@article {pmid41795148,
year = {2026},
author = {Shabana, H and Rodriguez-Wallberg, KA},
title = {The microbiome research in obstetrics and gynecology is getting attention-Some reasons why.},
journal = {Acta obstetricia et gynecologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/aogs.70184},
pmid = {41795148},
issn = {1600-0412},
}

@article {pmid41795122,
year = {2026},
author = {Kerr, EN and Yu, L and Hesse, RD and Roberts, CN and Bulone, V and Meyer, L and Edwards, RA and Doane, MP and Dinsdale, EA},
title = {Interactions of Mucus Monosaccharides and the Epidermal Microbiome in Four Benthic Elasmobranchs.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70303},
pmid = {41795122},
issn = {1758-2229},
support = {//Royal Society for South Australia/ ; RC2DK116713/NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; },
mesh = {Animals ; *Mucus/chemistry/metabolism/microbiology ; *Monosaccharides/metabolism/analysis ; *Microbiota ; *Epidermis/microbiology ; *Elasmobranchii/microbiology/metabolism ; Bacteria/genetics/classification/metabolism/isolation & purification ; Skin Microbiome ; },
abstract = {Epidermal mucus is a complicated mixture of macromolecules which acts as the first line of defence for organisms against abrasions and infections. We quantified the carbohydrate (monosaccharide) composition of the mucus from four Elasmobranchii hosts, including eagle rays (Myliobatis tenuicaudatus), Port Jackson sharks (Heterodontus portusjacksoni), Australian angelsharks (Squatina australis) and whitespotted skates (Dentiraja cerva). Elasmobranchii had low amounts of mucus and a low proportion of carbohydrates (< 10%) compared with other marine organisms. Four key monosaccharides: glucose, glucosamine, galactose and fucose, were identified in mucus samples. Hosts exhibited distinct, species-specific monosaccharide signatures. We identified key carbohydrate microbial genes from host and water microbiomes. Elasmobranch microbiomes had a higher relative abundance of carbon utilisation genes compared to the water column and contained gene pathways for the utilisation of specific monosaccharides found in host mucus, suggesting that the host mucus was a regulator of the microbiome. Elasmobranch epidermal microbiomes have the genetic machinery required for detecting, transporting and metabolising monosaccharides and other carbohydrates present in the host mucus, demonstrating the selective nature of Elasmobranch epidermal mucus.},
}

Animals
*Mucus/chemistry/metabolism/microbiology
*Monosaccharides/metabolism/analysis
*Microbiota
*Epidermis/microbiology
*Elasmobranchii/microbiology/metabolism
Bacteria/genetics/classification/metabolism/isolation & purification
Skin Microbiome

@article {pmid41794853,
year = {2026},
author = {Zhang, Z and Yu, L and Wu, C and Guo, J and Zhu, L and Wang, J and Zhou, C},
title = {Soil acidification dismantles a citrulline-mediated microbe-metabolite-host defense axis in watermelon, exacerbating Fusarium wilt.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00951-7},
pmid = {41794853},
issn = {2055-5008},
support = {20250586//where they are referenced/ ; 2023AH020024, gxyq2022053//Natural Science Foundation of Universities in Anhui Province/ ; XK-XJGY003//University-Level Advanced Discipline/ ; DTR2024033//Discipline (Major) Leader Development Program/ ; },
abstract = {Soil acidification disrupts the structure and function of soil microbiomes, resulting in increased vulnerability to soil-borne pathogens. While the link between soil acidification and disease susceptibility is well-established, the mechanisms underlying the suppression of plant defense remain poorly understood. In this study, we found that soil acidification perturbed the co-evolved assembly process of endophytic microbiomes in watermelon roots, leading to the collapse of a critical microbe-metabolite-host defense axis essential for resistance against Fusarium oxysporum f. sp. niveum (FON). Integrated field surveys and multi-omics analyses revealed that acidification-induced dysbiosis in the root endophytic microbiomes, characterized by the depletion of keystone Pseudomonas species (Pseudomonadaceae), strongly correlated with increased Fusarium wilt incidence. Central to this interaction was citrulline, a metabolite produced by root Pseudomonas endophytes that functioned as a symbiotic effector promoting bacterial colonization and a defense modulator inhibiting FON-induced oxidative burst. Disruption of citrulline biosynthesis abolished these protective effects, whereas exogenous citrulline application restored disease resistance. These findings underscored the role of root endophyte-derived citrulline in sustaining microbial fitness and plant defense, revealing a tripartite interaction impacted by soil acidification. Collectively, this study provides insights for developing microbiome-based strategies to enhance sustainable crop protection in degraded agroecosystems.},
}

@article {pmid41794812,
year = {2026},
author = {Müller, F and Wang, H and Reinhard, A and Omirbekova, A and Berzhanova, R and Mukasheva, T and Urich, T and Mikolasch, A},
title = {The hydrocarbon-degrading bacteria and fungi in oil contaminated soils of Kazakhstan: microbiome composition, enrichment, isolation and bioremediation potential.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00866-y},
pmid = {41794812},
issn = {2524-6372},
abstract = {BACKGROUND: Oil contamination in soils causes significant environmental impacts and risks to human health. Oil components can be naturally reduced by indigenous microorganisms, that are able to degrade such substrates. We used culture-independent and culture-dependent methods to examine the prokaryotic and the eukaryotic microbiome of different heavily oil contaminated soils in Kazakhstan. Bacteria and fungi were enriched and isolated from four soils contaminated with crude oil or hydrocarbons. Aliphatic, aromatic and condensed aromatic model hydrocarbons of crude oil and crude oil itself were used as substrates for the enrichment and the isolation experiments. The enrichment process was accompanied by culture-independent tests.

RESULTS: The results of the Illumina sequencing of the contaminated soils and the enrichment cultures were compared with the results of the culture-dependent isolation and determination of bacterial, yeast and filamentous fungal strains. The majority of these 110 strains from 45 different genera belong to well-described hydrocarbon degraders like Bacilli and Rhodococci as well as to Achromobacter, Gordonia, Pseudomonas, Stenotrophomonas, Aspergillus, Exophiala, Fusarium, Meyerozyma, Penicillium and Trichoderma species. The most abundant species was the ascomycetal yeast Meyerozyma guilliermondii followed by strains of the bacterial genus Peribacillus. Furthermore, we combined the microbiome insights on the enrichment procedures and the isolation of bacteria, yeasts and filamentous fungi with the in-fact degradation potential of the isolated species based on substrate consumption and metabolite formation. In addition to the well-described hydrocarbon degraders, the utilization spectrum of less-studied strains of the genera Leifsonia, Neorhizobium, Purpureocillium, Rhodotorula and Sarocladium could be broadened.

CONCLUSION: In the end a complex overview of the indigenous microorganisms and their degradation ability of crude oil components emerged and demonstrates the great potential of bioremediation for Kazakhstan soils.},
}

@article {pmid41794696,
year = {2026},
author = {Amsalu, A and Haidari, H and Mirco, B and Rudolph-Stringer, V and Walter, S and Antipov, A and Murrell, DF and Kopecki, Z},
title = {Characterisation of the wound microbiome and antimicrobial resistance profiles in clinical isolates from epidermolysis bullosa patients.},
journal = {Orphanet journal of rare diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13023-026-04295-5},
pmid = {41794696},
issn = {1750-1172},
support = {Channel 7 Children's Research Foundation//Channel 7 Children's Research Foundation/ ; DEBRA Australia//DEBRA Australia/ ; Epidermolysis Bullosa Medical Research Foundation//Epidermolysis Bullosa Medical Research Foundation/ ; },
}

@article {pmid41794620,
year = {2026},
author = {Iftikhar, N and Konig, I and Brammer-Robbins, E and Kozuch, M and Bisesi, JH and Hashmi, I and Martyniuk, CJ},
title = {Corrigendum to "Environmentally relevant levels of sulfamethoxazole (SMX) alter the skin and gastrointestinal microbiome of adult male and female zebrafish (Danio rerio)" [Aquatic Toxicology, Volume 288 (2025) 107546].},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {},
number = {},
pages = {107767},
doi = {10.1016/j.aquatox.2026.107767},
pmid = {41794620},
issn = {1879-1514},
}

@article {pmid41794500,
year = {2026},
author = {Hua, Q and Meng, Y and Hu, J and Wei, Y and Yi, H and Liang, X and Zhang, L and Zhang, Z},
title = {ILA-producing bifidobacterium bifidum ameliorates chronic kidney disease via AHR signaling by modulating the gut-kidney axis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118638},
doi = {10.1016/j.foodres.2026.118638},
pmid = {41794500},
issn = {1873-7145},
mesh = {Animals ; *Renal Insufficiency, Chronic/therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; *Gastrointestinal Microbiome ; Signal Transduction ; Mice ; *Probiotics/pharmacology ; *Bifidobacterium bifidum/metabolism/genetics ; *Indoles/metabolism ; Kidney/metabolism ; Male ; Disease Models, Animal ; *Lactic Acid/metabolism/analogs & derivatives ; Dysbiosis ; Mice, Inbred C57BL ; *Basic Helix-Loop-Helix Proteins/metabolism ; },
abstract = {Chronic kidney disease (CKD) is associated with gut microbiota dysbiosis and disruption of the gut-kidney axis, making probiotics-which can modulate host metabolism and the gut microbiome-a highly promising intervention strategy. Building on this premise, this study used High-Performance Liquid Chromatography (HPLC) to screen 39 candidate strains and successfully isolate two high indole-3-lactic acid (ILA)-producing strains of Bifidobacterium bifidum: FL228.1 and ZL.1. Whole-genome sequencing subsequently confirmed that both strains possess the aromatic lactate dehydrogenase (Aldh) gene, which is essential for ILA biosynthesis. The strains were then evaluated in an adenine-induced CKD mouse model. ZL.1 exhibited pronounced efficacy: it not only improved renal injury, restored gut barrier function, and corrected dysbiosis, as evidenced by an increased relative abundance of Muribaculaceae and a decreased abundance of Dubosiella, but also significantly elevated the level of the key metabolite ILA. In-depth mechanistic analysis revealed that ILA exerts its effects by activating the aryl hydrocarbon receptor (AHR) signaling pathway, which in turn inhibits NLRP3 inflammasome activation, thereby achieving the dual benefit of mitigating intestinal inflammation and alleviating renal fibrosis. Targeted metabolomics analysis supported the conclusion that high ILA production is a critical characteristic for B. bifidum's modulation of the gut-kidney axis. In contrast, the FL228.1 strain showed moderate effects, with its specific mechanism remaining unclear. In conclusion, our study suggests that ILA-producing B. bifidum may ameliorate CKD by regulating the gut-kidney axis via ILA and AHR signaling. This indicates a potential probiotic strategy targeting tryptophan metabolism for CKD.},
}

Animals
*Renal Insufficiency, Chronic/therapy/microbiology/metabolism
*Receptors, Aryl Hydrocarbon/metabolism
*Gastrointestinal Microbiome
Signal Transduction
Mice
*Probiotics/pharmacology
*Bifidobacterium bifidum/metabolism/genetics
*Indoles/metabolism
Kidney/metabolism
Male
Disease Models, Animal
*Lactic Acid/metabolism/analogs & derivatives
Dysbiosis
Mice, Inbred C57BL
*Basic Helix-Loop-Helix Proteins/metabolism

@article {pmid41794479,
year = {2026},
author = {Baheti, R and Deshkar, S and Jadhav, S and Mule, K and Jha, A and Giram, P and Mahore, J},
title = {Interplay of probiotics, prebiotics, synbiotics and postbiotics: a review of their therapeutic potential for gastrointestinal inflammation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118598},
doi = {10.1016/j.foodres.2026.118598},
pmid = {41794479},
issn = {1873-7145},
mesh = {*Prebiotics/administration & dosage ; Humans ; *Probiotics/therapeutic use/administration & dosage ; *Synbiotics/administration & dosage ; Gastrointestinal Microbiome ; Animals ; *Inflammation ; *Inflammatory Bowel Diseases/microbiology/therapy ; *Gastrointestinal Diseases/therapy ; },
abstract = {Gastrointestinal inflammation is a multifaceted condition deeply connected to the gut microbiota. The prebiotics, probiotics, synbiotics and their metabolites, termed postbiotics, have been explored extensively in the past as a novel approach in managing inflammatory bowel disorders. Prebiotics, probiotics, and postbiotics derived from food sources play crucial roles in modulating the gut microbiota and significantly impact gastrointestinal inflammation. Prebiotics are non-digestible, selectively fermented dietary fibers found in foods such as inulin-type fructans and galacto-oligosaccharides that promote the growth of beneficial gut bacteria like bifidobacteria and lactobacilli. These prebiotics contribute to the production of short-chain fatty acids which possess anti-inflammatory properties and enhance immune regulation in the gut. Together, prebiotics, probiotics, and postbiotics synergistically maintain and restore gastrointestinal health by modulating the gut microbiome composition, enhancing production of anti-inflammatory metabolites, strengthening the intestinal barrier, and regulating immune responses. These interventions show promise in preventing and managing gastrointestinal inflammatory conditions such as irritable bowel syndrome, Crohn's disease, and ulcerative colitis by counteracting dysbiosis and mucosal inflammation. Drawing from recent preclinical and clinical studies, these strategies have shown promising results in managing gastrointestinal inflammation. Despite the compelling evidence, significant challenges remain. These include the considerable variability of host responses, the necessity for standardized strains and precise dosages, and a lack of a unified regulatory framework. This comprehensive review integrates the current understanding of prebiotics, probiotics, synbiotics, and postbiotics, highlighting their mechanistic interplay and highly promising role in managing gastrointestinal inflammation. It provides an in-depth discussion on current limitations and future directions for research and clinical application.},
}

*Prebiotics/administration & dosage
Humans
*Probiotics/therapeutic use/administration & dosage
*Synbiotics/administration & dosage
Gastrointestinal Microbiome
Animals
*Inflammation
*Inflammatory Bowel Diseases/microbiology/therapy
*Gastrointestinal Diseases/therapy

@article {pmid41794478,
year = {2026},
author = {Chiarini, E and Buzzanca, D and Devizia, A and Giordano, M and Dipietro, F and Zeppa, G and Alessandria, V},
title = {Kombucha meets circular economy: A microbiome and metabolite perspective on second fermentation with plant by-products.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118597},
doi = {10.1016/j.foodres.2026.118597},
pmid = {41794478},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Kombucha Tea/microbiology/analysis/economics ; Food Microbiology ; Bacteria/metabolism/classification ; Yeasts/metabolism ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Kombucha is a traditional fermented beverage produced through the fermentation of sugared tea by a symbiotic culture of bacteria and yeasts (SCOBY). In recent years, the valorisation of plant-based by-products as fermentation substrates has gained attention as a sustainable approach to improving both the nutritional and economic efficiency of fermented beverages. The present study investigated the production of kombuchas supplemented with pineapple, fennel, and carrot by-products during the secondary fermentation phase, aiming to evaluate their influence on fermentation dynamics, microbial ecology, and the chemical and aromatic profiles of the final products. The experimental design integrated culture-dependent and culture-independent approaches, including amplicon sequencing, to characterize microbial community composition and evolution throughout fermentation. Chemical profiling was carried out using gas chromatography coupled with quadrupole mass spectrometry (GC-qMS) and high-performance liquid chromatography equipped with diode-array and refractive index detectors (HPLC-DAD/RI). The fermentation process was monitored during both the primary and secondary stages, and a shelf-life assessment was conducted over 14 days of refrigerated storage (4 °C) to evaluate product stability. Microbiological results indicated a predominance of Schizosaccharomyces spp., while Komagataeibacter spp. was the only bacterial genus identified. A significant reduction in α-diversity was observed over time, suggesting selective adaptation of the microbial community to the fermentation environment. β-diversity analysis revealed clear differences among samples collected after 8 and 22 days, reflecting the combined influence of time and substrate composition on microbial succession. Chemical analyses demonstrated an increase in acetic acid concentration and a progressive decline in pH throughout fermentation, consistent with the metabolic activity of acetic acid bacteria. Among volatile organic compounds (VOCs), alcohols and organic acids were the most abundant chemical classes detected. Several VOCs were associated with minor yeast genera, including Hannaella, Galactomyces, Aureobasidium, and Millerozyma, whereas Schizosaccharomyces spp. showed a strong correlation with specific aroma-active compounds, highlighting its key role in defining the sensory characteristics of the beverage. Overall, this study provides new evidence on how different vegetable by-products and microbial consortia influence the development of chemical and aromatic compounds in kombucha. The findings highlight the potential of using by-products as a sustainable, value-added strategy for producing fermented beverages, while also supporting the principles of the circular economy and resource-efficient food systems.},
}

*Fermentation
*Microbiota
*Kombucha Tea/microbiology/analysis/economics
Food Microbiology
Bacteria/metabolism/classification
Yeasts/metabolism
Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry

@article {pmid41794466,
year = {2026},
author = {Huang, S and Ding, H and Su, Y and Chen, Z and He, W and Chen, ZY and Zhu, H},
title = {Alpha-lipoic acid improves intestinal homeostasis and ameliorates colitis through modulation of gut microbiota and production of short chain fatty acids in mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118582},
doi = {10.1016/j.foodres.2026.118582},
pmid = {41794466},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fatty Acids, Volatile/metabolism ; *Thioctic Acid/pharmacology ; *Colitis/chemically induced/drug therapy/microbiology ; Mice, Inbred C57BL ; Male ; *Homeostasis/drug effects ; Mice ; Dextran Sulfate ; Fecal Microbiota Transplantation ; Oxidative Stress/drug effects ; NF-kappa B/metabolism ; Disease Models, Animal ; Antioxidants/pharmacology ; Cytokines/metabolism ; },
abstract = {α-Lipoic acid (ALA) is a natural antioxidant present in both plants and animal foods. It has attracted growing attention for its potential role in maintenance of intestinal homeostasis. This study was to investigate the protective effects of dietary ALA on experimental colitis, and to evaluate its modulating effect on gut microbiome in mice. Male C57BL/6 J mice with dextran sulfate sodium (DSS)-induced acute colitis were administered ALA (40 or 80 mg/kg) dissolved in corn oil. Results showed that dietary ALA ameliorated colitis severity, improved intestinal barrier integrity, and attenuated inflammation by reducing oxidative stress and suppressing NF-κB pathway activation and pro-inflammatory cytokines expression. Moreover, dietary ALA increased the microbial diversity (Shannon index), reshaped gut microbiota composition by suppressing pathogenic bacteria and promoting beneficial taxa such as Akkermansia, and elevated levels of short chain fatty acids (SCFA). Fecal microbiota transplantation (FMT) further confirmed that ALA could modulate gut microbiota and protect against colitis in mice. In conclusion, ALA could effectively maintain the intestinal homeostasis and ameliorate colitis at least in mice. Such protective effect of ALA in gut health was mediated through modulation of gut microbiota and enhancement of SCFA production.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Fatty Acids, Volatile/metabolism
*Thioctic Acid/pharmacology
*Colitis/chemically induced/drug therapy/microbiology
Mice, Inbred C57BL
Male
*Homeostasis/drug effects
Mice
Dextran Sulfate
Fecal Microbiota Transplantation
Oxidative Stress/drug effects
NF-kappa B/metabolism
Disease Models, Animal
Antioxidants/pharmacology
Cytokines/metabolism

@article {pmid41794462,
year = {2026},
author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V},
title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118577},
doi = {10.1016/j.foodres.2026.118577},
pmid = {41794462},
issn = {1873-7145},
mesh = {*Fermentation ; *Vitis/microbiology ; *Wine/microbiology/analysis ; *Mycobiome ; Italy ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metagenomics/methods ; Food Microbiology ; Metabolome ; Kluyveromyces/metabolism ; Multiomics ; },
abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.},
}

*Fermentation
*Vitis/microbiology
*Wine/microbiology/analysis
*Mycobiome
Italy
Metabolomics/methods
Greece
Saccharomyces cerevisiae/metabolism
Metagenomics/methods
Food Microbiology
Metabolome
Kluyveromyces/metabolism
Multiomics

@article {pmid41794383,
year = {2026},
author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G},
title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110327},
doi = {10.1016/j.jnutbio.2026.110327},
pmid = {41794383},
issn = {1873-4847},
abstract = {BACKGROUND: Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains scope for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden.

METHODS: We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45).

RESULTS: Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. Eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population.

CONCLUSIONS: Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.},
}

@article {pmid41794297,
year = {2026},
author = {Wang, T and Binion, B and Alves, JMP and Ridlon, JM},
title = {Characterization of an NADPH-dependent 17ɑ-hydroxysteroid dehydrogenase encoded by the desF gene from the gut bacterium Clostridium scindens VPI 12708.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106982},
doi = {10.1016/j.jsbmb.2026.106982},
pmid = {41794297},
issn = {1879-1220},
abstract = {Epitestosterone (epiT) is the isomer of the androgen testosterone. Historically, the role of epiT has remained unclear. Recently, it has been reported that epiT promotes nuclear androgen receptor (AR)-dependent prostate cancer cell proliferation. The gut bacterium Clostridium scindens VPI 12708 was shown to convert androstenedione (AD) to epiT over three decades ago. The bacterial enzymatic pathways involved in epiT formation have only recently been reported. The desF gene encodes 17α-hydroxysteroid dehydrogenase which converts AD to epiT using NADPH as a cofactor. In this study, we quantitatively characterized DesF kinetic parameters and substrate specificity. The results revealed that the optimal pH for the reductive reaction is 7.0, and for the oxidative reaction it is 7.5 and 8.0. The kinetic analysis showed that for the reductive reaction, the KM was 8.1 ± 1.8µM and the Vmax was 6.4 ± 0.3 µmol·min[-1]·mg[-1]; for the oxidative direction, the KM was 27.3 ± 3.3µM and the Vmax was 7.2 ± 0.3 µmol·min[-1]·mg[-1]. Moreover, the substrate specificity analysis revealed that 11-keto-AD is the most favourable substrate for DesF, and the 17-keto group of 11-keto-AD can be converted to the 17α-hydroxy group. The phylogenetic relation between DesF and other characterized hydroxysteroid dehydrogenases reveals common ancestry with human HSD17B10 and Eggerthella lenta 3β-HSDH. These results are a significant advance in understanding epiT formation by the gut microbiome.},
}

@article {pmid41794153,
year = {2026},
author = {Ma, Y and Ni, Z and Zhu, L and Yang, J and Zhang, Y and Liu, W and Wang, R and Sun, Y and Liu, J and Zhang, P and Yu, L and Huangfu, C and Gao, Y and Zhou, W},
title = {Skin commensal Cutibacterium acnes alleviates UVB-induced solar dermatitis via ceramide-mediated TLR4-MyD88-NF-κB.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2026.02.074},
pmid = {41794153},
issn = {1873-4596},
abstract = {BACKGROUND: The high-altitude environment is characterized by hypobaric hypoxia and intense ultraviolet B (UVB) radiation, contributing to increased incidence of UVB-induced skin injuries, including plateau solar dermatitis (PSD). The role of commensal skin microbiota in mediating photoprotection under such extreme conditions remains poorly understood. This study aimed to identify UVB-protective skin microbiota in high-altitude populations and to elucidate their potential mechanisms in mitigating UVB-induced skin damage.

METHODS: Skin microbiota profiles were analyzed by 16S rRNA gene sequencing in healthy plateau residents and PSD patients. Protective effects were evaluated using a murine model of UVB-induced skin injury and an in vitro UVB-exposed HaCaT keratinocyte model. Integrated transcriptomic, proteomic, and metabolomic analyses were performed to identify candidate bioactive microbial metabolites, followed by functional validation.

RESULTS: Cutibacterium acnes (C. acnes) was significantly enriched in healthy plateau residents compared with PSD patients. Topical application of C. acnes alleviated UVB-induced skin inflammation, collagen degradation, and DNA damage in mice. Multi-omics analyses revealed dysregulation of sphingolipid metabolism following UVB exposure and highlighted bacterial-derived ceramides as candidate protective metabolites. Two representative ceramides, CER2 and CER14, significantly reduced UVB-induced apoptosis, oxidative stress, and DNA damage in keratinocytes. These effects were associated with suppression of TLR4-MyD88-NF-κB signaling activity.

CONCLUSION: This study identifies C. acnes as a commensal bacterium with photoprotective potential against UVB-induced skin damage in high-altitude environments. Ceramide-related lipid metabolites derived from C. acnes contribute to attenuation of UVB-triggered inflammatory signaling and cellular injury, providing new insights into microbiome-based strategies for photoprotection.},
}

@article {pmid41794001,
year = {2026},
author = {Noor, S and Qureshi, A and Parvez, S and Ahmad, B},
title = {The dual binding of pantoprazole mitigates ceftriaxone-mediated misfolding of human serum albumin.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {355},
number = {},
pages = {127661},
doi = {10.1016/j.saa.2026.127661},
pmid = {41794001},
issn = {1873-3557},
abstract = {Proton pump inhibitors (PPIs) like pantoprazole are often prescribed alongside antibiotics to prevent antibiotic-induced gastritis, ulcers, and microbiome disturbances. In this study, we provide the first evidence of pantoprazole's (PTP) distinct protective role in preventing ceftriaxone (CTX) induced structural alterations and aggregation of human serum albumin (HSA). We have found strong binding of pantoprazole at domain-I and domain-III, whereas ceftriaxone binds in domain-II of HSA. The ceftriaxone binding was found to disrupt the tertiary structure of the protein and induces the non-native β-structures without affecting the thermal stability of the protein. Moreover, it was found to promote the thermal-induced formation of protofibrils. However, the addition of pantoprazole in HSA-CTX complex efficiently restored the structural alterations and aggregation reaction. This study highlights a previously unrecognized protective role of PPIs, particularly pantoprazole, in preserving protein structure and aggregation caused by antibiotic overuse.},
}

@article {pmid41793943,
year = {2026},
author = {Burns, GL and Roberts, F and Wark, JA and Fowler, S and Jones, MP and Duncanson, K and Talley, NJ and Keely, S},
title = {Serological and faecal markers of irritable bowel syndrome: a systematic review and meta-analysis.},
journal = {EBioMedicine},
volume = {126},
number = {},
pages = {106198},
doi = {10.1016/j.ebiom.2026.106198},
pmid = {41793943},
issn = {2352-3964},
abstract = {BACKGROUND: The irritable bowel syndrome (IBS) has long been considered a functional disorder, but recent work has demonstrated clear biological signatures in immune, microbiome and enteric nervous systems of patients with IBS. Despite this new knowledge, there is still no clear biological marker of IBS, with patient symptom reporting and exclusion of organic disease the main criteria for diagnosis. We aimed to perform a systematic review and meta-analysis to identify consistent biomarkers for IBS in serum and stool samples.

METHODS: We searched Medline, EMBASE, Cochrane Library, Web of Science and Scopus to obtain all relevant publications published between 1992 and January 2026. Original, peer-reviewed research articles including adults with IBS and healthy or outpatient controls, and/or patients with organic gastrointestinal conditions (e.g. IBD) were included. All articles had quantification of blood and faecal markers between IBS and controls. Descriptive data presented as median and range or median (interquartile range) was converted to mean ± SD. To account for methodological assay differences between studies, standardised mean difference (SMD) with 95% confidence interval was used as the primary outcome measure for the meta-analyses, with a random effects model fitted to the data.

FINDINGS: The search strategy identified 55,444 citations across all databases. 124 studies were included encompassing 14,930 patients with IBS, 7544 healthy/asymptomatic controls and 4317 patients with organic diseases. The top serum discriminators between IBS and healthy controls were TNF-⍺ (13 studies, 1025 controls and 1244 IBS, SMD = 2.74, 95% CI = 0.70, 4.70, p = 0.006), IL-6 (13 studies, 736 controls and 1022 IBS, SMD = 1.87, 95% CI = 0.13, 3.61, p = 0.035) and IFN-ɣ (4 studies, n = 195 controls, n = 372 IBS, SMD = 2.79, 95% CI = 1.07, 4.51, p = 0.002). For faecal markers calprotectin was significantly higher in patients with IBS over controls (11 studies, 1624 controls and 1383 IBS, SMD = 0.75, 95% CI = 0.30, 1.21, p = 0.001), while faecal valerate levels were lower in IBS versus controls (4 studies, 290 controls and 488 IBS, SMD = -0.79, 95% CI = -1.48, -0.11, p = 0.02). For discriminating IBS overall from organic diseases, serum albumin (4 studies, 282 IBS and 312 organic, SMD = 2.15, 95% CI = 0.20, 4.11, p = 0.031) and faecal calprotectin (16 studies, 1591 IBS and 1685 organic, SMD = -1.13, 95% CI = -1.51, -0.75, p < 0.0001) were significantly different. In discriminating IBS subtypes from controls, only diarrhoeal IBS (IBS-D) could be distinguished by albumin (3 studies, 248 controls and 219 IBS-D, SMD = -0.39, 95% CI = -0.68, -0.11, p = 0.007) and IL-6 (4 studies, 153 IBS-D and 169 controls, SMD = 2.53, 95% CI = 0.86, 4.21, p = 0.003). Heterogeneity across the studies ranged from moderate to high, but few overly influential studies were identified between comparisons.

INTERPRETATION: Patients with IBS exhibit increased peripheral cytokine levels that are consistent with reports of increased epithelial permeability and may be important in distinguishing subgroups of IBS patients. Patients with IBS also demonstrated higher faecal calprotectin levels than healthy individuals, although these levels were still significantly lower than patients with organic diseases. Similarly, patients with IBS-D have lower serum albumin levels compared to healthy controls, while patients with organic disease had lower levels compared to patients with IBS, irrespective of subtype. There are clear biological signatures at play in IBS patients that may be useful clinically in establishing IBS diagnosis and may indicate the mechanisms of disease symptoms.

FUNDING: National Health and Medical Research Council Centre for Research Excellence in Digestive Health (NJT, SK) G180219.},
}

@article {pmid41793899,
year = {2026},
author = {Amin, H and Cramer, C and Finster, K and Real, FG and Gislason, T and Holm, M and Janson, C and Jögi, NO and Jogi, R and Malinovschi, A and Modig, L and Norbäck, D and Shigdel, R and Sigsgaard, T and Svanes, C and Thorarinsdottir, H and Wouters, IM and Šantl-Temkiv, T and Schlünssen, V and Bertelsen, RJ},
title = {Indoor airborne bacterial communities and adult lung health: A cross-sectional study.},
journal = {International journal of hygiene and environmental health},
volume = {274},
number = {},
pages = {114780},
doi = {10.1016/j.ijheh.2026.114780},
pmid = {41793899},
issn = {1618-131X},
abstract = {BACKGROUND AND OBJECTIVE: Indoor microbial exposures influence respiratory health, yet how men and women respond differently to airborne bacterial communities remains unclear. This study aimed to assess sex-specific associations between indoor airborne bacteria, and lung function, and airway inflammation in adults.

METHODS: Airborne dust was collected from the bedrooms of 1038 adults (463 men, 575 women) across five Nordic cities as part of the European Community Respiratory Health Survey (ECRHS) III. Bacterial communities were profiled using 16S rRNA amplicon sequencing. Bacterial and endotoxin loads were quantified via quantitative PCR (qPCR) and the Limulus amebocyte lysate (LAL) assay, respectively. Multivariable linear regression models stratified by sex were used to examine associations with lung function and airway inflammation.

RESULTS: Greater indoor bacterial diversity was associated with higher lung function in men (FEV1 β = 0.17, 95% CI: 0.05 to 0.29, P = 0.003) and higher FeNO levels in women (β = 2.44, 95% CI: 0.73 to 4.15, P = 0.005). Endotoxin load was positively associated with FeNO in women (β = 0.37, 95% CI: 0.05 to 0.70, P = 0.02), but not in men. Genera from Actinobacteriota and Bacilli were associated with higher lung function, while Clostridia was linked to lower lung function and reduced FeNO. In contrast, several genera from Actinobacteriota and Gammaproteobacteria were positively associated with FeNO.

CONCLUSIONS: Indoor bacterial exposures were associated with respiratory health in a sex-specific pattern. These findings highlight the importance of microbial composition in shaping adult lung health and underscore the need for sex-specific approaches in future epidemiological research.},
}

@article {pmid41793893,
year = {2026},
author = {Narla, T and Nudurupati, U and Ou, Y},
title = {Developing fast scan cyclic voltammetry at carbon fiber microelectrodes to quantify short chain fatty acids in situ.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {171},
number = {},
pages = {109266},
doi = {10.1016/j.bioelechem.2026.109266},
pmid = {41793893},
issn = {1878-562X},
abstract = {Acetic, propionic, and butyric acids are short chain fatty acids (SCFAs) and the most abundant metabolites produced by gut bacteria. To uncover mechanistic insights of their function throughout the body, it is critical to measure rapid SCFA fluxes in sites of action such as brain, muscle, and skin. Current approaches have focused on fecal and plasma measurements, where SCFA levels are low and not representative of tissue-specific concentrations or fluxes. Thus, a rapid, in situ methodology is needed. Fast scan cyclic voltammetry (FSCV) at carbon fiber microelectrodes (CFMs) has the spatiotemporal resolution to fill this need. However, the electrochemical response of CFMs to SCFAs have not been explored until now. By coupling FSCV at CFMs with flow injection analysis of each SCFA, we demonstrate there are distinct peaks in the cyclic voltammograms for each fatty acid. Some of these peaks display faradaic behavior in scan rate, holding potential, and switching potential experiments. Interestingly, we identify several peaks that are concentration-sensitive and therefore are promising quantifiable markers of SCFA dynamics and fluxes. This work lays the foundation in understanding the response of CFMs to fatty acids and demonstrate the utility of FSCV at CFMs for the in situ quantitation of SCFAs.},
}

@article {pmid41793548,
year = {2026},
author = {Shahadha, MH and Voigt, A and Gruner, D and Marschner, U and Le Floch, M and Hampe, J and Brauer, F and Schostek, S and Luniak, M and Bock, K and Richter, A},
title = {Ingestible active capsule for gastrointestinal microbiome sampling.},
journal = {Biomedical microdevices},
volume = {28},
number = {1},
pages = {},
pmid = {41793548},
issn = {1572-8781},
abstract = {UNLABELLED: Various gastrointestinal disorders have been linked to gut microbiome dysbiosis, as it plays a critical role in immune regulation, metabolism, nutrient digestion, and pathogen suppression. However, the microbiome’s spatial variability across gastrointestinal segments and its intra- and interindividual differences complicate its study and clinical interpretation. While fecal DNA analysis is commonly used, stool samples only capture an accumulated signal and miss the spatial dynamics of microbial populations. To address this, we propose a modular sampling capsule capable of wirelessly collecting liquid. The capsule consists of two main modules: (i) an actuator module integrating a polymer-based microfluidic system with meltable wax-based opening valve, screen-printed microheater, cellulose membrane-based closing valve, evacuated sampling chamber with dried sample preservative material, filter membrane (size exclusion 150 μm), and sample extraction channel; and (ii) a control electronic module with communication, localization, and power supply units. The actuator module was validated in vitro using a diluted stool simulant (330 mg/mL) and an uncleaned porcine intestine. The opening valve activated within 3.6 ± 0.5 s at 120 ± 10 mA and 0.8 V. The sample was then filtered and aspirated into the sampling chamber within 1–2 s, and the closing valve sealed the inlet completely within 10 min. We overcame design, material, and fabrication challenges to construct an actuator module that functions effectively in liquids with variable physicochemical conditions (pH, chemical composition, viscosity, and particle size). These results demonstrate the feasibility of a controlled, segment-specific intestinal sampling capsule, representing a step towards precise and accurate microbiome profiling.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10544-026-00802-4.},
}

@article {pmid41793273,
year = {2026},
author = {Britos, M and Pellegrini, E and Hernández-Ríos, P and Garrido, M and Fernández, A and Tomás, I and León, R and Arredondo, A and Álvarez, G and Teuche, AH and Ríos, MH},
title = {Subgingival Microbial Signatures Associated With Apical Periodontitis Identified by Next Generation Sequencing and Predictive Modelling.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70131},
pmid = {41793273},
issn = {1365-2591},
support = {1200098//FONDECYT/ ; 1251739//FONDECYT/ ; ID24I10282//Vice-Rectorate for Research and Development (VID), University of Chile/ ; //Chilean Government/ ; },
abstract = {AIMS: To assess the relationship between endodontic and subgingival bacterial communities in individuals with apical periodontitis (AP), and to identify disease-associated subgingival microbial signatures. We propose that subgingival microbial communities exhibit a dysbiotic profile, defined by distinct bacterial signatures, which may provide complementary biological insights into AP.

METHODS: In this cross-sectional study, DNA was extracted from paired endodontic and subgingival samples from mesiobuccal sites of first molars in patients with AP (n = 25 sample pairs), and from subgingival samples from the same sites in healthy individuals (n = 34). Microbiota was explored using 16S rRNA sequencing. Alpha and beta diversity metrics were calculated. Differentially abundant taxa were identified using LEfSe. Random forest models based on the bacterial counts observed in the subgingival samples were trained to classify the individuals with AP from the controls.

RESULTS: Within AP individuals, the subgingival communities differed from those present in root canals. Subgingival communities exhibited higher alpha diversity than root canal communities, irrespective of the clinical diagnosis (p < 0.001). Subgingival microbial communities in AP individuals exhibited a dysbiotic profile associated with enrichment of anaerobic and inflammophilic species (p < 0.05). Beta diversity analyses showed compositional differences between AP and control individuals, with Jaccard distance reaching statistical significance (p < 0.05), and Bray-Curtis indicating a borderline effect (p = 0.07). The best predictive model (Streptococcus sanguinis and Prevotella maculosa) achieved an accuracy of 89.8%, sensitivity of 80%, specificity of 97%, precision of 95.2%, and an AUC of 0.98.

CONCLUSIONS: Subgingival profiles from AP individuals are distinct from those in healthy controls, showing AP-associated dysbiosis. Specific subgingival bacterial signatures achieved high diagnostic accuracy, supporting the potential broader impact of AP on the subgingival microbiota.},
}

@article {pmid41793176,
year = {2026},
author = {Zheng, L and Zhao, G and Zheng, L and Zou, Y and Zhang, S and Dong, J},
title = {Insights Into Highly Associated Co-Factors on HPV-Related Cervical Cancer.},
journal = {Reviews in medical virology},
volume = {36},
number = {2},
pages = {e70131},
doi = {10.1002/rmv.70131},
pmid = {41793176},
issn = {1099-1654},
mesh = {Humans ; *Uterine Cervical Neoplasms/virology/epidemiology/etiology ; Female ; *Papillomavirus Infections/complications/virology/epidemiology ; *Papillomaviridae/genetics/classification ; Prevalence ; Microbiota ; },
abstract = {Cervical cancer ranks among the most prevalent malignancies, representing a substantial threat to women's health. The incidence of cervical cancer is strongly correlated with persistent infections by high-risk human papillomavirus (HPV) types. Overall, the prevalence of HPV infection is high, with most cases being classified as recessive, latent, and subclinical. The predominant HPV types and overall infection rates exhibit variability across different tissue types, individuals, and regions. Numerous co-factors contribute to the processes underlying persistent HPV infection and carcinogenesis, including the microbiome, individual immune characteristics, and geographical population differences. Moreover, these factors affect the efficacy of chemotherapy and immunotherapy in cancer treatment. This review aims to summarise several key factors associated with HPV-related cervical cancer and discuss their mechanisms in promoting carcinogenesis in HPV-related malignancies. The insights gained may inform the development of more effective preventive and therapeutic strategies.},
}

Humans
*Uterine Cervical Neoplasms/virology/epidemiology/etiology
Female
*Papillomavirus Infections/complications/virology/epidemiology
*Papillomaviridae/genetics/classification
Prevalence
Microbiota

@article {pmid41793016,
year = {2026},
author = {Yin, J},
title = {Mechanistic Insights for Microbiome Application in Plant Disease Resistance.},
journal = {Molecular plant pathology},
volume = {27},
number = {3},
pages = {e70233},
pmid = {41793016},
issn = {1364-3703},
support = {//Xinyang Normal University Scientific Research Start-up Fund./ ; 5250046//2025 Key Pilot Research Projects in Natural Sciences, Xinyang Normal University/ ; },
mesh = {*Microbiota/physiology ; *Disease Resistance/physiology ; *Plant Diseases/microbiology/immunology ; *Plants/microbiology ; },
abstract = {Plant diseases caused by biotic and abiotic stresses pose a great threat to both plant health and yield. Plant microbiomes play a crucial role in improving disease resistance, representing a sustainable approach to enhance crop performance. Plant host factors, including genetic variation, metabolites and microRNA, shape the assembly and function of the plant microbiome, thereby augmenting disease resistance. This interplay presents opportunities for plant-mediated manipulation of microbiome to promote plant health. Multiple mechanisms are involved in the microbiome-mediated plant disease resistance, such as direct and indirect pathogen antagonism, niche pre-emption, alteration of microbiota and activation of plant defences. Nevertheless, the application of plant microbiome in the field remains limited due to the intrinsic complexity of plant-microbiome and environment-microbiome interactions. This review synthesises current knowledge on the roles of plant microbiomes in plant disease resistance. I further summarise the mechanisms underlying plant-guided microbiome modulation and probiotic-mediated disease suppression. I also raise work and challenges that should be addressed, with the ultimate goal of informing more efficient microbiome application in sustainable agriculture.},
}

*Microbiota/physiology
*Disease Resistance/physiology
*Plant Diseases/microbiology/immunology
*Plants/microbiology

@article {pmid41792922,
year = {2026},
author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD},
title = {Microbially Derived Essential Amino Acids Compensate for Dietary Deficiencies in an Ecologically Relevant Mammalian Host.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag044},
pmid = {41792922},
issn = {1751-7370},
abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.},
}

@article {pmid41792460,
year = {2026},
author = {Imre, A and Kovács, R and Jakab, Á and Harmath, A and Németh, B and Nagy, F and Forgács, L and Balázsi, D and Majoros, L and Benkő, Z and Crook, N and Pócsi, I and Pfliegler, WP},
title = {ENA1 deficiency attenuates Saccharomyces 'boulardii' probiotic yeast virulence in immunosuppressed mouse fungaemia model.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09763-z},
pmid = {41792460},
issn = {2399-3642},
abstract = {Recently, fungal infections originating from the probiotic Saccharomyces 'boulardii' yeast are increasingly reported. Here, we aimed to reveal the background of and to diminish the virulence of this yeast, mitigating infection risks in vulnerable patient groups. Product and human isolates of S. 'boulardii' were subjected to in-host selection and their subclone lineages were compared phenotypically to identify target phenotypes and associated genes. More virulent isolates showed signs of selection for high osmotic tolerance in immunosuppressed mouse model, hence the genes NHA1 and ENA1 were deleted in six different 'boulardii' backgrounds. Only ENA1 deletion diminished virulence in our mouse fungemia model and it retained the ability for gut colonization and its probiotic characteristics, including similar effects on the gut microbiome in gavaged mice. We also demonstrated the successful substitution of the ENA1 gene with an antilisterial bacteriocin, opening a strategy for safe strains with therapeutic effect. Our strain development approach highlighted the importance of testing various genetic backgrounds and resulted in engineered strains with drastically reduced capability to cause bloodstream infections even in immunosuppressed hosts, establishing the groundwork for safer probiotic yeast therapies in the future.},
}

@article {pmid41792406,
year = {2026},
author = {Llirós Dupré, M and Buxó, M and Virolés, S and Pujolassos, M and Serra, I and Martínez, J and Lluansí, A and Bahí, A and Calle, M and Aldeguer, X},
title = {Preliminary insights into gut microbiome shifts as screening proxy for MASLD disease progression.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42368-4},
pmid = {41792406},
issn = {2045-2322},
support = {2015 Research Initiation Grant #3//Societat Catalana de Digestologia/ ; Girona Townhall, 2017//Joan Bruguera Fund/ ; },
}

@article {pmid41792366,
year = {2026},
author = {Ikram, S and Ullah, M and Lee, J and Hasan, N and Yoo, JW and Khan, R and Naeem, M},
title = {Fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis of randomized controlled trials (2020-2025).},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41792366},
issn = {1568-5608},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has emerged as a therapeutic strategy for Inflammatory Bowel Disease (IBD) including ulcerative colitis (UC) and Crohn's disease (CD). Although multiple randomized controlled trials (RCTs) have been published in recent years, evidence remains fragmented regarding safety and efficacy. This systematic review and meta-analysis evaluated the efficacy and safety of microbiome-based interventions in Inflammatory Bowel Disease (IBD).

METHODS: A systematic search of PubMed, Cochrane CENTRAL and Embase was conducted for randomized controlled trials (RCTs) published between January 2020 and May 2025. Eligible studies compared donor FME with placebo, autologous FMT or standard therapy in adult patients with IBD. Primary outcomes were clinical remission and endoscopic improvement; secondary outcomes included maintenance of remission and adverse events. Risk of bias was assessed using the Cochrane RoB-2 tool. Meta-analyses were performed in R using the meta and meta for packages. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated using common-effects and random-effects models.

RESULTS: Six RCTs involving 220-230 patients were included (majority UC patients, two trials CD). For induction of clinical remission, FMT was associated with significantly higher rates vs controls (OR = 3.24, 95% CI 1.43-7.41, p = 0.005) under a common-effect model; random-effects model showed similar point estimate but wide CI overlapping unity. Endoscopic response was strongly increased with FMT (OR = 6.80, 95% CI 2.96-15.63, p < 0.0001). Serious adverse events were more common in FMT arms but not statistically significant (common-effects OR ~ 2.05, 95% CI 0.72-5.81, p = 0.18). Evidence for maintenance of remission from two trials was limited and inconsistent.

CONCLUSION: Microbiome-based therapies, particularly FMT, significantly improved clinical and endoscopic remission in IBD (especially in UC) compared with control interventions, but safety signals and maintenance efficacy remain uncertain. Larger and strictly designed UC and CD-specific RCTs are needed to confirm long-term efficacy, clarify safety and define the role of microbiome-targeted therapies in IBD management.},
}

@article {pmid41792350,
year = {2026},
author = {Gan, Y and Zhang, J and Yao, K and Jiang, R and Li, Z and Yang, Y},
title = {The microbiome of interstitial cystitis revealed by 2bRAD-M.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42249-w},
pmid = {41792350},
issn = {2045-2322},
support = {82103239//National Natural Science Foundation of China/ ; 7244419//Beijing Municipal Natural Science Foundation/ ; },
}

@article {pmid41792309,
year = {2026},
author = {Ntekas, I and Takayasu, L and McKellar, DW and Grodner, B and Holdener, C and Schweitzer, P and Park, YS and Sauthoff, M and Shi, Q and Brito, IL and De Vlaminck, I},
title = {Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41792309},
issn = {2058-5276},
abstract = {Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong intermicrobial interactions at short length scales and tumour-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.},
}

@article {pmid41792269,
year = {2026},
author = {Ray, K},
title = {HIV-associated gut microbiome influences gut mucosal immunity.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41792269},
issn = {1759-5053},
}

@article {pmid41792267,
year = {2026},
author = {Almeida, AP and Moncau-Gadbem, CT and Goes, CP and Garcia, IS and da Silva, TR and Clemente, LG and Coutinho, LL},
title = {Characterization of bacterial microbiome and molecular detection of rickettsiosis in free-living ticks (Amblyomma sculptum Berlese, 1888).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38069-7},
pmid = {41792267},
issn = {2045-2322},
abstract = {Amblyomma sculptum is a major tick species in southeastern Brazil and an important vector in the epidemiology of Brazilian Spotted Fever (BSF). This study characterized the bacterial microbiome of free-living A. sculptum ticks in a BSF-endemic area, focusing on differences among developmental stages and sexes, and investigated rickettsial agents using 16S rRNA gene (V3-V4) sequencing. A total of 154 ticks were collected and analysed as 13 pooled samples grouped by stage and sex. Sequencing identified a diverse bacterial community of 180 genera, dominated by Sphingomonas, Nocardioides, Actinomycetospora and Methylobacterium, alongside genera of potential zoonotic relevance such as Rickettsia, Anaplasma, Ehrlichia and Coxiella, mainly in nymph pools. Alpha and beta diversity analysis showed that microbial community composition differed among stages and sexes, with adult males exhibiting higher richness and compositional dispersion, whereas nymphs showed reduced diversity and tighter clustering. Because 16S sequencing does not allow species-level identification of rickettsiae, positive samples were further analysed by PCR amplification and sequencing of the gltA gene, which identified Rickettsia bellii. Together, these results highlight stage- and sex-associated patterns in the microbiome of free-living A. sculptum and support the use of integrated microbiome profiling and targeted rickettsial detection in ecological and epidemiological studies of tick-borne diseases.},
}

@article {pmid41792233,
year = {2026},
author = {Wu, Q and Hu, K and Wang, Q and Luo, T and Hu, L and Liu, J and Zou, D and Hu, J and Guo, Z},
title = {Proline/serine-rich coiled-coil 1 alleviates atherosclerosis via remodeling tryptophan metabolism mediated by Akkermansia muciniphila.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41792233},
issn = {2092-6413},
abstract = {Genome-wide association studies have implicated proline/serine-rich coiled-coil 1 (PSRC1) in coronary artery disease (CAD) pathogenesis. Our previous studies demonstrated that Psrc1 deficiency accelerates atherosclerosis via gut microbial dysbiosis, characterized by a substantial depletion of Akkermansia muciniphila. Recent studies implicate microbiome-dependent tryptophan metabolism as a novel checkpoint in atherosclerosis, with specific microbial taxa regulating metabolite-driven immune responses. The mechanism by which Psrc1 modulates atherosclerosis through A. muciniphila and its regulation of tryptophan metabolism remains unclear. Here Psrc1 knockout mice exhibited reduced colonic mucin content, altered tryptophan metabolic enzyme expression and diminished levels of Trp metabolites including indoleacetic acid (IAA), with concomitant suppression of Ahr signaling in macrophages. In vivo analysis revealed that Psrc1 knockout diminishes Ahr through A. muciniphila-dependent IAA depletion. In vitro experiments further uncovered that Psrc1 stabilizes Ahr protein via ubiquitin carboxyl terminal hydrolase L3 (Uchl3)-mediated deubiquitylation. In addition, we identified plasma IAA levels positively correlating with decreased PSRC1 expression in peripheral blood mononuclear cells from patients with CAD. Furthermore, therapeutic restoration of a live A. muciniphila-IAA axis through oral supplementation reversed atherosclerosis in Psrc1 knockout mice. Notably, oral IAA supplementation substantially ameliorated atherosclerosis in Psrc1 knockout mice by suppressing plaque macrophage apoptosis. Crucially, co-administration of the Ahr antagonist CH-223191 abolished these benefits, confirming Ahr dependence. Our findings position PSRC1 as a critical regulator of the A. muciniphila-IAA-Ahr axis and nominate microbiome-targeted Ahr activation as a precision therapeutic strategy for patients with CAD with PSRC1 loss-of-function variants.},
}

@article {pmid41791848,
year = {2026},
author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ},
title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337478},
pmid = {41791848},
issn = {1468-3288},
abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.},
}

@article {pmid41791791,
year = {2026},
author = {Corona, M and García-Vicente, R and Saez-Marin, AJ and Ancos-Pintado, R and Rodríguez-Garcia, A and Arroyo, A and Blanco, A and Chari, A and Martin, T and Wolf, J and Rey-Bua, B and Mateos, MV and Kortüm, KM and Riedhammer, C and Tamariz-Amador, LE and Valencia, E and Rodríguez-Otero, P and San Miguel, J and Ibarra, G and Oriol, A and Cedena, MT and López-Muñoz, N and Alonso, R and Calbacho, M and Sanchez-Pina, JM and Linares, M and Martínez-López, J},
title = {Antibiotic-associated dysbiosis and bispecific antibody outcomes in multiple myeloma.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {3},
pages = {},
doi = {10.1136/jitc-2025-014224},
pmid = {41791791},
issn = {2051-1426},
mesh = {Humans ; *Multiple Myeloma/drug therapy/mortality/immunology ; Male ; Female ; *Dysbiosis/chemically induced ; *Antibodies, Bispecific/therapeutic use/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Middle Aged ; Aged ; Retrospective Studies ; Gastrointestinal Microbiome/drug effects ; Adult ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiota plays a critical role in regulating immune homeostasis and modulating responses to cancer immunotherapies. However, the impact of antibiotic-induced dysbiosis in patients with multiple myeloma (MM) treated with bispecific antibodies (BsAbs) remains unexplored. This multicenter, international study investigated whether antibiotic exposure prior to BsAb initiation alters the gut microbiome and affects clinical outcomes in patients with relapsed or refractory MM.

METHODS: We retrospectively analyzed 237 adult patients with MM treated with CD3-engaging BsAbs across six academic institutions. Antibiotic exposure was defined as the administration of any broad-spectrum, non-prophylactic antibiotic within 30 days before BsAb initiation. Clinical outcomes included overall survival (OS), progression-free survival (PFS), and cumulative incidence of relapse, evaluated using Kaplan-Meier estimates, log-rank tests, and multivariable Cox and competing-risk regression models. Additionally, in a subset of 24 patients, peripheral blood samples were collected prior to BsAb infusion for immunophenotyping, cytokine profiling, and serum short-chain fatty acid (SCFA) quantification, while stool samples for 16S ribosomal RNA (rRNA) sequencing were collected in a subset of 19 patients.

RESULTS: Broad-spectrum antibiotic exposure prior to BsAb therapy was associated with significantly inferior 1-year OS (60% (95% CI 44% to 81%) vs 77% (95% CI 71% to 83%), p=0.004) and PFS (26% (95% CI 14% to 47%) vs 53% (95% CI 46% to 61%), p<0.001), and higher relapse incidence (68% (95% CI 48% to 82%) vs 43% (95% CI 36% to 50%), p=0.004). In multivariable analyses, antibiotic exposure remained independently associated with poorer OS, PFS, and higher relapse risk. These associations were also observed within the subgroup of patients treated with CD3/B-cell maturation antibody-targeted BsAbs (n=155). Immunoprofiling revealed lower CD4[+] T-cell counts (p=0.017) and reduced circulating cytokine levels among antibiotic-exposed patients. 16S rRNA sequencing demonstrated a marked depletion of SCFA-producing genera, including Roseburia and Eubacterium, accompanied by lower serum SCFA concentrations. Moreover, microbiota composition before BsAb treatment correlated with therapy response and treatment-related toxicity.

CONCLUSIONS: Antibiotic-induced dysbiosis prior to BsAb therapy is associated with impaired immune reconstitution and inferior clinical outcomes in MM. These findings underscore the importance of antibiotic stewardship and suggest that microbiota-preserving strategies could enhance the efficacy of BsAb therapy in MM.},
}

Humans
*Multiple Myeloma/drug therapy/mortality/immunology
Male
Female
*Dysbiosis/chemically induced
*Antibodies, Bispecific/therapeutic use/pharmacology
*Anti-Bacterial Agents/adverse effects
Middle Aged
Aged
Retrospective Studies
Gastrointestinal Microbiome/drug effects
Adult
Treatment Outcome

@article {pmid41791749,
year = {2026},
author = {Ribeiro, B and Duarte, G and Thomas, T and Reeves, S and Suggett, DJ and Peixoto, RS},
title = {Exploring the transformative potential of multi-trophic strategies to enhance coral restoration and mitigate disease.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1945},
pages = {},
doi = {10.1098/rstb.2024.0323},
pmid = {41791749},
issn = {1471-2970},
mesh = {Animals ; *Coral Reefs ; *Anthozoa/physiology/microbiology ; *Conservation of Natural Resources/methods ; Climate Change ; *Environmental Restoration and Remediation/methods ; *Food Chain ; Microbiota ; },
abstract = {Unprecedented coral reef degradation from climate change, local impacts and disease requires time-critical development of innovative, cost-effective and ecologically grounded restoration strategies. Conventional restoration strategies to recover coral reef ecosystems largely focus on coral propagation, often de-prioritizing the broader ecological interactions that underpin reef resilience. However, coral reefs are complex ecosystems where other reef-associated organisms have fundamental and connected roles in nutrient cycling, biofiltration, pathogen control and microbiome stewardship. Integrating these key functional groups into restoration efforts in both the production phase (co-cultivation) and ecological recovery phase (ecological reconstruction) is required to advance coral restoration efforts toward more holistic coral reef ecological restoration frameworks. Integrating multi-trophic strategies provides a multifunctional, nature-based solution to enhance coral survival, mitigate disease outbreaks and promote overall ecosystem health. Here, we discuss the benefits of such a multi-trophic approach, where filter feeders, suspension feeders, detritivores and grazers are incorporated into the processes of reef restoration efforts. By leveraging positive species interactions based on facilitation theory, a multi-trophic approach provides a tool that not only enhances microbiome stewardship and coral reef restoration success but also reinforces the long-term sustainability of reef ecosystems in a changing climate. This article is part of the theme issue 'Managing infectious marine diseases in wild populations'.},
}

Animals
*Coral Reefs
*Anthozoa/physiology/microbiology
*Conservation of Natural Resources/methods
Climate Change
*Environmental Restoration and Remediation/methods
*Food Chain
Microbiota

@article {pmid41791695,
year = {2026},
author = {Chandra, QM and Clister, D and Halim, P and Dalimunthe, A and Ichwan, M and Sari, DK and Umaya, C and Aktary, N and Rani, A and Park, MN and Kim, B and Syahputra, RA},
title = {Harnessing the gut-heart axis for cardiovascular drug innovation: microbiome, metabolites, and personalized treatment strategies.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {587},
number = {},
pages = {120941},
doi = {10.1016/j.cca.2026.120941},
pmid = {41791695},
issn = {1873-3492},
abstract = {Cardiovascular disease (CVD) remains the leading cause of mortality worldwide despite major advances in pharmacotherapy. Emerging evidence reveals a pivotal role for the gut-heart axis, wherein gut microbiota are and their metabolites influence CV physiology, pathology, and drug responsiveness. Dysbiosis in conditions such as hypertension, atherosclerosis, and heart failure has been associated with altered production of bioactive metabolites including trimethylamine N-oxide, short-chain fatty acids, bile acids, and tryptophan derivatives. These metabolites have been shown to modulate inflammation, endothelial function, lipid metabolism, and myocardial remodeling. This review synthesizes current knowledge on microbiome-drug interactions in CV pharmacology, including how gut bacteria may metabolize drugs (e.g., digoxin, aspirin, warfarin) and how CV agents can shape microbial communities. We further explore microbiome-targeted therapeutic strategies-probiotics, prebiotics, postbiotics, fecal microbiota transplantation, and small-molecule inhibitors of harmful metabolites-highlighting their mechanisms, preclinical evidence, and translational potential. Integrating microbiome profiling with multi-omics platforms and artificial intelligence may enable personalized treatment strategies that optimize CV outcomes. While the gut-heart axis presents an exciting frontier for drug innovation, challenges remain in establishing causality, addressing inter-individual microbiome variability, managing confounding factors such as diet and medication use, and meeting regulatory requirements. Harnessing this bidirectional relationship holds promise for transforming CV pharmacotherapy from a one-size-fits-all approach to precision medicine grounded in host-microbe interactions.},
}

@article {pmid41791635,
year = {2026},
author = {Laojun, S and Changbunjong, T and Bunchu, N and Chaiphongpachara, T},
title = {Microbial communities and wing variation associated with ectoparasitic mites in medically important Mansonia mosquitoes (Diptera: Culicidae) from coconut plantation habitats in central Thailand.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108042},
doi = {10.1016/j.actatropica.2026.108042},
pmid = {41791635},
issn = {1873-6254},
abstract = {This study presents the comprehensive assessment of the bacterial microbiome and the effects of ectoparasitic mites on wing morphometry in Mansonia mosquitoes, namely, Ma. annulifera, Ma. indiana, and Ma. uniformis from coconut-growing areas in central Thailand. High-throughput sequencing of the 16S ribosomal RNA gene (V3-V4 regions) generated 1,813,140 raw reads. Following quality control with the DADA2 pipeline, including filtering, denoising, merging, and chimera removal, 681,766 non-chimeric sequences were retained across nine libraries, yielding 467 unique amplicon sequence variants (ASVs). Distinct, species-specific bacterial community profiles were identified: Fructobacillus fructosus dominated Ma. annulifera (28.85% relative abundance), whereas Wolbachia was predominant in Ma. indiana (57.94%) and Ma. uniformis (80.87%). Although alpha diversity showed no significant interspecific differences (p > 0.05), beta-diversity analyses revealed clear species-specific clustering. Differential abundance testing further identified Rosenbergiella sp. as a biomarker for Ma. annulifera and Wolbachia sp. as highly enriched in Ma. indiana and Ma. uniformis. Geometric morphometric analysis revealed significant differences in mean centroid size among all mite infestation groups in Ma. annulifera (p < 0.05), but not in Ma. indiana or Ma. uniformis (p > 0.05). Shape analysis indicated that Ma. annulifera differed significantly only between the no-mite and high-intensity groups, Ma. indiana across all pairwise comparisons, and Ma. uniformis between the no-mite and high-intensity groups and between the low- and high-intensity groups (p < 0.05). This study provides new insights into Mansonia microbiome diversity and mite-associated morphological variation, with implications for mosquito ecology and disease transmission.},
}

@article {pmid41791375,
year = {2026},
author = {Shane, J and Evans, M and Rigas, Y and Shanks, RMQ and St Leger, AJ},
title = {Genetically engineered eye-colonizing microbes that deliver the anti-inflammatory cytokine interleukin-10 enhance corneal tissue repair.},
journal = {Cell reports},
volume = {},
number = {},
pages = {117064},
doi = {10.1016/j.celrep.2026.117064},
pmid = {41791375},
issn = {2211-1247},
abstract = {Barrier surfaces harbor tissue-colonizing microbes that can shape local physiology and immunity. During corneal injury, inflammation can delay healing, resulting in loss of visual acuity. Standards of care include topical applications of therapies, which are quickly washed away, requiring a laborious treatment regimen to maintain efficacy. To address this problem, we engineered an eye-colonizing microbe, Corynebacterium mastitidis, to act as a long-term therapeutic delivery vehicle by secreting bioactive interleukin (IL)-10 using a native secretion signal that we identified using transposon mutagenesis. Engineered microbes stably colonize the eye and release mouse (mIL-10) or human IL-10 (hIL-10) that modulates local immunity and accelerates wound repair after an initial inoculation event. Further, hIL-10 producing C. mast can regulate inflammatory cytokine production in immune cells, highlighting the immune-regulatory capabilities of this live biotherapeutic product. These findings demonstrate that genetically engineered eye-colonizing bacteria can serve as a self-sustaining therapeutic platform to control inflammation and promote tissue repair.},
}

@article {pmid41791329,
year = {2026},
author = {de Vicente, M and Tomás-Pejó, E and González-Fernández, C},
title = {From conventional to adapted microbiomes: Promoting high short-chain fatty acid yields and productivities from agricultural waste.},
journal = {Journal of environmental management},
volume = {403},
number = {},
pages = {129216},
doi = {10.1016/j.jenvman.2026.129216},
pmid = {41791329},
issn = {1095-8630},
abstract = {Microbial consortia play an essential role in anaerobic fermentation (AF) devoted to the production of short-chain fatty acids (SCFAs) from organic wastes. AF is usually performed by a conventional anaerobic microbiome (CM) sourced from anaerobic digestion reactors. During AF, the microbiome undergoes an adaptation period to the imposed operational conditions and substrate characteristics, leading to the bio-enrichment of certain microorganisms. This work compared the use of CM and a bio-enriched microbiome (BM) as inoculum for AF of agricultural wastes in continuous stirred tank reactors (CSTR) with hydraulic retention time (HRT) of 8 d. The novelty of this study lies in demonstrating that using a BM enhances the production rate of SCFAs when compared to CM. BM, composed of adapted microorganisms previously working at an HRT of 10 d, allowed the highest SCFAs productivity (1.97 g/L·d) and concentration (15.6 g/L). Bioconversion efficiencies achieved with BM and CM (60.1 % and 71.8 %, respectively) were among the highest reported in literature. Microbiome analysis revealed inoculum-driven changes in the microbial community. However, Clostridium and Megasphaera, which are involved in the hydrolysis and acidification steps of AF and are associated with acetic acid formation and chain elongation, predominated in all cases (up to 48 % of the microbial abundance within the total community). These results evidenced the feasibility of operating CSTRs at an HRT of 8 d with diverse inoculum sources to maintain exceptionally high SCFA productivity and bioconversion. The outcomes also highlighted the robustness of the microbial community, even under short HRT, providing a novel strategy for AF processes optimization.},
}

@article {pmid41791313,
year = {2026},
author = {Filippini, G and Bugnot, AB and O'Connor, W and Gribben, PE and Varkey, DR and Paulsen, IT and Dafforn, KA},
title = {Marine heatwaves alter shell microbiomes and denitrification capacity: An oyster family-specific response.},
journal = {Marine pollution bulletin},
volume = {227},
number = {},
pages = {119503},
doi = {10.1016/j.marpolbul.2026.119503},
pmid = {41791313},
issn = {1879-3363},
abstract = {Marine heatwaves (MHWs) are increasing in frequency and intensity, significantly affecting biodiversity and ecosystem processes. However, the impact of MHWs on microbiome structure and function, and whether such changes are influenced by intraspecific differences among hosts, remains unclear. This study investigated the effect of a simulated MHW on external shell microbiomes (alpha diversity, community and taxonomic compositions, and denitrification capacity) of four oyster families (1, 11, 14 and 15), with different levels of disease resistance and growth rate. Oysters were exposed to 29 °C (MHW) and 24 °C (control) temperatures for 6 days, followed by a 21-day recovery period. The MHW shifted bacterial community composition and decreased alpha diversity in Family 14, together with reductions in the relative abundance of Pseudomonadota and Planctomycetota, and in denitrification genes (nirK and nosZ). In Family 15, MHW exposure decreased the abundance of Rhizobiaceae and the denitrification gene nirS, which recovered within three weeks. Reduction in denitrification genes suggests a potential decline in nitrogen removal capacity, which could negatively affect coastal systems, as bioavailable nitrogen may accumulate and lead to eutrophication. Conversely, in Families 1 and 11 the shell microbiomes remained stable under heat stress. Although mechanisms were not directly assessed, these faster-growing families may possess physiological traits (e.g. efficient metabolism and filtration) that support the resilience of nitrogen-cycling microbes during thermal stress. This study highlights the importance of intraspecific differences among hosts in shaping microbiome responses to MHWs, suggesting that selecting certain oyster families could help maintain key microbial-driven processes like denitrification under climate stress.},
}

@article {pmid41790992,
year = {2026},
author = {Berendse, R and Verkleij, M and Daams, J and Hemmings, S and Lindauer, R and Korosi, A and Zantvoord, JB and Lok, A},
title = {The microbiome and PTSD: a scoping review across preclinical and clinical studies.},
journal = {European journal of psychotraumatology},
volume = {17},
number = {1},
pages = {2627060},
doi = {10.1080/20008066.2026.2627060},
pmid = {41790992},
issn = {2000-8066},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Stress Disorders, Post-Traumatic/microbiology/physiopathology ; Disease Models, Animal ; },
abstract = {BACKGROUND: Posttraumatic Stress Disorder (PTSD) is a psychiatric condition that substantially impairs quality of life and global health. Emerging evidence implicates that the human microbiome contributes to PTSD pathophysiology via gut-brain-immune interactions, although the underlying mechanisms and therapeutic implications remain unclear.

OBJECTIVE: This review aimed to systematically map the evidence linking microbiome alterations to PTSD, with a focus on mechanistic pathways, therapeutic potential, and research gaps.

METHODS: This scoping review was conducted in Medline, Embase, and PsychINFO from inception to 18-03-2025. Eligible studies included human participants with PTSD and preclinical rodent models employing validated PTSD paradigms. Outcomes of interest included microbiome diversity and composition, gut-brain axis biomarkers, and effects of microbiome-targeted interventions.

RESULTS: Fifty studies were included, comprising 20 human, 29 preclinical and one cross-species study. Human observational studies frequently observed reduced overall microbial diversity, along with a loss of short-chain fatty acid (SCFA)-producing bacteria, such as Ruminococcaceae and Lachnospiraceae, and an increased abundance of Veillonella, Odoribacter, and Catenibacterium linked to gut permeability and inflammation. Human intervention studies testing probiotics, prebiotics, fermented soy, and dietary fibre showed preliminary evidence for symptom and related metabolic and inflammatory marker improvements; however, microbiome effects were inconsistent. Preclinical models revealed stress-induced reductions in Bifidobacteria, Verrucomicrobia, and Parabacteroides, and increases in Coprobacillus and Anaeroplasma. Functional consequences included impaired barrier integrity, altered SCFA levels, and heightened immune activation. Preclinical interventions, particularly Mycobacterium vaccae, as well as probiotics, synbiotics, acetate, and MDMA, mitigated microbial alterations, reduced anxiety-like behaviours, and modulated neuroimmune pathways.

CONCLUSION: Current evidence supports an association between PTSD and microbiome alterations, with convergent human and preclinical findings. However, human research remains limited by small, cross-sectional designs, which preclude causal inferences. Rigorous longitudinal and interventional studies are required to establish causality and assess microbiome-targeted therapies as adjuncts in PTSD treatment.},
}

Humans
Animals
*Gastrointestinal Microbiome/physiology
*Stress Disorders, Post-Traumatic/microbiology/physiopathology
Disease Models, Animal

@article {pmid41790682,
year = {2026},
author = {Xie, RX and Ci, XY and Xue, YB and Liu, M and Zhang, MJ},
title = {Association between oral microbiota and inflammatory bowel disease: A 2-sample Mendelian randomization study in East Asian populations.},
journal = {Medicine},
volume = {105},
number = {10},
pages = {e47909},
doi = {10.1097/MD.0000000000047909},
pmid = {41790682},
issn = {1536-5964},
mesh = {Humans ; Mendelian Randomization Analysis ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; Asia, Eastern/epidemiology ; *Microbiota/genetics ; *Crohn Disease/microbiology/genetics ; *Mouth/microbiology ; Asian People/genetics ; *Inflammatory Bowel Diseases/microbiology/genetics/epidemiology ; *Colitis, Ulcerative/microbiology/genetics/epidemiology ; Saliva/microbiology ; Male ; Female ; East Asian People ; },
abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is increasingly prevalent in East Asia. Its pathogenesis is linked to microbiota dysbiosis via the oral-gut axis, but population-specific causal evidence remains scarce. This study aimed to clarify the causal associations between oral microbiota and UC/CD in East Asian populations using Mendelian randomization (MR), providing evidence for IBD etiology and precise prevention/treatment. A 2-sample MR approach was adopted, using genome-wide association study data of East Asian populations. Single nucleotide polymorphisms associated with tongue dorsum and salivary microbiota were selected as instrumental variables after rigorous screening (F-statistic > 10, linkage disequilibrium R2 = 0.001). Inverse variance weighted was the primary analysis method, supplemented by sensitivity tests (MR-PRESSO, MR-Egger intercept test, etc) and Benjamini-Hochberg multiple testing correction (false discovery rate < 0.05). A total of 82 oral microbiota taxa (22 families, 35 genera) were significantly causally associated with UC (FDR < 0.05), and 21 taxa (10 families, 12 genera) with CD (FDR < 0.05). High-risk taxa included Aggregatibacter and Streptococcus (OR > 1), while protective taxa included Fusobacterium_periodonticum_C_mgs_3022 and TM7x_unclassified_mgs_1084 (OR < 1). A distinct "mixed effect" was identified: the Streptococcus genus was risky for UC but protective for CD; genera such as Streptococcus (UC), Oribacterium (CD), and TM7x (CD) exhibited bidirectional risk/protective associations within a single IBD subtype; and the TM7x genus was risky for UC and showed bidirectional effects in CD. Other genera (e.g., Fusobacterium, Aggregatibacter) only had unidirectional associations. This study is the first to confirm the causal association between oral microbiota and IBD in East Asian populations, revealing the heterogeneity and "mixed effect" of this association. Identified high-risk and protective oral microbiota taxa provide new insights into IBD etiology and potential targets for clinical precise prevention and treatment.},
}

Humans
Mendelian Randomization Analysis
Polymorphism, Single Nucleotide
Genome-Wide Association Study
Asia, Eastern/epidemiology
*Microbiota/genetics
*Crohn Disease/microbiology/genetics
*Mouth/microbiology
Asian People/genetics
*Inflammatory Bowel Diseases/microbiology/genetics/epidemiology
*Colitis, Ulcerative/microbiology/genetics/epidemiology
Saliva/microbiology
Male
Female
East Asian People

@article {pmid41790596,
year = {2026},
author = {Srivastava, H and Sehgal, T and Sharma, V and Narang, H and Berinstein, J and Sood, A and Bishu, S and Goyal, MK},
title = {Beyond the binary: understanding inflammatory bowel disease in the context of HIV-Induced immunodeficiency.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2026.2642832},
pmid = {41790596},
issn = {1744-8409},
abstract = {INTRODUCTION: The coexistence of inflammatory bowel disease(IBD) and human immunodeficiency virus(HIV) represents a clinical paradox in which immune hyperactivity coexists with persistent immunodeficiency. Improved survival with antiretroviral therapy(ART) has led to increasing co-diagnoses, creating complex diagnostic and therapeutic challenges.

AREAS COVERED: A comprehensive literature search of PubMed/MEDLINE, Embase, Scopus, and the Cochrane Library from inception through December 2024 was conducted, supplemented by major gastroenterology and infectious disease conference proceedings through April 2025. This review synthesizes contemporary evidence on epidemiology, immunopathogenesis, clinical presentation, and management of IBD in people living with HIV. Key themes include immune reconstitution and Th17-cell depletion, diagnostic differentiation from infectious and noninfectious mimickers, underutilization of advanced IBD therapies despite emerging safety data, bidirectional interactions between intestinal inflammation and HIV viral dynamics, and clinically relevant ART - IBD interactions requiring multidisciplinary care.

EXPERT OPINION: Accumulating evidence supports the safe and appropriate use of immune-modulating therapies in virologically suppressed HIV-positive patients with IBD, challenging historical risk-averse approaches. Optimal management requires precision-based strategy incorporating CD4[+] cell thresholds, mucosal and inflammatory biomarkers, and individualized risk stratification. Future priorities include standardized diagnostic algorithms, longitudinal registries integrating immunological and virological parameters, and improved access to advanced therapies, moving beyond the traditional autoimmunity - immunodeficiency binary.},
}

@article {pmid41790425,
year = {2026},
author = {Kim, E and Kim, H and Lee, M and Kim, B and Kim, B and Kim, H and Kim, D and Kang, D and Shatta, A and Kim, JY and Holzapfel, WH and Yoon, H},
title = {Saccharomyces cerevisiae 48338 Suppresses Antibiotic-Induced Clostridioides difficile Infection in a Murine Model.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41790425},
issn = {1867-1314},
support = {RS-2025-16070149//National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; 202400440001//Handong Global University Research Grants/ ; },
abstract = {Clostridioides difficile infection (CDI) is a major cause of antibiotic-associated diarrhea and colitis, driven by toxin-mediated epithelial injury and inflammation. While antibiotics such as vancomycin remain the primary treatment, they can further disrupt the gut microbiota and promote recurrence. Probiotics, including yeast strains, have emerged as potential adjunctive therapies for mitigating CDI. In this study, several Saccharomyces cerevisiae strains were evaluated for their probiotic potential, and strain 48338 was identified as the most promising candidate based on its gastrointestinal tolerance, auto-aggregation ability, and antioxidant activity. Using a CDI mouse model, we found that treatment with S. cerevisiae 48338 reduced disease severity, as reflected by lower clinical sickness scores. Quantitative PCR analysis confirmed that the expression of the toxin gene tcdA was significantly decreased following 48338 treatment, whereas total C. difficile burden remained unchanged. In addition, 48338 treatment might enhance intestinal barrier integrity by upregulating occludin gene expression and also might attenuate production of pro-inflammatory cytokines, particularly the expression of IL-1β. The strain also increased the proportions of Foxp3[+] regulatory T cells and macrophages in both the spleen and mesenteric lymph nodes, as determined by flow cytometry, suggesting a shift towards an anti-inflammatory immune profile. Collectively, these findings suggest that the primary mechanism by which S. cerevisiae 48338 exerts its protective effect against C. difficile infection is not through direct reduction of C. difficile colonization, but primarily through modulation of the microbiome, host immune response, and maintenance of epithelial cell integrity. This study highlights the potential of yeast-based probiotics as adjunctive agents for the prevention or mitigation of CDI.},
}

@article {pmid41790398,
year = {2026},
author = {Sutton, S and Voskamp, S and Le, K and Hafez, A and Nelson, J and Palomo, P},
title = {Malondialdehyde Drives a Feed-Forward Reactive Oxygen Species Loop in Pediatric Crohn's Disease.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41790398},
issn = {1573-2568},
abstract = {PURPOSE: Crohn's disease (CD) is a chronic, relapsing inflammatory bowel disease with multifactorial etiology. Recent studies implicate reactive oxygen species (ROS) in pediatric CD. Expression of malondialdehyde (MDA), a biomarker of oxidative stress, is elevated in inflammatory diseases, including CD. This study aimed to evaluate genes driving ROS production in pediatric CD and MDA's role in shaping downstream gene expression.

METHODS: Using the Search Tag Analyze Resource for NCBI's Gene Expression Omnibus (STARGEO), we performed a tagged meta-analysis of publicly available gene expression data comparing pediatric CD with controls. Differentially expressed genes were restricted to p < 0.05 and absolute experimental log ratio of 0.2 for further analysis with Ingenuity Pathway Analysis (IPA), to explore biologic relationships.

RESULTS: Fifty-two pediatric CD samples and 24 healthy pediatric intestinal samples were identified and analyzed via STARGEO, yielding 1968 genes that met inclusion criteria. DUOX2, MMP3, and NOD2 were significantly upregulated in pediatric CD (log ratios of 2.521, 1.823, 0.524, respectively). Upstream regulators include TNF (z-score 11.195), TGFB1 (5.945), IFNG (9.983), and TLR4 (5.989). MDA was identified as a strongly activated regulator with a z-score of 10.909 and downstream targets including TGFB1, MMP3, TNF, and IL-6.

CONCLUSION: Our findings enhance the current understanding of the role of immune dysregulation, ROS, the gut microbiome, and epithelial barrier dysfunction in pediatric CD. DUOX2 functions as one of the central mediators of ROS-driven dysregulation, with TLR4-driven DUOX2 activity potentially overriding the NOD2 regulation. MDA formation stimulates inflammation and tissue injury, upregulating MMP3, which in turn increases ROS production to generate more MDA. This feed-forward inflammatory loop may accelerate fibrosis and chronic inflammation. This meta-analysis provides a preliminary framework of ROS-related gene programs in pediatric CD.},
}

@article {pmid41790338,
year = {2026},
author = {Shibuki, T and Yamashita, R and Hashimoto, T and Fujisawa, T and Imai, M and Yuda, J and Kuwata, T and Misumi, T and Nakamura, Y and Bando, H and Kojima, K and Tokioka, S and Chiba, I and Nakaya, N and Hozawa, A and Koshiba, S and Fuse, N and Saito, S and Shimizu, R and Park, WY and Kinoshita, K and Yoshino, T},
title = {Clinical development of molecular residual disease (MRD) and multi-cancer early detection (MCED) using liquid biopsy multiomics with artificial intelligence (AI).},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {41790338},
issn = {1437-7772},
support = {23tk0124005h0001//Japan Agency for Medical Research and Development/ ; 24tk0124005h0002//Japan Agency for Medical Research and Development/ ; 25tk0124005h0003//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: Early detection of cancer and precise recurrence monitoring remain major unmet needs in oncology. Conventional screening is limited to a few cancer types, leaving nearly half of cancers without established programs. Multi-cancer early detection (MCED) tests based on circulating tumor biomarkers have shown promise, but sensitivity for early-stage remains a challenge. In parallel, detection of molecular residual disease (MRD) using circulating tumor DNA (ctDNA) has emerged as a powerful prognostic and predictive tool, though current assays remain limited in sensitivity and specificity. This study aims to integrate multi-omics data to develop more refined and highly sensitive MCED and MRD assays.

METHODS: This study leverages clinical information and biospecimens from patients with cancer and cancer-naïve individuals. Samples from patients with cancers will be derived from the MONSTAR-SCREEN-3 study, while those from cancer-naïve individuals will be obtained from the Tohoku Medical Megabank Project. Comprehensive analyses will include whole-genome sequencing (WGS), whole-exome sequencing (WES), whole-transcriptome sequencing (WTS), proteomics, metabolomics, and microbiome profiling using stool and saliva. Artificial intelligence (AI)-based multi-omics integration will be performed to develop novel MCED and MRD assays and to evaluate their clinical performance. The primary endpoints are the sensitivity and specificity of MCED and MRD assays.

DISCUSSION: This is the first large-scale study to integrate comprehensive multi-omics profiling with AI for MCED and MRD assay development. The findings are expected to advance precision oncology by improving early diagnosis and recurrence monitoring.

TRIAL REGISTRATION: UMIN000053815, approved by the Institutional Review Board of the National Cancer Center Hospital East.},
}

@article {pmid41790238,
year = {2026},
author = {Zhao, S and Liu, B and Shi, Y and Zhou, Z and Chen, S and Saiding, Q and Xu, Q and You, X and Zhen, X and Chen, Q and Zhang, Y and An, S and Tao, N and Ouyang, J and Tao, W},
title = {Sprayable Lactococcus lactis-Nanocatalyst Gel for Postsurgical Immunomodulation in Preclinical Oral Squamous Cell Carcinoma.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.6c01542},
pmid = {41790238},
issn = {1520-5126},
abstract = {Oral squamous cell carcinoma (OSCC) is one of the most prevalent and aggressive head and neck cancers. Emerging evidence shows that distinct microbiomes coexist with tumor and immune cells in the tumor microenvironment (TME), shaping tumor progression and antitumor immunity. Harnessing probiotic-based immune modulation therefore represents a promising strategy to improve postoperative outcomes. Here, we develop a dual-channel sprayable Lactococcus lactis probiotic-nanocatalyst gel (L. lactis@Co4N/C@Gel) to potentiate postoperative immune reconstruction in OSCC. L. lactis can activate antitumor responses through Toll-like and NOD-like receptor pathways. However, its therapeutic benefit is constrained by lactate overproduction, which promotes tumor aggressiveness, immunosuppression, and therapy resistance. The incorporated Co4N/C nanoparticles efficiently scavenge L. lactis-derived lactate, thereby amplifying downstream immune activation. Benefiting from the thixotropic properties of calcium alginate, a sodium alginate solution containing L. lactis and CaCl2 solution containing Co4N/C nanoparticles can be cosprayed to achieve uniform wound coverage and rapid in situ gelation. In an orthotopic OSCC mouse model, L.lactis@Co4N/C@Gel effectively reconstructs postoperative antitumor immunity and markedly suppresses tumor recurrence. These findings highlight a microbiome-nanocatalyst synergistic strategy for improving postoperative immunotherapy in OSCC.},
}

@article {pmid41789971,
year = {2026},
author = {Zhang, D and Tian, S and Feng, B and Yang, F and Zhu, P and Wu, Q and Xu, J and Wang, H and Zhang, X},
title = {Rapid Classification of Pantoea spp. via Raman Flow Cytometry.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.6c00276},
pmid = {41789971},
issn = {1520-6882},
abstract = {Microorganisms play pivotal roles in ecosystems, where precise taxonomic identification is fundamental to understanding and harnessing their functions. Conventional microbial classification, however, relies on pure-culture techniques that suffer from prolonged cultivation cycles, low throughput, high costs, and limited resolution. To address these constraints, we developed an integrated platform combining positive dielectrophoresis-activated Raman-activated cell sorting (pDEP-RACS) with deep ResNet. Using the ecologically versatile and taxonomically challenging genus Pantoea as a model, we constructed a reference Ramanome database by pDEP-RACS that consists of 180 000 single-cell Raman spectra (SCRS) from 12 Pantoea species (22 strains) and two phylogenetically related species and established a classification model by ResNet-18. The model achieved optimal performance 96.9% mean accuracy and 97.3% recall for 24 SCRS colony isolates. Cross-batch validation shows the highest reproducibility in nutrient-starved samples, with 87.9% accuracy postpreprocessing with reduced batch effects. For optimal accuracy (97.6% ± 2.0%), classification accuracy plateaus at >1,500 SCRS of Raman detection depth. In synthetic communities, the model shows ≤3.21% absolute abundance error for species identification. For the rice seed microbiome, a good consistency was observed between Raman-derived Pantoea abundance (34.8%) and 16S rRNA sequencing results (45%). This platform enables species- and strain-level classification of Pantoea spp. cultures, acquiring >7,200 SCRS per hour to facilitate rapid identification in both synthetic microbial communities and field-derived samples.},
}

@article {pmid41789898,
year = {2026},
author = {Sharma, N and Singh, M and Radeny, J and Mukherjee, A and Sullivan, RF and Boyd, JM and Carabetta, VJ and Yang, JH and Yadavalli, SS},
title = {Insights into bacterial stress adaptation, host interactions, and drug resistance: key findings from the fall 2025 ASM Theobald Smith Society meeting.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0087825},
doi = {10.1128/msphere.00878-25},
pmid = {41789898},
issn = {2379-5042},
abstract = {The annual fall meeting for the Theobald Smith Society (TSS), the New Jersey Branch of the American Society for Microbiology (ASM), took place in November 2025 at Cooper Medical School of Rowan University in Camden, New Jersey. A total of 72 branch members from across New Jersey participated, including undergraduate and graduate students, postdoctoral trainees, faculty, and professionals from government and industry. This report highlights the scope and diversity of research carried out by TSS members and celebrates their impactful discoveries.},
}

@article {pmid41789894,
year = {2026},
author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N},
title = {Gut virome and metabolic associations in patients with acute pancreatitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0140025},
doi = {10.1128/msystems.01400-25},
pmid = {41789894},
issn = {2379-5077},
abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.},
}

@article {pmid41789806,
year = {2026},
author = {Nair, AV},
title = {Friend and Foe: Microbes in Orchestrating Immunity and Shaping Infection Dynamics.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00709},
pmid = {41789806},
issn = {2373-8227},
abstract = {Microbial communities, or microbiota, are fundamental regulators of host immunity and infection outcomes across diverse body sites, including the gut, skin, respiratory tract, and vagina. Despite advances, infectious diseases remain a global challenge, exacerbated by antimicrobial resistance and emerging pathogens. This review explores the dynamic interplay between microbiota, host immune responses, and pathogens, highlighting how microbial interactions shape immune homeostasis and colonisation resistance. The review discusses therapeutic approaches leveraging probiotics, prebiotics, defined microbial consortia, and fecal microbiota transplantation to enhance resistance against bacterial, viral, fungal, and parasitic infections. These microbiome-based strategies represent promising, sustainable alternatives to conventional antibiotics, offering scalable and mechanism-driven interventions. This review further underscores the potential of microbiota-informed therapies to contribute to effective infectious disease prevention and management while addressing global health challenges.},
}

@article {pmid41789608,
year = {2026},
author = {Marginean, SS and Radu, PA and Zurzu, M and Garofil, D and Paic, V and Tigora, A and Bratucu, M and And, FP},
title = {Advances and Ongoing Challenges in Colorectal Cancer.},
journal = {Chirurgia (Bucharest, Romania : 1990)},
volume = {121},
number = {1},
pages = {27-42},
doi = {10.21614/chirurgia.3262},
pmid = {41789608},
issn = {1221-9118},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/therapy/epidemiology/genetics ; Early Detection of Cancer/methods ; Biomarkers, Tumor/blood ; Prognosis ; Treatment Outcome ; },
abstract = {Colorectal cancer (CRC) remains a major global health concern, with a rising incidence among younger adults and persistently high mortality in advanced stages, despite significant scientific and technological progress. Its etiology is multifactorial, involving lifestyle factors, genetic susceptibility, chronic inflammation, and gut microbiome dysbiosis. Recent advances in screening, molecular profiling, surgery, and systemic therapies have substantially reshaped CRC management. This narrative review was conducted through a comprehensive literature search of PubMed/MEDLINE, Scopus, and Web of Science databases, covering publications from January 2015 to June 2025. Peer-reviewed articles addressing CRC epidemiology, molecular pathways, screening and diagnostic strategies, surgical management, systemic therapies, and emerging treatment modalities were selected. Evidence was qualitatively synthesized and organized into clinically relevant thematic domains. Recent progress in CRC screening, including advanced endoscopic imaging, fecal DNA testing, and blood-based biomarkers, has improved early detection, although implementation remains uneven. Molecular characterization such as MSI-H/dMMR status, RAS/RAF mutations, HER2 amplification, and consensus molecular subtypes â?" guides prognostic assessment and personalized therapy. Surgical resection remains the cornerstone of curative-intent treatment, with minimally invasive and robotic approaches reducing morbidity while maintaining oncologic safety. Techniques such as complete mesocolic excision and total mesorectal excision, along with multimodal strategies for advanced disease, have expanded therapeutic options. Despite these advances, challenges persist, including therapeutic resistance, tumor heterogeneity, limited immunotherapy efficacy in microsatellite-stable disease, and rising early-onset CRC. Future progress relies on precision medicine, ctDNA-guided monitoring, microbiome-targeted strategies, and optimized surgical selection.},
}

Humans
*Colorectal Neoplasms/diagnosis/therapy/epidemiology/genetics
Early Detection of Cancer/methods
Biomarkers, Tumor/blood
Prognosis
Treatment Outcome

@article {pmid41789481,
year = {2026},
author = {Stevenson, E and Susic, D and Craig, ME and Henry, A and Gow, M},
title = {Maternal antenatal health and infant growth outcomes: a Microbiome Understanding in Maternity Study.},
journal = {Journal of developmental origins of health and disease},
volume = {17},
number = {},
pages = {e15},
doi = {10.1017/S2040174425100378},
pmid = {41789481},
issn = {2040-1752},
mesh = {Humans ; Female ; Pregnancy ; Infant ; Adult ; *Child Development/physiology ; Infant, Newborn ; *Maternal Health/statistics & numerical data ; Longitudinal Studies ; Australia/epidemiology ; Male ; Life Style ; *Microbiota/physiology ; Weight Gain ; },
abstract = {The influence of the maternal antenatal environment on infant growth and development beyond the neonatal period is not well understood. This study investigated associations between maternal cardiometabolic health and lifestyle on infant growth during the first year of life. This sub-study of the longitudinal Microbiome Understanding in Maternity Study included 87 mother-infant dyads. Maternal anthropometrics were collected at each trimester. Lifestyle was assessed through the Australian Eating Survey (Trimester T1 and T3) and International Physical Activity Questionnaire (T1, T2 and T3). Infant anthropometrics were measured at birth, 6 weeks, 6 months and 12 months. Changes in weight, weight-for-age z-score, length-for-age z-score, rapid weight gain and conditional weight gain (CWG) were determined. Multiple linear regression was used to assess associations between maternal parameters and infant growth, adjusting for common confounders. Maternal T1 weight (CWG: p = 0.03), T3 weight (CWG: p = 0.03) and GWG (weight z-score change: p = 0.031) were positively associated with increased infant growth from 0 to 6 months. Greater maternal fat mass was associated with increased CWG (p = 0.042) from 6 weeks to 6 months. Higher quality maternal T1 diet was associated with increased infant growth (weight z-score change: p = 0.022, CWG: p = 0.013) from 0 to 12 months. Increased maternal physical activity was associated with increased CWG (p = 0.022) and length z-score change (p = 0.024) from 0 to 12 months in T1, and increased CWG from 6 to 12 months in T2 (p = 0.014) and T3 (p = 0.047). Markers of maternal cardiometabolic health risk and healthier lifestyle were associated with increased infant growth. Further investigation is required to confirm findings and investigate links with future health sequelae.},
}

Humans
Female
Pregnancy
Infant
Adult
*Child Development/physiology
Infant, Newborn
*Maternal Health/statistics & numerical data
Longitudinal Studies
Australia/epidemiology
Male
Life Style
*Microbiota/physiology
Weight Gain

@article {pmid41789431,
year = {2026},
author = {Priya, C and Jain, A and Shetty, DC and Pai Khot, AJ and Yadav, S and Jain, M and Gulati, N and Almalki, SA and Gowdar, IM},
title = {Analysis of Fusobacterium nucleatum Driven Modulation of c-Myc Pathways in Oral Carcinogenesis.},
journal = {F1000Research},
volume = {15},
number = {},
pages = {176},
pmid = {41789431},
issn = {2046-1402},
mesh = {Humans ; *Fusobacterium nucleatum/physiology ; *Mouth Neoplasms/microbiology/metabolism/pathology ; *Proto-Oncogene Proteins c-myc/metabolism ; Female ; Male ; *Carcinogenesis/metabolism/pathology ; Middle Aged ; Aged ; *Carcinoma, Squamous Cell/microbiology/metabolism/pathology ; Adult ; Fusobacterium Infections ; Signal Transduction ; },
abstract = {OBJECTIVE: To evaluate the association between Fusobacterium nucleatum and c-Myc expression in Oral Potentially Malignant Disorders (OPMDs) and Oral Squamous Cell Carcinoma (OSCC) and to explore its potential role in oral carcinogenesis.

MATERIALS AND METHODS: A total of 32 histopathologically confirmed cases (18 OPMDs and 14 OSCC) were analyzed. Anaerobic cultures and polymerase chain reaction (PCR) were used to detect F. nucleatum. Immunohistochemistry (IHC) was performed to assess c-Myc expression. Statistical analysis was conducted using Mann-Whitney and Chi-square tests, with p < 0.05 considered significant.

RESULTS: F. nucleatum was detected in eight OSCC and two OPMD cases, with higher colony counts in OSCC. All samples were positive for c-Myc, but their expression levels varied. In OPMDs, positivity was mainly observed in the basal and suprabasal epithelial layers, whereas OSCC showed both peripheral and central tumor cell localization. F. nucleatum-positive OSCC cases demonstrated strong nuclear c-Myc staining (50-75% positive cells). Tobacco habits, particularly combined smoking and smokeless use, were more common in F. nucleatum-positive OSCC cases.

CONCLUSION: F. nucleatum colonization correlates with increased c-Myc expression in OPMDs and OSCC, supporting its possible role in microbially driven oral carcinogenesis. These findings suggest its potential as a prognostic biomarker and a therapeutic target.},
}

Humans
*Fusobacterium nucleatum/physiology
*Mouth Neoplasms/microbiology/metabolism/pathology
*Proto-Oncogene Proteins c-myc/metabolism
Female
Male
*Carcinogenesis/metabolism/pathology
Middle Aged
Aged
*Carcinoma, Squamous Cell/microbiology/metabolism/pathology
Adult
Fusobacterium Infections
Signal Transduction

@article {pmid41789326,
year = {2026},
author = {Yu, H and Li, F},
title = {Multi-Omics Mechanisms of Trimethylamine Oxide and Cardiovascular Disease: A Review.},
journal = {Reviews in cardiovascular medicine},
volume = {27},
number = {2},
pages = {44420},
pmid = {41789326},
issn = {2153-8174},
abstract = {Cardiovascular diseases (CVDs) rank among the most prevalent conditions globally, encompassing coronary heart disease, hypertension, cardiomyopathy, and heart failure. The global prevalence of CVD continues to rise despite available therapies such as interventional procedures and pharmacotherapy, which remain associated with high rates of recurrence and mortality. In recent years, with a deepening understanding of the human gut microbiome, researchers have discovered that gut microbiota and their metabolites play a significant role in the development and progression of cardiovascular diseases. Among these, trimethylamine N-oxide (TMAO), a major metabolite of gut microbiota, has garnered extensive attention. Thus, this review leverages a multi-omics perspective to compare the commonalities and differences in TMAO-related mechanisms across various cardiovascular diseases. Moreover, this review aims to construct a TMAO-driven pathogenic network and critically evaluate the translational potential of this metabolite as a disease biomarker and therapeutic target, alongside current challenges.},
}

@article {pmid41788774,
year = {2026},
author = {Patel, E},
title = {Dietary interventions for modulating the gut microbiome in PCOS management.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1713408},
pmid = {41788774},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/diet therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; Insulin Resistance ; Dysbiosis/diet therapy ; },
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) is a multifactorial endocrine disorder affecting about 10% of reproductive-age women. It is defined by insulin resistance, androgen excess, and chronic inflammation, which drive both reproductive and metabolic complications. Growing evidence suggests that gut microbiome dysbiosis contributes to PCOS by altering intestinal permeability, promoting endotoxemia, and worsening hormonal and metabolic dysfunction. Diet, as a modifiable factor, may offer a therapeutic route to restore microbial balance and improve outcomes.

OBJECTIVES: This review aims to (1) synthesize evidence on how diet shapes gut microbiome composition in PCOS; (2) evaluate the effects of specific dietary patterns on microbial diversity, insulin sensitivity, lipid metabolism, and hormonal regulation; and (3) identify dietary components that may improve clinical outcomes.

METHODS: Evidence from observational studies, randomized trials, and meta-analyses was reviewed to assess how dietary interventions influence gut microbiome modulation and PCOS outcomes. Dietary patterns-including the Mediterranean diet, low-glycemic index diets, anti-inflammatory diets, time-restricted eating, and probiotic supplementation-were examined for their effects on microbiota and metabolic or hormonal measures.

RESULTS: Dietary interventions can beneficially alter gut microbiota, reduce systemic inflammation, improve insulin sensitivity, and lower androgen levels. The Mediterranean diet enhances microbial diversity and is associated with reduced PCOS risk. Low-glycemic index diets improve metabolic and hormonal profiles by lowering insulin demand. Anti-inflammatory diets and time-restricted eating may restore microbial rhythmicity and reduce inflammatory and endocrine imbalances. Probiotic supplementation, particularly with Lactobacillus and Bifidobacterium, strengthens gut integrity and benefits metabolic and hormonal outcomes. A multi-component dietary plan integrating high-fiber foods, probiotics, anti-inflammatory nutrients, low glycemic load, and structured eating patterns is proposed.

CONCLUSION: Modulating the gut microbiome through diet is a promising, non-invasive, cost-effective strategy for PCOS management. By targeting insulin resistance, androgen excess, and inflammation, nutrition-based interventions can improve metabolic and reproductive outcomes. Long-term randomized trials are needed to strengthen causal evidence and guide personalized dietary approaches.},
}

Humans
*Polycystic Ovary Syndrome/diet therapy/microbiology
*Gastrointestinal Microbiome/physiology
Female
Insulin Resistance
Dysbiosis/diet therapy

@article {pmid41788695,
year = {2026},
author = {Xu, J and Cheng, C and Yu, K and Wang, Q and Peng, Y and Li, Y and Yao, W and Pi, Y and Yu, S and Han, Z and Wei, J and Chen, T and Yu, Y},
title = {Ocular Surface Microbiota Alterations Following FS-LASIK and Their Association With Postoperative Dry Eye.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {2148587},
pmid = {41788695},
issn = {1712-9532},
abstract = {PURPOSE: Given the limited evidence on ocular surface microbiota (OSM) changes after femtosecond laser-assisted in situ keratomileusis (FS-LASIK) and their link to dry eye (DE), this study aimed to compare microbial profiles in patients with and without postoperative DE, offering a basis for early detection and targeted treatment.

METHODS: Patients undergoing FS-LASIK were evaluated 3 months postoperatively and stratified into DE (N = 30) and non-DE groups (N = 30) based on ocular surface disease index (OSDI), TBUT, and the Schirmer I test. Corneal nerve alterations were assessed using IVCM. Conjunctival sac samples were collected pre- and postoperatively, and microbiota profiles were analyzed via 16S rRNA sequencing.

RESULTS: Comparative analysis of the OSM revealed significantly higher α-diversity in the DE group compared to the NDE group. At the phylum level, a decrease in Proteobacteria and an increase in Bacteroidetes were observed. At the genus level, Veillonella, Streptococcus, and Aggregatibacter were enriched, whereas Pseudomonas and Lactobacillus were depleted. The abundance of Staphylococcus was positively correlated with OSDI scores and negatively correlated with corneal nerve fiber length (CNFL), corneal nerve branch density (CNBD), corneal nerve fiber area (CNFA), and corneal nerve fractal dimension (CFracDim) (all p < 0.05). In contrast, Lactobacillus was positively associated with the Schirmer I test values and corneal nerve fiber density (CNFD) (p < 0.05). At baseline, patients in the DE group exhibited lower abundances of Cyanobacteria and Acinetobacter but higher levels of Verrucomicrobia and Akkermansia. Postoperative within-group comparisons further showed that, relative to baseline, the DE group had increased abundances of Staphylococcus, Veillonella, Ralstonia, and Aggregatibacter, along with decreased levels of Pseudomonas, Corynebacterium, and Helicobacter.

CONCLUSIONS: In summary, dysbiosis between the Staphylococcus and Lactobacillus genera may represent both a biomarker of DE susceptibility and a therapeutic target. Additionally, the preoperative microbial composition may influence postoperative dynamics and DE risk.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT06448468.},
}

@article {pmid41788690,
year = {2025},
author = {Kozik, AJ and Henderson, K and Salameh, L and Mahboub, B and Al Bataineh, MT and Huang, YJ},
title = {Respiratory Microbiota Associations with Asthma Across American and Emirati Adults: A Comparative Analysis.},
journal = {Applied microbiology (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {},
pmid = {41788690},
issn = {2673-8007},
support = {R01 AI129958/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: Clinical features of asthma are associated with differences in the lower airway microbiome. However, knowledge is limited on whether airway microbiota composition differs between individuals residing in different geographic regions and if asthma-associated differences in lower airway microbiota are similar between distinct populations.

METHODS: Existing 16S rRNA gene sequence data, generated from sputum collected from adults with or without asthma (n = 74) from two single-center cohort studies in the U.S. and United Arab Emirates, were re-processed for merged computational analysis using standard available tools. Potential differences between study sites, asthma status and specific clinical factors (inhaled corticosteroid use, ICS; obesity) were examined.

RESULTS: Differences in sputum bacterial composition, assessed by alpha- and beta-diversity measures, were associated with study site. Despite this, asthma-related differences were discerned in both cohorts. Specifically, sputum microbiota of asthmatic patients on ICS treatment displayed reduced bacterial phylogenetic diversity, compared to those not on ICS treatment (p = 0.006). Sputum bacterial composition also differed by obesity status (unweighted Unifrac distance PERMANOVA, p = 0.004). Specific genera were identified in both cohorts that were differentially enriched between obese vs. non-obese subjects, including Rothia and Veillonella (obesity-associated) and Campylobacter (non-obesity-associated).

CONCLUSIONS: Our findings suggest clinical factors associated with differences in the lower airway microbiome in asthma may transcend variation related to geographic area of residence.},
}

@article {pmid41788459,
year = {2026},
author = {Gadara, D and Schwaiger-Haber, M and Jackstadt, MM and Song, MG and Guo, Q and Barr, M and Bakulski, KM and Shriver, LP and Patti, GJ},
title = {Transient exposure to bisphenol F in early life affects the metabolic health of adults.},
journal = {Exposome},
volume = {6},
number = {1},
pages = {},
pmid = {41788459},
issn = {2635-2265},
support = {R35 ES028365/ES/NIEHS NIH HHS/United States ; },
abstract = {Although bisphenol F (BPF) is widely used in plastic products, there are concerns about its potential health risks. Here, we aimed to understand the long-term effects of a brief BPF exposure during development. We treated zebrafish larvae 7 days post-fertilization with 1 mg/L BPF for 48 hours. We then maintained the animals under standard conditions for 5 months and compared them to control adults never exposed to BPF. In addition to sequencing the gut microbiome, we profiled six different tissues and serum by metabolomics and lipidomics. Strikingly, we found widespread alterations in metabolites and lipids throughout the animal that were both sex and tissue specific. For example, over 60 lipid species were depleted in the livers of BPF-treated females but no changes were observed in male livers. At the tissue level, BPF treatment altered fatty acid oxidation uniquely in skeletal and cardiac muscle. This study shows that transient exposures limited to the developmental phase of life can induce metabolic abnormalities later in adulthood. Our findings highlight the importance of profiling specimens from early life by exposomics and suggest that, even with the introduction of regulatory measures, the adverse effects of BPF could persist in the population for a generation.},
}

@article {pmid41726958,
year = {2026},
author = {Khanal, S and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, C},
title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41726958},
issn = {2692-8205},
abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Remarkably, time-lapse microscopy revealed that Archangium exhibited markedly reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate), while maintaining robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.},
}

@article {pmid39344767,
year = {2024},
author = {Slobodnikova, L and Halasa, AI and Kalmanova, S and Calkovsky, B and Juricek, R and Malachovsky, I and Repiska, V and Skerenova, M and Janickova, M},
title = {Genetic factors affecting susceptibility to dental caries.},
journal = {Bratislavske lekarske listy},
volume = {125},
number = {10},
pages = {635-647},
doi = {10.4149/BLL_2024_98},
pmid = {39344767},
issn = {0006-9248},
mesh = {Humans ; *Dental Caries/genetics ; *Genetic Predisposition to Disease ; Dental Caries Susceptibility/genetics ; },
abstract = {Dental caries remains the most prevalent chronic, oral biofilm-associated disease affecting majority of the globe's population in all age categories. Despite enormous and revolutionary progress in omics technologies, it´s aetiology is not fully understood. The interest of current research is primarily focused on the identification and understanding of the crosstalk between main players such as host cell genome, oral microbiome´s genome, factors of immune response, saliva content and nutrition. For accurate, multi-omix analyses, it is essential to know which patient´s genes enter into crucial interactions. Identifying genes and understanding the mechanism of their action is the key for deeper understanding of their involvement in the pathogenesis of this disease. Serious alterations of these genes should be consequently used as markers to determine the extent of genetic predisposition to dental caries and identify susceptible patients. That should significantly improve the prevention, diagnostic and therapy of the disease with an individual approach and provide more efficient and effective implementation of newer preventive measures and novel therapeutic approaches in the management of the disease. This review focuses on contemporary evidence on genetics factors affecting dental caries and to provide an up-to-date comprehensive description and classification of the genes and their alterations influencing the disease. It also aims to delineate and discuss evidence gaps and potential novel applications of genetics in the context of recent advances (Tab. 2, Ref. 113). Text in PDF www.elis.sk Keywords: dental caries, candidate gene, genetic variation, multifactorial disease.},
}

Humans
*Dental Caries/genetics
*Genetic Predisposition to Disease
Dental Caries Susceptibility/genetics

@article {pmid41788329,
year = {2026},
author = {Wang, M and Huo, Y and Zhao, Y and Du, X and Yun, BW and Wu, J and Ying, X and Wei, F and Wang, Y and Lu, R and Chen, J and Wang, X and Yang, Q and Liu, L},
title = {Responses of Panax notoginseng (Burk.) F.H. Chen to cadmium stress: hormetic effects on growth, antioxidant systems, and rhizosphere microbial dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741415},
pmid = {41788329},
issn = {1664-302X},
abstract = {BACKGROUND: Cadmium (Cd) contamination poses a major threat to Panax notoginseng (Burk.) F.H. Chen cultivation, yet the dose-dependent thresholds separating adaptive responses from toxicity remain poorly understood, particularly at the level of rhizosphere microbial processes.

METHODS: A 75-day pot experiment was conducted using eight soil Cd concentrations (0-100 mg kg[-1]). Plant growth traits and antioxidant enzyme activities (SOD, POD, CAT) were measured. Rhizosphere microbial communities were characterized in terms of alpha and beta diversity, co-occurrence network structure, and predicted functional potential using PICRUSt2 and FAPROTAX.

RESULTS: Moderate Cd exposure (∼30 mg kg[-1]) enhanced plant growth and antioxidant enzyme activities, whereas high Cd (≥ 80 mg kg[-1]) caused physiological inhibition, consistent with a hormetic response. Microbial alpha diversity also peaked under moderate Cd but declined sharply at high Cd levels. Beta diversity differentiation was primarily driven by shifts in relative abundance rather than taxonomic turnover. Severe Cd stress reduced co-occurrence network connectivity and increased negative correlations, although several persistent core taxa (e.g., Granulicella) were maintained. Functional predictions indicated substantial functional redundancy, with key nutrient-cycling pathways largely retained despite pronounced network simplification.},
}

@article {pmid41788326,
year = {2026},
author = {Yin, X and Zeng, J and Li, Z and Chen, S and Xie, C and Li, X and Zhang, L and Pan, Y and An, J},
title = {Gut bacteriome alterations during high altitude exposure: a comprehensive analysis of different species.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762563},
pmid = {41788326},
issn = {1664-302X},
abstract = {With the increase of high-altitude sojourn population, more and more studies on hypoxia have been conducted, but the associated changes in gut bacteriome in different hypoxic environments need to be further investigated. Gut bacteriome plays an important role in host adaptation to high-altitude hypoxia, but the contribution of gut bacteriome in high-altitude hypoxia adaptation is still controversial and may be influenced by multiple factors. In this study, we reviewed the changes in diversity and composition of the gut bacteriome of different populations of animals in different highland hypoxic environments, clarified the dynamics of the gut bacteriome during exposure to high altitude, identified the core bacteriome that may contribute to host adaptation to hypoxic environments, and comprehensively considered the effects of multiple factors on the gut bacteriome.},
}

@article {pmid41788296,
year = {2026},
author = {Guo, ZL and Cui, MW and Dong, YL and Wang, S},
title = {The oral microbiome as a regulatory hub for systemic health: a systematic review of mechanistic links and clinical implications.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2635233},
pmid = {41788296},
issn = {2000-2297},
abstract = {BACKGROUND: The human oral microbiome is a highly diverse ecosystem with important roles in oral and systemic health. Beyond dental caries and periodontitis, oral dysbiosis has been increasingly implicated in the development of multiple non-communicable diseases.

OBJECTIVE: To systematically synthesize evidence on the mechanisms linking oral dysbiosis to systemic diseases and to summarize its diagnostic and therapeutic implications.

DESIGN: A systematic review was performed using major electronic databases. We screened 1,128 records and included 104 studies that met predefined eligibility criteria.

RESULTS: Evidence indicates that oral dysbiosis may influence systemic health through several mechanisms, including hematogenous dissemination of oral pathogens and virulence factors (e.g. lipopolysaccharide), chronic systemic inflammation, molecular mimicry in autoimmune disorders, and microbial metabolic byproducts. The reviewed studies support associations between oral microbiome alterations and atherosclerotic cardiovascular disease, type 2 diabetes, Alzheimer's disease, rheumatoid arthritis, and gastrointestinal cancers. The literature also highlights the promise of non-invasive oral microbiome-based biomarkers for early detection and disease monitoring. Emerging microbiome-modulating interventions, including probiotics, prebiotics, and bacteriophage therapy, show potential for restoring oral eubiosis and improving systemic outcomes.

CONCLUSIONS: Oral dysbiosis is an important regulator of systemic disease processes and a promising target for diagnosis, prevention, and therapy. Integrating oral health and oral microbiome assessment into broader disease management may improve outcomes, although methodological standardization and stronger causal evidence are still needed.},
}

@article {pmid41788258,
year = {2026},
author = {Keles, E and Celik, O},
title = {Metagenomic and microbiological analyses of historical manuscripts for bacterial community profiling and bacteria-related biodeterioration assessment.},
journal = {Microbial cell (Graz, Austria)},
volume = {13},
number = {},
pages = {117-130},
pmid = {41788258},
issn = {2311-2638},
abstract = {Bacteria are important agents in the biodeterioration of cultural heritage objects, including historical manuscripts. Characterizing bacterial communities and generating robust microbiological data has therefore become crucial for conservation and restoration strategies. In this study, we investigated the bacterial communities associated with biodeterioration in six historical manuscripts using both culture-dependent and culture-independent (Illumina MiSeq) approaches. Culture-dependent methods yielded only 16 viable and culturable isolates, highlighting the limitations of traditional techniques. In contrast, metagenomic analysis revealed a far richer and more diverse bacterial community, capturing both living and non-living microbial traces accumulated over centuries. Bacterial genera with known cellulolytic and/or proteolytic activities, such as Bacillus, Stenotrophomonas, Pseudomonas and Acinetobacter, were identified as part of a core microbiome commonly associated with paper deterioration. High abundances of gut-associated bacteria (Prevotella, Faecalibacterium, Bacteroides, Porphyromonas) and human-related taxa (Staphylococcus, Streptococcus, Cutibacterium) indicated extensive historical human handling. A notable finding was the detection of Pseudonocardia broussonetiae, an endophytic bacterium associated with paper mulberry (Broussonetia papyrifera), suggesting the possible use of this plant as a papermaking material in one manuscript. This represents an important contribution to understanding Islamic paper production. Overall, our results demonstrate that effective conservation strategies require a detailed understanding of each manuscript's microbial ecology, together with evidence of past environmental conditions, handling history, and production materials.},
}

@article {pmid41788170,
year = {2026},
author = {Koh, YC and Pan, MH},
title = {Pterostilbene-mediated microbiota shifts: Implications and opportunities.},
journal = {Journal of traditional and complementary medicine},
volume = {16},
number = {2},
pages = {131-142},
pmid = {41788170},
issn = {2225-4110},
abstract = {Pterostilbene, a natural stilbene compound present in blueberries and several medicinal plants, has been increasingly studied for its ability to influence gut microbiota composition across different disease contexts. In a variety of animal and cell-based models, researchers have observed notable shifts in microbial profiles following pterostilbene supplementation. These changes are thought to be, at least in part, responsible for the compound's health-promoting properties, especially in relation to disease prevention and immune regulation. Despite these findings, no in-depth review has yet compiled the specific bacterial taxa most consistently affected by pterostilbene, nor analyzed the broader physiological significance of such changes. In this narrative review, we aim to address that gap by synthesizing current knowledge on the gut microbiota-modulating effects of pterostilbene. Particular focus is placed on beneficial genera that are frequently enriched, such as Akkermansia, Bifidobacterium, Faecalibacterium prausnitzii, Roseburia, and Lactobacillus. These microbes are often associated with key functions like intestinal barrier support, immune homeostasis, and the production of short-chain fatty acids. By linking microbial alterations to potential host benefits, we hope this review will inform future studies that explore pterostilbene as a microbiota-targeted therapeutic agent. Moreover, considering that this compound is found in many herbal medicines, our discussion may also offer valuable insights for research at the intersection of microbiome science and traditional medicine.},
}

@article {pmid34333553,
year = {2022},
author = {Howard, MM and Bass, E and Chautá, A and Mutyambai, D and Kessler, A},
title = {Integrating plant-to-plant communication and rhizosphere microbial dynamics: ecological and evolutionary implications and a call for experimental rigor.},
journal = {The ISME journal},
volume = {16},
number = {1},
pages = {5-9},
pmid = {34333553},
issn = {1751-7370},
mesh = {Plant Roots ; Plants ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {The perception of airborne chemical signals by plants can trigger reconfigurations of their metabolism that alter their biotic interactions. While plant-to-plant chemical communication has primarily been studied in the context of eliciting defenses to herbivores and pathogens, recent work suggests that it can also affect plants’ interactions with their rhizosphere microbiomes. In this perspective, we discuss the potential for integrating the fields of plant-to-plant communication and microbial ecology to understand the chemical ecology of plant−microbiome interactions. As an introduction for microbial ecologists, we highlight mechanistic knowledge gaps in plant volatile organic compound (VOC) perception and provide recommendations for avoiding common experimental errors that have plagued the plant communication field. Lastly, we discuss potential implications of plant VOCs structuring rhizosphere microbiomes, particularly effects on plant community and evolutionary dynamics. As we continue to discover links between plant metabolism and their microbiomes—from molecular to community scales—we hope that this perspective will provide both motivation and words of caution for researchers working at the intersection of these two fields.},
}

Plant Roots
Plants
*Rhizosphere
*Soil Microbiology

@article {pmid41788069,
year = {2026},
author = {Fedosova, N and Symchych, T and Gogol, S and Cheremshenko, N and Virych, P and Voyeykova, I and Chekhun, V},
title = {INFLUENCE OF BIFIDOBACTERIUM ANIMALIS SUBSP. LACTIS BB-12 AND LACTOBACILLUS RHAMNOSUS GG ON POLARIZATION OF TUMOR-ASSOCIATED MACROPHAGES.},
journal = {Experimental oncology},
volume = {47},
number = {4},
pages = {451-458},
doi = {10.15407/exp-oncology.2025.04.451},
pmid = {41788069},
issn = {2312-8852},
mesh = {Animals ; *Lacticaseibacillus rhamnosus ; Female ; Mice ; *Carcinoma, Ehrlich Tumor/pathology/immunology/microbiology ; *Probiotics/pharmacology ; Mice, Inbred BALB C ; *Bifidobacterium animalis ; Nitric Oxide/metabolism ; *Tumor-Associated Macrophages/immunology/metabolism ; Reactive Oxygen Species/metabolism ; Arginase/metabolism ; },
abstract = {BACKGROUND: The microbiota has a significant impact on the host's immune system. However, the influence of the microbiome is heavily dependent on species, strain, and context. The aim of this study was to evaluate the influence of Bifidobacterium animalis subsp. lactis BB-12 (BB-12) and Lactobacillus rhamnosus GG (LGG) supplementation on the polarization of tumor-associated macrophages (TAMs) in mice with Ehrlich carcinoma.

MATERIALS AND METHODS: Female Balb/c mice bearing solid Ehrlich carcinoma were administered via gavage with BB-12, LGG, or 0.9% NaCl. On days 14, 21, and 28 of tumor growth, macrophages from tumor tissue were isolated and subjected to functional analysis. The nitric oxide (NO) production was measured using the standard Griess reaction. The arginase activity was determined based on the urea measurements. The reactive oxygen species (ROS) production was checked using flow cytometry. The cytotoxic activity was estimated by an MTT assay.

RESULTS: The application of different probiotic bacteria elicited different TAM polarization states. The TAMs in the group supplemented with LGG demonstrated M1 polarization with low arginase activity but high production of NO and ROS, as well as cytotoxic activity toward Ehrlich carcinoma cells. The TAMs of BB-12-treated mice exhibited M2 (supposedly M2b) polarization, characterized by high arginase activity alongside the preserved cytotoxic activity toward Ehrlich carcinoma cells in vitro.

CONCLUSION: The results indicate that the consumption of two probiotics, BB-12 and LGG, affects the polarization of TAMs in distantly located experimental tumors.},
}

Animals
*Lacticaseibacillus rhamnosus
Female
Mice
*Carcinoma, Ehrlich Tumor/pathology/immunology/microbiology
*Probiotics/pharmacology
Mice, Inbred BALB C
*Bifidobacterium animalis
Nitric Oxide/metabolism
*Tumor-Associated Macrophages/immunology/metabolism
Reactive Oxygen Species/metabolism
Arginase/metabolism

@article {pmid41788021,
year = {2026},
author = {Mezera, CC and Steffan, S and Holland, LA},
title = {Pollinator Visitation Alters Cranberry Flower Fungal Communities in Wisconsin Cranberry Agroecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70310},
pmid = {41788021},
issn = {1758-2229},
support = {AWD00000457//U.S. Department of Agriculture/ ; },
mesh = {*Vaccinium macrocarpon/microbiology/physiology ; Animals ; *Flowers/microbiology ; *Pollination ; *Fungi/classification/isolation & purification/genetics ; Wisconsin ; Bees/microbiology/physiology ; *Mycobiome ; Plant Diseases/microbiology ; Diptera/microbiology ; },
abstract = {Pollinators are known dispersal agents of microbial communities between flowering plants, although the role of insect-mediated microbial assembly in flowering agricultural crops is not well understood. In cranberry (Vaccinium macrocarpon Ait.) agroecosystems, the blossom period is a vulnerable time for infection from pathogens within the cranberry fruit rot fungal disease complex, and understanding the components and assembly dynamics in cranberry flower fungal communities may provide important insights to the relationship between the cranberry microbiome and crop health. This 2-year study uses a combination of culture-dependent and next-generation sequencing approaches to compare the community structure of cranberry flowers, honey bees (Apis mellifera), bumble bees (Bombus sp.), wild solitary bees, hover flies (Syrphidae), and nearby wildflowers to identify shared fungal associates. Compared to a tenting treatment in cranberry flowers used to prevent insect visitation, cranberry flowers with access to pollinators have higher detection of fungal genera in culture, as well as more fungal genera identified through culture-independent methods. Fungi associated with the cranberry fruit rot complex were identified in several insect groups, with the highest proportion of identified fruit rot fungi detected in Toxomerus fly samples. This research provides the first evidence of shared fungal communities between pollinators and managed cranberry flowers.},
}

*Vaccinium macrocarpon/microbiology/physiology
Animals
*Flowers/microbiology
*Pollination
*Fungi/classification/isolation & purification/genetics
Wisconsin
Bees/microbiology/physiology
*Mycobiome
Plant Diseases/microbiology
Diptera/microbiology

@article {pmid41788004,
year = {2026},
author = {Kumar, D and Gupta, V and Jaiswal, NK and Tanwar, R},
title = {Antibiotics and Metabolic Dysregulation After Surgery: Exploring an Overlooked Connection.},
journal = {Current diabetes reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733998425015260116113449},
pmid = {41788004},
issn = {1875-6417},
abstract = {Hypertension and hyperglycemia are common in patients without metabolic disease even after surgery and are generally considered to have been caused by surgical stress and inflammation. Nonetheless, in the case of long-term or repeated exposure to perioperative antibiotics, this can be a hidden cause of disturbances. Broad-spectrum antibiotics may interfere with gut microbiota, decrease short-chain fatty acid synthesis, and impair mitochondrial function and vascularity, thereby facilitating the development of insulin resistance and metabolic instability. Observational cohort evidence associates cumulative exposure to antibiotics with the risk of developing type 2 diabetes, whereas experimental models show that antibiotics cause glucose intolerance via the mechanism of dysbiosis. There are also clinical observations that, in certain patients, suitable parameters of the metabolic condition return to normal only on removal of antibiotics. These mechanisms can interact with surgical stress, especially in metabolically vulnerable individuals. This hypothesis-generating editorial demonstrates the need to explore antibiotic-related metabolic changes during postoperative care and to implement microbiome-informed interventions in perioperative practice and antibiotic stewardship.},
}

@article {pmid41787837,
year = {2026},
author = {Orozco-Mosqueda, MDC and Flores-Piña, A and Kumar, A and Parra-Cota, FI and de Los Santos-Villalobos, S and Mitra, D and Babalola, OO and Santoyo, G},
title = {Impact of Fire and Heat Stress on Soil Microorganisms: A Review of Community Changes, Molecular Responses and Plant-Beneficial Roles.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70247},
pmid = {41787837},
issn = {1758-2229},
mesh = {*Soil Microbiology ; *Fires ; Fungi/genetics/classification/metabolism ; Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Soil/chemistry ; *Heat-Shock Response ; Plants/microbiology ; Hot Temperature ; },
abstract = {Fire, whether occurring on the surface or underground, significantly influences soil microbial dynamics by reshaping community composition, functional diversity and overall soil and plant health. This review examines the effects of fire on soil-beneficial microbial communities, with particular attention to how surface and underground fires drive shifts in microbial diversity and functional roles within the agroecosystems. These changes impact key processes such as nutrient cycling, soil physicochemical structure and organic matter decomposition, ultimately affecting crop production. Bacterial groups such as Firmicutes and Actinobacteria often increase in abundance following fire events, while others lacking survival strategies tend to decline. Resilient fungal groups, including Ascomycota (such as Aspergillus, Penicillium and Trichoderma), frequently play pivotal roles during the recovery process. Fire can also enhance microbial metabolic activity, particularly in pathways involved in organic matter degradation, leading to short-term increases in nutrient availability that support plant regrowth. Finally, the review discusses the molecular responses of microbes to fire and outlines perspectives for better understanding this type of stress and how it affects the beneficial soil microbiota in agricultural edaphic systems.},
}

*Soil Microbiology
*Fires
Fungi/genetics/classification/metabolism
Bacteria/genetics/classification/metabolism/isolation & purification
*Microbiota
Soil/chemistry
*Heat-Shock Response
Plants/microbiology
Hot Temperature

@article {pmid41787816,
year = {2026},
author = {Shi, Y and Lin, X and Wang, L and Ou, Y and Wu, Q and Song, M},
title = {Engineered Biomimetic Nanoparticles With Targeted Delivery of Chlorothiazide for the Treatment of Inflammatory Bowel Disease.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e25914},
doi = {10.1002/anie.202525914},
pmid = {41787816},
issn = {1521-3773},
support = {82201873//National Natural Science Foundation of China/ ; 2408085QH239//Natural Science Foundation of Anhui Province/ ; 2025AHGXZK31379//University Natural Science Research Key Project of Anhui Province/ ; 2025AHGXZK31514//University Natural Science Research Key Project of Anhui Province/ ; BK20241589//Natural Science Foundation of Jiangsu Province/ ; BK20220202//Natural Science Foundation of Jiangsu Province/ ; 2022M723510//Project funded by China Postdoctoral Science Foundation/ ; 2022ZB294//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; LH250104002//Longhu Talent Project of Bengbu Medical University/ ; bsqd202427//Research Foundation for Advanced Talents from Bengbu Medical University/ ; 2025SYKFD15//Anhui Provincial Engineering Research Center for Biochemical Pharmaceuticals/ ; },
abstract = {While conventional treatment strategies for inflammatory bowel disease (IBD) focus primarily on suppressing overactive immunity, there is still a lack of definitive interventions targeting key pathological mechanisms, such as intestinal barrier dysfunction, dysbiosis of the gut microbiome, and disrupted mucosal immune regulation. Using a high-throughput drug screening platform, the present study successfully identified chlorothiazide (Chl), a lead compound with anti-inflammatory potential, from a library of 3152 natural compounds. To further increase the bioavailability of Chl and mitigate its potential toxicity, we constructed a biomimetic delivery system based on engineered bacterial membrane-encapsulated reactive oxygen species (ROS)-responsive biomimetic nanoparticles (CHM NPs). This delivery system achieved targeted accumulation in inflamed colonic tissue in a mouse model of acute colitis and effectively facilitated the restoration of epithelial barrier function. Moreover, CHM NPs significantly altered the gut microbiome, increasing overall microbial abundance and diversity while increasing the abundance of gut Lactobacillus, which plays a crucial role in maintaining gut microecological homeostasis. We systematically elucidated the multifaceted mechanisms by which CHM NPs regulate gut homeostasis, remodel the microbial composition, and modulate innate immunity. These findings provide novel theoretical foundations and potential intervention strategies for the treatment of IBD and other related inflammatory conditions.},
}

@article {pmid41787616,
year = {2026},
author = {Stoehr, MC and Martin, EM and Babalola, JT and Xue, J and Kern, MJ and Li, NY and Winters, MF and Bhagwagar, S and Smith, CJ},
title = {Effects of combined prenatal exposure to air pollution and maternal stress on social behavior and oxytocin and vasopressin systems in male and female mice.},
journal = {Journal of neuroendocrinology},
volume = {38},
number = {3},
pages = {e70151},
pmid = {41787616},
issn = {1365-2826},
support = {R00ES033278/ES/NIEHS NIH HHS/United States ; },
abstract = {Prenatal exposures to air pollution and maternal psychosocial stress are each associated with increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), and epidemiological work suggests that concurrent exposure to these risk factors may be particularly harmful. This is important given that the same populations often bear the brunt of both toxicant and psychosocial stress burdens. Social impairments are a defining symptom in ASD. Previous work modeling combined prenatal exposure to diesel exhaust particles (DEPs) and maternal stress (MS) in rodents has found male-biased social deficits in offspring, as well as changes to neuroimmune processes and the gut microbiome. However, the precise neural circuits on which these exposures converge to impact social behavior are unclear. Oxytocin (OXT) and vasopressin (AVP) are neuropeptides critical to the regulation of social behavior across species, signaling primarily at the oxytocin receptor (Oxtr) and vasopressin V1a receptor (V1aR) in the brain. Here, we hypothesized that OXT and/or AVP expression would be reduced in the brain following DEP/MS exposure. Following prenatal exposure to DEP/MS or the vehicle/control condition (VEH/CON), we measured maternal and offspring outcomes during the perinatal period, social and anxiety-like behavior during adolescence, OXT and AVP cell/fiber density, and Oxtr and Avpr1a mRNA expression in early adulthood in several brain regions in both males and females. We observed a decrease in interaction time in DEP/MS males as compared to VEH/CON in the sociability assay and a decrease in social novelty preference in DEP/MS females as compared to VEH/CON. No effects of sex or treatment were observed on OXT or AVP cell number or fiber density in the hypothalamic regions assessed. However, numerous sex differences were observed in Oxtr and Avpr1a mRNA. Moreover, Avpr1a mRNA was significantly increased following DEP/MS exposure in the nucleus accumbens in both sexes and trended towards increasing in the dorsal hippocampus. Together, these findings suggest that DEP/MS exposure has a stronger impact on female social behavior than previously observed. Moreover, while DEP/MS exposure does not appear to impact OXT or AVP expression in the brain, V1aR expression is modulated by DEP/MS exposure in the nucleus accumbens.},
}

@article {pmid41787564,
year = {2026},
author = {Luo, F and Cai, Y and Cui, Y and He, X and Xu, J and Tang, W and Wang, X and Cai, Y and Xie, H and Chen, W and Li, W and Ding, X},
title = {Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02359-z},
pmid = {41787564},
issn = {2049-2618},
support = {CARS-01-09//the earmarked fund for the China Agriculture Research System/ ; 32260023, 31560041//National Natural Science Foundation of China/ ; 20232ACB205006//Key Project of Jiangxi Natural Science Foundation/ ; },
abstract = {BACKGROUND: Crop wild relatives and their microbiomes are essential for sustainable crop production. However, the co-evolution of wild rice species and their microbiomes remains poorly understood. Herein, we investigated microbiome assembly across 17 wild rice and one cultivated rice species under controlled conditions spanning ~15 million years of evolution.

RESULTS: Our data reveal distinct eco-evolutionary patterns for bacteria and fungi. Host divergence time was the predominant driver of root microbiota structure, outweighing polyploidy and life cycle, and exerted a stronger effect on bacteria than fungi. Bacterial community exhibited a significant phylosymbiosis with its host, but fungi did not. Over evolutionary time, bacterial diversity decreased while phylogenetic clustering increased. Deterministic and stochastic processes co-drove bacteria assembly, whereas stochastic processes strongly drove fungi assembly. Potentially functional taxa, including nitrogen-fixing and methane-cycle bacteria, were differentially enriched across evolutionary time and polyploidization events. Notably, co-speciating bacteria better predicted grain weight than fungi, with core species making a major contribution. Using a synthetic community (SynCom) derived from the wild rice core microbiome and four nitrogen-fixing strains enriched in early- and medium-diverging Oryza species, we demonstrated that the SynCom strongly promoted rice growth, with the removal of key members markedly reducing its impact.

CONCLUSIONS: These results reveal co-phylogenetic patterns between Oryza and root-associated bacteria, highlighting the closer functional linkage between rice traits and bacteria than fungi, likely due to their co-evolution. Our findings provide new insights into crop-microbiome symbiosis from an eco-evolutionary perspective and underscore the importance of co-speciating microbiomes from wild relatives in supporting crop growth. Video Abstract.},
}

@article {pmid41787488,
year = {2026},
author = {Gu, C and Qi, Y and Xie, Y and Yang, L and Wang, G and Zhou, J and Ren, J and Liu, S and Zhu, G and Li, W and Hu, W and Chen, Y and Liu, D},
title = {A lung microbial signature for postoperative recurrence in stage I-II non-small cell lung cancer.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03609-2},
pmid = {41787488},
issn = {1465-993X},
support = {82300011//National Natural Science Foundation of China/ ; 82173182//National Natural Science Foundation of China/ ; 2024ZD0529501 / 2024ZD0529500//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2023NSFSC1939//Science and Technology Program of Sichuan Province/ ; },
}

@article {pmid41787302,
year = {2026},
author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W},
title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12725-8},
pmid = {41787302},
issn = {1471-2164},
support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; },
}

@article {pmid41787261,
year = {2026},
author = {Dühr, H and Pärnänen, K and Kucháriková, N and Werner, P and Pershagen, G and Lahti, L and Alenius, H and Bergström, A and Ruuskanen, MO and Fyhrquist, N},
title = {Lifestyle associates with unique resistome and microbiome signatures in children.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04665-2},
pmid = {41787261},
issn = {1471-2180},
}

@article {pmid41787031,
year = {2026},
author = {Jiang, EX and Quarta, G and Delau, O and Shaukat, A},
title = {Mutations in Exon 29 of Ring Finger Protein 213 Are Associated with Early-Onset Colorectal Cancer.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41787031},
issn = {1573-2568},
abstract = {BACKGROUND AND AIMS: Growing evidence suggests that the gut microbiome plays a role in carcinogenesis for early-onset colorectal cancer (EOCRC). The novel Ring Finger Protein 213 (RNF213) gene has broad antimicrobial properties. Our study aimed to compare RNF213 mutation rates in EOCRC and late-onset colorectal cancer using data from the cBioPortal for Cancer Genomics.

METHODS: All participants from the cBioPortal with CRC samples that profiled the RNF213 gene were included. Multivariable logistic regression was used to assess the association between EOCRC and primary tumor RNF213 mutation. Cox proportional hazards models were used to evaluate the influence of RNF213 mutation on all-cause mortality risk. All tests were two-sided.

RESULTS: 1594 participants with CRC from six cohorts were included, of which 7.8% (N = 125) had EOCRC. Participants with EOCRC were more likely to have late-stage CRC (p < 0.001) and left-sided tumors (p < 0.001). Participants with a mutation in exon 29 of RNF213 had significantly increased odds of EOCRC diagnosis (adjOR 3.82, 95% CI 1.82, 7.54) compared to participants with wild-type RNF213, while mutations in other exons did not confer significantly increased odds of EOCRC diagnosis (adjOR 1.61, 95% CI 0.72, 3.22). There was no significant difference in all-cause mortality risk by RNF213 mutation status.

CONCLUSIONS: Primary tumor mutations in exon 29 of the RNF213 gene are associated with significantly increased odds of EOCRC diagnosis in a multicohort sample of participants with CRC. Future studies of germline and precancerous RNF213 mutations are needed to elucidate its possible role in EOCRC tumorigenesis.},
}

@article {pmid41786774,
year = {2026},
author = {Moiseyenko, A and Antonello, G and Schonhoff, AM and Boktor, JC and Long, K and Dirks, B and Oguienko, AD and Winnett, AV and Simpson, P and Daeizadeh, D and Ismagilov, RF and Krajmalnik-Brown, R and Segata, N and Waldron, LD and Mazmanian, SK},
title = {Faecalibacterium prausnitzii, depleted in the Parkinson's disease microbiome, improves motor deficits in α-synuclein overexpressing mice.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01287-x},
pmid = {41786774},
issn = {2373-8057},
support = {ASAP-020495; ASAP-000375//Aligning Science Across Parkinson's/ ; },
abstract = {Gut microbiome composition is altered in Parkinson's disease (PD), the fastest-growing neurological condition, that is characterized by neurodegeneration, motor dysfunction, and is frequently accompanied by gastrointestinal (GI) symptoms. Notably, microbial taxa with anti-inflammatory properties are consistently depleted in PD patients compared to controls. To explore whether specific gut bacteria may be disease-protective, we assembled a microbial consortium of 8 human-associated taxa that are reduced in individuals with PD. Treatment of α-synuclein overexpressing (Thy1-ASO) mice, an animal model of PD, with this consortium improved motor and GI deficits. A single bacterial species from this consortium, Faecalibacterium prausnitzii, was sufficient to correct gut microbiome deviations in Thy1-ASO mice, induce anti-inflammatory immune responses, and promote protective colonic gene expression profiles. Accordingly, oral treatment with F. prausnitzii robustly ameliorated motor and GI deficits and reduced α-synuclein aggregates in the brain. These findings support the emerging hypothesis of functional contributions by the microbiome to PD outcomes, and embolden the development of potential probiotic therapies to treat motor and non-motor symptoms.},
}

@article {pmid41786764,
year = {2026},
author = {Franciosa, I and Castelnuovo, G and Cantele, C and Cardenia, V and Bo, S and Ponzo, V and Goitre, I and Pontonio, E and Tortarolo, D and Verni, M and Bugianesi, E and Cordero, F and Beccuti, M and Cocolin, L and Ferrocino, I},
title = {Gut microbiome modulation by cricket, pea, and whey protein using the SHIME in vitro simulator.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00785-9},
pmid = {41786764},
issn = {2396-8370},
support = {D17G22000150001//NODES funding from the MUR - M4C2 1.5 of PNRR, funded by the European Union - NextGenerationEU, Mission 4 Component 1.5 - ECS00000036/ ; },
abstract = {Entomophagy is increasingly popular, and Acheta domesticus offers an ecologically sustainable protein alternative, but the effects on the human gut microbiome need further investigation. In this study, we investigated the impact of the intake of three isolated proteins: pea (plant), whey (animal), and cricket (insect) on gut microbiome of a single-donor using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®). Cricket protein intake was associated with potential beneficial taxa such as Bifidobacterium and Lactobacillus, genes related to vitamin biosynthesis and bacteriocin transport, and short and medium-chain fatty acids. Pea protein intake was associated with Faecalibacterium and Slackia, while whey protein with Butyricimonas and Lactobacillus. Metagenomic analysis revealed that pea intake led to increased lysine degradation genes, promoting SCFAs production. Each protein has its own unique characteristics that may contribute positively to gut health. Specifically, cricket protein intake appears to have beneficial effects, promoting the growth of potentially beneficial taxa and enhancing short-chain fatty acid production. The results of this study indicate that cricket protein does not exhibit any detrimental effects compared to pea and whey proteins.},
}

@article {pmid41786749,
year = {2026},
author = {Chechi, K and Chakaroun, R and Myridakis, A and Forslund-Startceva, SK and Fromentin, S and Nielsen, T and Aron-Wisneswky, J and Belda, E and Prifti, E and Lassen, PB and Falony, G and Vieira-Silva, S and Chilloux, J and Sonomura, K and Hoyles, L and Martinez-Gili, L and Pallotti, F and Andrikopoulos, P and Puig-Castellví, F and Tapia, RP and Castro-Dionicio, I and Roume, H and Pons, N and Le Chatelier, E and Quinquis, B and Galleron, N and Berland, M and Olanipekun, MT and Jia, M and Manolias, A and Holmes, B and Adriouch, S and Blüher, M and Coelho, LP and Da Silva, K and Galan, P and Ji, B and Neves, AL and Rouault, C and Salem, JE and Tremaroli, V and Hansen, TH and Søndertoft, NB and Lewinter, C and Pedersen, HK and , and Mark, PD and Goetze, JP and Køber, L and Vestergaard, H and Hansen, T and Zucker, JD and Sato, TA and Hercberg, S and Bäckhed, F and Letunic, I and Oppert, JM and Nielsen, J and Raes, J and Tzoulaki, I and Dehghan, A and Zuber, V and Bouzigon, E and Lathrop, M and Raina, P and Froguel, P and Matsuda, F and Demenais, F and Gauguier, D and Stumvoll, M and Bork, P and Pedersen, O and Ehrlich, SD and Clément, K and Dumas, ME},
title = {A gut microbiome-kidney-heart axis predictive of future cardiovascular diseases.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69405-0},
pmid = {41786749},
issn = {2041-1723},
support = {HEALTH-F4-2012-305312//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
abstract = {Cardiovascular diseases (CVD) remain a major global health challenge. Early markers of disease initiation and progression are urgently needed. We, and others, have previously shown changes in the gut microbiome in association with metabolic and CVD. Here, we demonstrate that gut microbiome-related changes can be detected in association with subclinical variations in heart and kidney function. Markers related to gut microbial metabolism of aromatic amino acids, phenylalanine and tyrosine, associate with circulating pro-atrial natriuretic peptide and estimated glomerular filtration rate in a metabolically healthy European population. Observational and genetic evidence further identify microbiome-related metabolites as mediators of this gut microbiome-kidney axis, with their baseline levels associating with incident CVD in an external Canadian population. Altogether, our work suggests that the gut microbiome interacts with the cardiorenal axis and participates in an interorgan crosstalk affecting host physiology and risk of CVD.},
}

@article {pmid41786640,
year = {2026},
author = {Santana, AE and Torres, SMF and Costa, MO},
title = {Skin Commensal Microbiota Does Not Influence the Clinical Course of Dermatophyte Infection in Persian Cats.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.70058},
pmid = {41786640},
issn = {1365-3164},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {BACKGROUND: Dermatophytes can be isolated from both symptomatic and asymptomatic cats, yet the role of skin commensals in modulating disease expression remains unclear. This study investigates whether microbial skin communities influence the clinical presentation (symptomatic or asymptomatic) of dermatophyte infection in Persian cats.

HYPOTHESIS/OBJECTIVES: We hypothesised that the fungal and bacterial skin microbiota differ between Persian cats with and without clinical signs of dermatophytosis. The objectives of this study were to compare the fungal and bacterial skin microbiota among healthy, symptomatic, and asymptomatic cats with dermatophytosis and to evaluate the performance of two skin sampling methods (carpet and toothbrush) for microbiome analysis.

ANIMALS: Forty-five cats.

MATERIAL AND METHODS: Cats were grouped according to clinical presentation: Persian cats with skin lesions characteristic of dermatophytosis (multifocal alopecia and scaling) and a positive fungal culture (symptomatic group; n = 15), Persian cats with no skin lesions and a positive fungal culture (asymptomatic group; n = 15), and domestic short hair cats with no history and clinical signs of skin disease and negative fungal culture (negative group; n = 15). Hair and scale samples were collected using carpet and toothbrush techniques from all animals. Fungal and bacterial communities were investigated using high-throughput sequencing targeting internal transcribed spacer (ITS)1 and 16S ribosomal (r)RNA genes.

RESULTS: Our data showed that the taxonomic composition of fungal and bacterial communities was similar between symptomatic and asymptomatic cats, regardless of the sampling method used. No notable differences were identified in the relative abundance of Microsporum spp. between symptomatic and asymptomatic cats.

Our findings suggest that the commensal microbiota may not influence the clinical presentation of dermatophyte infection. Instead, other factors, such as the host immune response, appear to play a pivotal role in determining disease outcomes.},
}

@article {pmid41786560,
year = {2026},
author = {Albright, JD and Haug, LI},
title = {Bidirectional Communication: The Gut-Brain Axis in Companion Animal Health.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2026.01.008},
pmid = {41786560},
issn = {1878-1306},
abstract = {The microbiome-gut-brain axis (MGBA) is a complex network of gastrointestinal (GI) microbiota and host enteric, immune, neural, endocrine, and metabolic pathways. Disruptions to homeostasis promote dysbiosis, immune dysregulation, inflammation, and vagal signal disruption. Many disease states and behavioral disorders are associated with a change in GI microbial composition and diversity. Psychoactive treatments may specifically target the MGBA to reduce systemic and neuroinflammation linked to the pathogenesis of many GI and neuropsychiatric conditions.},
}

@article {pmid41786542,
year = {2026},
author = {Kobayashi, S and Nakagawa, H and Komai, M},
title = {Comprehensive analysis of tonsillar gene expression and the tonsillar microbiota in patients with palmoplantar pustulosis and pustulotic arthro-osteitis.},
journal = {Journal of dermatological science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jdermsci.2026.01.006},
pmid = {41786542},
issn = {1873-569X},
abstract = {BACKGROUND: Tonsillectomy improves symptoms in patients with palmoplantar pustulosis (PPP) and suppresses disease progression in patients with pustulotic arthro-osteitis (PAO), highlighting the important role of tonsils in the pathogenesis of PPP/PAO.

OBJECTIVE: To identify inflammatory pathways involved in the tonsil tissue of patients with PPP/PAO, and to clarify the characteristics of tonsillar microbiota.

METHODS: We assessed gene expression in tonsil tissue obtained from PPP/PAO or recurrent tonsillitis (RT)/sleep apnea syndrome (SAS) patients using microarray and quantitative reverse transcription polymerase chain reaction analysis. We also performed a comprehensive analysis of the tonsillar microbiota using next-generation sequencing. Potential associations between tonsillar gene expression and bacterial composition or disease activities were evaluated.

RESULTS: Twenty-five tonsils from PPP/PAO patients and 15 tonsils from RT/SAS patients were included. The gene expression of inflammatory cytokines and molecules involved in the Th17, Th2, and Treg pathways was significantly higher in PPP/PAO tonsils than in RT/SAS tonsils. A significant positive correlation between Streptococcus spp. and the expression of Th17 and Th2 pathway genes was revealed both in PPP/PAO and RT/SAS, however, different correlation patterns were observed between these groups for the other genera. PAO disease activity showed a negative correlation with the expression of CCR4, FOXP3, and CXCR3 genes.

CONCLUSION: PPP/PAO tonsils exhibit enhanced Th17, Th2, and Treg responses relative to RT/SAS, indicating a complex inflammatory condition. Streptococcus genus may be associated with inflammation, and interaction between microbiota and T cell immunity would be suggested in PPP/PAO tonsils. PAO disease activity inversely correlated with Treg response.},
}

@article {pmid41786183,
year = {2026},
author = {Long, Z and Li, J and Zhu, F and Liu, X and Zhoua, J and Li, J and Xu, W},
title = {From intestinal messenger to next-generation therapeutics: A review on mechanisms and prospects of host metabolic regulation mediated by P9, a secreted protein from Akkermansia muciniphila.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {151199},
doi = {10.1016/j.ijbiomac.2026.151199},
pmid = {41786183},
issn = {1879-0003},
abstract = {P9, a protein secreted by Akkermansia muciniphila (A. muciniphila), serves as a key bioactive effector and exhibits promising therapeutic potential for metabolic disorders. This review systematically elucidates the molecular mechanisms by which P9 mediates microbe-host interactions through activation of the intercellular adhesion molecule-2 (ICAM-2) and interleukin-6 (IL-6) signaling pathways. It also summarizes recent advances in P9 biomanufacturing, summarizing advances in its heterologous expression in Escherichia coli (E. coli) and Lactobacillus lactis (L. lactis), and proposes innovative delivery strategies using engineered probiotics or nanocarriers to bypass gastrointestinal barriers. In addition, we explore the modular structure of P9 proteins predicted by AlphaFold, revealing potential domains amenable to functional optimization through protein engineering. By combining mechanistic insights with bioengineering approaches, this review positions engineered P9 as a multifunctional candidate for developing oral, targeted, and sustained-release therapies against obesity and type 2 diabetes mellitus (T2DM). This strategy offers new avenues for linking fundamental gut microbiome research with translational metabolic medicine applications.},
}

@article {pmid41786113,
year = {2026},
author = {Huang, P and Gao, J and Cao, L and Li, J and Du, J and Xu, G},
title = {Effects of subchronic exposure to PFOA and nanoplastics on the gills of Eriocheir sinensis: Perspectives from the transcriptome, microbiome and physiology.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110502},
doi = {10.1016/j.cbpc.2026.110502},
pmid = {41786113},
issn = {1532-0456},
abstract = {PFOA and NPs are recognized as persistent organic pollutants with potential ecological risks in aquatic ecosystems, and they exhibit specific toxic effects on benthic invertebrates. As a vital respiratory organ of aquatic animals, the gill plays a key role in gas exchange and osmoregulation. However, studies on the potential adverse impacts of these two pollutants on the gill tissue remain scarce. In the present study, we conducted a 28-day stress experiment with the Eriocheir sinensis as a research model and systematically investigated the toxic effects of PFOA/NPs on gill organs by multi-omics sequencing. At the biochemical level, PFOA/NPs inhibited the activity and transcription of antioxidant enzymes (CAT, T-SOD, and GSH) or genes (gpx, gstd7), while triggering oxidative stress (MDA) and causing morphological damage. Moreover, PFOA/NPs induced inflammation (TNF-α, hil-6), apoptosis, autophagy (bnip3, stk17a, lc3a, epg5), suppression of immune responses (fcn, lyz), and disruption of glycolipid metabolism (fasn, acsl14, srebf1, acsly). In addition, the PFOA-NPs co-exposure disrupted the microbial flora structure in gill tissues, including reduced community evenness, increased dominance of specific species, and heightened abundances of both environmental organic pollutant-degrading microbes and opportunistic pathogens (Acidovorax, Sphaerotilus, Candidatus_Bacilloplasma). Furthermore, PFOA-NPs may disrupt microbial physiological homeostasis by suppressing the "LPS biosynthesis-antibiotic production-GAG degradation-lysosomal function" axis. These findings indicate that the gill organs of aquatic crustaceans are highly sensitive to organic pollutants such as PFOA and NPs, and long-term exposure disrupts their tissue physiology and microbial community homeostasis, thereby providing critical data to support the ecotoxicological assessment of PFOA/NPs in aquatic ecosystems.},
}

@article {pmid41785880,
year = {2026},
author = {Petersen, AØ and Damholt, B and Grove, M and Hink, J and Marotte-Hurbon, T and Söderqvist, J and Troy, A and Zdravkovic, M and Bayer, L and Brunner, K and Bryde, T and Clube, J and Gencay, YE and Gram, A and Haaber, JK and Hallström, B and Jasinskytė, D and Pascal, R and Petersen, M and Semsey, S and Torio, AS and Turcu, IC and Smrekar, F and Taur, Y and Satlin, MJ and Sommer, MOA and van der Helm, E and Grøndahl, C},
title = {Safety, recovery, and pharmacodynamics of CRISPR-Cas therapeutic SNIPR001: a phase 1, randomised, double-blind, first-in-human, dose-escalation study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101257},
doi = {10.1016/j.lanmic.2025.101257},
pmid = {41785880},
issn = {2666-5247},
abstract = {BACKGROUND: Patients with haematological cancer who receive stem-cell transplantation are at risk of bloodstream infections, often caused by multidrug resistant gut pathogens such as Escherichia coli. SNIPR001 is a cocktail of four CRISPR-Cas-armed bacteriophages that reduce colonisation of E coli in the gastrointestinal tract in animal models and is designed to not affect other members of the commensal microbiota. We aimed to investigate the safety and tolerability of SNIPR001 in healthy participants.

METHODS: In this randomised, placebo-controlled, double-blind, first-in-human, dose-escalation trial conducted at a single centre (Medpace Clinical Pharmacology Unit; Cincinnati, OH, USA), we sequentially enrolled healthy participants (aged 18-65 years) with more than 10[7]E coli colony-forming units per gram of stool into cohorts 1, 2, and 3, pending a safety review of the previous enrolment group where applicable. Participants in each cohort were randomly assigned to treatment or placebo using a unique three-digit participant identification number. Participants were orally administered 10[8] plaque-forming units (PFU) per dose (cohort 1), 10[10] PFU per dose (cohort 2), and 10[12] PFU per dose (cohort 3) of SNIPR001 or placebo (phosphate-buffered saline buffer), twice daily for 7 days. All personnel, except for a pharmacy staff member who prepared both SNIPR001 and placebo vials, were masked to the administered dose and assignment; masking was ensured by fully covering the surface of each vial. Participants were followed up to day 187. The primary outcome was the incidence and severity of adverse events and medically attended adverse events from the first administration of the study drug until 4 weeks after the last dose administration on day 35 of the study. Recovery and biodistribution of SNIPR001 in faeces, blood, and urine; pharmacodynamics, including the ability of SNIPR001 to reduce E coli levels in stool (assessed using a linear mixed-effects model); and microbiome composition (using Bray-Curtis dissimilarity) were secondary outcomes. Primary safety analyses were assessed per-protocol (ie, all enrolled participants who received at least one administration of the study drug). This trial was conducted under an Investigational New Drug application from the US Food and Drug Administration, is registered with ClinicalTrials.gov (NCT05277350), and is closed to new participants.

FINDINGS: The trial was carried out between March 24, 2022, and Nov 30, 2022. 36 eligible participants were randomly assigned to receive SNIPR001 or placebo in cohorts 1 (six assigned to 10[8] PFU per dose and two assigned to placebo), 2 (six to 10[10] PFU per dose and two to placebo), and 3 (12 to 10[12] PFU per dose and eight to placebo). The mean age of participants was 42·1 years (SD 13·8), with 14 (39%) female participants and 22 (61%) male participants. During the trial and 4-week follow-up period, only mild and moderate adverse events were observed, with most adverse events occurring in the placebo group (13, six, one, and nine for participants receiving either placebo or SNIPR001 at 10[8], 10[10], and 10[12] PFU twice a day, respectively). The number of participants who had adverse events was not significantly higher in treatment groups than in the placebo group (p=0·94, one-sided Fisher's exact test). The most frequently reported adverse events were headaches and diarrhoea. No grade 3-4 adverse events were reported and no serious adverse events were reported in the SNIPR001 dose groups. During and after the dosing period, the gut microbiota composition did not significantly differ between the treatment and placebo groups (p>0·05, two-sided Mann-Whitney U test of Bray-Curtis distances, false discovery rate [FDR]-corrected). Functional SNIPR001 was recovered from stool samples in concentrations proportional to the administered dose but was not meaningfully detected in plasma (only one sample) or urine (only one sample). SNIPR001 was undetected in all samples 6 months after the last dosing, which is a favourable pharmacokinetic property and meets regulatory expectations. We observed the largest reduction in E coli levels compared with placebo 2 weeks after treatment initiation at day 14 (78%; -0·65 log10 [SE 0·64] for 10[12] PFU SNIPR001 twice-daily group), according to a linear mixed-effects model for the highest dose population; however, this change was not statistically significant (p=0·811, linear mixed-effects model, FDR-corrected).

INTERPRETATION: This first-in-human study of SNIPR001 supported its safety, tolerability, and restriction to the gastrointestinal tract, while not systemically disrupting the gut microbiome. These results justify further clinical development of SNIPR001 in an ongoing phase 1b/2a trial.

FUNDING: Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator (CARB-X) and SNIPR Biome.},
}

@article {pmid41785672,
year = {2026},
author = {Chen, Q and Feng, X and Wang, J and Zhu, H and Bo, Z and Wang, B and Zhao, Z},
title = {Impact of gut microbiota on hepatocellular carcinoma: Pathogenesis, diagnosis, prognosis, and therapeutic prospective.},
journal = {European journal of cancer (Oxford, England : 1990)},
volume = {237},
number = {},
pages = {116581},
doi = {10.1016/j.ejca.2026.116581},
pmid = {41785672},
issn = {1879-0852},
abstract = {Advances in sequencing technology have elucidated the complex role of the gut microbiota in hepatocellular carcinoma (HCC). Communication between the gut and the liver occurs via the gut-liver axis, and dysbiosis of the gut microbiota has been implicated in both the promotion and suppression of HCC. Furthermore, through interactions with host metabolism and immune system, the gut microbiota significantly influences treatment responses and prognostic outcomes of HCC. Despite progress in therapeutic strategies, clinical efficacy remains suboptimal, underscoring the need for a deeper understanding of the gut microbiota's role. This review highlights the potential of gut microbiota as novel biomarkers for the diagnosis and prognostic prediction of HCC, and explores its therapeutic implications. We summarize current insights into the molecular mechanisms underlying the gut microbiota-HCC interplay, and emphasize the relationship between gut microbiota and the efficacy of various treatments, including surgery, chemotherapy, radiotherapy, immunotherapy, and targeted agents. Microbiome-targeting interventions like probiotics, fecal microbiota transplantation (FMT), and dietary changes as emerging adjuvant strategies are also discussed in detail to provide potential resources for advancing translational hepatology. Although challenges remain, this review aims to provide valuable perspectives for developing individualized therapeutic strategies in HCC management.},
}

@article {pmid41785480,
year = {2026},
author = {Shekarriz, S and Vigod, SN and Bianco, T and Bala, A and Hao, C and Allard, JP and Hota, S and Poutanen, S and Surette, MG and Taylor, VH},
title = {The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437261420877},
pmid = {41785480},
issn = {1497-0015},
abstract = {BackgroundThe gut microbiome has been proposed as a potential modifiable target to treat mental illness. This double-blind randomized control trial investigated fecal microbiota transplant (FMT) in bipolar disorder (BD) to assess efficacy, safety, and feasibility. The primary outcome evaluated the effectiveness of standard approved therapy for BD depression + FMT in individuals not responding to standard treatment, measured by change in the Montgomery-Åsberg Depression Rating Scale (MADRS) score from baseline to week 24. Secondary outcomes included FMT's impact on anxiety, global function, side-effects, and safety. The feasibility of this novel intervention was also assessed. Microbial analysis utilized whole-genome shotgun metagenomic sequencing, comparing outcomes between allogenic (donor) and autologous (participants own) FMT.MethodsA total of 35 participants (28 women and 7 men) with at least moderate depressive-phase BD (MADRS) were randomized to receive either allogenic FMT (n = 17) or autologous FMT (n = 18) via colonoscopy and were followed for 24 weeks.ResultsMADRS scores significantly improved from baseline to the last visit in both treatment arms. There was no significant difference between allogenic FMT (16.74-point improvement) and autologous FMT (15.4-point improvement) regarding clinical efficacy (t = -0.47, p-value = .64, 95% confidence interval [CI] = -7.3-4.6). Microbiota analysis showed that allogenic FMT let to a bacterial profile similar to the healthy donor and increased bacterial diversity at the 6-month mark, whereas those receiving autologous FMT did not. The intervention was well tolerated with no significant adverse events. Recruitment, randomization, and retention metrics support feasibility of a larger trial.ConclusionFeasibility and tolerability data indicate further investigation into microbial manipulation in BD is warranted. The absence of efficacy differences between the two types of FMT, despite microbial change, highlights the importance of a true placebo in future studies, as well as the importance of understanding exactly what bacteria are linked to improvements. ClinicalTrials.gov, NCT0327922.},
}

@article {pmid41770403,
year = {2026},
author = {D'Souza, R and Pujare, K and Balu, SK and Kanojiya, D and Garg, Y and Ghag, SB},
title = {Differential Response of Banana Root Exudates and its Components on the Growth and Development of Banana Wilt Pathogen.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41770403},
issn = {1432-184X},
abstract = {UNLABELLED: Plant roots and rhizospheric microbes share an intricate relationship. Plants produce a complex mixture of root exudates that significantly affect the rhizospheric microbiome. Understanding the composition and functional significance of root exudates is essential for elucidating ecological mechanisms that can be leveraged to reduce disease severity. The significance of banana root exudates in Fusarium wilt disease caused by Fusarium oxysporum f. sp. cubense (Foc) remains poorly understood. This study investigates the differential effects of root exudates and their specific constituents derived from resistant and susceptible banana cultivars on the growth and development of Foc. Root exudates collected from four banana cultivars were evaluated for their effect on Foc mycelial growth, conidiospore germination and chemotropism. Exudates from susceptible cultivars (Rasthali, Red banana) significantly stimulated Foc conidiospore germination and chemotropism index as compared to those from resistant cultivars (Grand Naine, cv. Rose). Among the components, fumaric and salicylic acid showed dose-dependent increase in Foc conidia germination and chemotropism index. Conversely, oxalic and malic acid showed inhibition of Foc conidia germination at 0.5 µM, while phthalic acid showed inhibitory effects at 5 µM. Interestingly, oxalic, malic and phthalic acid treatment showed increased chemotropism index at 0.5 µM whereas, cinnamic acid showed a dose-dependent decrease. Mass spectrometric analysis revealed distinct profiles of organic acids among the four cultivars, while phenolic acids were detected in all four samples. This study enhances our understanding of the banana-Fusarium interaction and offer valuable insights into natural defense mechanisms and potential biocontrol strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-025-02693-z.},
}

@article {pmid41639642,
year = {2026},
author = {Unrug-Bielawska, K and Dziełak, M and Sandowska-Markiewicz, Z and Piątkowska, M and Czarnowski, P and Goryca, K and Zeber-Lubecka, N and Dąbrowska, M and Bałabas, A and Statkiewicz, M and Rumieńczyk, I and Pyśniak, K and Wójcik-Trechcińska, U and Tyl-Bielicka, A and Ziemska-Legięcka, J and Mikula, M and Ostrowski, J},
title = {Sex- and mouse strain-related differences in body weight gain, composition of the gut microbiota, and levels of selected metabolites in response to a Western-style diet.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {},
pmid = {41639642},
issn = {1471-230X},
support = {2018/29/B/NZ7/00809//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Recent studies reveal an association between the mitochondrial Amidoxime Reducing Component (MTARC) 1 and 2 proteins and metabolism in Mtarc1/2-deficient mice that are resistant to diet-induced obesity; however, the impact of Mtarc1/2 knockout (KO) on the gut microbiota and metabolome has not been explored in the context of sex and diet.

AIM: To compare the effects of a Western diet (WD) or a Novel Gubra Amylin NASH (GAN) diet on body weight gain, and on the composition of the gut microbiome and metabolome, between the background mouse strain and male and female Mtarc1- or Mtarc2-KO mice.

METHODS: Seventy-two 8-week-old male and female mice from each strain were fed a WD or a corresponding control normal diet (ND/WD), or a GAN diet or a corresponding control normal diet (ND/GAN), for 16 weeks. Fecal samples were collected at the beginning and end of the experiments, and 16 S rRNA-based microbiota profiling-based analysis was performed by sequencing the variable V3 and V4 regions of the bacterial 16 S rRNA gene. Mass spectrometry was used to measure short-chain fatty acids (SCFAs) and amino acids (AAs).

RESULTS: Compared with a control ND, GAN feeding increased the body weight of all groups of mice, whereas the WD increased the body weight of all groups except Mtarc2-KO female mice. The most significant weight gain was observed for male and female C57BL6/NTac mice fed a WD or GAN. Differences in body weight were mirrored in the microbiota profiles. In each of the mouse strains tested, the number of differentially abundant taxa between the GAN- and ND/GAN-fed groups was greater than that between WD- and ND/WD-fed mice. Both the GAN and WD also altered the levels of SCFAs and AAs in feces in a manner dependent on the mouse strain and sex.

CONCLUSIONS: Significant differences in body weight gain and changes in the composition of the gut microbiome and metabolome between the background mouse strain and Mtarc1-KO or Mtarc2-KO mice were further modified by sex and diet. Therefore, preclinical studies using animal models of obesity should ensure the selection of the appropriate mouse strain and sex, and be mindful of diet composition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12876-026-04647-2.},
}

@article {pmid41639630,
year = {2026},
author = {Bansaghi, S and Gulyás, G and Járay, T and Tombácz, D and Boldogkői, Z and Klein, J},
title = {Effect of long-lasting antimicrobial surface sprays in real-life environment.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41639630},
issn = {1471-2334},
abstract = {Antimicrobial surfaces have the potential to continuously self-decontaminate, which can play a key role in infection control. Various surface treatment sprays are available on the market today, differing in their chemical compositions and active ingredients. This study aimed to evaluate the effectiveness of these surface treatment sprays in real-life settings. The effects of the sprays were examined both in vitro, using bacterial suspensions, and in real-life settings. Effectiveness was measured by the number of colony-forming units (CFU) and by ATP tests. Additionally, the microbiome of one door opener was sequenced to identify the predominant microbes on that surface. Sequencing revealed that the microbiome of the door openers is mainly composed of skin bacteria. Staphylococcus (49.2%) and Micrococcus (33.6%) were the dominant genera identified in the sample. In vitro experiments demonstrated that all spray treatments were effective when tested against bacteria in suspension. However, in real-life settings, none of our measurements detected a significant reduction in microbial presence following spray treatment. We hypothesize that this discrepancy is due to the presence of a fatty substance, likely from fingerprints, on surfaces. This oily layer may act as a barrier that physically separates microbes from the treated surfaces, thereby diminishing the efficacy of the antimicrobial sprays.},
}

@article {pmid41785450,
year = {2026},
author = {Sun, QQ and Bao, MY and Gao, R and Wang, SK and Zhang, Y and Wang, LB and Zhang, Y and Li, X},
title = {Advances in Understanding Lipid Metabolism in Oligodendrocyte Development and Neurodegenerative Diseases.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20258150},
pmid = {41785450},
issn = {1470-8736},
support = {82471421,82271199,82571568//National Natural Science Foundation of China/ ; 23JHQ057//Scientific Research Program Funded by Education Department of Shaanxi Provincial Government/ ; GK202501001, GK202505004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Lipids are indispensable architectural and functional components of central nervous system (CNS) myelin, with cholesterol, sphingolipids, and phospholipids collectively constituting 70-80% of myelin membrane composition. Oligodendrocytes (OLs), the sole myelin-producing cells in the CNS, exhibit exquisite metabolic specialization to sustain lifelong myelination and remyelination. Mounting evidence implicates lipid metabolic dysregulation-spanning cholesterol efflux defects, sphingolipid imbalance, and peroxisomal dysfunction-as a convergent mechanism underlying OL differentiation failure and progressive demyelination in neurodegenerative diseases. This review explores the role of lipid metabolic rewiring in governing oligodendrocyte precursor cells (OPCs) fate determination, highlighting three crucial axes: the interplay between mitochondria and peroxisomes in lipid biosynthesis, the potential toxicity of accumulated myelin debris in the microenvironment, and the regulation of OPC differentiation through lactylation modification on lipid metabolism and the interaction between glycolipid metabolisms. We further synthesize emerging therapeutic strategies targeting these pathways, including immunometabolism modulators, precision lipid interventions; diet-microbiome synergies: ketogenic diets combined with butyrate-producing probiotics to amplify endogenous remyelination. By integrating lipidomics datasets and recent clinical trial evidence, we propose a shift from broad metabolic suppression to spatially resolved modulation of lipid flux. This synthesis not only clarifies the dual roles of lipids in OL development and degeneration but also highlights druggable targets for personalized treatment of neurodegenerative diseases.},
}

@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
doi = {10.1371/journal.pcbi.1013185},
pmid = {41785249},
issn = {1553-7358},
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}

@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag017},
pmid = {41785052},
issn = {1477-4054},
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}

@article {pmid41784969,
year = {2026},
author = {Chen, Y and Xing, Z and Sheng, J and Liu, X and Ding, W and Chen, X},
title = {Trends in the Application of Multiomics Based on Machine Learning in the Development of Probiotics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15387},
pmid = {41784969},
issn = {1520-5118},
abstract = {With the rapid development of computational methods and high-throughput multiomics technologies, machine learning (ML) has emerged as an important analytical approach in probiotic research. This review summarizes recent ML-assisted applications across genomics, transcriptomics, metabolomics, microbiome profiling, and culturomics, and organizes current studies around four functional objectives: probiotic selection, functional prediction, metabolic activity prediction, and probiotic effectiveness optimization. We discuss how ML facilitates the integration of heterogeneous omics data to enable more systematic and quantitative probiotic development and highlight representative analytical tools and workflows. At the same time, key limitations remain, including cross-platform data heterogeneity, imbalanced functional labels, and limited robustness in capturing complex microbial and environmental interactions. Consequently, experimental validation remains essential for ensuring biological relevance. Future progress will rely on standardized multiomics integration and iterative computational-experimental frameworks to support rational probiotic optimization.},
}

@article {pmid41784899,
year = {2026},
author = {Colaco, VS and Boleij, A},
title = {The gut microbiome as a biomarker and modifiable risk factor in Lynch Syndrome.},
journal = {Familial cancer},
volume = {25},
number = {1},
pages = {},
pmid = {41784899},
issn = {1573-7292},
support = {WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; WO24-54//Dutch Digestive Diseases Foundation (MDL-Fonds)/ ; KUN2015-7739//KWF Kankerbestrijding/ ; },
}

@article {pmid41784851,
year = {2026},
author = {Yoshioka, H and Mary-Huard, T and Aubert, J and Toda, Y and Ohmori, Y and Yamasaki, Y and Tsujimoto, H and Takahashi, H and Nakazono, M and Takanashi, H and Fujiwara, T and Tsuda, M and Kaga, A and Inaba, J and Fuji, Y and Hirai, MY and Nose, Y and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Narukawa, M and Ichihashi, Y and Iwata, H},
title = {Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {139},
number = {3},
pages = {},
pmid = {41784851},
issn = {1432-2242},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JP22K21352//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Corporation/ ; JPMJAN23D1//Japan Science and Technology Corporation/ ; },
abstract = {Intermediate omics traits, which mediate the effects of genetic variation on phenotypic traits, are increasingly recognized as valuable components of genetic evaluation. In particular, rhizosphere microbiota play a crucial role in plant health and productivity; however, their complex interactions with host genetics remain challenging to model. Although two-step modeling frameworks have been proposed to integrate intermediate omics traits into phenotype prediction, existing approaches do not incorporate nonlinear relationships between different omics layers. To address this, we have proposed a two-step phenotype prediction framework that integrates genomic, rhizosphere microbiome, and metabolome (meta-metabolome) data, while explicitly capturing omics-omics nonlinearities. The first step is to predict meta-metabolome traits from genetic and microbial features, thus effectively isolating them from the environmental noise. In this process, intermediate "proxy" omics traits are generated as general biological information to provide robust models. The second step utilizes this "proxy" to enhance the accuracy of the phenotype prediction. We compared a linear mixed model (Best Linear Unbiased Prediction, BLUP) and a nonlinear model (Random Forest, RF) at each step, as demonstrated through simulations and empirical analysis of a multi-omics soybean dataset in which nonlinear modeling captures intricate omics interactions. Notably, our approach enables phenotype prediction without requiring the original meta-metabolome data used in model training, thereby reducing reliance on costly omics measurements. This framework integrates intermediate omics traits into genomic prediction to improve prediction accuracy and provide solutions for deeper insights into plant-microbiome interactions.},
}

@article {pmid41784506,
year = {2026},
author = {Ivanov, VA and Hartman, WH and Soheilypour, M},
title = {Decoding the Microbiome-Disease Axis with Interpretable Graph Neural Networks.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag063},
pmid = {41784506},
issn = {1365-2672},
abstract = {AIMS: The human gut microbiome is a complex ecosystem whose disruption is implicated in a wide spectrum of diseases, yet translating microbiome research into actionable therapeutics is hindered by a critical trade-off: existing models either prioritize predictive accuracy at the expense of interpretability or sacrifice performance for mechanistic insight, limiting their ability to pinpoint specific disease-driving microbial interactions and taxa.

METHODS AND RESULTS: To address this, we introduce Graph neural network for Interpretable Microbiome (GIM), a graph neural network framework that integrates minimally processed taxonomic metadata as sparse node embeddings within an unweighted complete graph, enabling direct modeling of high-order microbial interactions through message passing. GIM achieves state-of-the-art classification performance on microbiome-disease prediction tasks (e.g. healthy vs. allergic states) while generating finegrained, experimentally validated attributions at the level of taxonomic ranks, driver microbes, and putative microbe-to-microbe interactions.

CONCLUSIONS: By bridging the gap between predictive accuracy and biological interpretability, GIM overcomes a key limitation in current approaches, offering a unified framework to both predict dysbiosis-associated disease states and identify actionable microbial targets for therapeutic intervention. This dual capability represents a critical advance toward precision microbiome engineering and scalable hypothesis generation in translational microbiome research.},
}

@article {pmid41784373,
year = {2026},
author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A},
title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0369125},
doi = {10.1128/spectrum.03691-25},
pmid = {41784373},
issn = {2165-0497},
abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.},
}

@article {pmid41784222,
year = {2026},
author = {Barr, SA and Davis, LJ and Vidar, W and Williamson, RT and Strangman, WK},
title = {Assessing Digestive Transformations of Withania somnifera Extracts via LC-MS/MS Profiling with a Focus on Bioactive Compounds Withaferin A, Withanolide A, Withanoside IV, and Untargeted Metabolomics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09897},
pmid = {41784222},
issn = {1520-5118},
abstract = {Botanical extracts are widely employed as health care agents but lack the rigorous vetting required for FDA-approved pharmaceuticals. Research on phytochemical bioavailability and transformation has mainly focused on liver metabolism and plasma binding, while gastrointestinal and microbiome metabolism studies remain limited. This study combined digestive in vitro assays with mass spectrometry-based metabolomics and molecular networking to analyze metabolites in Withania somnifera leaf and root extracts, along with three known bioactive reference standards: withaferin A, withanolide A, and withanoside IV. Both withaferin A and withanoside IV underwent significant in vitro transformation, while withanolide A remained stable across conditions. Molecular networking revealed that withanolides in the root extract were largely stable, whereas many in the leaf extract were more labile under the assay conditions. Detailed network analysis also enabled the identification of specific metabolite transformations. These findings support the refinement of in vitro models to better predict in vivo behavior in complex botanical mixtures.},
}