilzey, A and El-Ajouz, M and Dong, J and Daley, C and Olivares, CI},
title = {Surface water microbiome response to pyrogenic carbon after a wildland-urban interface fire.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5em00803d},
pmid = {41536159},
issn = {2050-7895},
abstract = {Fires in the wildland-urban interface (WUI) introduce pyrogenic organic contaminants to surface waters, but their impacts on microbial dynamics have not been evaluated. We studied the interactions between microbial communities and pyrogenic carbon during post-fire storms in a WUI fire-impacted creek in Orange County, CA. The first storms following the fire (low intensity) brought about the highest discharges of polycyclic aromatic hydrocarbons (PAHs), e.g. benzo[a]pyrene, benz[a]anthracene. Dissolved organic carbon (DOC) loads reached up to 11.2 g-C s[-1] during the more severe storms. PAHs correlated with each other but not with DOC or fluctuations in turbidity, suggesting these two variables might not be good predictors of PAH flushes, especially in low-intensity storms. Microbial genera with known PAH-degrading members were differentially abundant during post-fire storms (Pseudomonadota, Bacteroidota, Cyanobacteriota, Actinobacteriota, Bacillota). In addition, predicted metabolic pathways related to the PAH biodegradation intermediates, catechol and protocatechuate, increased significantly at sites downstream of the fire. Overall, our findings suggest pyrogenic carbon from the fire resulted in a detectable shift in microbial community function and composition to favor PAHs degradation just a few months after the fire. This response suggests that PAH-degrading microorganisms are readily found after WUI fires.},
}

@article {pmid41536136,
year = {2026},
author = {Yu, J and Zhang, Y and Wells, JCK and Wei, Z and Nielsen, DS and Fewtrell, M},
title = {Maternal and infant microbiota in early infancy: Longitudinal findings from a randomised controlled trial.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70342},
pmid = {41536136},
issn = {1536-4801},
support = {//NIHR Great Ormond Street Hospital Biomedical Research Centre/ ; },
abstract = {OBJECTIVES: To characterise early postnatal microbial development across maternal gut, breast milk, and infant gut compartments, and explore potential modulation by maternal stress in a cohort of Chinese mothers practising traditional postpartum confinement.

METHODS: This secondary analysis draws on a randomised controlled trial of a maternal relaxation intervention in late preterm and early-term dyads. Vaginally delivered mothers (34 + 0 to 37 + 6 weeks) and their exclusively breastfed infants were followed from 1 to 8 weeks postpartum. Maternal stool, breast milk, and infant stool samples were collected at both time points and analysed via 16S rRNA gene amplicon sequencing. Changes in gut microbiome diversity and composition (alpha andbeta diversity metrics) and the relative abundance of dominant genera were assessed overall and by intervention group.

RESULTS: Microbiome diversity (alpha diversity metrics) remained stable across all sample types. However, we observed a compositional temporal shift in breast milk microbiota (p = 0.039), driven primarily by changes in the control group. Infant gut microbiota showed increased Bifidobacterium and decreased Staphylococcus and Enterobacteriaceae with time. A significant reduction in Staphylococcus was observed in breast milk of the intervention group only. Maternal gut microbiota remained stable.

CONCLUSIONS: Microbial composition in breast milk and infant gut shifted over the first 8 weeks postpartum, while maternal gut remained stable. Findings suggest maternal stress-reduction interventions may influence breast milk microbiota. Further research is warranted to confirm these effects and investigate mechanisms.},
}

@article {pmid41535980,
year = {2026},
author = {Wang, Z and Guo, H and He, J and Zhang, Z and Huws, S and Guo, T and Shen, W and Wan, F},
title = {Responses of rumen bacterial microflora to aflatoxin B1 challenge: potential roles of AHLs/AI-2 mediated quorum sensing.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00515-2},
pmid = {41535980},
issn = {2524-4671},
support = {32302764//National Natural Science Foundation of China/ ; 2024JJ5179//Hunan Provincial Natural Science Foundation/ ; 2024JJ5179//Hunan Provincial Natural Science Foundation/ ; XJSLSW-2023001//Key laboratory for the feed and biology technique of Xinjiang Uygur Autonomous Region/ ; XJSLSW-2023001//Key laboratory for the feed and biology technique of Xinjiang Uygur Autonomous Region/ ; XJSLSW-2023001//Key laboratory for the feed and biology technique of Xinjiang Uygur Autonomous Region/ ; XJSLSW-2023001//Key laboratory for the feed and biology technique of Xinjiang Uygur Autonomous Region/ ; 2022A02001-1//Science and Technology Department of Xinjiang Uygur Autonomous Region/ ; },
}

@article {pmid41535879,
year = {2026},
author = {Xu, Y and An, L and Xie, J and Luo, C and Zhang, H and Zhang, Q and Luo, G},
title = {Investigating the impact of gut microbiota-derived metabolites on benign prostatic hyperplasia using network pharmacology approaches.},
journal = {BMC pharmacology & toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40360-025-01059-y},
pmid = {41535879},
issn = {2050-6511},
abstract = {BACKGROUND: The gut microecosystem represents the most abundant and complex microbial ecosystem in the human body. Maintaining homeostasis of gut microbiota and their metabolites is essential for human health. As a chronic metabolic disorder, the association between benign prostatic hyperplasia (BPH) and gut microbiota remains unclear. Growing evidence suggests that modulating the composition and function of gut microbiota may influence the gut-prostate axis, thereby affecting the development and progression of prostatic hyperplasia. In this study, we employed network pharmacology to systematically elucidate the complex interactions among gut microbiota, microbial metabolites, and BPH-related therapeutic targets.

METHODS: In this study, we first retrieved information on gut microbial metabolites from the gutMGene database. Subsequently, we identified overlapping targets of these metabolites using the SEA and STP databases. To further clarify targets related to BPH, we integrated data from authoritative databases such as Genecard and OMIM. Based on this information, we constructed a protein-protein interaction (PPI) network to screen for core targets. In addition, we performed systematic GO and KEGG functional enrichment analyses of these targets using the DAVID database. we constructed a network model to illustrate the interactions among microbiota, substrates, metabolites, and targets.Finally, molecular docking validation was performed between the core targets and gut microbiota metabolites.

RESULTS: We identified 43 overlapping targets between gut microbial metabolites and BPH. Subsequently, we selected AKT1, IL-6, and IL-1B as core therapeutic targets for BPH. By constructing an MSMT comprehensive network, we found that these three core targets exert therapeutic effects on BPH through interactions with 11 metabolites, 2 substrates, and 4 gut microbial species. Furthermore, GO analysis revealed that gut microbial metabolites influence prostatic hyperplasia by regulating inflammation, immune responses, and the activation of oxidoreductase activity. KEGG analysis indicated that the AGE-RAGE signaling pathway, Toll-like receptor signaling pathway, HIF-1 signaling pathway, C-type lectin receptor signaling pathway, and PI3K/Akt signaling pathway are the major pathways involved in BPH.The molecular docking results demonstrated that butyrate may influence prostatic hyperplasia by modulating the AKT1 gene.

DISCUSSION: This study employs a network pharmacology approach to elucidate the intricate "Microbiota-Substrate-Metabolite-Target" (M-S-M-T) network in Benign Prostatic Hyperplasia (BPH), identifying key hub genes (AKT1, IL-6, IL-1B), signaling pathways (PI3K/Akt, AGE-RAGE, HIF-1), and gut microbiota-derived metabolites (butyrate, propionate, TMAO) as central regulators. It further characterizes the functional significance of the Bifidobacterium-tryptophan and Clostridium sporogenes-tyrosine axes, highlighting their probiotic potential for microbiota-targeted BPH therapy. While demonstrating the therapeutic promise of modulating the gut microbiome, the study underscores the need for future experimental validation to decipher the precise mechanistic links within the M-S-M-T network and its role in BPH pathogenesis CONCLUSION: IL-6, AKT1, and IL-1B serve as the primary targets through which gut microbiota metabolites exert their therapeutic effects on benign prostatic hyperplasia.},
}

@article {pmid41535843,
year = {2026},
author = {Pappert, FA and Newrzella, N and Roth, O},
title = {Parental fasting effects on offspring immune gene expression, epigenetic patterns, and gut microbiota in a species with male pregnancy (Syngnathus typhle).},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02509-7},
pmid = {41535843},
issn = {1741-7007},
support = {RTG 2501 TransEvo//Deutsche Forschungsgemeinschaft/ ; MALEPREG: eu-repo/grantAgreement/EC/H2020/755659//HORIZON EUROPE European Research Council/ ; CRC 1182 Origin//Metaorganisms/ ; },
abstract = {BACKGROUND: Intermittent fasting is widely promoted for its potential to improve health and extend lifespan, yet these benefits may come at a reproductive cost, potentially reducing parental fitness and offspring quality. While the inter- and transgenerational effects of fasting are increasingly studied, they remain poorly understood in species with unconventional reproductive roles. Investigating such effects in these systems is crucial, as the evolutionary trade-offs between somatic maintenance and reproductive investment may differ from those in species with conventional reproductive roles. In this study, we investigated the effects of intermittent fasting (IF) in a species with male pregnancy, Syngnathus typhle, by exposing mothers and fathers to either IF or ad libitum (AL) feeding before mating. Upon transfer of maternal eggs to paternal brood pouches, males remained on their assigned diets throughout pregnancy.

RESULTS: Offspring from all parental diet combinations AL(p) × AL(m), IF(p) × IF(m), AL(p) × IF(m), and IF(p) × AL(m) (with p = paternal and m = maternal) were analyzed at birth before first feeding alongside parents for morphology, immune and epigenetic candidate gene expression, and gut microbiota composition. Mothers under IF showed greater condition loss, leading to reduced offspring condition regardless of paternal diet, highlighting the importance of maternal provisioning through eggs. However, IF fathers exhibited increased immune activation and microbiome shifts that were mirrored in offspring, suggesting paternal priming via epigenetic and microbial inheritance. Offspring from mismatched parental diets showed disrupted immune-microbiome correlations, indicating that aligned parental cues support more stable offspring development.

CONCLUSION: These findings highlight how parental nutritional history differentially shapes offspring phenotype through maternal and paternal pathways in a species with male pregnancy. Our results emphasize the value of studying species with diverse reproductive strategies and life histories to understand the full spectrum of trans-generational plasticity in nature.},
}

@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {},
number = {},
pages = {},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}

@article {pmid41535594,
year = {2026},
author = {Govender, P and Cason, E and Ghai, M},
title = {Characterization of the oral microbiome in the diverse South African population by PacBio HiFi sequencing.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {23},
pmid = {41535594},
issn = {1432-0614},
mesh = {Adult ; Humans ; South Africa ; *Microbiota/genetics ; *Mouth/microbiology ; Middle Aged ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Adolescent ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Phylogeny ; Biodiversity ; },
abstract = {Mounting evidence supports population-specific variation in the microbiome. This study applied PacBio HiFi 16S rRNA amplicon sequencing to profile the oral microbiome of 62 individuals (aged 18-55 years) from the four major South African population groups (Black, Coloured, Indian and White). Bioinformatics analysis was performed using QIIME2 with taxonomic classification based on the SILVA database. Across all groups, Firmicutes was the most dominant phylum (80.92%), followed by Proteobacteria (8.94%) and Bacteroidota (4.22%). A total of 236 genera and 376 species were identified. Veillonella was the most abundant genus (27.57%), followed by Streptococcus (25.08%) and Granulicatella (15.54%). Streptococcus (30.40%) and Veillonella (41.82%) were the most abundant in the Indian and Coloured populations, respectively. Significant microbiome variation was observed between groups (β-diversity, p < 0.001), highlighting distinct population-specific microbial profiles. The Coloured population exhibited the highest microbiome diversity, likely due to complex genetic makeup and diverse cultural influences. The White population displayed the lowest microbiome diversity, likely due to more uniform lifestyle patterns. Despite these differences, three bacterial species, namely, Streptococcus salivarius, Veillonella atypica, and Prevotella melaninogenica were present in the majority of individuals across the populations, suggesting a core component of the South African oral microbiome. No significant associations were observed between factors such as sex, age, diet antibiotic use, lifestyle and oral microbiome variation. Several undetermined factors, such as psychological factors, stress, level of exercise, host genetics and immunity, could have contributed to the observed diversity. Our results present the first report of oral microbiome analysis of healthy South African populations by PacBio HiFi sequencing and warrant further research to provide insight into how these differences influence health disparities and potential application in forensics. KEY POINTS: • First report of the oral microbiome of healthy South Africans by PacBio HiFi sequencing • S. salivarius, P. melaninogenica and V. atypica define South Africa's core oral microbiome • Population-specific microbiome signatures can guide forensics and health research.},
}

Adult
Humans
South Africa
*Microbiota/genetics
*Mouth/microbiology
Middle Aged
Young Adult
RNA, Ribosomal, 16S/genetics
Adolescent
*Bacteria/classification/genetics/isolation & purification
Male
Female
DNA, Bacterial/genetics
Sequence Analysis, DNA
Phylogeny
Biodiversity

@article {pmid41535558,
year = {2026},
author = {Zhang, M and Ding, R and Jia, T and Wu, Z and Hussain, M and Wang, L and Gan, GY and Zhang, J},
title = {Synergy of FeNPs and PGPR Strain Enhances Nitrogen Fixation by Linking Root Metabolites and Rhizosphere Microbiome Assembly in Alfalfa.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70387},
pmid = {41535558},
issn = {1365-3040},
support = {32471768//National Natural Science Foundation of China/ ; 22ZD6NA007//Key Science & Technology Project of Gansu Province, China/ ; },
abstract = {Increasing evidences show plant growth-promoting rhizobacteria (PGPR) benefit legume-rhizobium symbiosis, and iron-based nanoparticles (FeNPs) act as rhizobia microenvironment stabilizers. However, few studies explored if their combination exerts synergistic effects on the symbiosis in legume. Here, we compared the effects of FeNPs, Pseudomonas rhizovicinus M30-35, and their co-application (Fe + M) on alfalfa growth, nitrogen fixation, root metabolites, and rhizosphere microbiome. Compared with FeNPs and M30-35, Fe + M increased shoot height, root length, root activity, chlorophyll content, and net photosynthetic rate (Pn) by 63.2% and 45.4%, 61.1% and 70.6%, 56.2% and 47.1%, 20.1% and 18.6%, and 41.1% and 30.6%, respectively; the nodule number, nitrogenase activity, ureide content, and leghemoglobin content rose by 29.6% and 31.4%, 58.5% and 78.7%, 20.4% and 15.1%, and 9.7% and 12.4%, respectively. Metabolomic analysis showed that Fe + M enhanced the accumulation of benzenoid compounds in roots, while microbial co-occurrence network analysis indicated reduced complexity and connectivity of rhizosphere bacterial and fungal communities. Importantly, core microbes, such as Hydrogenophaga, Nocardioides, unidentified_Mitochondria, and Scedosporium, were positively associated with benzenoid compounds, which contribute to nutrient cycling in the rhizosphere. Our findings demonstrate that FeNPs and PGPR strain together achieve synergistic effects on the nitrogen fixation in alfalfa.},
}

@article {pmid41535415,
year = {2026},
author = {Sambolín-Pérez, CA and Montes-Jiménez, SM and Montes-Jiménez, HM and Rosa-Morales, Y and Aybar-Batista, R and Núñez-Marrero, ÁR and Rivera-Vicéns, RE and Ríos-Velázquez, C and Negrón-Berríos, JA},
title = {Revealing and characterizing bacterial communities of in vitro Musa species through 16S rDNA metabarcoding and culture dependent approaches.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35510-9},
pmid = {41535415},
issn = {2045-2322},
support = {Award No. P031S220125//U.S. Department of Education/ ; },
abstract = {Bananas and plantains, part of the Musa genus, are key global food crops that are threatened by various factors, including hurricanes and microbial infections. The production of phytopathogen-free plants in Temporary Immersion Bioreactors (TIB) has gained attention due to improved yield and health. However, the impact of TIB on Musa spp. microbiomes remains poorly understood. Thus, elucidating the role of in vitro Musa spp. microbiome is crucial for developing healthier plantlets with beneficial microbes, such as plant growth-promoting bacteria (PGPB), which are essential for plant development and might help Musa spp. thrive in abiotic and biotic stresses after in vitro development. To reveal the potential association of PGPB, we aimed to identify and characterize the bacterial communities from in vitro (TIB) Musa spp. varieties (Maiden, Dwarf, and Maricongo) pseudostems using both culture-independent (16S rDNA-metabarcoding) and culture-dependent methods to elucidate their diversity and roles in plant health. Our results identified four bacterial phyla, with Bacillota being the most dominant, followed by Pseudomonadota, Actinobacteriota, and Bacteroidota. Brevibacillus sp. and Xylella sp. were the dominant genera. The isolates included Lysobacteraceae and Terribacillus spp., and the microbiomes metabolic pathways featured cofactors and amino acid biosynthesis. These findings enhance the understanding of bacterial communities in Musa spp. under in vitro conditions, highlighting the potential effects of artificial environments on host microbiomes, and encouraging innovative research into bacterial-plant interactions. This may aid in identifying specific bacteria with potential PGPB traits in Musa spp., offering new ways to enhance production and protection.},
}

@article {pmid41535303,
year = {2026},
author = {Hall, AN and Manuja, S and Payling, LM and Romero, LF and Hoerr, FJ and Shields, J and Hofacre, C and Susanti, D and Gangaiah, D and Plata, G and Kumar, A},
title = {Lactobacillus-vectored nanobodies improve broiler productivity under sub-clinical necrotic enteritis with associated microbiome and transcriptome changes.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00916-w},
pmid = {41535303},
issn = {2055-5008},
abstract = {Sub-Clinical Necrotic Enteritis (SCNE), caused by toxin-producing Clostridium perfringens, is a major challenge in poultry production. SCNE has traditionally been managed with in-feed antibiotics; however, increasing concerns about the spread of antimicrobial resistance call for antibiotic-free strategies for its control. We recently described an NE control strategy leveraging Limosilactobacillus reuteri probiotic strains genetically engineered to deliver nanobodies against alpha toxin and NetB from C. perfringens in the poultry gut. Here, in a controlled study under SCNE conditions, we found that the engineered strains significantly improved feed conversion ratios and weight gain of broilers, outperforming treatment with either a prophylactic antibiotic or the wild-type probiotic strains. To investigate the systemic factors contributing to these performance differences, we analyzed histomorphometrics of the small intestine, microbial metatranscriptomics of jejunal contents, and gene expression from the jejunum and liver tissues. Our results confirmed the in situ expression of the nanobodies and provided evidence that nanobody delivery mitigates SCNE-associated inflammation in the jejunum and toxin-induced damage in the liver, leading to a more quiescent immune state, lower oxidative stress, and improved growth performance. Our findings demonstrate the potential of probiotic-vectored nanobody delivery as an effective strategy for targeting gut antigens across a range of diseases.},
}

@article {pmid41535289,
year = {2026},
author = {Panah, FM and Støving, RK and Sjögren, M and Micali, N and Maschek, S and Reis, KD and Mirsepasi-Lauridsen, HC and Petersen, AM and Nielsen, DS and Helms, M and Rasmussen, MA and Barfod, KK},
title = {Impact of a single fecal microbiome transplantation in adult women with anorexia nervosa: an open-label feasibility pilot trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68455-8},
pmid = {41535289},
issn = {2041-1723},
support = {R370-2021-863//Lundbeckfonden (Lundbeck Foundation)/ ; },
abstract = {Anorexia nervosa (AN) is a severe mental disorder characterized by restrictive eating and disturbance in the way one's body weight or shape is experienced, often accompanied by depression and anxiety. Current evidence-based treatments for AN have limited efficacy, with less than half of the patients achieving full recovery in long-term follow-up studies. Recent findings have identified gut microbiota (GM) dysbiosis as a potential contributor to AN pathology through the gut-brain axis. This open-label, non-randomized, feasibility trial (Clinicaltrials.gov Identifier: NCT05834010) evaluated the feasibility of utilizing fecal microbiota transplantation (FMT) to modify the GM and GM-associated signaling in females with AN and to examine biological effects following a single FMT procedure. Adult female participants diagnosed with AN were recruited. FMT was administered either orally via capsules or as rectal enema. Stool and blood samples were collected pre- and one week post-FMT to assess GM composition, hormonal changes, and biomarkers. Primary endpoints: Feasibility of FMT in individuals with AN and preferred route of FMT. Secondary endpoints: A single FMT treatment can alter GM composition in individuals with AN short term and relevant gut brain signaling in serum. 18/22 participants (81%) completed FMT and sampling and 19/22 participants chose oral capsules, with no serious adverse effects reported. GM analysis showed significant shifts toward donor composition 1-week post-FMT, with improved stool consistency. No significant changes were observed in psychopathology measures or appetite-related biomarkers. Oral FMT is a feasible intervention for adult women with AN, leading to changes in GM profile. Future studies should focus on placebo-controlled trials to assess the efficacy of repeated oral treatments and explore long-term effects on GM, appetite, body weight, sex hormones, disorder-specific symptoms, and overall well-being.},
}

@article {pmid41535271,
year = {2026},
author = {Klümpen, L and Mantri, A and Philipps, M and Seel, W and Schlautmann, L and Yaghmour, MH and Wiemann, V and Stoffel-Wagner, B and Coenen, M and Weinhold, L and Hasenauer, J and Fließwasser, T and Burgdorf, S and Thiele, C and Stehle, P and Simon, MC},
title = {Cholesterol-lowering effects of oats induced by microbially produced phenolic metabolites in metabolic syndrome: a randomized controlled trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {598},
pmid = {41535271},
issn = {2041-1723},
support = {01EA1707//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 432325352 - SFB 1454, EXC 2151-390873048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 432325352 - SFB 1454//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Avena/metabolism/chemistry ; *Metabolic Syndrome/diet therapy/blood/microbiology/metabolism ; Male ; Coumaric Acids/blood ; Middle Aged ; Female ; *Phenols/metabolism ; Adult ; *Cholesterol/blood ; Gastrointestinal Microbiome ; },
abstract = {Oats have various positive effects on human health, but the underlying mechanisms are not fully understood. To identify oat-microbiome-host interactions contributing to metabolic improvements, we conducted two randomized controlled dietary interventions in parallel-design in individuals with metabolic syndrome, comparing a short-term, high-dose and a six-week, moderate oat intake with respective controls (DRKS00022169). Both oat diets lead to an increase in plasma ferulic acid (0.64 [0.26, 1.02], P = 0.002; 0.55 [0.21, 0.89], P = 0.003), while the high-dose oat-diet also increased dihydroferulic acid (1.23 [0.44, 2.01], P = 0.003). Here we show that microbial phenolic metabolites are driving factors for the cholesterol-lowering effect of oats, which might be of relevance since short-term, high-dose oat-diet is a suitable approach to alleviate obesity-related lipid disorders.},
}

Humans
*Avena/metabolism/chemistry
*Metabolic Syndrome/diet therapy/blood/microbiology/metabolism
Male
Coumaric Acids/blood
Middle Aged
Female
*Phenols/metabolism
Adult
*Cholesterol/blood
Gastrointestinal Microbiome

@article {pmid41534821,
year = {2026},
author = {Cadaxo, AS and Cotrin, JC and Valente, AP and Lopes, FG and Veras, RP and Torres, DS and Molina da Costa, RQ and Dos Santos Junior, GC and Santos-Rebouças, CB},
title = {Multi-biofluid metabolomics coupled with gene network reveals stage-specific alterations in mild cognitive impairment and Alzheimer's disease in an ethnically mixed cohort.},
journal = {Brain research},
volume = {1874},
number = {},
pages = {150167},
doi = {10.1016/j.brainres.2026.150167},
pmid = {41534821},
issn = {1872-6240},
abstract = {Alzheimer's disease (AD) is the most prevalent age-related neurodegenerative disorder worldwide. A prodromal stage, often manifested as Mild Cognitive Impairment (MCI), can precede dementia onset. Metabolomics provides a powerful approach to detect metabolic alterations capturing combined genetic, epigenetic, dietary, gut microbiota, and environmental influences on AD pathogenesis and progression from MCI to AD. In this study, we analysed plasma, urine, and saliva metabolomes of 94 ethnically diverse Brazilian individuals (30 AD, 16 MCI and 48 healthy controls), all comorbidity-free, using Nuclear Magnetic Resonance (NMR)-based metabolomics. Cross-sectional analysis employed multivariate modelling (PLS-DA) and univariate Mann-Whitney U tests. We identified distinct group-specific metabolic signatures involving amino acids (phenylalanine, glutamine, asparagine, valine, alanine), energy-related metabolites (pyruvate, citrate, glucose), compounds linked to lipid/redox pathways (acetate, glutamate, aspartate), epigenetic regulation (betaine), neuroinflammation, immune fitness, and gut microbiome-influenced metabolites (scyllo-inositol). Valine increased progressively (controls < MCI < AD), while alanine showed a biphasic pattern (reduced in MCI, elevated in AD). These consistent, biofluid-spanning alterations highlight their potential as minimally invasive biomarkers for diagnosis and monitoring. Integration of metabolite data with AD-associated genes from genome-wide association studies (GWAS) revealed six genes (CYCS, NFAT5, GRIN2B, SLC43A2, MAPT, and SLC38A1) common to all biofluids, reinforcing convergent systemic pathways. Collectively, these findings underscore the importance of integrating metabolomics with genetic networks to enhance understanding of AD pathophysiology, identify potential therapeutic targets, and guide future clinical validation and precision medicine strategies for dementia in ethnically mixed populations.},
}

@article {pmid41534759,
year = {2026},
author = {Deng, L and Tian, L and Su, D and Li, Y and Zhang, S and Wang, S and Liu, Z},
title = {(R)-bambuterol ameliorates DSS-induced colitis in mice fed a high-fat diet via modulating immune response, intestinal barrier integrity, gut microbiota, and metabolomic profiles.},
journal = {Archives of biochemistry and biophysics},
volume = {777},
number = {},
pages = {110734},
doi = {10.1016/j.abb.2026.110734},
pmid = {41534759},
issn = {1096-0384},
abstract = {The consumption of a high-fat diet is currently thought to be closely related to the onset of ulcerative colitis. (R)-bambuterol ((R)-BMB) has anti-inflammatory effects in the treatment of respiratory system related diseases. However, the therapeutic effect of (R)-BMB against in high-fat diet-related colitis remain undocumented. Therefore, in this study, the alleviation effect of (R)-BMB in mice with dextran sulfate sodium (DSS)-induced colitis fed a high-fat diet and its potential mechanism was explored. The results demonstrated that (R)-BMB markedly ameliorated the symptoms of colitis, such as body weight loss, spleen swelling and colon shortening. Moreover, (R)-BMB obviously mitigated the levels of inflammatory cytokines. Further research exhibited that (R)-BMB inhibited the NF-κB signaling pathway, regulated the balance of Th17 and Treg cells, elevated activated the Nrf-2/HO-1 signaling pathway, and increased the expression of related to tight junction proteins to increase the integrity of the intestinal barrier. In addition, 16S rDNA sequencing results indicated that (R)-BMB regulated the structure of the intestinal microbiome and relieved imbalances in this microbiome, and non-targeted metabolomics analysis revealed that (R)-BMB reversed the metabolic changes in mice with colitis fed a high-fat diet. In summary, these results indicate that (R)-BMB can serve as a novel alternative strategy for treating colitis in the context of high-fat diet consumption.},
}

@article {pmid41534752,
year = {2026},
author = {van der Merwe, L and Bester, M and Serem, J and Apostolides, Z},
title = {Alleviation of adverse effects associated with α-glucosidase inhibitors by Ocimum basilicum L., Matricaria chamomilla L., and Salvia officinalis L. reveals novel selective inhibition of Bacillus α-glucosidase by acarbose.},
journal = {Journal of ethnopharmacology},
volume = {360},
number = {},
pages = {121182},
doi = {10.1016/j.jep.2026.121182},
pmid = {41534752},
issn = {1872-7573},
abstract = {Ocimum basilicum L., Matricaria chamomilla L., and Salvia officinalis L. have literature-supported ethnobotanical claims of reducing hyperglycaemia and gastrointestinal discomfort. Thus, they contain potent potential for reducing gastrointestinal adverse side effects associated with the use of the type 2 diabetes medication, acarbose. The adverse effects are predominantly theorised to be caused by excess carbohydrate fermentation by gut bacteria. Therefore, the aim of this study was to subject herbal extracts as well as compounds identified in the herbs to in silico and in vitro investigation for selective inhibition of a gut bacterial enzyme, Bacillus α-glucosidase, compared with human α-glucosidase. In silico molecular docking was employed to filter and select top performing compounds that exhibited the highest selective Bacillus α-glucosidase inhibition, followed by pharmacokinetic examination of the selected compounds. In vitro enzyme kinetics, hepatocellular carcinoma cell line cytotoxicity and the reduction of hepatic lipid accumulation in a hepatocellular carcinoma/oleic acid cellular model of metabolic dysfunction-associated fatty liver disease was examined. A metabolomic study on the concentration of the selected compounds in the herbs as well as a comparative analysis on abundant metabolites between herbs were analysed through an ultra-performance liquid chromatography-mass spectrometry-based study. Molecular docking revealed cinnamic acid, coumaric acid, epicatechin, hesperetin, linalool, menthol, octenol, terpineol, umbelliferone, and vanillic acid as the top predicted compounds with the highest predicted selective inhibition of Bacillus α-glucosidase. These findings were validated through in vitro assessment, in which the primary finding and the most unexpected result was obtained through enzyme kinetics, where compared with all compounds, acarbose exhibited the most potent inhibition and selectivity towards Bacillus α-glucosidase. Only umbelliferone significantly reduced cell viability and therefore validated its predicted toxicity that was obtained through pharmacokinetic studies. O. basilicum, M. chamomilla, and S. officinalis were evaluated against Camellia sinensis (L.) Kuntze for cytotoxic effects, where only M. chamomilla produced a significantly higher EC50, substantiating the herbs potent anti-cancerous abilities. Compounds and herb extracts were not found to reduce hepatic lipid accumulation. The novel finding was related to acarbose inhibition and specifically its potent selectivity of Bacillus α-glucosidase which discredits and disproves the theory that excess bacterial fermentation is the cause behind acarbose's reported adverse effects. Thus, this research study rather proves that acarbose negatively affects gut bacterial enzymes, promoting microbiome dysbiosis and therefore future research should at the forefront focus on the rehabilitation of diabetic patients' gut microbiome and intestinal health.},
}

@article {pmid41534698,
year = {2026},
author = {Baldi, S and Bertorello, S and Cei, F and Iurato La Rocca, A and Scianaro, V and Bartolucci, G and Mannaioni, G and Amedei, A and Gerace, E},
title = {Gender-Specific Gut Microbiota Alterations in Adolescent C57BL/6 Mice Following Prenatal Alcohol Exposure.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115929},
doi = {10.1016/j.fct.2026.115929},
pmid = {41534698},
issn = {1873-6351},
abstract = {Fetal Alcohol Spectrum Disorder (FASD), caused by prenatal alcohol exposure (PAE), produces lasting physical, cognitive, and behavioral impairments. The present study examined effects of early PAE on the gut microbiome (GM) in adolescent mice to identify targets for early intervention. Female C57Bl/6 dams received 10% ethanol during the first 10 days of gestation while controls received water. Fecal and blood samples from adolescent offspring were profiled by 16S rRNA sequencing and gas chromatography-mass spectrometry to characterize microbial composition and short-chain fatty acids (SCFAs). PAE reduced microbial alpha diversity and produced distinct beta diversity patterns versus controls. Metabolomic profiling revealed increased fecal acetate and reduced anti-inflammatory SCFAs in PAE mice, though circulating SCFA levels remained unchanged. Sex-stratified analyses showed that these alterations were driven predominantly by males, who exhibited greater microbial and metabolic disruptions, enrichment of pro-inflammatory genera (Parasutterella, Parabacteroides, Clostridioides), and elevated serum medium-chain fatty acids. Cluster analysis of PAE males identified a dysbiotic subgroup with severe alpha diversity loss, increased pro-inflammatory taxa, diminished beneficial SCFAs, and enrichment of catabolic and fatty acid biosynthesis pathways. Together, the results reveal sex- and individual-specific susceptibility to PAE-induced GM dysbiosis and justify further mechanistic studies to develop sex-tailored microbiota-targeted strategies for FASD.},
}

@article {pmid41534598,
year = {2026},
author = {Irfan, Z and Halder, J and Giri, S and Molla, EA and Khanam, S},
title = {Therapeutic potential of prebiotics in modulating postprandial GLP-1, GLP-2, and glucose homeostasis in type 2 diabetes mellitus: Targeting gut dysbiosis and insulin resistance.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113102},
doi = {10.1016/j.diabres.2026.113102},
pmid = {41534598},
issn = {1872-8227},
abstract = {Type 2 diabetes mellitus is associated with gut dysbiosis, decreased microbial diversity, short-chain fatty acid synthesis, and altered GLP secretion, which are crucial for intestinal integrity, insulin sensitivity, and postprandial glucose control. Evidence from peer-reviewed mechanistic studies, observational research, clinical trials, and meta-analyses was summarised in this review. Prebiotics, an emerging potential treatment, increase the formation of SCFA during fermentation, thereby enhancing the release of GLP through FFAR2/3 signalling. This chain of events enhances glucose-dependent insulin production, inhibits glucagon secretion, delays stomach emptying, strengthens the intestinal barrier, and reduces inflammation throughout the body. Human trials demonstrate statistically significant but clinically modest improvements in HbA1c, postprandial glucose fluctuations, and an increased response to incretin-based treatments, with meta-analytic evidence reporting decreased fasting glucose and HbA1c levels. Prebiotics effect on incretin hormones in humans appears to be diverse, depending on the type, dose, duration, and baseline microbiota composition. Resistant starch and inulin-type fructans have the most consistent effects for lowering postprandial glucose. Prebiotics are viable supplementary therapy for improving glycaemic management by regulating the gut microbiota-SCFA-incretin axis. While the molecular evidence is substantial, clinical effects are moderate and diverse. Long-term microbiome-specific trials are required to understand therapeutic potential and optimise tailored therapies fully.},
}

@article {pmid41534526,
year = {2026},
author = {Jalkanen, J and Zhong, J and Nono Nankam, PA and Bhalla, N and Elmastas, M and Luo, J and Weinbrenner, S and Frendo-Cumbo, S and Pesti, B and Gourash, W and Courcoulas, A and Yang Loureiro, Z and Dietrich, A and Bäckdahl, J and Thorell, A and Buggert, M and Kalucka, J and Emont, MP and Rosen, ED and Blüher, M and Kovacs, P and Ståhl, PL and Massier, L and Rydén, M and Mejhert, N},
title = {Cytoarchitectural multi-depot profiling reveals immune-metabolic crosstalk in human colon-associated adipose tissue.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.12.008},
pmid = {41534526},
issn = {1932-7420},
abstract = {While it is well established that the cellular composition of white adipose tissue (WAT) varies between depots, the functional relevance of this heterogeneity remains unclear. By combining spatial and single-nucleus RNA sequencing, we provide a comprehensive map of subcutaneous and visceral (omental, mesenteric, mesocolic, and epiploic) WAT in both men and women. Our analyses reveal shared features, such as the spatial organization of adipogenesis, alongside depot-specific characteristics, including distinct cell-type enrichments and unique cell-cell communication routes. Epiploic WAT stands out by harboring high proportions of serum amyloid A expressing fat cells (encoded by SAA1/SAA2) and several leukocyte populations. Through mechanistic studies, we demonstrate that adipocyte SAA1/SAA2 expression is induced by inflammatory signals, including lipopolysaccharide, and that SAA1 activates immune responses in adipose-resident myeloid cells. Collectively, our findings suggest that visceral WAT exhibits distinct cytoarchitectural properties, with those located near the colon adapting by developing specialized adipocytes and immune cell populations.},
}

@article {pmid41534266,
year = {2026},
author = {Yang, SB and Kwack, KH and Lee, JH and Moon, JH},
title = {Oral live microbial therapeutics: A synthetic biology roadmap toward durable oral microbiome-based therapies.},
journal = {Archives of oral biology},
volume = {183},
number = {},
pages = {106515},
doi = {10.1016/j.archoralbio.2026.106515},
pmid = {41534266},
issn = {1879-1506},
abstract = {OBJECTIVES: Oral live microbial therapeutics (LMTs) show promise for halitosis, caries, and adjunctive periodontal care, yet benefits often fade after dosing stops. We synthesized evidence across indications and reframed development around quantifying and engineering persistence at intraoral sites, while outlining safety-by-design and delivery considerations for the oral niche.

DESIGN: This narrative review integrated randomized trials, observational studies, and in vitro/ex vivo investigations to characterize clinical outcomes, persistence-related metrics, and engineering principles relevant to oral LMT development. Sources included PubMed/MEDLINE, Web of Science, Embase, and ClinicalTrials.gov, with backward/forward citation tracking. We included studies on LMTs in oral or gut contexts when mechanistically informative for oral applications (e.g., persistence, delivery, or biocontainment). Eligibility required clinical outcomes or persistence-related readouts. Two reviewers screened records and resolved disagreements by consensus. Reporting and assay principles were informed by STORMS and MIQE to support transparent, reproducible methods.

RESULTS: Across indications, effects typically peak during dosing and attenuate after cessation, varying with strain, delivery format, and co-interventions (e.g., tongue dorsum debridement; standardized periodontal care). Persistence is rarely co-measured with clinical endpoints, limiting mechanistic interpretation. We outline a site-resolved measurement set, including time above the limit-of-detection, colonization area under the curve, apparent half-life (t½), and t½ under oral-mimetic shear, together with an engineering toolkit combining mucoadhesive/enamel-interactive carriers, single-cell coatings, and multilayer biocontainment (e.g., logic-gated/CRISPR kill switches, synthetic auxotrophy), and chemistry, manufacturing, and controls considerations.

CONCLUSIONS: Embedding persistence metrics and safety-by-design into study protocols may support more durable outcomes, and standardized, site-resolved reporting will be essential for clinical translation.},
}

@article {pmid41534185,
year = {2026},
author = {de Torres, CS and Elias, E and Vaghi, C and González, NS and García, A and Alcaraz, A and Rodríguez-Castells, M and Baraibar, I and Ros, J and Salvà, F and Tabernero, J and Élez, E and Sanz-Garcia, E},
title = {Exploring resistance to immune checkpoints inhibitors in mismatch repair-deficient or microsatellite-instable colorectal cancer.},
journal = {Cancer treatment reviews},
volume = {143},
number = {},
pages = {103089},
doi = {10.1016/j.ctrv.2026.103089},
pmid = {41534185},
issn = {1532-1967},
abstract = {Colorectal cancer (CRC) with mismatch-repair deficiency (dMMR) or high microsatellite instability (MSI-H) represents a distinct molecular subtype highly sensitive to immune checkpoint inhibitors (ICIs). Landmark clinical trials have established ICIs as standard-of-care in this setting, demonstrating durable responses and improved survival. However, up to one-third of patients will exhibit primary or acquired resistance, highlighting the urgent need for predictive biomarkers and novel therapeutic strategies. This review summarizes the clinical evidence supporting ICIs in dMMR/MSI-H CRC, explores mechanisms of resistance-including intrinsic and extrinsic modulators-and evaluates the role of potential predictive biomarkers of response. Finally, we discuss innovative therapeutic approaches to overcome resistance, including combination strategies, DNA repair pathway inhibitors, immune-oncology drugs beyond checkpoint inhibitors and microbiome-targeted interventions. Together, these insights aim to refine patient selection, optimize therapeutic benefit, and guide the development of next-generation therapies for dMMR/MSI-H CRC.},
}

@article {pmid41534145,
year = {2026},
author = {Das, M and Rath, S and Gorepatti, R and Dash, R and Akella, A and Gaur, AS and Venugopal, G and Khan, ZH and Ramadass, B and Nayak, P},
title = {Microbiome-linked transcriptomic signatures in NMIBC: Toward personalized uro-oncology.},
journal = {Urologic oncology},
volume = {44},
number = {3},
pages = {110977},
doi = {10.1016/j.urolonc.2025.12.013},
pmid = {41534145},
issn = {1873-2496},
abstract = {BACKGROUND: Nonmuscle Invasive Bladder Cancer (NMIBC) is a prevalent malignancy marked by high recurrence and progression rates. Emerging evidence suggests that demographic and environmental factors may alter the bladder's native oncobiome, influencing tumor behavior. This exploratory pilot study examined whether paired tumor and adjacent normal bladder mucosa exhibit distinct host transcriptomic and microbial signatures that may illuminate early tumor-microbiome interactions in NMIBC.

METHODS: A meta-transcriptomic analysis was conducted on paired tumor and adjacent normal bladder mucosa from 6 NMIBC patients. Shotgun RNA sequencing was used to profile differential gene expression and microbial composition. Functional annotation and correlation analyses were performed to explore gene-microbe interactions.

RESULTS: Fifty-seven differentially expressed genes (DEGs) across 6 patients and 12 paired samples were identified, including 45 downregulated and 12 upregulated genes, primarily involved in extracellular matrix organization and structural integrity. Tumor tissues exhibited significantly reduced microbial species richness compared to the adjacent normal mucosa (P = 0.026). Propionibacterium acnes showed increased abundance in tumor sites (23.88%) versus the adjacent normal mucosa (13%), suggesting a protumorigenic role. Veillonella dispar and Corynebacterium durum were strongly associated with matrix-regulating genes, while Bifidobacterium longum-more abundant in the adjacent normal tissues-correlated with genes linked to extracellular homeostasis, indicating a potential protective role.

CONCLUSION: This pilot study reveals distinct transcriptomic and microbial signatures in NMIBC, highlighting the role of microbial dysbiosis, which denotes an altered microbial community; reduced diversity and shifts in key taxa relative to the adjacent bladder mucosa, in extracellular matrix remodeling and tumor progression. These host-microbe interactions may contribute to disease pathogenesis and recurrence. Further studies are warranted to elucidate the underlying mechanisms and therapeutic implications.},
}

@article {pmid41534121,
year = {2026},
author = {Zalomova, LV and Fesenko, EE},
title = {Effectiveness of FBS-DMSO cryoprotectant composition in artificial microbiome models mimicking key gut microbiota enterotypes.},
journal = {Cryobiology},
volume = {122},
number = {},
pages = {105582},
doi = {10.1016/j.cryobiol.2026.105582},
pmid = {41534121},
issn = {1090-2392},
abstract = {The ratio of microorganisms in the composition of the microflora of the small and large intestines plays a crucial role in human health. Therefore, it is essential to preserve the original proportions of species over an extended period for their further therapeutic application. It has previously been established that three primary enterotypes dominate the human gut microbiota: Bacteroides, Prevotella, and Ruminococcus. However, there is no precise information on how their species ratios are affected by deep freezing. In our study, we examined the preservation of the ratios of microorganisms in the human gut before and after cryopreservation, represented as distinct clusters consisting of four different bacterial species dominant in the gut microbiome. Using photometric registration of optical density and fluorescent staining methods, we demonstrated that the viability of most bacteria remained high in the cryoprotective medium of 5 % Me2SO/FBS. Additionally, the calculation of the Pattern Comparison Index (PCI) showed good results in maintaining the community structure of bacteria in each of the artificial models. Thus, this modeling of microbiocenoses allows for the identification of patterns in the preservation of their quantitative composition during long-term storage in liquid nitrogen.},
}

@article {pmid41533849,
year = {2026},
author = {Su, T and Cai, W and Shen, T and Yu, D and Zhu, M and Liu, C and Yu, J},
title = {Comprehensive Analysis of the Conjunctival Sac Microbiome in Patients With Evaporative Dry Eye and Mixed Dry Eye.},
journal = {Translational vision science & technology},
volume = {15},
number = {1},
pages = {4},
pmid = {41533849},
issn = {2164-2591},
mesh = {Humans ; *Microbiota/genetics ; *Dry Eye Syndromes/microbiology ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Conjunctiva/microbiology ; Adult ; *Bacteria/genetics ; Aged ; DNA, Bacterial/genetics ; },
abstract = {PURPOSE: This study aimed to investigate the differences in the microbial community of the conjunctival sac (CS) between patients with evaporative dry eye (EDE) and patients with mixed dry eye (DE), then, to compare it with previously reported ocular surface microbial of healthy people.

METHODS: CS swabs were collected from 10 patients with EDE and 10 patients with mixed DE. Bacterial DNA from these swabs were analyzed using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Alpha diversity analysis assessed the microbial community diversity, while beta diversity was evaluated. Bioinformatic analysis of relative abundances and the functional annotations were performed at the genus level.

RESULTS: Results indicated no significant difference in alpha diversity, but a significant difference in beta diversity was observed (P = 0.001). Notably, Ralstonia and Corynebacterium exhibited significant differences. At the species level, the colonization rates and abundances of bacteria, including Comamonas denitrificans, Raoultella planticola (R. planticola), Pseudomonas mosselii, and Pseudomonas aeruginosa were significantly different. Functional annotation revealed that disparities in the microbial composition from CS between the two groups were accompanied by differences in the expression levels of genes involved in carbohydrate metabolism and histidine kinases, which were elevated in the mixed DE group.

CONCLUSIONS: The microbial community structure of the EDE group was comparable to that of the mixed DE group. However, notable differences were observed in the relative abundance and colonization rate of certain specific microorganisms. These variations were associated with alterations in carbohydrate metabolism and histidine kinase expression.

TRANSLATIONAL RELEVANCE: Corynebacterium, and Ralstonia may play important roles in the pathogenesis of dry eye disease (DED).},
}

Humans
*Microbiota/genetics
*Dry Eye Syndromes/microbiology
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
*Conjunctiva/microbiology
Adult
*Bacteria/genetics
Aged
DNA, Bacterial/genetics

@article {pmid41533724,
year = {2026},
author = {Li, H and Jin, YT and Ye, DX and Liu, Q and Su, X and Zhang, HQ and Yang, H},
title = {Machine Learning-based Diagnostic Potential of Bipolar Disorder Using Gut Microbiota Signatures.},
journal = {IET systems biology},
volume = {20},
number = {1},
pages = {e70056},
doi = {10.1049/syb2.70056},
pmid = {41533724},
issn = {1751-8857},
support = {32270786//National Natural Science Foundation of China/ ; 62371403//National Natural Science Foundation of China/ ; 62402207//National Natural Science Foundation of China/ ; 2024D008//the Municipal Government of Quzhou/ ; },
mesh = {*Bipolar Disorder/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Machine Learning ; Humans ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Male ; Female ; Adult ; },
abstract = {Bipolar disorder (BD) is a chronic psychiatric illness associated with significant cognitive and social dysfunction, contributing substantially to the global disease burden. Recent evidence suggests that the gut microbiota may play a role in the pathophysiology of BD through the microbiota-gut-brain axis. To clarify this potential link and explore diagnostic applications, we investigated gut microbial alterations in BD and evaluated their predictive value using 16S rRNA sequencing and machine learning approaches. We first assessed microbial diversity and composition, revealing significantly reduced α-diversity and altered β-diversity in BD compared to healthy controls (HC), alongside weakened microbial co-occurrence network connectivity. Given these compositional differences, we systematically benchmarked 12 classification algorithms to discriminate BD from HC. Ensemble-based models, particularly the random forest (RF) classifier, achieved the best diagnostic performance. To further improve predictive accuracy, we compared multiple feature selection methods: RF feature importance ranking, independent t-tests and MaAsLin2 analysis, identifying 35 optimal microbial biomarkers based on RF. This feature set demonstrated excellent classification performance (AUC = 0.9316, AUPR = 0.9497). Furthermore, based on the taxonomic findings, we applied PICRUSt2 functional prediction using KEGG and MetaCyc annotations, which revealed marked alterations in pathways related to neurodegeneration, lipid metabolism and heme biosynthesis. Finally, to capture both compositional and functional aspects of microbial dysbiosis, we combined these functional features with the selected microbial biomarkers in an RF model, achieving further improved diagnostic performance (AUC = 0.9499, AUPR = 0.9586). In conclusion, our results demonstrate substantial compositional and functional disturbances in the gut microbiota of BD and highlight the value of machine learning-driven, microbiome-based models for noninvasive BD diagnosis. The identified microbial and metabolic markers also provide mechanistic insights into the microbiota-gut-brain axis, offering promising directions for precision psychiatry and microbiome-targeted interventions.},
}

*Bipolar Disorder/diagnosis/microbiology
*Gastrointestinal Microbiome
*Machine Learning
Humans
RNA, Ribosomal, 16S/genetics
Biomarkers
Male
Female
Adult

@article {pmid41533698,
year = {2026},
author = {Vargas-Robles, D and Yap, YR and Singha, B and Tien, J and Purandare, M and Rojas-Correa, M and Madziar, C and Picker, M and Dumont, T and Leftwich, HK and Frisard, CF and Ward, DV and Peter, I and Olendzki, B and Maldonado-Contreras, A},
title = {Association of vaginal IL-4, IL-6, IL-8, IL-17, IFN-γ, and dietary intake with IBD status and vaginal microbiota in pregnant individuals.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0335178},
pmid = {41533698},
issn = {1932-6203},
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology/metabolism ; Adult ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Microbiota ; Interferon-gamma/metabolism ; Diet ; Interleukin-6/metabolism ; Interleukin-4/metabolism ; Interleukin-17/metabolism ; Interleukin-8/metabolism ; *Cytokines/metabolism ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {BACKGROUND: Pregnant individuals with inflammatory bowel diseases (IBD) exhibit gut inflammation and dysbiosis; however, there is limited knowledge about their vaginal environment. This is important as vaginal inflammation and high vaginal microbiota diversity are associated with adverse pregnancy outcomes.

OBJECTIVES: We aimed to compare vaginal inflammatory markers and microbiota diversity of pregnant individuals with and without IBD in their third trimester of pregnancy and determine the role of diet in the vaginal microbiota diversity.

METHODS: We recruited pregnant individuals who provided vaginal swabs at 27-29 weeks of pregnancy. We characterized the vaginal microbiota by sequencing the V3-V4 region of the 16S rRNA and surveyed nine key pro and anti-inflammatory cytokines by qRT-PCR from the vaginal mucosa. Participants completed three validated interviewer-led nutrition assessments of 24-hour dietary intake around the same time as the collection of vaginal samples. The nutritional assessments were used to estimate dietary quality using the validated Healthy Eating Index (HEI-2015).

RESULTS: The cohort included 23 pregnant individuals with IBD (18 with Crohn's disease and 5 with ulcerative colitis) and 25 healthy controls (HC); 56.5% of the IBD cases were in remission. Vaginal microbiota diversity and composition did not differ significantly between individuals with IBD and HC. However, the vaginal mucosa of the IBD individuals showed increased expression of Th17 pro-inflammatory cytokines (i.e., IL-6, IL-8, IL-17) and decreased expression of Th1 (IFN-γ) and Th2 (IL-4) compared to HC. Expression of IL-6 and TNF- α correlated positively with vaginal microbial diversity. The beneficial Lactobacillus crispatus dominated the vaginal microbiota of individuals with either high dietary quality or those consuming more vegetables or low added sugar, regardless of IBD status. In IBD cases, consumption of vegetables and added sugars were associated with reduced expression of the pro-inflammatory IFN-γ and an increased expression of anti-inflammatory IL-4.

CONCLUSION: The vaginal microbiome did not differ between individuals with IBD and HC; however, IBD cases exhibit a pro-inflammatory tone in the vagina (high IL-6) that is associated with higher vaginal microbial diversity. Regardless of IBD status, healthier diets are positively associated with an increased abundance of the beneficial L. crispatus in the vagina.},
}

Humans
Female
Pregnancy
*Vagina/microbiology/metabolism
Adult
*Inflammatory Bowel Diseases/microbiology/metabolism
*Microbiota
Interferon-gamma/metabolism
Diet
Interleukin-6/metabolism
Interleukin-4/metabolism
Interleukin-17/metabolism
Interleukin-8/metabolism
*Cytokines/metabolism
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid41533261,
year = {2026},
author = {Aron, S and Meagher, M and Azari, S and Baker, B and Nasseri, R and Bagrodia, A and Stewart, T and Liss, M and Salmasi, A},
title = {Beyond Sterility: the Urinary Microbiome in Bladder Cancer Carcinogenesis and Treatment.},
journal = {Current urology reports},
volume = {27},
number = {1},
pages = {8},
pmid = {41533261},
issn = {1534-6285},
mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/therapy ; *Microbiota ; *Carcinogenesis ; },
abstract = {PURPOSE OF REVIEW: Emerging evidence has challenged the paradigm of bladder sterility, opening new opportunities for understanding bladder cancer biology.

RECENT FINDINGS: Disruption of commensal intravesical bacterial communities appears to increase risk of carcinogenesis, while the presence of specific bacterial strains has been linked to differential treatment responses. However, the interplay between urinary microbiome and bladder cancer remains incompletely defined. This review summarizes the current literature regarding the role of urinary microbiome in the pathogenesis and treatment outcomes, highlights limitations of existing studies, and outlines future directions for incorporating microbiome profiling into personalized management strategies.},
}

Humans
*Urinary Bladder Neoplasms/microbiology/therapy
*Microbiota
*Carcinogenesis

@article {pmid41532953,
year = {2026},
author = {Maggo, J and Ng, HM and Bayer, SB and Wall, CL and Hoad, CL and Marciani, L and Mullaney, J and Cabrera, D and Fraser, K and Cooney, JM and Günther, CS and Trower, T and Tang, J and Gasser, O and Milan, A and McNabb, WC and Spiller, R and Conner, T and Frampton, C and Foster, M and Roy, NC and Gearry, RB},
title = {Normalization of Gastrointestinal Symptoms in Adults With Constipation With Daily Green Kiwifruit Consumption: Protocol for an Open-Label Intervention Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e75286},
pmid = {41532953},
issn = {1929-0748},
mesh = {Humans ; *Actinidia ; *Constipation/diet therapy ; Adult ; *Irritable Bowel Syndrome/diet therapy/complications ; Female ; Male ; *Fruit ; Middle Aged ; Abdominal Pain/diet therapy ; Quality of Life ; Randomized Controlled Trials as Topic ; },
abstract = {BACKGROUND: Irritable bowel syndrome with constipation (IBS-C) and functional constipation (FC) have significant personal, health care, and social impacts, affecting patients' quality of life. Treatment of these conditions is challenging. While green kiwifruit is a promising natural alternative to laxatives, its effectiveness in managing abdominal pain and the underlying mechanism of action is yet to be substantiated.

OBJECTIVE: This study investigates the effect of consuming 2 green kiwifruit daily for 4 weeks (the habitual serving) on abdominal pain and discomfort in individuals with IBS-C and FC.

METHODS: This study is a 2-arm parallel, open-label, placebo-controlled randomized study. This study's duration was 9 weeks, with a 3-week lead-in phase, a 4-week intervention phase, and a 2-week follow-up phase. A total of 60 participants with IBS-C and FC were randomized to consume either 2 Zespri green kiwifruit (Actinidia deliciosa "Hayward," ~150 g per serving, ~90 kcal) or maltodextrin (calorie-matched to the fruit, ~25 g per serving, ~90 kcal) per day for 4 weeks. The participants completed validated questionnaires assessing digestive and general health and well-being parameters, underwent magnetic resonance imaging to determine colon physiological measures, ingested a blue food dye, provided blood and fecal samples to measure microbial, immunological, and biochemical parameters, and ingested wireless motility devices (selected participants only) to assess physiological processes.

RESULTS: Recruitment for this study began in May 2021 and was completed in May 2022. A total of 63 participants were randomized, and 57 were analyzed using intention-to-treat analysis. Data analysis is complete, and full results are expected to be published in a peer-reviewed journal by April 2026.

CONCLUSIONS: This study aims to evaluate the effectiveness of green kiwifruit consumption in managing abdominal pain in individuals with IBS-C and FC. It will provide new insights into the mechanisms behind the habitual consumption of green kiwifruit for digestive comfort in this population.},
}

Humans
*Actinidia
*Constipation/diet therapy
Adult
*Irritable Bowel Syndrome/diet therapy/complications
Female
Male
*Fruit
Middle Aged
Abdominal Pain/diet therapy
Quality of Life
Randomized Controlled Trials as Topic

@article {pmid41532887,
year = {2026},
author = {Liao, Z and Parumasivam, T and Xiao, Z and Zhu, X and Yeoh, YK and Ye, X and Tan, TC},
title = {Emerging therapeutic and cosmeceutical applications of phenylalanine and its metabolites.},
journal = {Cutaneous and ocular toxicology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/15569527.2026.2612999},
pmid = {41532887},
issn = {1556-9535},
abstract = {OBJECTIVE: This review aims to comprehensively examine and integrate the extant knowledge pertaining to phenylalanine (Phe) and its key metabolites, namely tyrosine (Tyr), phenylpyruvic acid (PPA), phenyllactic acid (PLA), and phenylacetic acid (PAA). The primary focus of this review will be on the emerging pharmacological and cosmetic applications of these metabolites.

RATIONALE: Phe-derived compounds have garnered increasing attention due to their diverse pharmacological effects, including antioxidant, antimicrobial, anti-inflammatory, and neuromodulatory properties. Their relevance to skin health, pigmentation regulation, microbiome modulation, and mood-related dermatoses provides a compelling basis for reviewing their functional potential in both therapeutic and cosmetic contexts.

METHODS: A systematic literature review was conducted using PubMed, Web of Science, and Scopus up to 2025. The review was guided by predefined keywords related to Phe and its metabolites. The inclusion criteria were tailored to encompass experimental, clinical, and translational studies that explore pharmacological or cosmetic applications of Phe.

MAIN FINDINGS: The review presents compelling evidence substantiating the bioactivity of Phe and its metabolites across multiple skin-related pathways. These compounds exhibit promising efficacy in preserving skin homeostasis, regulating pigmentation, harmonizing cutaneous microbiota, and mitigating psychosomatic skin conditions. Their structural and functional diversity renders them versatile agents with extensive translational potential.

CONCLUSIONS AND IMPLICATIONS: The multifunctional nature of Phe-derived compounds presents substantial potential for incorporation into advanced skincare and pharmaceutical formulations. However, limitations persist in safety and toxicological data, particularly concerning prolonged human exposure. Future research should prioritize (i) mechanistic elucidation of biological effects, (ii) standardized toxicological and clinical validation, and (iii) formulation optimization to facilitate safe and effective applications. These endeavors have the potential to bridge the gap between biochemical research and practical innovation, thereby fostering novel solutions for skin health and emotional well-being.},
}

@article {pmid41532678,
year = {2026},
author = {Le Dréan, ME and Ganachaud, B and Rebion, M and Marchix, J and Le Berre-Scoul, C and Hulin, P and Feyeux, M and Talon, S and Neunlist, M and Caillaud, M and Boudin, H},
title = {The Microbiota-Derived Metabolite Deoxycholic Acid Regulates Enteric Neuron Activity and Connectivity.},
journal = {Journal of neurochemistry},
volume = {170},
number = {1},
pages = {e70351},
doi = {10.1111/jnc.70351},
pmid = {41532678},
issn = {1471-4159},
support = {R20056NN//Conseil Régional des Pays de la Loire/ ; R23066NN//Conseil Régional des Pays de la Loire/ ; //Fondation SantéDige/ ; //Ministère de l'enseignement supérieur, de la recherche et de l'espace/ ; ANR-10-INBS-04//Agence Nationale de la Recherche/ ; ANR-22-CE14-0043//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; *Neurons/drug effects/metabolism/physiology ; *Enteric Nervous System/drug effects/metabolism ; Rats ; *Deoxycholic Acid/pharmacology/metabolism ; *Gastrointestinal Microbiome/physiology ; Cells, Cultured ; Receptors, G-Protein-Coupled/metabolism ; Rats, Sprague-Dawley ; },
abstract = {Secondary bile acids (BAs) are metabolites produced by the gut microbiota and shown to impact digestive functions, at least in part through the enteric nervous system (ENS). In the ENS, enteric neurons express the BA receptor Takeda G protein-coupled receptor 5 (TGR5), making them potential direct cellular targets of secondary BAs, although their effects on enteric neuronal functions remain poorly understood. Enteric neuronal activity and connectivity form the basis of the regulatory control exerted by the ENS on gut functions. Yet, the influence of microbiota-derived metabolites, such as secondary BAs, on enteric neuron connectivity and synaptic activity remains largely unexplored. To address this question, we studied the effects of secondary BAs on neuronal connectivity using a model of rat primary culture of enteric neurons. We found that exposure to deoxycholic acid (DCA) increased the expression of key presynaptic proteins, synapsin-1 and synaptophysin, and enhanced synaptic density in enteric neurons. Moreover, DCA enhanced synaptic activity by increasing synaptic vesicle exocytosis upon KCl depolarisation, potentially through amplified phosphorylation of synapsin-1 at the Ser62-67 sites. In addition, we found that DCA modulated the intracellular Ca[2+] response induced by acetylcholine, a major excitatory neurotransmitter in enteric neurons, through a mechanism mediated by the TGR5 receptor. Overall, this study identifies DCA as a microbiota-derived compound capable of reshaping the enteric neuronal functional network. These findings highlight the potential of bacterial metabolites like DCA to link the microbiome with modulation of enteric neuronal activity and connectivity, supporting the relevance of secondary BAs in digestive physiology and their possible roles in gastrointestinal disorders.},
}

Animals
*Neurons/drug effects/metabolism/physiology
*Enteric Nervous System/drug effects/metabolism
Rats
*Deoxycholic Acid/pharmacology/metabolism
*Gastrointestinal Microbiome/physiology
Cells, Cultured
Receptors, G-Protein-Coupled/metabolism
Rats, Sprague-Dawley

@article {pmid41532647,
year = {2026},
author = {Cuozzo, M and O'Connor, C and Power, E and Gleeson, E and O'Mahony, S},
title = {Gut-Brain Communication in Menopause: Insights into Neuroendocrine and Microbiome Interactions.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-35},
doi = {10.1017/S0029665126102201},
pmid = {41532647},
issn = {1475-2719},
abstract = {This review synthesizes current evidence linking alterations in the gut microbiome to menopausal transition. The gut microbiota plays a crucial role in numerous physiological processes, particularly due to its bidirectional communication with the brain via multiple neural, endocrine, and immune pathways. Menopause-associated oestrogen decline disrupts this axis, influencing not only gastrointestinal function and microbial diversity but also mood, cognition, and inflammation.The estrobolome is a community of gut bacteria capable of modulating circulating estrogen levels. Taken together, research suggests a complex dynamic interplay between the intestinal microbiota and sex hormones, potentially contributing to menopausal symptoms and related comorbidities.Understanding these interactions offers promising avenues for intervention, as dietary strategies (such as isoflavones), lifestyle modifications, and targeted probiotic and prebiotic therapies may help restore balance within the gut-brain axis and optimize brain health by influencing neurotransmitter synthesis, stress responses, and hormonal regulation during and after the menopausal transition.Here, we highlight the importance of an integrative, microbiome-informed approach to midlife women's health, emphasizing innovative, non-pharmacological strategies to promote long-term well-being in women.},
}

@article {pmid41532636,
year = {2026},
author = {Jangra, M and Travin, DY and Kaur, M and Hackenberger, D and Koteva, K and Polikanov, YS and Wright, GD},
title = {An Acetyltransferase Conferring Self-Resistance of the Producer to Lasso Peptide Antibiotic Lariocidin.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00885},
pmid = {41532636},
issn = {2373-8227},
abstract = {The soil microbiome, a reservoir of antibiotic-producing bacteria, also harbors resistance determinants encoded within antibiotic biosynthetic gene clusters (BGCs). Studying self-resistance mechanisms, which have evolved in producers to protect against their own toxic metabolites, provides critical insights into the evolution of resistance and the potential vulnerabilities of new antibiotics and can facilitate the production of natural products in heterologous hosts. Here, we describe the self-resistance mechanism to lariocidin (LAR), a recently discovered lasso peptide antibiotic that inhibits the ribosomal machinery and exhibits antibacterial activity against key pathogens. We identified and characterized an N-acetyltransferase enzyme (LrcE) encoded within the LAR BGC that mediates self-resistance in LAR-producing Paenibacillus sp. M2. LrcE is a member of the GCN5-related N-acetyltransferase (GNAT) superfamily and performs site-specific acetylation of LAR at a critical lysine residue. This modification disrupts ribosomal binding, thereby reducing LAR's antibacterial activity. Using in silico modeling, we predicted a conserved acetyl-CoA-binding motif and an LAR-binding region on LrcE. Bioinformatic analysis revealed LrcE homologues in environmental but not clinically relevant pathogens, suggesting a limited risk of horizontal gene transfer and, therefore, supporting the further development of LAR as a next-generation antibiotic.},
}

@article {pmid41532519,
year = {2026},
author = {Zhu, M and Huang, K and Wang, X and Yang, F and Ni, K},
title = {Enhanced Nitrogen Use Efficiency and Reshaped Phyllosphere Microbiome through Biochar Application and Nitrogen Fertilizer Reduction.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10538},
pmid = {41532519},
issn = {1520-5118},
abstract = {Paper mulberry (Broussonetia papyrifera), a high-protein forage species, exhibits low nitrogen use efficiency (NUE) under conventional nitrogen fertilization. This study conducted a field experiment to systematically evaluate the effects of coapplying biochar with reduced nitrogen fertilizer on paper mulberry by integrating plant physiological measurements, soil property analysis, and phyllosphere microbiome profile. Results demonstrated that moderate biochar addition significantly enhanced plant growth, forage quality, and soil health, while improving NUE. Notably, coapplying biochar with a 15% reduced nitrogen emerged as a sustainable fertilization strategy, reducing nitrogen inputs without compromising plant performance. 16S rRNA gene sequencing revealed that biochar treatment reshaped the phyllosphere microbiome by increasing diazotroph abundance, suppressing pathogens, and enhancing microbial network complexity. Overall, this study demonstrates that coapplying biochar with 15% reduced nitrogen not only improves NUE, but also enhances plant performance and soil properties, while reshaping the phyllosphere microbiome into a more plant-beneficial community.},
}

@article {pmid41532472,
year = {2026},
author = {Lim, S and Kim, SH and Jeong, HJ and Park, S and Koo, BK and Lee, JH and Shin, W},
title = {Gastric cancer organoids and their convergence in engineering approaches.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70272},
pmid = {41532472},
issn = {1873-3468},
support = {RS-2023-00221122//National Research Foundation of Korea/ ; RS-2024-00414004//National Research Foundation of Korea/ ; RS-2025-23022973//National Research Foundation of Korea/ ; IBS-R021-D1//Institute for Basic Science/ ; },
abstract = {Gastric cancer research has rapidly progressed due to interdisciplinary advances in stem cell biology and bioengineering. Gastric organoid models, particularly those derived from adult stem cells, have emerged as powerful tools that recapitulate the cellular complexity of the human stomach. This review highlights the development of various gastric organoid platforms, with a specific focus on the convergence of engineering strategies to overcome the limitations of conventional organoid systems. We explore how CRISPR-based functional genomics, matrix innovations, co-culture systems, microphysiological systems (MPS), and big data integration are collectively enhancing organoid models. Furthermore, we examine how artificial intelligence may refine the clinical relevance and precision of gastric organoid models. By assessing both current capabilities and future directions, this review offers a perspective on how gastric organoid systems may reflect human physiology more accurately and improve therapeutic outcomes.},
}

@article {pmid41532467,
year = {2026},
author = {Ruan, C and Zheng, X and Wang, L},
title = {Letter to the Editor: integrating oral microbiome biomarkers into global disease burden assessments to enhance early-onset type 2 diabetes prevention strategies.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004750},
pmid = {41532467},
issn = {1743-9159},
}

@article {pmid41532465,
year = {2026},
author = {Ferri, A and Schneider, E and Lucey, A and Hennessy, Á and Cotter, PD and Balasubramanian, R and Clarke, G and Cryan, JF},
title = {Development and Validation of a Food Frequency Questionnaire to Assess Fermented Food Consumption in Adults.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {39},
number = {1},
pages = {e70183},
pmid = {41532465},
issn = {1365-277X},
support = {SFI/12/RC/2273_P2//Science Foundation Ireland grant to APC Microbiome Ireland through the Irish Government's National Development Plan/ ; },
mesh = {Humans ; Adult ; Male ; Middle Aged ; Female ; *Fermented Foods/statistics & numerical data ; Young Adult ; Surveys and Questionnaires/standards ; Reproducibility of Results ; Adolescent ; *Diet/statistics & numerical data ; United Kingdom ; *Diet Surveys/methods/standards ; Ireland ; Australia ; *Feeding Behavior ; New Zealand ; United States ; Canada ; },
abstract = {BACKGROUND: Fermented foods can confer benefits to human health and modulate the microbiota-gut-brain axis. Fermented foods are gaining popularity in Western cultures, with increasing calls for their inclusion in national dietary guidelines. As no specific validated measure to capture fermented food intake exists, this study aimed to develop and validate a fermented food intake questionnaire (FFIQ) to assess habitual intake in adults from the United States, Canada, the United Kingdom, Ireland, Australia and New Zealand, aged 18-60 years.

METHODS: A 32-item self-administered FFIQ, informed by available international food consumption data for adults, was developed and subsequently validated in an online sample of 167 adults using six online 24-h automated dietary recalls (intake24.com) as the reference method. Correlation and Bland-Altman analyses were used to assess agreement and bias between the FFIQ and the 24-h dietary recalls.

RESULTS: The most frequently consumed fermented foods were cheeses, yoghurt, kefir and kombucha. Median (Interquartile range) intake of total fermented food was 85.4 (42.3, 143.0) g/day for the FFIQ and 54.9 (20.8, 112.1) g/day for the average of the 24-h dietary recalls, respectively and showed good agreement for total fermented food consumption (r = 0.56, p < 0.001) and for most individual fermented foods and food categories. The FFIQ classified 93.4% of participants in the same or adjacent tertile of total fermented food intake. Bland-Altman plots for total intake of fermented food demonstrated good agreement between the FFIQ and the 24 h recalls. The FFIQ also showed good to excellent reliability upon re-administration for most fermented foods as indicated by the intraclass correlation coefficients.

CONCLUSIONS: The FFIQ provides a robust estimate of fermented food consumption among adults from English-first language countries. This will be a valuable resource with potential applications in clinical and epidemiological research aimed at exploring associations between fermented foods and health outcomes.},
}

Humans
Adult
Male
Middle Aged
Female
*Fermented Foods/statistics & numerical data
Young Adult
Surveys and Questionnaires/standards
Reproducibility of Results
Adolescent
*Diet/statistics & numerical data
United Kingdom
*Diet Surveys/methods/standards
Ireland
Australia
*Feeding Behavior
New Zealand
United States
Canada

@article {pmid41532096,
year = {2025},
author = {Xie, L and Li, X and Liu, L and Zhao, J and Luo, L and Qiao, W and Chen, L},
title = {Oral administration of Lacticaseibacillus rhamnosus HM126 alleviates DNFB-induced atopic dermatitis in BALB/c mice by modulating immunity, gut microbiota, and metabolites.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1739967},
pmid = {41532096},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Dermatitis, Atopic/immunology/chemically induced/therapy/metabolism/microbiology ; *Lacticaseibacillus rhamnosus/immunology ; Administration, Oral ; *Probiotics/administration & dosage ; Mice ; Disease Models, Animal ; Mice, Inbred BALB C ; Cytokines/blood ; Female ; Feces/microbiology ; Metabolomics ; },
abstract = {INTRODUCTION: Probiotics have emerged as a promising and safe alternative therapy for atopic dermatitis (AD) by regulating the gut microbiota-immune axis, correcting type 1/type 2 imbalance, and repairing the skin barrier.

METHODS: A mouse model of AD was established using diphenylnitromethane (DNFB). Low, medium, and high doses of human milk-derived Lacticaseibacillus rhamnosus HM126 were administered to investigate its effects on the model. We observed the scratching frequency and skin lesion scores after 28 days of continuous oral administration. Serum biochemical indicators and inflammatory cytokines were measured using ELISA, whereas the gut microbiota in feces was analyzed using 16S rDNA sequencing. Non-targeted metabolomics was used to assess the changes in fecal metabolites.

RESULTS AND DISCUSSION: Compared to the DNFB group, high-dose L. rhamnosus HM126 significantly reduced scratching frequency in AD mice. The low-dose group showed significantly reduced IgE levels. Additionally, the IFN-γ/IL-4 ratio significantly increased, indicating that L. rhamnosus HM126 modulates type 1/type 2 immune factors toward equilibrium. 16S rDNA analysis revealed that L. rhamnosus HM126 significantly reduced the ACE index and Chao 1 index of the gut microbiota in mice with AD, thereby reshaping the composition of the gut microbiome. Metabolomics analysis suggested that L. rhamnosus HM126 may improve AD by influencing the levels of asiatic acid, phytosphingosine, Ser-Glu, prostaglandin F2 alpha ethylamide (PGF(2α)EA), argininosuccinic acid, L-rhamnose, and gamma-L-glutamyl-L-glutamic acid. This study demonstrated that L. rhamnosus HM126 maintains the type 1/type 2 balance and effectively modifies the gut microbiota structure and metabolic changes to improve AD. Our findings provide a scientific basis for the development of probiotic therapeutics to prevent and treat this condition.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Dermatitis, Atopic/immunology/chemically induced/therapy/metabolism/microbiology
*Lacticaseibacillus rhamnosus/immunology
Administration, Oral
*Probiotics/administration & dosage
Mice
Disease Models, Animal
Mice, Inbred BALB C
Cytokines/blood
Female
Feces/microbiology
Metabolomics

@article {pmid41532068,
year = {2026},
author = {Aghdam, R and Shan, S and Lankau, R and Solís-Lemus, C},
title = {A hybrid framework for disease biomarker discovery in microbiome research combining Bayesian networks, machine learning, and network-based methods.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpaf089},
pmid = {41532068},
issn = {2396-8923},
abstract = {Microbiome research faces two central challenges, namely constructing reliable networks, where nodes represent microbial taxa and edges represent their associations, and identifying significant disease-associated taxa. To address the first challenge, we developed CMIMN, a novel R package that applies a Bayesian network framework based on conditional mutual information to infer microbial interaction networks. To further enhance reliability, we construct a consensus microbiome network by integrating results from CMIMN and three widely used methods, including Sparse Inverse Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Semi-Parametric Rank-based correlation and partial correlation Estimation (SPRING), and Sparse Correlations for Compositional Data (SPARCC). This consensus approach, which overlays and weights edges shared across methods, reduces inconsistencies and provides a more biologically meaningful view of microbial relationships. To address the second challenge, we designed a multi-method feature selection framework that combines machine learning with network-based strategies. Our machine learning pipeline applies distinct algorithms and identifies key taxa based on their consistent importance across models. Complementing this, we employ two network-based strategies that prioritize taxa based on centrality differences between networks constructed from healthy samples and disease-affected samples, as well as a composite scoring system that ranks nodes using integrated network metrics. We applied CMIMN on soil microbiome data from potato fields affected by common scab disease. Bootstrap analysis confirmed the robustness of CMIMN, and the consensus network further improved stability and interpretability. The multi-method framework enhances confidence in identifying soil microbial taxa associated with potato disease. Notably, we identified Bacteroidota, WPS-2, and Proteobacteria at the Phylum level; Actinobacteria, AD3, Bacilli, Anaerolineae, and Ktedonobacteria at the Class level; and C0119, Defluviicoccales, Bacteroidales, and Ktedonobacterales at the Order level as key taxa associated with disease status.},
}

@article {pmid41531645,
year = {2026},
author = {Fernandes, LA and de Souza, AO and Nukui, Y and Marcusso, RM and de Oliveira, ACP and Casseb, J and Clissa, PB and Villas-Boas, SG and Sanabani, SS},
title = {Gut Microbiome Dysbiosis is Associated With Human T-Lymphotropic Virus Type 1 (HTLV-1) Infection and Disease Progression to HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis: A Cross-Sectional Study.},
journal = {Smart medicine},
volume = {5},
number = {1},
pages = {e70024},
pmid = {41531645},
issn = {2751-1871},
abstract = {Human T-lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic neuroinflammatory disease. Given the established role of the gut-brain axis in other neurological diseases such as multiple sclerosis, the role of the gut microbiome in the pathogenesis of HAM/TSP remains a critical unexplored area. The aim of this study was to characterize alterations in the gut microbiome associated with HTLV-1 infection and its clinical stages. We performed a cross-sectional analysis of the gut microbiome from 112 Brazilian individuals, including 24 healthy controls and 88 HTLV-1-infected individuals at different disease stages: 38 HAM patients, 17 patients with intermediate syndromes, and 33 asymptomatic carriers. Fecal samples were collected and analyzed using Illumina MiSeq sequencing to assess bacterial composition and diversity. Functional analysis was performed to identify differentially enriched gene categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) modules. Significant dysbiosis was observed in HTLV-1-infected individuals, characterized by reduced bacterial diversity, an inverted Firmicutes/Bacteroidetes ratio, and specific changes in bacterial genera. Notably, HAM patients exhibited decreased Faecalibacterium and increased Ruminococcus_g2 abundance. These associations should be interpreted with caution, as patient cohorts were significantly older and differed in sex distribution from healthy controls. Functional analysis revealed 13 differentially enriched gene categories and five KEGG modules that were more abundant in HAM patients, indicating alterations in metabolic processes. These findings provide the first comprehensive insight into gut microbiome changes associated with HTLV-1 infection and disease progression. This study provides the first comprehensive insight into gut microbiome changes associated with HTLV-1 infection and disease progression. The identified microbial signatures and functional alterations highlight potential diagnostic and therapeutic targets for HTLV-1-associated diseases, particularly HAM. These findings open new avenues for further research and clinical applications.},
}

@article {pmid41436826,
year = {2025},
author = {Biţă, A and Turcu-Ştiolică, A and Scorei, IR and Pisoschi, CG and Biţă, CE and Rău, G and Ciocîlteu, MV and Ştefănescu, S and Dincă, L and Neamţu, J and Rogoveanu, I and Mogoşanu, GD and Gheonea, DI},
title = {Targeting biological age with bioactive, microbiota-accessible nutritional complexes: a pilot study on healthspan extension in medically healthy adults.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1901},
pmid = {41436826},
issn = {2045-2322},
support = {The Article Processing Charges were funded by the University of Medicine and Pharmacy of Craiova, Romania.//Universitatea de Medicină şi Farmacie din Craiova/ ; },
abstract = {UNLABELLED: Microbiota-accessible nutritional complexes (MAC), a formulation comprising prebiotics, postbiotics, autophagy stimulators, senolytic activators, and natural probiotics, may influence systemic biomarkers and biological aging in healthy individuals. This pilot interventional study aimed to evaluate the effects of a 60-day MAC supplementation on serum biomarkers and biological age (BioAge) in medically healthy adults. Methods: Of 13 screened, 12 enrolled; 3 were excluded from the final analysis. Nine participants (five females, four males; mean age 61 ± 9.29 years) completed 60 days of daily MAC supplementation and were included in the analyses. Serum biomarkers were measured at baseline and post-intervention. BioAge was estimated using three machine-learning regressors: Support Vector Regression (SVR), Random Forest (RF), and eXtreme Gradient Boosting (XGBoost). Feature importance analysis was conducted to identify key predictors of BioAge. Results: No adverse events occurred. A significant reduction in high-sensitivity C-reactive protein (hs-CRP) levels was observed from 2.66 ± 4.65 to 0.84 ± 0.54 mg/L (-69%; p = 0.009; Cohen’s d ≈ 0.55; post-mean 95% CI: 1.44 to 5.10), indicating decreased systemic inflammation. Lactate dehydrogenase (LDH) also declined significantly from 171.11 ± 21.32 to 159.44 ± 26.86 U/L (-6.8%; p = 0.038; Cohen’s d ≈ 0.22; post-mean 95% CI: 0.97 to 22.37). Other biomarkers, including gamma-glutamyl transferase (GGT), alkaline phosphatase (ALP), and glucose, showed trends toward improvement without reaching statistical significance. Stratified analysis revealed that females experienced a significant reduction in hs-CRP (p = 0.043) and a mild increase in creatinine (p = 0.042), whereas males exhibited non-significant trends toward improved inflammatory and metabolic markers. AI modeling indicated a reduction in BioAge for several participants. The XGBoost model consistently captured moderate improvements (e.g., Participant 7: 3.3 years), while the RF model showed more variability. SVR did not detect significant changes. An independent empirical model confirmed a statistically significant reduction in BioAge post-intervention (p < 0.0001). Top predictors were low-density lipoprotein cholesterol (LDL-C), glucose, and total cholesterol (TC) as key predictors in the RF and SVR models, while ferritin and hs-CRP ranked highest in the XGBoost model. Conclusions: Sixty days of MAC was safe and associated with clinically relevant hs-CRP reductions and small LDH decreases, alongside AI-inferred BioAge improvements most stably detected by XGBoost. Limitations include small sample size (n = 9), single-arm design, 60-day duration, non-fasting sampling, and a multicomponent intervention that precludes mechanistic attribution, with no microbiome/postbiotic readouts. Larger randomized trials with microbiome/metabolomic profiling and pre-registered, externally validated AI pipelines are required to confirm causality. Trial registration: ISRCTN, ISRCTN85957759. Registered 04 February 2025, https://www.isrctn.com/ISRCTN85957759.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-31590-1.},
}

@article {pmid41531549,
year = {2026},
author = {Barnea, ER and Nazareth, A and Purandare, CN and Pinheiro-Borovac, A and Carluccio, RD and Purandare, NC and McAuliffe, FM and , },
title = {Optimizing Maternal Microbiome: Role in Improved Conception and Pregnancy Outcome.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70014},
doi = {10.1002/rmb2.70014},
pmid = {41531549},
issn = {1445-5781},
abstract = {PURPOSE: To evaluate the role of optimizing the maternal microbiome in improving pregnancy outcomes, focusing on preconception and early gestation, and to propose practical diagnostic and preventive strategies, particularly in low- and middle-income countries (LMIC).

METHODS: A comprehensive review of peer-reviewed literature was conducted, analyzing the impact of vaginal, endometrial, gastrointestinal, urinary, and oral microbiomes on fertility and pregnancy. Key factors included microbial dysbiosis, sexually transmitted infections (STIs), and lifestyle interventions. Diagnostic approaches (cultures, gene sequencing) and preventive measures (nutrition, probiotics, vaccinations) were assessed for efficacy in optimizing the microbiome.

RESULTS: An optimized microbiome, particularly with Lactobacillus crispatus dominance, enhances fertility and reduces pregnancy complications like miscarriage, preterm birth, and congenital infections. Dysbiosis, linked to obesity, antibiotic overuse, and poor nutrition, increases STI susceptibility and pregnancy risks. Preconception screening and targeted treatments (e.g., antibiotics for STIs, probiotics) improve outcomes. Nutritional interventions, including Mediterranean diets and supplements, support microbial health. LMIC face challenges due to limited access to care and nutrition, exacerbating adverse outcomes to be addressed.

CONCLUSIONS: Preconception microbiome optimization through diagnostics, lifestyle changes, and targeted therapies significantly improves pregnancy outcomes. Simple, cost-effective measures are critical also in LMIC to prevent and reduce maternal and fetal morbidity and mortality.},
}

@article {pmid41531391,
year = {2026},
author = {Liang, J and Li, S and Dai, Y and Pi, Z and Liu, J and Li, P and Sun, W and Jiang, T and Xu, T and Yu, P},
title = {Integrating Transcriptomics and Gut Microbiota Analysis Reveals the Anti-Osteoporotic Mechanisms of Wine and Oil Co-Processed Epimedium.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71319},
doi = {10.1096/fj.202501534RR},
pmid = {41531391},
issn = {1530-6860},
support = {20230204034YY//Jilin Provincial Scientific and Technological Development Program (Jilin Scientific and Technological Development Program)/ ; 2024128//Administration of Traditional Chinese Medicine of Jilin Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Epimedium/chemistry ; Female ; *Osteoporosis/drug therapy/metabolism/microbiology ; *Transcriptome/drug effects ; Ovariectomy ; *Wine ; *Drugs, Chinese Herbal/pharmacology ; STAT3 Transcription Factor/metabolism ; Mice, Inbred C57BL ; Gene Expression Profiling ; },
abstract = {Wine- and suet oil co-processed Epimedium (WSOEP) is a traditional Chinese herbal preparation produced by processing raw Epimedium with wine and suet oil as adjuvants. Although WSOEP has been used clinically for the treatment of osteoporosis, its precise therapeutic indications and underlying molecular mechanisms remain incompletely defined. This study integrates transcriptomic profiling with gut microbiota analysis to systematically elucidate the anti-osteoporotic efficacy of WSOEP and its mechanistic basis. In a mice model of osteoporosis induced by bilateral ovariectomy (OVX), WSOEP administration significantly attenuated bone loss and improved multiple key bone parameters compared to the Mod group. Mechanistically, WSOEP treatment markedly downregulated SRC protein expression while simultaneously upregulating both total STAT3 and p-STAT3, indicating restoration of the dysregulated SRC/STAT3 signaling axis. Furthermore, WSOEP effectively modulated gut microbial homeostasis by enriching beneficial taxa, including Bacilli, Verrucomicrobiae, and Bacteroidales, while suppressing potentially detrimental lineages such as Proteobacteria, Clostridia, and Akkermansia. This is the first study to demonstrate that WSOEP exerts robust protective effects against OVX-induced osteoporosis through dual modulation of the SRC/STAT3 pathway and the gut microbiome. These findings not only position WSOEP as a promising candidate for osteoporosis therapy but also offer a novel paradigm for multi-component herbal interventions targeting the gut-bone axis in metabolic bone diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Epimedium/chemistry
Female
*Osteoporosis/drug therapy/metabolism/microbiology
*Transcriptome/drug effects
Ovariectomy
*Wine
*Drugs, Chinese Herbal/pharmacology
STAT3 Transcription Factor/metabolism
Mice, Inbred C57BL
Gene Expression Profiling

@article {pmid41531341,
year = {2026},
author = {Mellor, D and McArdle, P and Spiro, A and Stanner, S and Marsland, N and Kudzin, S and Twenefour, D},
title = {Summary of the Development of a Joint Position Statement on Low and No-Calorie Sweeteners (LNCS) From the British Dietetic Association (BDA), British Nutrition Foundation (BNF) and Diabetes UK.},
journal = {Nutrition bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1111/nbu.70044},
pmid = {41531341},
issn = {1467-3010},
abstract = {Low and no-sugar sweeteners (LCNS) are used in the food supply, notably within the beverage industry in many countries, where sugar reduction is a key public health concern. In the UK, following the announcement and implementation of the Soft Drinks Industry Levy (SDIL), nearly 9 out of 10 soft drinks contain < 5 g sugar per 100 mL, most of which now contain LNCS. In 2023, the World Health Organisation (WHO) issued a guideline with a conditional recommendation advising that LNCS should not be used as 'a means of achieving weight control or reducing the risk of non-communicable disease' (NCDs). This recommendation potentially conflicted with existing recommendations from several authoritative sources at the time, including the Diabetes UK position statement published in 2018 (developed in collaboration with the British Dietetic Association, BDA and the British Nutrition Foundation, BNF), as well as information on the NHS website, which suggests that LCNS can be helpful in reducing sugar intake. More recently, a working group comprising the BDA, BNF and Diabetes UK produced an updated insight document. This review included a re-evaluation of the WHO's systematic review and meta-analysis, alongside the Scientific Advisory Committee on Nutrition (SACN) statement on the guideline. The narrative review outlines the relationship between LNCS and a range of public health outcomes, including weight management, dental health, cardiovascular disease, type 2 diabetes (T2D), cancer and related risk markers such as appetite and gut microbiome composition. The insights document also considered the safety of LNCS and their impact on overall dietary quality. The insight document informed a subsequent joint position statement from the three organisations, highlighting research gaps and providing practical guidance for healthcare professionals to support individuals living with obesity and diabetes in reducing sugar intake. It also includes recommendations for policymakers and identifies actions for the food industry. The Position Statement emphasises that, while LNCS may not directly promote weight loss or reduce disease risk, they can serve as a useful tool for reducing sugar intake at both individual and population levels, at least acting as a 'stepping stone' from sugar-sweetened foods and unsweetened food and beverages.},
}

@article {pmid41530974,
year = {2026},
author = {Xu, XY and Wang, CL and Xu, JY and Dong, CJ and Tan, C and He, YX and Hu, HW and Shu, K and Dai, CC and Chen, ZH and Sun, K},
title = {Seed-microbiome interactions: Mechanistic insights and utilization toward seed performance for sustainable agriculture.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101716},
doi = {10.1016/j.xplc.2026.101716},
pmid = {41530974},
issn = {2590-3462},
abstract = {Global climate change poses increasing threats to seed production and thus food security. The seed microbiome plays an essential role in regulating the whole seed life cycle. Specific seed endophytes and spermosphere microorganisms orchestrate the maintenance and termination of dormancy towards the synchronization of germination plasticity to meet agricultural demands. In this review, we summarize recent advances by linking seed-microbiome interactions with seed processes. We review the sources of seed microbiomes and their physiological regulation on dormancy and germination in response to environmental changes with a focus on phytohormone crosstalk. We also discuss the molecular mechanisms by which seed-microbe interactions affect seed destiny. Finally, we explore emerging precision applications of microbiomes in the seed industry by integrating cutting-edge technologies such as microbial seed coatings and artificial intelligence (AI) in seed science and technology. In conclusion, harnessing microbiome-based strategies to manipulate seed life cycle holds immense promise for sustainable food production in a changing global climate.},
}

@article {pmid41530889,
year = {2026},
author = {Bonacolta, AM and Keeling, PJ},
title = {Modern microbialites harbor an undescribed diversity of chromerid algae.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00852-4},
pmid = {41530889},
issn = {2524-6372},
support = {GBMF9201//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.},
}

@article {pmid41530845,
year = {2026},
author = {Liu, CM and Erikstrup, LT and Edslev, SM and Park, DE and Salazar, JE and Aziz, M and Rendboe, AK and Pham, T and Dinh, KM and Roach, K and Onos, A and Sung, E and Weber, NO and Andersen, PS and Ullum, H and Skov, R and Hungate, BA and Stegger, M and Erikstrup, C and Price, LB},
title = {Composition and dynamics of the adult nasal microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02250-3},
pmid = {41530845},
issn = {2049-2618},
abstract = {BACKGROUND: The nasal microbiome, a dynamic assemblage of commensals and opportunistic pathogens, is crucial to human health.

RESULTS: Using cross-sectional data from 1,608 adults and longitudinal sampling of 149 individuals over 8-22 months, we identified nine nasal community state types (CSTs), defined by bacterial density and indicator taxa, with varying stability and transition patterns. Core taxa such as Staphylococcus epidermidis and Cutibacterium acnes were highly stable, while opportunistic pathogens like Staphylococcus aureus and Moraxella catarrhalis had shorter residence times. Interactions between Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum/propinquum were linked to reduced S. aureus colonization. Host factors, including age and biological sex, significantly shaped microbiome dynamics: men exhibited higher bacterial densities and pathogen colonization, while women showed more stable commensal-dominated CSTs. Aging was associated with shifts in CST frequencies, with declining S. aureus and increasing Enterobacterales.

CONCLUSIONS: These findings reveal potential strategies by modulating nasal microbiome dynamics to reduce pathogen colonization and improve health. Video Abstract.},
}

@article {pmid41530829,
year = {2026},
author = {Yan, D and Yu, Y and Liang, C and Cui, Z and Shi, L and Li, G and Ren, C},
title = {Intratumoral microbiome: the double-edged sword in remodeling cancer immunotherapy.},
journal = {Molecular cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12943-025-02566-6},
pmid = {41530829},
issn = {1476-4598},
support = {82172345//National Natural Science Foundation of China/ ; BK20221281//Natural Science Foundation of Jiangsu Province/ ; SBJC22003//Crosscooperation project of Subei Peoples' Hospital of Jiangsu Province/ ; },
abstract = {Emerging evidence reveals that intratumoral microbial (ITM) communities within the tumor immune microenvironment (TIME) critically influence tumor progression and immunotherapy response. Studies have shown that resident bacteria within tumors, such as Sphingobacterium multivorum, regulate the secretion of chemokines like CCL20 and CXCL8, promoting the infiltration of regulatory T cells (Tregs) and inhibiting the function of cytotoxic T cells (CD8[+] T cells)-thereby weakening the efficacy of immune checkpoint inhibitors. Additionally, microbial metabolites may serve as potential biomarkers for predicting sensitivity to immunotherapy. Concurrently, engineered bacteria (e.g., oncolytic mineralizing bacteria) demonstrate significant antitumor effects by activating innate immunity and enhancing antitumor-specific immune responses, providing new strategies to overcome immunotherapy resistance. These findings highlight the dual role of ITM in tumor immune evasion and immunotherapy sensitivity, laying an important theoretical foundation for developing novel immunotherapy strategies targeting tumoral microbiota metabolism.},
}

@article {pmid41530817,
year = {2026},
author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y},
title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {33},
pmid = {41530817},
issn = {1749-8546},
support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; },
abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.

PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.

METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.

RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.

CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.},
}

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41530658,
year = {2026},
author = {Kaloterakis, N and Braun-Kiewnick, A and Rashtbari, M and Giongo, A and Babin, D and Zamberlan, PM and Razavi, BS and Smalla, K and Reichel, R and Brüggemann, N},
title = {Bacillus seed coating mitigates early growth reduction in successive winter wheat without altering rhizosphere bacterial and archaeal communities.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08128-2},
pmid = {41530658},
issn = {1471-2229},
abstract = {The soil legacy of successively grown winter wheat (WW) often leads to lower plant growth and yield. In this study, we assessed the effect of Bacillus pumilus seed inoculation on the early growth of successively grown WW. We conducted an outdoor experiment using newly designed temperature-regulated rhizotrons. WW was grown in soil from two rotational positions, i.e., first WW after oilseed rape (W1) and second WW after oilseed rape (W2), until the end of tillering. We measured several plant and soil biochemical parameters. In addition, amplicons of the 16S rRNA gene were sequenced to account for bacterial and archaeal community shifts in the rhizosphere, and functional genes involved in the nitrogen cycle were quantified to estimate possible changes in N cycling due to B. pumilus inoculation. B. pumilus seed coating significantly compensated for the early growth reduction of W2, and this effect was primarily linked to changes in root plasticity with a higher root length density and a smaller specific root length in inoculated W2 compared with non-inoculated W2. There was a higher LAP activity in the rhizosphere of inoculated W2 plants than in the rhizosphere of non-inoculated W2 plants and this was followed by a reduction in soil NO3[-], most probably due to an enhanced plant N uptake capacity. This was also shown in the increased potassium content of the inoculated W2 plants compared with their non-inoculated counterparts. B. pumilus seed coating did not influence the bacterial and archaeal alpha and beta diversity, but differential abundance analysis identified differences in the relative abundance of certain taxa between non-inoculated and inoculated W2. While B. pumilus seed coating significantly improved root growth and nutrient uptake in W2, this was not accompanied by a higher absolute abundance of bacterial or archaeal genes involved in N-cycling. Our study suggests that certain plant-beneficial microbes can reverse the negative plant-soil feedback in successive WW rotations and provides strong evidence of B. pumilus seed coating to promote WW productivity under such rotations.},
}

@article {pmid41530607,
year = {2026},
author = {Miller, CB and Bader, GA and Kay, CL},
title = {Fecal Microbiota Transplantation in 2025: Two Steps Forward, One Step Back.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {5},
pmid = {41530607},
issn = {1534-312X},
mesh = {*Fecal Microbiota Transplantation/trends/methods ; Humans ; *Irritable Bowel Syndrome/therapy ; *Clostridium Infections/therapy ; *Inflammatory Bowel Diseases/therapy ; },
abstract = {PURPOSE OF REVIEW: This review summarizes the history and current landscape of fecal microbiota transplantation (FMT), with an emphasis on use of the therapy for Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS). We clarify indications, evidence, and current recommendations for FMT-highlighting major advances and minor setbacks that have led to the state of FMT in 2025.

RECENT FINDINGS: After decades of steady progress, the U.S. Food and Drug Administration (FDA) approved the first FMT-based therapies: fecal microbiota, live-jslm and fecal microbiota spores, live-brpk-in 2022 and 2023, respectively. The 2024 American Gastroenterological Association (AGA) Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases made specific recommendations for conventional FMT and these FDA-approved therapies for multiple CDI presentations, as well as for IBD and IBS. Conventional FMT remains an option for CDI; however, OpenBiome's halt of shipped, frozen FMT preparations on December 31, 2024, has made access more challenging in 2025. Although first reported almost seventy years ago, extensive efforts over the last two decades have placed FMT in routine algorithms for many patients with CDI. While understanding of the intestinal microbiome's role in other gastrointestinal conditions is expanding, and FMT may modulate these pathways, additional evidence is needed before FMT becomes routine outside CDI.},
}

*Fecal Microbiota Transplantation/trends/methods
Humans
*Irritable Bowel Syndrome/therapy
*Clostridium Infections/therapy
*Inflammatory Bowel Diseases/therapy

@article {pmid41530574,
year = {2026},
author = {Deng, YH and Liu, Q and Luo, XQ},
title = {The gut-kidney axis in pediatric acute kidney injury: a review of pathophysiological mechanisms and therapeutic frontiers.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41530574},
issn = {1432-198X},
support = {2024JJ6595//Natural Science Foundation of Hunan Province/ ; },
abstract = {Acute kidney injury (AKI) is a frequent and severe condition in hospitalized children, leading to significant morbidity, mortality, and long-term risk of chronic kidney disease. This review explores the gut-kidney axis, a concept describing the bidirectional relationship between the gut microbiome and kidney function, as a critical driver of pediatric AKI. In critically ill children, interventions such as broad-spectrum antibiotics and necessary nutritional support strategies (e.g., parenteral nutrition or fasting) can cause profound gut microbial imbalance (dysbiosis). This dysbiosis initiates a deleterious feedback loop, exacerbating kidney injury. Key mechanisms include the disruption of the intestinal barrier (leaky gut), which allows bacterial endotoxins to enter the bloodstream, triggering renal inflammation via Toll-like receptor 4 signaling. Concurrently, the dysbiotic gut increases production of directly nephrotoxic gut-derived uremic toxins, such as indoxyl sulfate and p-cresyl sulfate, while failing to produce protective anti-inflammatory metabolites like short-chain fatty acids. While therapies targeting the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, are theoretically promising, their clinical use in pediatric AKI is unsupported by evidence and carries substantial risks, particularly iatrogenic infection. A significant knowledge gap exists due to a relative lack of pediatric-specific clinical research. The conclusion emphasizes an urgent need for longitudinal, multi-omics studies in children to understand this axis, identify functional biomarkers, and develop safe, targeted therapies to improve outcomes.},
}

@article {pmid41530533,
year = {2026},
author = {Ning, J and Zhao, Y and Lu, G and Wei, L},
title = {Melatonin Alleviated Cadmium Induced Microbiota-Gut-Brain Disorder in Adult Zebrafish: Insights from Transcriptomic and Microbiome Analysis.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
pmid = {41530533},
issn = {1559-0720},
support = {KYQD(ZR)21138//Scientific Research Start-up Fund of Hainan University/ ; },
abstract = {Cadmium (Cd), a toxic metal, poses significant threats to ecological and human health due to its neurotoxic and gut toxicity effects. However, the mechanisms by which Cd disrupts brain-gut axis interactions remain unclear, and strategies to mitigate these effects are limited. Melatonin (MT), known for its anti-inflammatory and antioxidant properties, has shown promise in counteracting heavy metal toxicity. This study investigated the protective mechanisms of MT against Cd-induced toxicity in adult zebrafish using histopathological analysis, 16 S rRNA sequencing, RNA-sequencing, and qRT-PCR. Results showed that MT significantly alleviated Cd-induced structural damage in brain spongiosa and restored intestinal villi integrity. 16 S rRNA sequencing revealed that MT reduced pathogenic bacteria and increased beneficial bacteria in the gut microbiota. Transcriptomic analysis identified 31 differentially expressed genes (DEGs) in brain, KEGG enrichment analysis showed these DEGs are associated with neurodegenerative diseases pathways. Concurrently, 8 DEGs in gut were linked to oxidative phosphorylation signaling pathways. Correlation analysis showed pathogenic Legionella and Aeromonas were positively correlated with htr2b, il21r.2, il2rb, il21r.2, cyp46a1.3 cyp2ad3, cyp46a1.3 in brain, Candidatus_Protochlamydia was positively correlated with il7r, drd3 in gut, those are down regulated DEGs, whereas beneficial Acinetobacter and Achromobacter were positively correlated with cyp2 × 8 in gut, this is up regulated DEG. These suggests that Legionella, Candidatus_Protochlamydia, Achromobacter and Acinetobacter may be key bacterial that mediate the MT reduction in neurotoxicity and immunotoxicity induced by Cd. These findings highlight MT's potential to mitigate Cd-induced toxicity by modulating the gut microbiota, offering therapeutic insights for reducing Cd toxicity risks in aquaculture.},
}

@article {pmid41530470,
year = {2026},
author = {El-Sayed, ASA and Mohamed, NZ and Safan, S and Yassin, MA and Shaban, L and Shindia, AA and Shad Ali, G and Sitohy, MZ},
title = {Retraction Note: Restoring the Taxol biosynthetic machinery of Aspergillus terreus by Podocarpus gracilior Pilger microbiome, with retrieving the ribosome biogenesis proteins of WD40 superfamily.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1752},
doi = {10.1038/s41598-026-35501-w},
pmid = {41530470},
issn = {2045-2322},
}

@article {pmid41530275,
year = {2026},
author = {Wöber, D and Wernicke, M and Cerqueira, F and Wechselberger, K and Hansel-Hohl, K and Manhalter, S and Molin, EM},
title = {Intestinal microbiome interactions influence Metarhizium-based biocontrol efficacy against the sugar beet weevil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36038-8},
pmid = {41530275},
issn = {2045-2322},
abstract = {The sugar beet weevil is considered one of the most economically important insect pests in sugar beet cultivation. A promising biological control strategy involves the natural interaction between entomopathogenic fungi and arthropods. The successful application of M. brunneum as part of integrated biological control strategies against the sugar beet weevil has already been demonstrated resulting in lethal mycosis. However, the efficacy of this strain is affected by multiple factors. The intestinal microbiome of insects harbours beneficial microbes that possess various functions, such as defence mechanisms against insect-pathogens. Thus, investigating intestinal microbial interactions in combination with Metarhizium-application could reveal microbes that modulate susceptibility to pathogens. This study investigated whether intestinal microbial interactions influence mycosis caused by M. brunneum and M. robertsii. We analysed the intestinal microbiome of both treated and untreated sugar beet weevils, distinguishing between mycotic and non-mycotic individuals at the time of death. Notably, Pantoea and Enterobacter were significantly associated with mycotic individuals and may act as a potential antagonist to Metarhizium. In contrast, healthy individuals harboured diverse microbial communities that may provide a protective barrier against entomopathogens. However, the intestinal microbiome of non-mycotic specimens also comprised genera with presumed insecticidal properties, including Serratia, Penicillium and Cladosporium. The last two were also observed in the intestines of male individuals, which were generally at a higher risk of mortality. Further investigation is needed to confirm their insecticidal potential in the sugar beet weevil. A combined application could improve the efficacy of Metarhizium-based biocontrol, contributing to more sustainable pest management strategies.},
}

@article {pmid41530269,
year = {2026},
author = {Ludyga, S and Pedrini, L and Sarbach, L and Topyürek, B and Köhler, H and Furlano, R and Légeret, C},
title = {A comparative study of cognitive function among children with coeliac disease and healthy controls.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34500-7},
pmid = {41530269},
issn = {2045-2322},
abstract = {Coeliac disease (CD) is an immune-mediated systemic disorder triggered by gluten in genetically predisposed patients. The only available treatment is a strict life long gluten-free diet (GFD), which has been linked to a reduced quality of life (QOL) and causes alterations in the gastrointestinal microbiome. Abnormal compositions of the microbiome are now recognized as factors in the pathogenesis of neuropsychological disorders via gut-brain-axis. The aim of this study was to assess the QOL and the mental performance of children and teenagers with CD and compare it to healthy controls (HC). Children between the ages of 6 and 18 years with CD and age-and-sex-matched healthy controls (HC) filled in a questionnaire to assess QOL and performed the Flanker task, a standardized test to assess cognitive performance. A total of 444 children (210 CD patients and 234 HC) were included in the study. CD patients reported feeling statistically significantly more comfortable at school (p = 0.02) and being less exposed to bullying (p = 0.01); otherwise, no difference in QOL and sleep pattern was found compared to HC. The analysis of Flanker task revealed no difference in accuracy (HC: mean 0.97, CI 0.96-0.97; CD patients: mean 0.96, CI 0.96-0.97; p = 0.79), but there was a difference in reaction time (HC: mean 495.4 ms, CI 476.34-514.46; CD patients: mean 514.03, CI 493.68-534.39; p = 0.19). Children with CD in Switzerland have the same QOL as HC. There was a statistically non-significant difference in reaction time, therefore this study suggests that a GFD is not associated with impaired cognitive function.},
}

@article {pmid41530203,
year = {2026},
author = {Huang, X and Xu, B and Lei, Y and Qin, H and Zheng, J and Xu, Y and Zhao, D and Su, J and Li, J and Zhao, J},
title = {Bacillus velezensis mitigates deoxynivalenol-induced intestinal inflammation and liver injury via modulating the gut microbiota.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00707-9},
pmid = {41530203},
issn = {2396-8370},
abstract = {Deoxynivalenol (DON), a prevalent mycotoxin in food and feed, induces gastrointestinal and liver damage. The potential probiotic Bacillus velezensis may mitigate DON toxicity, though its precise mechanisms remain unknown. Our study demonstrates that B. velezensis WMCC10514 effectively survives and degrades DON within simulated gastrointestinal fluid. Fluorescently labeled WMC10514-GFP colonized murine intestines and persisted in simulated intestinal fluid (SIF), confirming its colonization capacity. In vivo, WMCC10514 alleviated DON-induced anorexia, restored murine growth, and reduced liver injury. Furthermore, the strain elevated ZO-1 and Occludin expression, enhanced intestinal barrier integrity and reduced DON accumulation in host tissues. Integrated transcriptomic and microbiome analyses revealed that the strain suppressed TLR4/NF-κB pathway activation in the intestine and liver, increased Lactobacillus abundance, restored SCFAs level, and modulated liver energy metabolism. These findings elucidate B. velezensis's role in mitigating mycotoxin toxicity through gut microbiota-driven regulation of the gut-liver axis.},
}

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68255-6},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

@article {pmid41530012,
year = {2026},
author = {Lechien, JR},
title = {Emerging Microbiome Findings in Laryngopharyngeal Reflux Disease: A Scoping Review.},
journal = {Journal of voice : official journal of the Voice Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jvoice.2025.12.023},
pmid = {41530012},
issn = {1873-4588},
abstract = {OBJECTIVE: To review the current literature linking laryngopharyngeal reflux disease (LPRD) with microbiome impairments.

METHODS: Two independent investigators conducted a systematic literature search for studies reporting microbiome findings in LPRD patients through PubMed, Scopus, and Cochrane Library databases. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement and the Population, Intervention, Comparison, Outcome, Timing, and Setting (PICOTS) framework were followed. A methodological bias analysis was conducted with the Tool to Assess the Risk of Bias in Cohort Studies.

RESULTS: Of the 585 identified papers, eight studies met the inclusion criteria, including 245 patients with suspected or confirmed LPRD. Two studies using objective diagnostic approaches confirmed that LPRD is associated with significantly reduced alpha and beta diversities compared to controls. Streptococcus and Actinomyces emerged as key taxa consistently differentiating LPRD patients from controls across multiple studies. However, significant methodological heterogeneity was observed in LPRD diagnosis, microbiome assessment methods, and control group definitions.

CONCLUSION: Preliminary literature suggests that patients with suspected or confirmed LPRD exhibit salivary microbiome alterations characterized by reduced diversity and selective microbial shifts. Future high-quality methodological studies are needed to elucidate the mechanistic relationship and clinical consequences of LPRD-related dysbiosis.},
}

@article {pmid41529744,
year = {2026},
author = {Li, J and Tang, G and Xie, Z and Yang, L and Zhou, Z and Guo, K},
title = {Identification of oral microbial biomarkers for prediabetes in young adults: A two-stage population-based study.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113101},
doi = {10.1016/j.diabres.2026.113101},
pmid = {41529744},
issn = {1872-8227},
abstract = {AIM: This study aims to identify oral microbial signatures associated with prediabetes in young adults and to investigate potential oral risk factors for early-onset diabetes, as well as to pinpoint targets for monitoring and intervention.

METHODS: The study involved a large cross-sectional analysis of 3,142 participants from two independent cohorts. The discovery cohort consisted of 334 prediabetes cases and 1,266 controls, while the validation cohort had 325 prediabetes cases and 1,217 controls. We compared the basic and clinical characteristics of the different groups. Additionally, 16S rRNA gene sequencing was conducted on oral rinse samples.

RESULTS: Prediabetes-enriched taxa comprised Bacteroidetes, Prevotella_7, and Veillonella. In contrast, normoglycemic controls showed a higher presence of Firmicutes and Streptococcus. The combined models, constructed from indicators identified by LASSO regression, including BMI, HOMA-IR, and specific microbiota (Prevotella_7 or Veillonella), demonstrated discriminatory performance. In the discovery set, the AUC values were 0.761 and 0.758, respectively, whereas in the validation set, the AUC values were 0.693 and 0.696, respectively.

CONCLUSION: Reproducible alterations and enrichment of Prevotella_7 and Veillonella are linked to prediabetes in young adults. Furthermore, the combined interaction between specific bacterial genera and core clinical indicators may be crucial in the development of prediabetes in young individuals.},
}

@article {pmid41529362,
year = {2026},
author = {Le, VV and Taj, M and Esterhuizen, M and Kim, YJ and Jung, MY and Lee, SA},
title = {Shape-driven toxicity of polystyrene microplastics: Impacts on physiology and gut microbiota in Daphnia magna.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119218},
doi = {10.1016/j.marpolbul.2026.119218},
pmid = {41529362},
issn = {1879-3363},
abstract = {Microplastic pollution has emerged as a global issue that poses serious risks to aquatic ecosystems. Although Daphnia spp. are widely used as model organisms to study the effects of microplastics on their fitness, their microbiome response remains largely unexplored. This study investigated the effects of ground polystyrene microplastics (G-PS; fragments below the EC10 value) and commercial polystyrene microplastics (C-PS; beads below the EC10 value) on the physio-biochemical responses and gut microbiota of Daphnia magna. The toxicity of polystyrene microplastics to D. magna was shape-dependent, with G-PS being more toxic than C-PS. Exposure to G-PS and C-PS triggered Reactive oxygen species (ROS) production in D. magna. Although G-PS increased the abundance of both harmful (Fusobacterium) and beneficial bacteria (Blautia and Subdoligranulum) in the gut microbiota of Daphnia, C-PS only increased the abundance of beneficial bacteria (Lactobacillus, Ligilactobacillus, and Aerococcus), which may mitigate the toxicity of microplastics. Functional predictions based on amplicon sequencing suggested that altered microbiota may support the growth of D. magna by modulating associated metabolic pathways. D. magna exposed to G-PS exhibited a significantly higher abundance of gut microbiota pathways and enzymes associated with the detoxification of harmful compounds than those exposed to C-PS. This suggests that the higher toxicity of G-PS requires a stronger adaptive response from the gut microbiota. Overall, these findings highlight microplastic shape as a key factor influencing toxicity in D. magna and its associated microbiota.},
}

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}