@article {pmid42899671,
year = {2026},
author = {Ke, X and Huang, X and Zhang, N and Yang, X and Chen, Y and Shao, J and Shi, J and Xu, J and He, Y},
title = {Combined Residues of Frequently Detected Herbicides are Stronger Predictors of Soil Resistome and Virulence Potential than Single Residues.},
journal = {Environmental science & technology},
volume = {60},
number = {41},
pages = {29555-29568},
doi = {10.1021/acs.est.6c03454},
pmid = {42899671},
issn = {1520-5851},
support = {2023C02004//Key Research and Development Program of Zhejiang Province/ ; 226-2025-00064//Fundamental Research Funds for the Central Universities/ ; 42225705//National Natural Science Foundation of China (NSFC)/ ; CARS-04//the earmarked fund for CARS/ ; JYB2025XDXM703//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Herbicides ; Soil Microbiology ; Soil/chemistry ; China ; Virulence ; },
abstract = {Overuse of herbicides has resulted in a global epidemic of evolved resistance in soil ecosystems. While single herbicide risk has been documented, the impact of multiple herbicide residues on the soil resistomes remains poorly understood. Our study quantified the residues of 24 herbicides, profiled antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and reconstructed 1086 metagenome-assembled genomes (MAGs) from 93 agricultural soils across China. The analytical results demonstrate that the frequently detected herbicide residues (e.g., 60-90% detection frequency) are stronger predictors of soil antibiotic resistomes than total herbicide load, unsupervised mixture based on principal component analysis (PCA), or single-herbicide models. For VFG abundance, the same mixture outperformed the best single herbicide and total herbicide concentration, although PCA-PC1 showed a moderately stronger correlation. Specifically, these commonly detected herbicides showed positive associations with ARG abundance through both direct linkages and bacterial community-dependent indirect pathways. Similar patterns were observed for virulence potential, where frequently detected residues maintained strong predictive performance and were predominantly associated with indirect pathways. Functional annotation patterns further suggest a concurrent enrichment of traits related to antioxidant defense, mobility, adherence, and immune modulation under elevated herbicide exposure. Notably, multiple herbicide residues were linked to the abundance of a Trinickia taxon, which was identified as a candidate ARG-VFG co-occurrence MAG carrying a high ARG load. Our findings highlight the need to integrate compound exposure of frequently detected herbicides into future risk assessment methodology for preventing the dissemination of ARGs in agricultural soils.},
}

*Herbicides
Soil Microbiology
Soil/chemistry
China
Virulence

@article {pmid42899700,
year = {2026},
author = {Amar, Y and Baumann, D and Niedermeier, S and Silva, RL and Walch, S and Schloter, M and Köberle, M and Biedermann, T and Volz, T},
title = {Hidradenitis suppurativa skin microbiome: In-depth analysis and modulation by systemic therapies.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70813},
pmid = {42899700},
issn = {1468-3083},
support = {MAIN457_FVJE032//Novartis/ ; 580001886//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease with a multifactorial pathogenesis involving genetic, lifestyle and microbial factors. While cutaneous microbiome shifts have been reported for this disease, the impact of systemic immunomodulators and antibiotics on HS microbiome remains poorly defined.

OBJECTIVE: To characterize species-level cutaneous dysbiosis in HS and evaluate the effects of three standard-of-care systemic therapies, clindamycin/rifampicin (ATB), adalimumab (ADA) and secukinumab (SEC) on skin microbial composition.

METHODS: We performed 16S rRNA sequencing on 251 skin swabs from lesional and non-lesional sites of 52 HS patients and 31 healthy matched controls. In a sub-cohort of 28 patients, microbial shifts were evaluated following 12 weeks of therapy with ATB (n = 8), ADA (n = 12) and SEC (n = 8).

RESULTS: HS skin exhibited profound dysbiosis defined by the depletion of homeostatic commensals (Cutibacterium acnes, Staphylococcus hominis, S. epidermidis) and a synergistic expansion of anaerobic pathogens, primarily Gram-positive anaerobic cocci (GPAC; Finegoldia magna, Peptoniphilus grossensis and Fenollaria massiliensis), Lawsonella clevelandensis and Campylobacter ureolyticus. A 13-taxa microbial signature accurately discriminated the HS phenotype (AUC = 0.92). Following 12 weeks of treatment, ATB markedly attenuated dysbiosis by reducing pathogen loads and significantly increasing microbial richness. In contrast, ADA and SEC did not alter pathogen abundance and were associated with a slight decline in protective commensals.

CONCLUSIONS: Systemic antibiotics partially restore cutaneous microbiome homeostasis in HS by targeting anaerobic pathogens while preserving beneficial commensals, an effect not observed with the tested biologics. These findings highlight the need for microbiome-directed adjuvant therapies to complement immunomodulation in HS management.},
}

@article {pmid42899707,
year = {2026},
author = {Luo, M and Dong, M and Qiao, H and Jin, D and Chang, S and Ullah, F and Yin, M and Shen, J and Yin, Y and Yan, S},
title = {Nanoscale pesticide delivery suppresses pathogens and enriches beneficial microbiomes for safer crop protection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag273},
pmid = {42899707},
issn = {1751-7370},
abstract = {Nanocarrier-based pesticide delivery platforms substantially boost agrochemical utilization efficiency, yet their cascading ecological repercussions for rhizosphere and soil microbial ecology remain insufficiently understood. Here, a star polycation (SPc) nanocarrier was employed to construct a matrine nano-formulation (MT@SPc) with typical nano-pesticide characteristics. MT@SPc and commercial matrine formulation (MT SL) were employed as representative systems to further evaluate their impacts on rhizosphere and soil microbial ecosystems. Compared with MT SL, MT@SPc reshaped rhizosphere microbial communities by suppressing phytopathogens and promoting the enrichment of beneficial bacteria. Further validation using four representative bacterial isolates obtained from soil demonstrated that MT@SPc significantly inhibited the growth of the phytopathogen Pectobacterium carotovorum, whereas enriched beneficial bacteria exhibited lower susceptibility to MT@SPc. Multi-scale mechanistic analyses revealed that MT@SPc could interact with bacterial cell surfaces through physicochemical interactions, resulting in pronounced surface deformation and structural damage in P. carotovorum. Multi-omics analyses associated with physiological and biochemical assays further demonstrated that MT@SPc disrupted cell wall and membrane integrity, leading to ionic imbalance, metabolite leakage and oxidative stress. However, beneficial bacteria maintained higher stability, and their enrichment was associated with microbial community shifts following pathogen suppression. Overall, this study reveals that nano-pesticides drive rhizosphere community restructuring through differential microbial responses, providing mechanistic insights into nano-pesticide-microbiome interactions in complex ecological systems.},
}

@article {pmid42899777,
year = {2026},
author = {Li, C and Miao, C and Chen, D and Zhou, Q and Chen, C and Jiang, X and Hou, J and Wu, W and Yang, K and Lin, D and Zhu, L and Xu, J},
title = {Arsenic Fingerprint and Microbiome Reconstruction of Rhizosphere-Specific Nanophases in Flooded Paddy Soil.},
journal = {ACS nano},
volume = {20},
number = {41},
pages = {27795-27806},
doi = {10.1021/acsnano.6c10025},
pmid = {42899777},
issn = {1936-086X},
support = {JYB2025XDXM909//Ministry of Education of the People's Republic of China/ ; LR26B070002//Natural Science Foundation of Zhejiang Province/ ; 226-2025-00064//Fundamental Research Funds for the Central Universities/ ; 226-2025-00246//Fundamental Research Funds for the Central Universities/ ; 22436006//National Natural Science Foundation of China (NSFC)/ ; 22494680//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Rhizosphere ; *Arsenic/analysis/chemistry/metabolism ; *Microbiota ; *Soil Microbiology ; *Soil/chemistry ; Oryza/metabolism ; *Nanoparticles/chemistry ; Floods ; *Soil Pollutants/analysis/chemistry ; Particle Size ; },
abstract = {Ubiquitous arsenic (As) nanophases in soils are metastable due to the size effect and become readily available to rice under flooded conditions, making substantial contributions to the As pool. Here, the chemical characteristics of As nanophases in the rhizosphere as a hotspot for rice-soil-microbe interactions were fingerprinted at a single-particle resolution, revealing their chemical speciation and interactions with soil microbiota. The initial As particle characteristics (speciation and size) governed bioavailability through distinct transformation pathways mediated by particle-specific elemental associations. Specifically, nanoscale As sulfide and ferrihydrite with adsorbed As resulted in greater rice uptake than their microscale treatments, whereas nanoscale scorodite exhibited a comparable bioavailability. Analyses at the individual nanoparticle level revealed that 75-90% of As-bearing particles were associated with other metals regardless of the initial particle type. Within the As particles associated with Fe, the Fe-to-As mass ratios ranged from 27 to 41 despite low co-occurrence probabilities (<30%). The redistributions of As, Fe, and associated elements (e.g., Si/Mn/Zr) observed at the individual particle level aligned with the metabolic capacity of enriched rhizosphere microbiomes to drive biogeochemical cycling. Such microscale interactions might contribute to As transformation and plant resistance. By resolving metastable nanophase behavior at critical soil-plant interfaces, this work provides mechanistic insights into their dynamic speciation and bioavailability during key agricultural phases, advancing predictive frameworks for As mobility in agroecosystems.},
}

*Rhizosphere
*Arsenic/analysis/chemistry/metabolism
*Microbiota
*Soil Microbiology
*Soil/chemistry
Oryza/metabolism
*Nanoparticles/chemistry
Floods
*Soil Pollutants/analysis/chemistry
Particle Size

@article {pmid42899795,
year = {2026},
author = {Dai, Y and Song, P and Cheng, C and Cheng, L and Dai, C and Lu, W},
title = {Schaftoside, a functional flavonoid from fenugreek (Trigonella foenum-graecum L.), alleviates depression and cognitive deficits via the microbiome-gut-brain axis in stressed mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo04156f},
pmid = {42899795},
issn = {2042-650X},
abstract = {Depression involves dysregulation of central and peripheral networks, with gut microbiota alterations increasingly implicated in pathogenesis. Trigonella foenum-graecum L. (fenugreek), a functional food and medicinal herb, has been used traditionally for neurological disorders, yet its specific neuroprotective constituents remain poorly characterized. This study evaluated the antidepressant potential of schaftoside, the predominant flavonoid of fenugreek seed flavonoids, and explored its mechanisms involving the microbiome-gut-brain axis in a chronic restraint stress (CRS) mouse model. Male Kunming mice were subjected to CRS and orally administered schaftoside (20, 50, and 125 mg kg[-1]) or fluoxetine (10 mg kg[-1]) for 28 days. Behavioral assessments (tail suspension, forced swim, novel object recognition, and Y-maze) demonstrated that schaftoside dose-dependently ameliorated depressive-like behaviors and cognitive impairments. It attenuated hippocampal neuronal damage and neuroinflammation, restoring hippocampal 5-HT, NE, and ACh levels. Intestinal barrier integrity was improved, evidenced by enhanced tight junction proteins (ZO-1, occludin) and mucin (MUC2) expression, alongside reduced colonic pro-inflammatory cytokines and elevated IL-10. 16S rRNA profiling revealed that schaftoside reshaped gut microbiota composition, notably suppressing stress-enriched Bacteroides and promoting butyrate-producing Butyricicoccus. Untargeted metabolomics identified restoration of tryptophan and α-linolenic acid metabolism pathways. Spearman correlation analysis revealed significant associations between specific gut genera, fecal metabolites, and host inflammatory/neurochemical markers. Hippocampal transcriptomics indicated enrichment of cAMP signaling, dopaminergic, and serotonergic synapse pathways. Fecal microbiota transplantation (FMT) from schaftoside-treated donors partially recapitulated the behavioral, anti-inflammatory, and intestinal barrier-protective effects in antibiotic-pretreated recipient mice, accompanied by restoration of the gut microbiota and metabolite profiles. These findings demonstrate that schaftoside, the major flavonoid of fenugreek seeds, exhibits promising antidepressant-like potential through modulation of the microbiome-gut-brain axis, supporting the functional food application of fenugreek-derived flavonoids for stress-related mood disorders.},
}

@article {pmid42899815,
year = {2026},
author = {Li, J and Xin, Y and You, W and Zhou, J and Wu, Z and Fang, X and Zhang, W},
title = {Mechanisms by which cannabidiol promotes peripheral nerve regeneration.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRRONLINE-D-26-00882},
pmid = {42899815},
issn = {1673-5374},
abstract = {Cannabidiol, a cannabis-derived non-psychoactive compound, possesses neuroprotective potential; however, the specific mechanisms by which it promotes peripheral nerve repair remain unclear. This study aimed to elucidate the mechanisms underlying the neurorepair effects of cannabidiol, focusing on the regulation of nerve injury and repair through the "gut-nerve axis." We used a sciatic nerve crush model, combined with multi-omics analyses and molecular validation, to investigate and verify the mechanisms underlying cannabidiol mediated peripheral nerve injury repair both in vivo and in vitro. Following peripheral nerve injury, the abundance of the probiotic Akkermansia muciniphila was significantly reduced. cannabidiol treatment restored Akkermansia muciniphila abundance and was accompanied by increased levels of 3-hydroxyphenylacetic acid in both the serum and injured sciatic nerve. Oral administration of cannabidiol promoted PNI repair by improving the morphology of the injured nerve, increasing the static sciatic index in mice, and alleviating gastrocnemius muscle atrophy. Importantly, antibiotic-induced dysbiosis significantly attenuated the therapeutic efficacy of cannabidiol, whereas Akkermansia muciniphila supplementation restored these neuroregenerative effects. Mechanistically, transcriptomic sequencing indicated that 3-hydroxyphenylacetic acid effectively inhibited MAPK signaling activation in Schwann cells, thereby reducing the secretion of inflammatory factors and alleviating inflammation to create a favorable microenvironment for repair of peripheral nerve injury. Exogenous 3-hydroxyphenylacetic acid supplementation similarly promoted recovery of peripheral nerve injury. This study reveals, for the first time, a novel "cannabidiol-Akkermansia muciniphila-3-hydroxyphenylacetic acid-mitogen-activated protein kinase axis" that plays a pivotal role in peripheral nerve repair. These findings deepen our understanding of the neuroprotective mechanisms of cannabidiol and provide an important theoretical foundation for developing novel therapeutic strategies targeting the gut microbiome to promote repair of peripheral nerve injury.},
}

@article {pmid42900262,
year = {2026},
author = {Low, JL and Nyo, YL and Chan, M and Koh, ZJ},
title = {The urinary microbiome after paediatric bladder augmentation: a scoping review with comparative insights from adult urinary diversion surgeries.},
journal = {Pediatric surgery international},
volume = {42},
number = {1},
pages = {},
pmid = {42900262},
issn = {1437-9813},
mesh = {Adult ; Child ; Humans ; *Microbiota ; *Urinary Bladder/surgery/microbiology ; *Urinary Diversion ; },
abstract = {Bladder augmentation is a lifelong reconstructive procedure for children with severe lower urinary tract dysfunction, but recurrent urinary tract infection, urolithiasis and mucus-related complications remain incompletely understood. This scoping review mapped evidence on the urinary microbiome after paediatric bladder augmentation and assessed transferable insights from adult bowel-derived urinary diversion. A PRISMA-ScR-guided search of PubMed, Embase and Web of Science identified peer-reviewed studies and conference abstracts published from January 2016 to April 2026 that used culture-independent sequencing. Seven studies were included: two paediatric and five adult, comprising three cross-sectional studies, two reports from one prospective cohort and two case reports. Paediatric studies reported contrasting enteric-dominant and native-bladder-like communities, with no consistent clinical associations. Adult studies more consistently suggested time-dependent restructuring, reservoir-specific microbial patterns and fungal involvement, although associations with urinary tract infection remained inconsistent. The paediatric evidence is insufficient to define microbiome composition, temporal behaviour or clinical significance after augmentation. Adult findings primarily provide a methodological template for future prospective, longitudinal, within-patient paediatric studies incorporating standardised urine and mucosal sampling, bacterial and fungal sequencing, metabolomics and predefined clinical outcomes.},
}

Adult
Child
Humans
*Microbiota
*Urinary Bladder/surgery/microbiology
*Urinary Diversion

@article {pmid42900352,
year = {2026},
author = {Desvennes, C and Loranger-Merciris, G and Gourdine, JL and Montout, L and Moreau, F and Thouin, J and Pruneau, L},
title = {Impacts of farming practices on pig gut microbiota and their interactions with soil microbial communities in tropical agroecosystems.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {11},
pages = {},
pmid = {42900352},
issn = {1572-9699},
mesh = {Animals ; *Soil Microbiology ; Swine/microbiology ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Agroecology ; *Gastrointestinal Microbiome ; Tropical Climate ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Biodiversity ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; Ecosystem ; },
abstract = {Livestock farming systems are associated with differences microbial communities in both animals and soils, yet the ecological mechanisms linking these compartments remain poorly understood. This study investigated the effects of contrasting farming systems (intensive vs. agroecological) on the gut microbiota of Creole pigs and associated soil microbial communities in farms located in Guadeloupe (French West Indies). Fecal and soil samples were analyzed using 16S and 18S Ribosomal Ribonucleic Acid (rRNA) genes metabarcoding to characterize bacterial, archaeal and fungal diversity. Pig gut microbiota was dominated by Bacillota (63.44% and 67.55% for intensive and agroecological raised pigs respectively) and Bacteroidota (24.70% and 18.56% for intensive and agroecological raised pigs respectively), whereas soils were mainly dominated by Acidobacteriota (14.61% and 17.48% for plowed and unplowed soil respectively), Actinomycetota (7.61% and 9.05% for plowed and unplowed soil respectively), and Bacillota (6.62% and 9.87% for plowed and unplowed soil respectively), indicating limited taxonomic overlap. Agroecological management was associated with higher relative abundances of Bacillota and Euryarchaeota in pigs and greater fungal diversity in soils. A total of 234 operational taxonomic units (OTUs) were common to all four groups (pig gut-agroecological, pig gut-intensive, plowed soil and unplowed soil), representing the microbial taxa shared between gut and soil environments; however, these taxa were generally abundant in the gut and rare in soils. These results suggest an ecological link between pigs and soil microbial communities that may be mediated by environmental processes. This underscores the interconnectedness of animal and environmental health within a One Health framework.},
}

Animals
*Soil Microbiology
Swine/microbiology
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Agroecology
*Gastrointestinal Microbiome
Tropical Climate
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Biodiversity
Agriculture/methods
RNA, Ribosomal, 18S/genetics
Ecosystem

@article {pmid42900414,
year = {2026},
author = {Almeida, KA and Guimarães, RA and Porto, VBC and Góes, LFM and de Moreira, FMS and Quensen, J and Tiedje, J and de Medeiros, FHV},
title = {Effects of a three-year maize-soybean rotation on soil bacterial diversity and fumonisin-producing Fusarium spp. inoculum potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42900414},
issn = {1573-0972},
support = {152719/2024-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CAG 03787/18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
mesh = {*Zea mays/microbiology/growth & development ; *Soil Microbiology ; *Fusarium/metabolism/genetics ; *Glycine max/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Fumonisins/metabolism ; Seasons ; Rhizosphere ; Brazil ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Agriculture/methods ; },
abstract = {Maize-soybean succession dominates grain production in tropical Brazil, and rotation is often recommended to improve soil health. However, few field studies have followed both soil bacterial diversity and fumonisin-producing pathogens over several seasons in tropical no-till systems. We compared continuous maize, continuous soybean and maize-soybean rotation for three seasons (2016-2017 to 2018-2019). In a fourth season (2019-2020), maize was grown in all plots to test legacy effects. Bacterial communities were profiled by 16 S rRNA (V3-V4) amplicon sequencing. The fum1 gene of fumonisin-producing Fusarium spp. was quantified by qPCR in soil and in maize stalks left on the soil surface. In the first three seasons, rotation did not detectably increase bacterial diversity, although statistical power was low (n = 4 plots; post-hoc power 12-61%). Community composition differed among seasons and was associated with antecedent precipitation as Actinobacteria were most abundant in the driest season. In the fourth season, a continuous-soybean history was associated with higher bacterial richness and Shannon diversity in the maize rhizosphere at tasselling than a rotation history, whereas bulk-soil diversity did not differ among land uses. A rotation history was associated with lower fum1 abundance in bulk soil. In contrast, continuous maize was associated with lower fum1 in stalks (third season), less stalk rot and fewer infected grains. Soil and crop residues therefore responded differently to rotation. Given the single site and limited plot-level replication, these findings should be regarded as hypothesis-generating.},
}

*Zea mays/microbiology/growth & development
*Soil Microbiology
*Fusarium/metabolism/genetics
*Glycine max/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification/metabolism
*Fumonisins/metabolism
Seasons
Rhizosphere
Brazil
Biodiversity
RNA, Ribosomal, 16S/genetics
Soil/chemistry
Agriculture/methods

@article {pmid42900725,
year = {2026},
author = {Byrd, EE and Harris, BW and Zhang, H and Warren, WE and Kolli, SH and Putelo, AM and McGinty, MT and Solga, MD and Rutkowski, MR and Kendall, MM},
title = {Methanogenic archaea Methanobrevibacter smithii and Methanosphaera stadtmanae promote mucosal homeostasis and protect from colitis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {43},
pages = {e2610622123},
doi = {10.1073/pnas.2610622123},
pmid = {42900725},
issn = {1091-6490},
support = {AI162696//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI146888//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T35AI060528//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Animals ; *Methanobrevibacter/metabolism/physiology ; *Colitis/microbiology/prevention & control/chemically induced/immunology ; Homeostasis ; Mice ; *Intestinal Mucosa/microbiology/immunology/metabolism ; *Methanobacteriaceae/metabolism/physiology ; Humans ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Dextran Sulfate ; Germ-Free Life ; T-Lymphocytes, Regulatory/immunology ; Male ; Colon/microbiology ; Methane/metabolism ; },
abstract = {The intestinal microbiota is a critical determinant of mucosal homeostasis, yet the functional contributions of Archaea-which constitute up to 10% of the anaerobic community-remain largely undefined. Here, we provide evidence that the human methanogens Methanobrevibacter smithii (MSm) and Methanosphaera stadtmanae (MSt) promote colonic health. Transcriptomic analysis of germ-free mice reveals that MSm and MSt induce distinct colonic programs important for epithelial integrity. Using gnotobiotic and antibiotic-treated specific-pathogen-free mouse models, we show that MSm and MSt reinforce the epithelial barrier, characterized by increased goblet cell expansion, mucus thickening, and enhanced epithelial regeneration. Furthermore, methanogens expand Foxp3[+] regulatory T cell (Treg) populations without inducing pro-inflammatory TH17 responses. Notably, MSm and MSt protect against dextran sodium sulfate-induced colitis. While MSt-mediated protection requires adaptive immunity, MSm retains partial efficacy in lymphocyte-deficient mice, revealing nonredundant protective mechanisms. These findings indicate that methanogenic archaea promote mucosal integrity during host association and suggest that methanogens may hold therapeutic potential for inflammatory bowel disease, though translation to human disease remains to be established.},
}

Animals
*Methanobrevibacter/metabolism/physiology
*Colitis/microbiology/prevention & control/chemically induced/immunology
Homeostasis
Mice
*Intestinal Mucosa/microbiology/immunology/metabolism
*Methanobacteriaceae/metabolism/physiology
Humans
Gastrointestinal Microbiome
Mice, Inbred C57BL
Dextran Sulfate
Germ-Free Life
T-Lymphocytes, Regulatory/immunology
Male
Colon/microbiology
Methane/metabolism

@article {pmid42900755,
year = {2026},
author = {Naeem, M},
title = {Reduced Crude Protein Nutrition in Poultry: Mechanistic Links Between Nitrogen Metabolism, Gut Microbial Ecology, and Intestinal Physiology.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70116},
pmid = {42900755},
issn = {1439-0396},
abstract = {Reducing dietary crude protein (CP) has emerged as an effective nutritional strategy to improve nitrogen utilisation efficiency and reduce environmental nitrogen losses in poultry production. Beyond these practical benefits, dietary protein concentration and digestibility influence nitrogen flow, microbial substrate availability, and metabolic interactions within the gastrointestinal tract, thereby shaping host-microbiota function. This review synthesises current evidence on the mechanistic links between reduced crude protein nutrition, nitrogen metabolism, gut microbial ecology, and intestinal physiology in poultry. Quantitative evidence indicates that responses depend strongly on the magnitude of CP reduction and dietary formulation. For example, a 2-percentage-point CP reduction with balanced lysine, methionine, and threonine improved growth and intestinal morphology, whereas a 3-percentage-point reduction has been associated with decreased duodenal and ileal villus height; in contrast, a 1.5-percentage-point reduction produced no significant morphological impairment. Recent evidence further shows that a 2% lower-protein diet can increase ileal microbial richness and diversity, while bacteriophage supplementation significantly improves nitrogen digestibility (p = 0.045), and dietary protein level itself affects nitrogen digestibility (p = 0.017). Collectively, moderate CP reduction supported by adequate digestible amino acids and highly digestible ingredients can decrease undigested nitrogen flow and proteolytic fermentation while maintaining intestinal function. However, excessive protein restriction, poor amino acid balance, or reduced ingredient digestibility may disrupt microbial metabolism and compromise intestinal integrity. These findings position reduced crude protein nutrition as a precision nutritional strategy in which the magnitude of protein reduction, amino acid adequacy, digestibility, and microbial substrate availability collectively determine productive, intestinal, and environmental outcomes.},
}

@article {pmid42901017,
year = {2026},
author = {Hotta, M and Hosomi, K and Uchiyama, K and Furuta, M and Tojima, Y and Kishino, S and Shibuya, N and Ogawa, J and Kunisawa, J},
title = {Longitudinal profiling of host- and microbe-derived lipid metabolites in human breast milk.},
journal = {Early human development},
volume = {224},
number = {},
pages = {106697},
doi = {10.1016/j.earlhumdev.2026.106697},
pmid = {42901017},
issn = {1872-6232},
abstract = {OBJECTIVE: Breast milk contains lipid metabolites and is indispensable for the growth and development of neonates and infants. However, studies investigating interindividual variations in human breast milk composition and the longitudinal changes in its constituent lipid metabolites remain limited. The temporal and individual patterns of variations in these metabolites were characterized to provide a foundation for future research on precision nutrition in infants.

STUDY DESIGN: Samples of human breast milk were collected shortly after birth and at 1 and 6 months postpartum, from participants who delivered healthy, full-term infants. Lipidomic analysis involving liquid chromatography coupled with tandem-mass spectrometry was used to quantify the levels of host- and microbe-derived fatty acid metabolites in the samples. The population was classified into five groups and analyzed based on the distribution of fatty acid substrate at 0 months.

RESULTS: Breast milk samples from 116 participants were analyzed. The group-specific metabolite profiles were classified into three distinct patterns. The concentrations of substrates and many metabolites increased from birth to 1 month, particularly among samples with lower baseline concentrations, whereas from 1 to 6 months, some metabolites remained stable, while others decreased. These patterns were associated with differences in the metabolic pathways.

CONCLUSIONS: Longitudinal lipid metabolites, including microbe-derived metabolites, in human breast milk and presented characteristic patterns. These findings provide foundational data for future research on precision nutrition for infants based on the metabolic profiles of breast milk.},
}

@article {pmid42901084,
year = {2026},
author = {Singh, N and Mohanta, YK and Priyadarshi, N and Das, D and Sharifi-Rad, M},
title = {Endophytes for climate-resilient agriculture: Mechanisms and systems-level insights.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111850},
doi = {10.1016/j.plaphy.2026.111850},
pmid = {42901084},
issn = {1873-2690},
abstract = {Endophytic bacteria and fungi that asymptomatically colonise plant tissues represent promising biological resources for developing sustainable and climate-resilient agricultural systems. These beneficial microorganisms establish intimate associations with crops and modulate plant growth, nutrient acquisition, immune responses, and stress physiology through diverse biochemical and molecular mechanisms. Endophytes enhance crop performance by producing phytohormones, solubilising and mobilising essential nutrients, improving nutrient-use efficiency, suppressing phytopathogens, inducing systemic resistance, and regulating plant metabolic and antioxidant responses. These functions can improve crop tolerance to major climate-associated stresses, including drought, salinity, heat, and nutrient limitations, while contributing to stable growth and yield under changing environmental conditions. Their potential as biofertilizers, biocontrol agents, biostimulants, and components of integrated crop management offers opportunities to reduce dependence on synthetic fertilisers and pesticides and promote environmentally sustainable agricultural production. This review critically synthesises current knowledge of endophyte diversity, crop colonisation, host specificity, plant-microbe signalling, and mechanisms underlying growth promotion, disease suppression, nutrient acquisition, and abiotic stress tolerance. Particular emphasis is placed on multi-omics and systems-level approaches that reveal endophyte-mediated regulation of plant metabolism, immunity, and microbiome assembly. The review also evaluates major constraints limiting agricultural translation, including inconsistent field performance, environmental adaptability, formulation and delivery, host microbe compatibility, ecological interactions, biosafety, and regulatory requirements. Finally, integration of multi-omics, microbiome engineering, synthetic biology, and precision agriculture is proposed as a pathway for developing robust endophyte-based technologies and microbial consortia. Such approaches could facilitate the transition toward low-input, resource-efficient, productive, and climate-resilient agriculture while strengthening long-term food security.},
}

@article {pmid42901222,
year = {2026},
author = {Trentin, AB and Dos Santos, SLS and Bendix, AF and Lopes, LC and Mota, TFM and de Souza, SS and Ghisi, NC and Leite, DCA},
title = {Functional Redundancy Enables Stable Treatment Performance Across Taxonomically Diverse Dairy Wastewater Microbiomes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70448},
pmid = {42901222},
issn = {1758-2229},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Universidade Tecnológica Federal do Paraná/ ; },
mesh = {*Wastewater/microbiology ; *Microbiota ; Dairying ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Bioreactors/microbiology ; },
abstract = {Biological treatment of dairy wastewater depends on complex microbial communities that vary widely across reactors, influent sources and operating conditions. Whether stable treatment performance arises from conserved taxa or from redundancy in functional potential remains unclear. In this study, we conducted a meta-analysis and reprocessing of 239 samples from nine independent studies spanning six countries and multiple reactor configurations. Taxonomic profiles showed extreme heterogeneity, with no ASV detected in at least 50% of samples and most genera exhibiting strong study-specific patterns. In contrast, the predicted functional repertoire was highly conserved. PICRUSt2 analysis identified 196 MetaCyc pathways present in at least 90% of samples, and these pathways accounted for approximately 90% of total predicted functional abundance. Generalised linear latent variable models showed that temperature and pH created consistent but modest ecological gradients, while study- and reactor-level factors dominated community structure. Despite substantial taxonomic turnover, functional signatures associated with fermentation, biosynthesis, nitrogen cycling, and degradation of complex substrates remained stable across systems. Treatment-stage transitions also followed predictable metabolic trajectories. These results show that dairy wastewater treatment systems are taxonomically flexible but functionally robust, and that extensive redundancy supports consistent metabolic capacity across diverse operational and environmental contexts.},
}

*Wastewater/microbiology
*Microbiota
Dairying
*Bacteria/classification/genetics/metabolism/isolation & purification
Bioreactors/microbiology

@article {pmid42901310,
year = {2026},
author = {Wiafe, MN and Ahmad, F and Berhanu, A and Dar, MA and Bai, Y and Zhu, D},
title = {Termite-microbiome symbiosis as a bioreactor model for lignocellulosic biomass pretreatment and biorefinery.},
journal = {Biotechnology advances},
volume = {94},
number = {},
pages = {109080},
doi = {10.1016/j.biotechadv.2026.109080},
pmid = {42901310},
issn = {1873-1899},
abstract = {Lignocellulosic biomass conversion is still limited by pretreatment strategies that are energy-intensive, chemically harsh, and difficult to scale. In contrast, termites and their symbiotic microbiota represent one of the most efficient natural systems for lignocellulose deconstruction, achieving rapid biomass conversion under mild physicochemical conditions. This review synthesizes current knowledge on termite-bacteria symbiosis and interprets it from a bioprocess engineering perspective, positioning it as a model for the design of engineered lignocellulosic biorefineries. By integrating gut compartmentalization, microbial community organization, enzymatic repertoires, and interaction networks, we develop a systems-level view of how spatial organization, physicochemical gradients, and cooperative metabolism jointly enable efficient biomass processing. Comparative analysis with conventional microbial platforms and industrial pretreatment technologies highlights the process advantages of termite-inspired systems in energy demand, process integration, and scalability. Rather than providing a purely descriptive synthesis, this review translates biological organization into engineering logic, outlining practical design principles for reactor architecture, consortium assembly, and enzyme deployment. We further identify key bottlenecks that constrain industrial translation, including transport limitations, gradient control, and community stability. Together, these insights provide a structured foundation for the rational development of robust, scalable, and sustainable termite-inspired lignocellulosic bioprocesses.},
}

@article {pmid42901334,
year = {2026},
author = {Wu, Y and Fan, W},
title = {Context Is Everything: Tumour-Type-Dependent Prioritisation of Tumour-Intrinsic, Microenvironmental and Host Determinants of Response to Immune-Checkpoint Blockade.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105654},
doi = {10.1016/j.critrevonc.2026.105654},
pmid = {42901334},
issn = {1879-0461},
abstract = {Predicting who benefits from immune-checkpoint blockade remains unsolved, and the search for a single universal biomarker has repeatedly failed: tumour mutational burden has no threshold that transfers across tumour types, PD-L1 expression is inconsistent, and the determinants of response lie on three interacting axes - tumour, microenvironment and host - studied in isolation. We argue that the predictive weight of each determinant is not fixed but depends on tumour type, and we integrate the axes into a determinant-weight matrix: an evidence-graded, falsifiable synthesis ranking, for each histology, which factor most plausibly governs baseline response. It is a hypothesis-generating framework for prioritising which determinants to measure, not a validated decision algorithm. Four regimes recur: mutation-led tumours such as melanoma, non-small-cell lung, mismatch-repair-deficient and urothelial cancers; microenvironment-led tumours such as renal-cell carcinoma, where mutational burden is paradoxically misleading, together with sarcoma and head-and-neck cancer; host-sensitive contexts in which the gut microbiome and concomitant medications become rate-limiting; and cold tumours in which no single axis suffices. These weightings follow from the axes converging on one effector pathway, explaining why single-axis biomarkers are unstable and why integrative scores, though largely retrospective, outperform them. Each cell records the weight, evidence tier, context, predictive-versus-prognostic and validation status of the determinant, with an explicit rule where axes disagree. The framework covers baseline determinants at the point where first-line treatment is chosen, and sets immune-related toxicity aside. Presented as a scaffold rather than a decision rule, it reframes biomarker selection from a universal panel to a tumour-type-calibrated sequence.},
}

@article {pmid42901599,
year = {2026},
author = {Katchhi, MS and Ming, LC and N, D and Bhandari, BS and Ahmad, A and Dhoddametikurke Siddappa, U and Krishna, M},
title = {Protocol for mixed methods study exploring the gut-brain health among South Indian population.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e114625},
pmid = {42901599},
issn = {2044-6055},
abstract = {INTRODUCTION: Depressive disorders are a major cause of disability worldwide and are frequently accompanied by somatic manifestations, particularly gastrointestinal (GI) symptoms. Emerging evidence implicates the gut–brain axis in the pathophysiology of depression, yet domain-wise characterisation of GI symptoms across stratified depression severity remains underexplored in the Indian context. Variations in diet, microbiota composition and cultural patterns of somatisation further necessitate region-specific evidence. This study aims to perform domain-wise analysis of GI symptoms across varying levels of depression severity among adult psychiatric outpatients.

METHODS/DESIGN: This hospital-based mixed-method study will be conducted in the psychiatry outpatient department of a tertiary care centre in South India. Approximately 300 adults (18–60 years) with newly diagnosed depression and Hamilton Depression Rating Scale-17 (HAMD-17) score ≥8 will be recruited. GI symptoms will be assessed using the GI Symptom Rating Scale (GSRS) across five domains: reflux, abdominal pain, indigestion, diarrhoea and constipation. Sociodemographic and clinical variables including body mass index, lifestyle factors, dietary habits and sleep duration will be recorded. Primary analysis will assess the correlation between total GSRS and HAMD-17 scores, while secondary analyses will compare domain-wise GI symptoms across depression severity groups and identify independent predictors using multivariable regression. A qualitative subsample will undergo semi-structured interviews to explore perceived gut–brain interactions. Statistical analysis will be performed using SPSS and R, with p<0.05 considered significant.

ETHICS AND DISSEMINATION: This study has been approved by the Institutional Ethics Committee (IEC) of KLE College of Pharmacy, Bengaluru. Study results will be disseminated through national and international meetings and peer-reviewed publications (IEC reference number: KLECOPBLR/2025-26).},
}

@article {pmid42901975,
year = {2026},
author = {Pérez-Escamilla, R and Hernández-Cordero, S and Franco-Lares, B and Lara-Mejía, V},
title = {Food insecurity in the development of metabolic diseases.},
journal = {Nature reviews. Endocrinology},
volume = {},
number = {},
pages = {},
pmid = {42901975},
issn = {1759-5037},
abstract = {This Review discusses the current evidence on the relationship between food insecurity, obesity, metabolic syndrome and type 2 diabetes mellitus (T2DM), and identifies potential interventions to mitigate the effect of food insecurity on these conditions. Studies in adults (mainly cross-sectional) have consistently found associations between food insecurity and several cardiometabolic diseases, including obesity (mainly among women), hyperlipidaemia, metabolic syndrome, hypertension, cardiovascular disease and T2DM. These associations represent plausible causal relationships given that food insecurity can be a powerful psycho-emotional stressor that can cause distress, anxiety and depressive symptoms across the life course; poor dietary quality can increase the risk of metabolic syndrome and T2DM through increased visceral adiposity and insulin resistance, inflammation and an unhealthy microbiome; and food insecurity can cause healthcare behavioural trade-offs such as prioritizing purchasing food over medications for T2DM prevention or management. Community-based, healthy lifestyle promotion, early-life nutrition and Food as Medicine programmes could mitigate the negative effect of food insecurity on T2DM risk and metabolic health. There is a need to rigorously evaluate the results of promising large-scale interventions on food insecurity and cardiometabolic health outcomes.},
}

@article {pmid42902048,
year = {2026},
author = {Wang, W and Feng, Y and Wang, Y and Wang, G and Wang, X},
title = {Metagenomic analysis of oral microbiota in Chinese children with obesity.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42902048},
issn = {1618-1905},
support = {2025JC-YBMS-1085//Natural Science Basic Research Program of Shaanxi Province/ ; },
abstract = {Childhood obesity represents an increasingly severe global public‑health concern, whose precise etiology remains incompletely elucidated and is likely multifactorial. In addition to genetic and lifestyle factors, mounting evidence indicates that the microbes in the digestive tract play a crucial role in the development and progression of obesity. Among them, the oral microbiota may contribute to obesity through mechanisms such as inducing systemic chronic inflammation and promoting gut microbiota dysbiosis. In the present study, saliva samples were collected from 9 obese children and 9 normal-weight children. Using metagenomic sequencing, we aimed to analyze the structural characteristics and functional profiles of the oral microbiota in Chinese school‑age children with obesity, so as to comprehensively dissect the oral microbiome ecology of this population from structural and functional perspectives. The results revealed that the microbiota diversity was similar between the two groups. At the species level, Dialister invisus, Treponema porcinum, Moraxella sp., Moraxella sp. VT 16 12, Moraxella lacunata, and Moraxella caprae were significantly enriched in the normal-weight group. Conversely, Campylobacter concisus, Veillonella sp. oral taxon 158, Veillonella rogosae, Veillonella sp. S13053 19, Streptococcus ilei, and Streptococcus australis were significantly enriched in the obese group. Functional annotation analysis demonstrated significant enrichment of functional genes associated with the hypoxia-inducible factor-1 (HIF-1) signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, beta-alanine metabolism, AMP-activated protein kinase (AMPK) signaling pathway, and apoptosis in the normal-weight group. In contrast, functional genes related to biofilm formation-Vibrio cholerae, selenocompound metabolism, RNA polymerase, xylene degradation, and dioxin degradation were significantly enriched in the obese group. Correlation analysis further revealed strong positive correlations between Veillonella sp. oral taxon 158, Veillonella sp. S13053 19, Streptococcus ilei, Streptococcus australis and the functional pathways of biofilm formation-Vibrio cholerae, selenocompound metabolism, xylene degradation, and dioxin degradation. These observations suggest that the oral microbiome undergoes compositional and functional alterations in children with obesity, implying a potential role of oral microbiota in the etiology of childhood obesity.},
}

@article {pmid42902157,
year = {2026},
author = {Li, X and Shi, C and Zhang, W and Na, R and Gu, M and Zhu, L and Zhao, S and Xiong, L and Wang, T},
title = {Integrative microbiome and transcriptome analyses identify parity-associated alterations in rectal fecal microbiota and peripheral immune transcriptional signatures in dairy cows.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42902157},
issn = {1471-2180},
support = {2025YFDZ0043//Inner Mongolia Autonomous Region Science and Technology Program/ ; 2023MS03052//Inner Mongolia Autonomous Region Natural Science Foundation/ ; },
mesh = {Animals ; Cattle ; Female ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; *Parity ; *Gene Expression Profiling ; *Rectum/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Pregnancy ; Phylogeny ; },
abstract = {BACKGROUND: Increasing parity in dairy cows is accompanied by cumulative physiological, reproductive, lactational, and management exposures that may coincide with changes in metabolic and immune status. However, the relationships among parity group, distal hindgut microbial communities, peripheral immune-related transcription, and their coordinated variation remain incompletely understood. In this cross-sectional observational study, 40 nonpregnant Holstein cows in mid-lactation without recorded disease were randomly selected from an eligible population within a commercial dairy herd and classified into naturally occurring parity groups: primiparous cows (PrC; parity = 1; n = 20) and multiparous cows (MuC; parities = 2-5; n = 20). Rectal fecal 16S ribosomal RNA (16S rRNA) gene sequencing and peripheral whole-blood RNA sequencing were integrated to characterize microbial and immune-related transcriptional differences between the two groups.

RESULTS: Multiparous cows had lower Shannon diversity, Chao1 richness, and observed amplicon sequence variant (ASV) richness than primiparous cows, but a higher Simpson dominance index (D), consistently indicating lower α-diversity and greater community dominance in multiparous cows. A one-factor permutational multivariate analysis of variance (PERMANOVA) based on Bray-Curtis distances indicated that parity-group membership was associated with a modest proportion of the variation in rectal fecal microbial composition (R² = 0.0581, permutation p = 0.004). Using linear discriminant analysis effect size (LEfSe), random forest, and analysis of compositions of microbiomes with bias correction 2 (ANCOM-BC2), 13 candidate genera were identified by at least two analytical approaches. Prevotellaceae_UCG-003 was more abundant in PrC, whereas Turicibacter, Clostridium_sensu_stricto_1, Acetitomaculum, and Lachnospiraceae_NK3A20_group were more abundant in MuC. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2)-based inference indicated group differences in predicted functional potential related to protein synthesis, amino acid and carbohydrate metabolism, bacterial motility, chemotaxis, and signal transduction; these results represent predicted rather than directly measured microbial functions. Whole-blood RNA sequencing identified 189 differentially expressed genes in the comparison between MuC and PrC, including 116 genes with higher transcript abundance in MuC and 73 with higher transcript abundance in PrC. Overall KEGG analysis of the complete DEG set identified 38 significantly enriched pathways, many of which were related to immune and inflammatory processes. Direction-stratified KEGG analysis further indicated that broad significant immune-related enrichment was mainly associated with genes showing higher transcript abundance in PrC cows, whereas only one KEGG term remained significantly enriched among the MuC-higher genes after Benjamini-Hochberg correction. Integration of differential expression, weighted gene co-expression network analysis, and protein-protein interaction analysis prioritized matrix metallopeptidase 9 (MMP9), mitogen-activated protein kinase 13 (MAPK13), and WD repeat domain, phosphoinositide interacting 1 (WIPI1) as candidate hub genes, all of which showed higher transcript abundance in MuC. Sparse partial least squares integration further identified a multivariate association structure involving selected candidate fecal genera and immune-related genes.

CONCLUSIONS: This study provides exploratory multi-omics evidence of differences in rectal fecal microbial composition, predicted microbial functional potential, and peripheral blood immune-related transcription between primiparous and multiparous cows. The coordinated microbiome-transcriptome patterns identify candidate microbial and transcriptional features for future investigation. Because this was a cross-sectional observational study, the findings should be interpreted as associations rather than causal effects of parity. Longitudinal studies and validation in independent herds are required.},
}

Animals
Cattle
Female
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
*Parity
*Gene Expression Profiling
*Rectum/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
*Gastrointestinal Microbiome/genetics
Pregnancy
Phylogeny

@article {pmid42902375,
year = {2026},
author = {Yahia, S and Murugesan, S and Al Khodor, S},
title = {Decoding the human milk virome: a comparative analysis of composition, colonization, and health impacts.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42902375},
issn = {1479-5876},
mesh = {Humans ; *Milk, Human/virology ; *Virome ; Female ; *Health ; },
abstract = {BACKGROUND: Breast milk (BM) is a complex biological system that not only delivers essential nutrition to the baby, but is also a rich collection of microorganisms, including bacteria, viruses and fungi. Dominated by bacteriophages and eukaryotic viruses, the BM virome plays a role in shaping the infant gut microbiome composition, influencing immune development and long-term health outcomes. Emerging research confirms the vertical transmission of bacteriophages from the mother to her infant via breastfeeding, and the shared viral taxa suggest functional roles in modulating bacterial populations and maintaining gut homeostasis. Disruptions in this early life virome, driven by factors such as maternal health, mode of delivery, and geographic location, have been linked to dysbiosis and disease susceptibility for conditions ranging from inflammatory bowel disease to metabolic disorders.

METHODS: A systematic literature search was conducted in NCBI/PUBMED and the European Nucleotide Archive (ENA) using the keywords "Milk virome," "Milk phage," "Milk phageome," and "Milk metagenome". After applying our inclusion and exclusion criteria, two studies remained. This comparative analysis explores the composition and diversity of the BM virome across two geographically distinct cohorts-Turkey and the United States-revealing significant differences in viral diversity and composition.

RESULTS: The Turkish cohort exhibited a significantly higher viral richness and unique taxonomic distributions compared to the USA group. Notably, bacteriophage families like Myoviridae, Siphoviridae, and Podoviridae were shown to be abundant in both populations. The Turkish BM virome featured a higher prevalence of plant- and insect-derived viruses (e.g. Partitiviridae, Tospoviridae), likely tied to dietary or regional agricultural practices.

CONCLUSIONS: Despite limitations related to sample size and methodological variability, this study emphasizes how dietary habits, environmental exposures, and geographic location may shape the breast milk virome. Further research integrating longitudinal data from a multi-ethnic population, cohorts is essential to fully harness the diagnostic and therapeutic potential of the human milk virome.},
}

Humans
*Milk, Human/virology
*Virome
Female
*Health

@article {pmid42902431,
year = {2026},
author = {Tang, S and Xing, Y and Yan, Z and Nyirenda, K and Zhao, J},
title = {Spatiotemporal plasticity of the gut microbiome facilitates redbelly tilapia (Coptodon zillii) invasion in China.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42902431},
issn = {2524-4671},
support = {2022YFC2601302//the National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The redbelly tilapia (Coptodon zillii) is a highly invasive fish species posing serious ecological risks to freshwater systems in China. To uncover mechanisms behind its invasion success, this study investigated spatiotemporal plasticity of its gut microbiome and explored the drivers of such plasticity. Using high-throughput 16 S rRNA sequencing, gut microbiota of C. zillii from five water bodies (two rivers, three reservoirs) and from Shuikou Reservoir across four seasons were compared.

RESULTS: Among populations from different habitats, 6 of the top 10 abundant phyla and 17 of the top 30 genera varied significantly (P < 0.05). Gut microbiota differed significantly (P < 0.05) in all pairwise population comparisons. Alpha diversity indices also showed significant differences among some populations (P < 0.05). Of 24 digestion-related KEGG pathways identified, 23 exhibited significant abundance variations across populations. Relative gene abundances of beta-glucosidase (P = 0.0025) and chitinase (P = 0.022) also differed significantly. Water temperature, dissolved oxygen, and conductivity were key environmental drivers of gut microbiota variation. Notably, microbial community assembly was predominantly governed by deterministic processes (> 60%), with heterogeneous selection contributing 42%-63%. In seasonal samples from Shuikou Reservoir, 6 of the top 10 phyla and 15 of the top 30 genera showed significant seasonal variation (P < 0.05). PERMANOVA indicated significant differences (P < 0.05) in all pairwise seasonal comparisons. Of 19 digestion-related KEGG pathways, 13 exhibited significant abundance variations across seasons. Chitinase-coding gene abundance varied significantly among populations (P < 0.0001). Key factors driving seasonal differentiation were pH, conductivity, turbidity degree, and total nitrogen.

CONCLUSIONS: The gut microbiome of invasive C. zillii displays significant spatiotemporal variation in structure, diversity, and functional gene composition. This pronounced plasticity-rather than a stable, specialized microbiota-likely serves as a key adaptive strategy, enabling the species to thrive in heterogeneous environments.},
}

@article {pmid42902790,
year = {2026},
author = {Fang, L and Ye, C and Wang, Y},
title = {Integrating complementary datasets for constructing microbiome-metabolome-disease pathways.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag787},
pmid = {42902790},
issn = {1367-4811},
abstract = {MOTIVATION: Microbiome-metabolome-disease pathways play a central role in host health, but studying them is limited by the data available. Large clinical microbiome cohorts often lack metabolomic measurements, while multi-omics studies with paired profiles are typically small or incompletely phenotyped. Combining such complementary datasets is challenging: the metabolite is not measured in the clinical cohort, microbiome data are high-dimensional and compositional, and log-ratio analyses depend on an arbitrarily chosen reference taxon.

RESULTS: We propose a framework that integrates a large target cohort that has microbiome and outcome data with a smaller external study that has paired microbiome-metabolome profiles. A high-dimensional structural equation model jointly links the microbiome, the metabolome and the disease outcome. It allows for unmeasured confounding and groups microbes into functional categories. We address compositionality with the additive log-ratio (ALR) transformation, estimate parameters by penalized two-stage least squares, and test metabolite-disease associations with a regularized permutation test. A novel multiple-reference procedure treats each microbe in turn as the ALR reference. It combines the resulting p-values with the Cauchy combination test and classifies microbes by stability selection, which makes inference robust to the choice of reference. In simulations, the method controls the type I error rate, and its power increases with both target and external sample sizes. An application to inflammatory bowel disease, integrating the FRAN and iHMP cohorts, reveals biologically interpretable microbiome-metabolome-disease links.

The method is implemented in the R package MMDP, freely available at https://github.com/lei-fang-stat/MMDP.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42902928,
year = {2026},
author = {Bayer, IS},
title = {Beyond Antibacterial Activity: Engineering Multifunctional Biomaterials for Multidrug-Resistant Infections.},
journal = {Journal of biomedical materials research. Part B, Applied biomaterials},
volume = {114},
number = {10},
pages = {e70166},
doi = {10.1002/jbm.b.70166},
pmid = {42902928},
issn = {1552-4981},
mesh = {Humans ; *Biocompatible Materials/chemistry/therapeutic use ; Animals ; *Bacterial Infections/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology/chemistry ; Biofilms ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria ; },
abstract = {Antimicrobial resistance is increasingly limiting the effectiveness of conventional antibiotic therapy, particularly in chronic wounds, biofilm-associated infections, and implant-related infections. Antimicrobial biomaterials have emerged as promising alternatives; however, much of the field remains organized around material classes or pathogen killing alone, with comparatively limited consideration of the complex biological environment in which infection develops and persists. This review proposes a function-based framework in which antimicrobial biomaterials are designed as integrated therapeutic systems rather than as passive antimicrobial carriers. Six complementary engineering functions are identified: infection targeting, overcoming bacterial defenses, multimodal pathogen eradication, host immune modulation, tissue regeneration, and adaptive or stimuli-responsive behavior. For each function, key design principles, representative strategies, and translational challenges are critically examined. Particular attention is given to the extent to which these functions have been experimentally integrated, including a systematic assessment of demonstrated versus largely conceptual pairwise combinations. Because the relative importance of each function varies by clinical application, the review also considers how these priorities shift across tissue and device context, including skin and soft tissue, bone, and short-term devices such as indwelling catheters. Rather than emphasizing efficacy alone, the review also examines translational limitations and failure points, including inadequate activity against clinically relevant organisms, limited clinical validation of established antimicrobial technologies, and regulatory failure of promising antimicrobial candidates. These examples highlight the persistent gap between laboratory performance and clinical utility. The review further considers the emerging tension between broad-spectrum antimicrobial strategies and approaches designed to preserve the host microbiome through species-selective targeting. Special emphasis is placed on halogen-based antimicrobial systems, catalytic nanozymes, and the emerging application of artificial intelligence to biomaterial design. Finally, a prioritized roadmap is proposed for advancing multifunctional antimicrobial biomaterials from mechanistic proof-of-concept toward clinically relevant therapeutic systems, while identifying key assumptions and knowledge gaps that remain to be validated.},
}

Humans
*Biocompatible Materials/chemistry/therapeutic use
Animals
*Bacterial Infections/drug therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology/chemistry
Biofilms
*Drug Resistance, Multiple, Bacterial/drug effects
Bacteria

@article {pmid42902965,
year = {2026},
author = {Jung, O and Stritt, K and Fleury, N and Erard, V},
title = {[Intrauretheral devices and infection : common beliefs and scientific evidence].},
journal = {Revue medicale suisse},
volume = {22},
number = {978},
pages = {1621-1623},
doi = {10.53738/REVMED.2026.22.978.49213},
pmid = {42902965},
issn = {1660-9379},
mesh = {Humans ; *Urinary Tract Infections/etiology/microbiology/epidemiology ; *Catheter-Related Infections/etiology/epidemiology/microbiology ; Biofilms ; *Urinary Catheters/adverse effects/microbiology ; *Urinary Catheterization/adverse effects/instrumentation ; Risk Factors ; },
abstract = {Intrauretheral catheters, used for drainage of the upper urinary tract, are associated with mechanical and infectious complications. The risk of infection is associated with the duration of catheterization, the presence of comorbidities, and the clinical context. Microbial colonization of synthetic material, via the formation of a biofilm, is a known and expected phenomenon that is most often clinically insignificant but may be associated with an increased risk of infection, even though a direct causal link between colonization and symptomatic infection has not been established. The management of urinary tract infection and the interpretation of bacteriuria associated with an intrauretheral catheter, rely on an understanding of the interactions between the microbiome and synthetic materials.},
}

Humans
*Urinary Tract Infections/etiology/microbiology/epidemiology
*Catheter-Related Infections/etiology/epidemiology/microbiology
Biofilms
*Urinary Catheters/adverse effects/microbiology
*Urinary Catheterization/adverse effects/instrumentation
Risk Factors

@article {pmid42903061,
year = {2026},
author = {Xiang, Z and Chen, Y and Ji, R and Wei, X and Xu, X},
title = {Editorial: Gut microbiome-driven pathogenesis and intervention strategies in liver diseases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1973834},
pmid = {42903061},
issn = {2296-858X},
}

@article {pmid42903070,
year = {2026},
author = {Vincent, KL and Moss, JA and Marzinke, MA and Pyles, RB and Dawson, L and Olive, TJ and Butkyavichene, I and Castonguay, AE and Cortez, JM and Remedios-Chan, M and Galvan, P and Rivera, S and Webster, S and Gunawardana, M and Adler, AP and Ramirez, CM and Spiegel, HML and Hendrix, CW and Anton, PA and Baum, MM},
title = {An intravaginal ring for HIV pre-exposure prophylaxis: assessment of safety and pharmacokinetics in a randomized, placebo-controlled clinical trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1955105},
pmid = {42903070},
issn = {2235-2988},
mesh = {Humans ; Female ; *Pre-Exposure Prophylaxis/methods ; *HIV Infections/prevention & control ; Tenofovir/pharmacokinetics/administration & dosage/adverse effects ; Adult ; Emtricitabine/pharmacokinetics/administration & dosage/adverse effects ; Cross-Over Studies ; *Anti-HIV Agents/pharmacokinetics/administration & dosage/adverse effects ; Double-Blind Method ; Young Adult ; Administration, Intravaginal ; *Contraceptive Devices, Female/adverse effects ; Adolescent ; Vagina ; },
abstract = {INTRODUCTION: In Eastern and Southern Africa, 63% of new HIV infections occurred in women and girls, with adolescent girls and young women representing a particularly vulnerable subpopulation. Effective vaginal products for HIV prevention are desirable because they are underrepresented in the currently approved portfolio and have attributes motivating product use. In this trial, we evaluated an innovative intravaginal ring (pod-IVR) as a platform for HIV pre-exposure prophylaxis (PrEP).

OBJECTIVE: To measure the safety and multicompartment pharmacokinetics (PKs) of a pod-IVR delivering tenofovir disoproxil fumarate (TDF) combined with emtricitabine (FTC) in healthy women over 28 days.

METHODS: The Phase 1 clinical trial consisted of a randomized order, controlled, double-blinded, crossover design. Ten women received either an active TDF-FTC pod-IVR or a placebo pod-IVR for 28 days, determined by 1:1 randomization, followed by product crossover for another 28 days. Safety was assessed in terms of adverse events related to product use, colposcopic examination, cervicovaginal epithelium thickness measurement by optical coherence tomography, and culture-independent assessment of the vaginal microbiome. Drug and/or drug metabolite concentrations were measured in cervicovaginal fluid (CVF), vaginal tissue, rectal tissue, rectal fluid, and plasma.

RESULTS: There was no evidence of a statistically significant difference in related adverse-event counts between study products. There also was no evidence suggesting the study product altered the vaginal microbiome systematically or reproducibly. Systemic plasma exposure to tenofovir (TFV) and FTC was low, consistent with topical delivery. High median CVF concentrations of TFV (38.9 ng mg[-1]; 135×10[3] fmol mg[-1]) and FTC (239 ng mg[-1]; 966×10[3] fmol mg[-1]) were measured. Median vaginal tissue concentrations of the anabolites responsible for inhibition of HIV reverse transcriptase exceeded our target concentrations: TFV diphosphate 0.651×10[3] fmol mg[-1] and FTC triphosphate 0.180×10[3] fmol mg[-1]. Drug concentrations in rectal tissue samples generally were below the analytical lower limits of quantification, but were quantifiable in rectal fluids, 130 (TFV) and 300 (FTC) times lower than in CVF.

CONCLUSIONS: The TDF-FTC pod-IVRs were safe and well-tolerated over the 28 days of consecutive use. The PK data met the target benchmarks associated with protection from vaginal HIV infection.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT03255915, identifier NCT03255915.},
}

Humans
Female
*Pre-Exposure Prophylaxis/methods
*HIV Infections/prevention & control
Tenofovir/pharmacokinetics/administration & dosage/adverse effects
Adult
Emtricitabine/pharmacokinetics/administration & dosage/adverse effects
Cross-Over Studies
*Anti-HIV Agents/pharmacokinetics/administration & dosage/adverse effects
Double-Blind Method
Young Adult
Administration, Intravaginal
*Contraceptive Devices, Female/adverse effects
Adolescent
Vagina

@article {pmid42903147,
year = {2026},
author = {Su, W and Ma, ZS},
title = {Ecological drivers of the colon cancer microbiome: evidence for niche-based selection over stochastic colonization.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1888804},
pmid = {42903147},
issn = {2234-943X},
abstract = {Colon cancer is a leading global malignancy influenced by genetic, environmental, and microbial factors. This study integrates ecological theories, including Hubbell's neutral theory, augmented by Ning et al.'s (2019, PNAS) stochasticity analysis framework, and classic niche theory, to assess the contributions of stochastic colonization and deterministic niche selection in shaping microbiome assembly and dynamics in colon cancer tissues. Specialist species were identified using Levins' niche breadth analysis. By reanalyzing the datasets from Nejman et al., including 22 normal adjacent tissue (NT) and 22 primary tumor (PT) samples, we find: (i) deterministic niche selection appears to dominate community assembly and diversity maintenance in both NT and PT microbiomes, as demonstrated by the normalized stochasticity ratio (NSR: 0.267 for NT, 0.287 for PT; both below 0.5; Wilcoxon PT>NT, p=0.027). Only 18.2% NT and 27.3% PT samples fit the neutral model, confirming stochastic drift plays a limited role and niche selection predominates in structuring tissue microbiomes. (ii) Through niche breadth analysis, we identified 106 specialist species, of which 14 are known CRC-associated taxa, including Fusobacterium nucleatum, Escherichia coli, Enterococcus faecalis, and Peptostreptococcus anaerobius. These species have established roles in inflammation, genotoxicity, immune modulation, and chemoresistance. (iii) These findings suggest that deterministic niche-based selection, rather than stochastic colonization, appears to govern microbial community assembly in colon cancer tissues. (iv) We postulate that the tumor microenvironment imposes biochemical filters-including hypoxia, lactate accumulation, and altered pH-that select for specialist species capable of adapting to these conditions. (v) While the sample size is modest and validation in independent cohorts is needed, our study demonstrates an integrative framework for understanding colon cancer microbiome dynamics. We propose testable hypotheses for future research: (i) specialist species abundance may correlate with tumor stage or patient survival; (2) depletion of specialists may alter tumor progression in preclinical models; and (3) hybrid neutral-niche models may better fit larger longitudinal datasets. By integrating ecological theory with microbiome research, this study offers insights into the forces driving microbial community assembly in tumor tissues and highlights potential targets for microbiome-based diagnostics and therapeutics.},
}

@article {pmid42903294,
year = {2026},
author = {Almoghrabi Ramirez, S and Karousa, MM and Yassin, E and AlOrjan, A and Shebbo, S and Al-Haidose, A and Zeidan, A and Abdallah, AM},
title = {Autophagy as a Proposed Regulatory Interface in the Gut Microbiota-Cardiovascular Axis.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {590787},
pmid = {42903294},
issn = {1178-7031},
abstract = {The gut-cardiovascular axis is increasingly recognized as a contributor to cardiovascular disease (CVD) risk; however, most available evidence remains associative, and the mechanistic links between gut dysbiosis, autophagy, and cardiovascular pathology require further validation. This review proposes a conceptual framework in which autophagy may serve as a regulatory interface linking gut microbiota-derived signals with vascular and cardiac dysfunction. We summarize evidence that microbial metabolites, including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), bile acids, and dysbiosis-associated products such as lipopolysaccharide (LPS), may influence autophagic flux in intestinal epithelial cells, endothelial cells, macrophages, and myocardium through pathways involving TLR-MyD88-NF-κB/NLRP3 signaling, AMPK-mTOR-ULK1-Beclin-1 regulation, and FXR/TGR5-associated mechanisms. These pathways may contribute to oxidative stress, lipid dysregulation, gut barrier dysfunction, endothelial activation, foam cell formation, and cardiovascular inflammation. We also discuss selected inflammatory and metabolic biomarkers, including PCSK9, MPO, Lp-PLA2, TMAO, and CRP, while emphasizing that their relationships with autophagy are context-dependent and, in several cases, indirect. Emerging therapeutic opportunities, including microbiome remodeling, prebiotics, probiotics, postbiotic SCFAs, high-purity eicosapentaenoic acid, PCSK9 inhibition, and autophagy-targeted nanocarriers, are evaluated with attention to their current evidence level. As many of these approaches remain supported mainly by preclinical, mechanistic, or indirect clinical evidence, future translation will require longitudinal human studies, standardized autophagy-flux assessment, multi-omics integration, and well-designed clinical trials using clinically relevant cardiovascular endpoints. Overall, this review positions the gut microbiota-autophagy-cardiovascular axis as a testable conceptual model to guide future mechanistic and translational research in CVD.},
}

@article {pmid42903311,
year = {2026},
author = {Yu, SY and Bak, JE and Oh, BS and Ryu, SW and Park, H and Yu, DJ and Lee, J and Kim, JS and Lee, JH},
title = {Butyrate-associated antiproliferative and antitumor effects of Eubacterium limosum KGMB01548 in colorectal cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1973432},
pmid = {42903311},
issn = {1664-302X},
abstract = {INTRODUCTION: Recent work has shown that Eubacterium limosum suppresses colorectal cancer (CRC), but the contribution and cellular actions of its short-chain fatty acids remain incompletely defined.

METHODS: We characterized E. limosum KGMB01548, a human gut isolate, and examined the antitumor activity of its cell-free culture supernatant (ElCFS).

RESULTS: ElCFS preferentially inhibited the proliferation of human HCT116 and murine CT26 CRC cells while having little effect on non-malignant CCD 841 CoN colonic cells. The activity persisted after heat and enzymatic treatments, and pH-dependent liquid-liquid extraction indicated that a small organic acid was a major bioactive component. High-performance liquid chromatography detected 13.77 mM butyrate and 23.33 mM acetate in ElCFS. At approximately the concentration delivered by 10% ElCFS, sodium butyrate (NaB; 1.3 mM) produced comparable antiproliferative activity, whereas sodium acetate did not, supporting butyrate as a major candidate contributor to ElCFS activity. ElCFS and approximately concentration-matched NaB increased histone H3 acetylation, consistent with histone deacetylase inhibition, and induced apoptosis, as evidenced by PARP and caspase-3 cleavage and p53 phosphorylation. Their antiproliferative effects were markedly attenuated under glucose-depleted conditions. In a CT26 syngeneic tumor model, peritumoral administration of ElCFS reduced tumor growth, indicating that secreted E. limosum metabolites retained local antitumor activity outside the intestinal route. Oral pre-administration of live E. limosum also reduced subsequent tumor burden. Furthermore, 16S rRNA gene profiling suggested modest changes in several putative short-chain-fatty-acid-producing taxa and in PICRUSt2-predicted butyrate-biosynthesis potential, without a major change in alpha diversity.

DISCUSSION: Together, these findings link E. limosum KGMB01548 to butyrate-associated histone acetylation, apoptosis, glucose-sensitive antiproliferative activity, and tumor suppression, supporting further investigation of this gut commensal and its secreted metabolites as microbiome-derived approaches for CRC control.},
}

@article {pmid42903418,
year = {2026},
author = {Pang, Y and Jiang, P and Liu, K and Suo, X and Zhang, D and Xu, Y and Ge, Y and Fu, Q and Gao, S},
title = {Molecular mechanisms and therapeutic strategies of immunotherapy resistance in esophageal cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1973515},
pmid = {42903418},
issn = {1664-3224},
mesh = {Humans ; *Esophageal Neoplasms/immunology/therapy/metabolism/drug therapy ; Tumor Microenvironment/immunology/drug effects ; *Drug Resistance, Neoplasm/immunology/genetics ; *Immunotherapy/methods ; Metabolic Reprogramming ; Animals ; *Immune Checkpoint Inhibitors/therapeutic use ; Epigenesis, Genetic ; },
abstract = {Immunotherapy, particularly immune checkpoint inhibitors (ICIs), has transformed the treatment landscape for advanced esophageal cancer (EC). Nevertheless, clinical benefits are constrained by primary and acquired resistance driven by a dynamic immunosuppressive tumor microenvironment (TME), extensive metabolic reprogramming, and epigenetic dysregulation. This review provides a comprehensive analysis of the molecular mechanisms underlying immunotherapy resistance in EC, including TME remodeling by cancer-associated fibroblasts, tumor-associated macrophages, and immunosuppressive cell populations; metabolic reprogramming encompassing glucose, amino acid, and lipid metabolism; epigenetic regulation involving DNA methylation, histone modifications, and non-coding RNAs; and compensatory immune checkpoint upregulation. We further highlight the emerging role of the microbiome and critically evaluate combination strategies designed to overcome resistance, including anti-angiogenic agents, ADCs, and personalized approaches guided by multi-omics and organoid models.},
}

Humans
*Esophageal Neoplasms/immunology/therapy/metabolism/drug therapy
Tumor Microenvironment/immunology/drug effects
*Drug Resistance, Neoplasm/immunology/genetics
*Immunotherapy/methods
Metabolic Reprogramming
Animals
*Immune Checkpoint Inhibitors/therapeutic use
Epigenesis, Genetic

@article {pmid42903427,
year = {2026},
author = {Sun, X and Ma, X and Ma, Y and Wang, X and Li, X and Ji, M},
title = {Correction: The oral immune and inflammatory network under circadian clock control.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1992894},
doi = {10.3389/fimmu.2026.1992894},
pmid = {42903427},
issn = {1664-3224},
abstract = {[This corrects the article DOI: 10.3389/fimmu.2026.1894302.].},
}

@article {pmid42903450,
year = {2026},
author = {Fyhrquist, N and Gugescu, L and Wincent, E and Alenius, H},
title = {Chemical-Specific Metabolic Disruption during Early Zebrafish Development is Modulated by the Microbiome.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {10},
pages = {2401-2415},
pmid = {42903450},
issn = {2833-8278},
abstract = {Environmental contaminants such as per- and polyfluoroalkyl substances, bisphenols, and agricultural fungicides are increasingly recognized as metabolic disruptors, yet how individual chemicals perturb metabolic pathways during early development remains incompletely understood. Here, we used targeted and untargeted metabolomics and pathway analysis in zebrafish embryos to characterize metabolic disruption induced by perfluorooctanesulfonic acid (PFOS), boscalid (BOS), and bisphenol F (BPF). Each compound elicited a distinct metabolic fingerprint, indicating chemical-specific patterns of metabolic stress rather than a uniform response across toxicants. Comparative analysis demonstrated divergence in central metabolic pathways, including mitochondrial metabolism, amino acid and nucleotide turnover, redox balance, and tryptophan metabolism. PFOS induced the most extensive metabolic perturbation, whereas BOS and BPF produced more restricted but distinct metabolic profiles. Comparison of germ-free and conventionally colonized embryos showed that host microbial status modulated the magnitude, but not the direction, of chemical-induced metabolic changes. These metabolic alterations align with exposure-specific transcriptional network modules, supporting distinct chemical modes of action. Together, these findings demonstrate that early life exposure to PFOS, BOS, and BPF results in chemically distinct metabolic stress phenotypes during development and illustrate how integrated metabolomic profiling can resolve compound-specific metabolic effects while accounting for contextual modifiers such as host microbial status.},
}

@article {pmid42903469,
year = {2026},
author = {Ponce-Cusi, R and Barletta-Carrillo, C and Pilco-Ferreto, N},
title = {Microplastics and nanoplastics as potential ecological oncogenic co-drivers: rewiring host-microbe interactions in cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1923626},
pmid = {42903469},
issn = {2235-2988},
mesh = {Humans ; *Neoplasms/microbiology/etiology/chemically induced/pathology ; *Microplastics/adverse effects/toxicity ; *Host Microbial Interactions/drug effects ; Tumor Microenvironment/drug effects ; Animals ; *Carcinogenesis ; Microbiota/drug effects ; Environmental Exposure/adverse effects ; Host-Pathogen Interactions ; },
abstract = {Microplastics and nanoplastics (MPs/NPs) are increasingly recognized as biologically active interfaces that may reshape host-microbe interactions in carcinogenesis. This review proposes a hypothesis-generating mechanistic framework in which MPs/NPs may influence cancer-related processes through the integration of environmental exposure, epithelial barrier disruption, immune dysregulation, and tumor microenvironment remodeling. Although applicable to multiple epithelial interfaces, the framework primarily focuses on the intestinal mucosa, where the most substantial evidence exists. Through plastisphere formation, MPs/NPs adsorb pollutants, virulence factors, and microbial communities, potentially facilitating pathogen persistence, horizontal gene transfer, and antibiotic resistance enrichment. Upon host exposure, MPs/NPs have been associated with compromised epithelial integrity, enhanced microbial translocation, and activation of inflammatory pathways involving pattern recognition receptors, NF-κB, and the NLRP3 inflammasome. At the microbiome level, MPs/NPs may promote dysbiosis, alter microbial metabolism, and favor pro-inflammatory and genotoxic metabolites that could reinforce oncogenic signaling. These processes may converge to sustain chronic inflammation, immune evasion, extracellular matrix remodeling, angiogenesis, and tumor-permissive niches. While experimental and biomarker-based evidence support this axis, direct human data remain limited. Collectively, this review provides a conceptual basis for understanding environmentally associated carcinogenesis through MPs/NPs as ecological mediators bridging the environmental exposures, microbiome, and cancer biology.},
}

Humans
*Neoplasms/microbiology/etiology/chemically induced/pathology
*Microplastics/adverse effects/toxicity
*Host Microbial Interactions/drug effects
Tumor Microenvironment/drug effects
Animals
*Carcinogenesis
Microbiota/drug effects
Environmental Exposure/adverse effects
Host-Pathogen Interactions

@article {pmid42903480,
year = {2023},
author = {Wang, J},
title = {A roadmap for exploring the untouched protein space for biology and medicine.},
journal = {hLife},
volume = {1},
number = {2},
pages = {93-97},
pmid = {42903480},
issn = {2949-9283},
abstract = {Proteins are the major carriers of biological processes and extant proteome contains tremendous diversity. However, the theoretical diversity of proteins greatly outnumbered the currently known, largely due to evolutionary constraints. Here, we propose that untouched protein space, either extant yet with unknown function, or unnatural proteins could have many proteins of desired functions, and outlined a roadmap for exploring such protein space with artificial intelligence. Particularly with the methods developed in natural language processing (NLP), we can first identify a large number of functional proteins and peptides encrypted in biological big data, for instance microbiome and virome data. Secondly, larger scale mutations and directed evolution can be carried out and facilitated by NLP, to achieve improved function based on known proteins. Lastly, sampling random sequences and applying NLP might reveal the more complete landscape of protein functions and enable de novo protein design.},
}

@article {pmid42903521,
year = {2026},
author = {Chen, K and Li, Q and Xing, Y and Liu, C and Yang, F},
title = {Gut microbiota dysbiosis in pediatric acute lymphoblastic leukemia: clinical consequences, mechanistic insights, and microbiota-targeted interventions.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1928304},
pmid = {42903521},
issn = {2296-2360},
abstract = {Gut microbiota dysbiosis has emerged as a key feature in pediatric acute lymphoblastic leukemia (ALL), driven by chemotherapy, antibiotic exposure, and treatment-related nutritional impairment. Increasing evidence indicates that disruption of microbial diversity and depletion of short-chain fatty acid-producing bacteria are closely associated with infectious complications, gastrointestinal toxicity, and potentially reduced treatment efficacy. This review synthesizes current evidence on the interplay between gut microbiota and pediatric ALL across four dimensions: clinical outcomes, treatment-related toxicity, pharmacological interactions, and prognosis. We further summarize how leukemia therapy reshapes microbial ecosystems through cytotoxic agents, antimicrobial exposure, and dietary alterations. In addition, we discuss microbiota-centered therapeutic strategies, including probiotics, prebiotics, synbiotics, postbiotics, dietary interventions, and fecal microbiota transplantation. While promising, these approaches require careful validation in pediatric oncology due to safety considerations and limited clinical trial data. Finally, we highlight methodological advances such as multi-omics integration and machine learning approaches, which may enable microbiome-based risk stratification and precision supportive care in the future. Overall, gut microbiota represents a potential modifiable factor influencing clinical outcomes in pediatric ALL.},
}

@article {pmid42903525,
year = {2025},
author = {Zhang, Y and Guo, J and Zhu, R and Hu, L and Li, T and Cao, X and Shen, H and Wu, W},
title = {Skin microbiome dysbiosis in Prototheca wickerhamii infection.},
journal = {hLife},
volume = {3},
number = {8},
pages = {410-412},
pmid = {42903525},
issn = {2949-9283},
}

@article {pmid42903607,
year = {2026},
author = {Cossu, C and Adamo, M and Di Lorenzo, A and Conti, L},
title = {The intratumoral microbiome in breast cancer: an actionable component of the tumor immune microenvironment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1944056},
pmid = {42903607},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Breast Neoplasms/microbiology/immunology/therapy ; Female ; *Microbiota/immunology ; Animals ; },
abstract = {Breast cancer remains one of the leading causes of cancer-related deaths in women. The discovery of a breast tumor microbiota has deeply changed our understanding of the breast tumor microenvironment, identifying microorganisms as active players in tumor progression. Increasing evidence suggests that intratumoral bacteria may influence multiple hallmarks of breast cancer, including chronic inflammation, immune modulation, metabolic reprogramming, epithelial plasticity, metastatic dissemination, and therapeutic response. Distinct microbial communities have been associated with specific breast cancer subtypes and clinical outcomes, and some mechanistic studies have demonstrated that individual bacterial species and their metabolites can directly regulate oncogenic signaling pathways, reshape the tumor immune microenvironment, and alter sensitivity to chemotherapy and immunotherapy. These findings have generated growing interest in exploiting the breast tumor microbiota as a source of novel diagnostic, prognostic, and predictive biomarkers, as well as a therapeutic target for breast cancer treatment. In this review, we summarize current knowledge on the composition and origin of the breast tumor microbiota, discuss the molecular mechanisms through which tumor-associated microorganisms may influence breast cancer initiation and progression, examine their impact on treatment response, and highlight emerging microbiota-based therapeutic strategies. Finally, we discuss the major technical and biological challenges that currently limit clinical translation, including low microbial biomass, contamination, lack of methodological standardization, and patient-related confounding factors, and outline future perspectives for integrating microbial profiling into precision oncology. A deeper understanding of host-microbe interactions within the breast tumor microenvironment may ultimately enable microbiome-informed approaches for personalized prevention, diagnosis, prognostication, and treatment of breast cancer.},
}

Humans
*Tumor Microenvironment/immunology
*Breast Neoplasms/microbiology/immunology/therapy
Female
*Microbiota/immunology
Animals

@article {pmid42903643,
year = {2026},
author = {Domagała, SK and Kania, K and Nocoń, J and Spyrka, A and Marcinek, M and Tkocz, M},
title = {Impact of the urinary microbiome on urinary tract infection progression.},
journal = {Central European journal of urology},
volume = {79},
number = {3},
pages = {463-471},
pmid = {42903643},
issn = {2080-4806},
abstract = {INTRODUCTION: Urinary tract infections (UTIs) remain a significant challenge in modern urology, increasingly complicated by the shift away from the "sterile bladder dogma." This narrative review summarizes current knowledge (2020-2026) on the urinary microbiome in women, men, and children, emphasizing the transition toward personalized urological care.

MATERIAL AND METHODS: We conducted a comprehensive synthesis of 48 peer-reviewed articles from PubMed, Scopus, and Google Scholar. This narrative review evaluates the interplay between the urinary microbiome, host immune response, and pathogen virulence, while critically comparing traditional urine cultures with advanced diagnostic tools, such as next-generation sequencing (NGS) and expanded quantitative urine cultures (EQUC).

RESULTS: Our analysis highlights the role of dysbiosis in UTI progression and the increasing threat of multidrug-resistant pathogens within the ESKAPEE group. Findings reveal that while modern diagnostics offer a more detailed microbial profile, clinical implementation remains constrained by technical and standardization challenges.

CONCLUSIONS: Standard urine culture may be insufficient for managing recurrent or atypical UTIs. We advocate for a personalized diagnostic and therapeutic approach that integrates molecular insights, aiming to curb antibiotic overuse and improve patient outcomes in the era of rising drug resistance.},
}

@article {pmid42903831,
year = {2027},
author = {López-Contreras, BE and León-Mimila, P and Villamil-Ramírez, H and Morán-Ramos, S and Cerqueda-García, D and Del-Río-Navarro, BE and Aguilar-Salinas, CA and Villarreal-Molina, T and Camacho-Barrón, M and García, OP and Canizales-Quinteros, S},
title = {Gut microbiota profile in school-aged children with vitamin A depletion and vitamin E deficiency: A cross-sectional study.},
journal = {Gut microbes reports},
volume = {4},
number = {1},
pages = {2747503},
pmid = {42903831},
issn = {2993-3935},
abstract = {Vitamin A (VitA) and vitamin E (VitE) deficiencies can result in significant health consequences in children. The role of the intestinal microbiota in these vitamin deficiencies has been scarcely explored. This cross-sectional study aimed to analyze the relationship of VitA depletion and VitE deficiency with metabolic traits, dietary intake, and the gut microbiota composition in 179 school-age children. Serum VitA depletion and VitE deficiency were present in 8.4% and 20.7% of children, respectively. No significant relationship between tocopherol or retinol intake and VitA depletion or VitE deficiency was found. Linear discriminant analysis effect size (LEfSe) and analysis of compositions of microbiomes with bias correction 2 (ANCOM-BC2) analysis revealed no differences in the gut microbiota composition according to VitE status. However, we observed significant enrichment of Veillonella, Haemophilus, and Streptococcus in children with VitA depletion as compared to those with normal VitA levels. The enrichment of these oropharyngeal genera in VitA depletion resembles the gut microbiome composition previously described in childhood stunting. Future functional studies are required to elucidate whether these bacteria play a role in vitamin A metabolism.},
}

@article {pmid42903950,
year = {2024},
author = {Qin, N and Ehrlich, SD},
title = {Advancements for microbiome research in human health and disease: From composition to functionality.},
journal = {hLife},
volume = {2},
number = {10},
pages = {542-545},
pmid = {42903950},
issn = {2949-9283},
}

@article {pmid42903982,
year = {2025},
author = {Ma, YJ and Sun, YC and Wang, L and Xu, WX and Fan, XD and Ding, J and Heeschen, C and Wu, WJ and Zheng, XQ and Liu, NN},
title = {Dissection of intratumor microbiome-host interactions at the single-cell level in lung cancer.},
journal = {hLife},
volume = {3},
number = {8},
pages = {391-406},
pmid = {42903982},
issn = {2949-9283},
abstract = {The intratumor microbiome, one of the hallmarks of cancer, plays a crucial role in cancer progression through its interaction with the host. However, the underlying mechanisms remain poorly understood. In this study, six publicly available single-cell transcriptomic lung cancer datasets (comprising 178 samples) from multiple centers (Shanghai, New York, Seoul) were integrated to investigate the heterogeneity of host-microbiome interactions at the single-cell level using single-cell analysis of host-microbiome interactions (SAHMI). The results indicate that primary tumor tissues have a high proportion of fungi-associated cells, whereas metastatic brain tissues predominantly contain bacteria-associated cells. There are also distinct microbial distributions across cell types. Notably, the presence of specific bacteria significantly influences the transcriptome of resident host cells, including T cells and macrophages, by modulating pathways related to ribosomal RNA (rRNA) processing, cellular responses to stress and stimuli, and RNA and protein metabolism. Finally, specific cell-associated bacteria are significantly correlated with clinical features, such as lung cancer stages and smoking frequency. These single-cell insights into microbiome-host interactions improve current understanding about lung cancer development and progression and offer potential micro-ecological and diagnostic insights.},
}

@article {pmid42904169,
year = {2026},
author = {Zhang, Y and Gao, F and Gao, P and Fan, Y and Wang, X and Yang, Y and Gagnon, A and Martinez, G and Gillet, V and Zhu, J and Bellenger, JP and Baccarelli, AA and Takser, L and Shen, Y},
title = {Halogenated flame retardant exposure was associated with pediatric gut microbiome profiles in a Canadian cohort.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2747517},
pmid = {42904169},
issn = {2993-3935},
abstract = {Environmental chemical exposures have been linked to gut microbiome dysregulation and adverse health outcomes in children. Halogenated flame retardants (HFRs) are persistent chemicals with substantial early-life exposure, yet evidence on their effects on the pediatric gut microbiome remains limited. We examined associations between HFR exposures and the gut microbiome among 8-12-y-old children from the GESTation and Environment (GESTE) cohort in Sherbrooke, Canada. In a multi-matrix, multi-omics design, 10 HFRs were quantified in plasma (n = 140) and stool (n = 182), with shotgun metagenomic and metatranscriptomic sequencing characterized microbial species and functional pathways. After false discovery rate correction, plasma BDE-47 and BDE-99 were inversely associated with Clostridium sp. CAG:221 and Bacteroides dorei, respectively (q < 0.2). Stool BDE-153 was negatively associated with short-chain fatty acid-producing taxa, including Eubacterium spp. and Roseburia intestinalis, and positively associated with Alistipes putredinis and Faecalibacterium spp. Stool BDE-153 and anti-DP were associated with higher activity of pathways involved in phospholipid homeostasis and 4-aminobutanoate degradation. Mediation analysis suggested that Faecalibacterium spp. partly mediated the association between stool BDE-153 and cytidine diphosphate-diacylglycerol biosynthesis. Our findings suggest that childhood HFR exposure is associated with alterations in gut microbiome composition and function, with potential implications for pediatric health.},
}

@article {pmid42904260,
year = {2026},
author = {Li, X and Shao, S and He, Y and Zhang, Q},
title = {Microbiome, anti-infectives, and artificial intelligence: Decoding host-microbe dynamics.},
journal = {Infectious diseases & immunity},
volume = {6},
number = {4},
pages = {248-250},
pmid = {42904260},
issn = {2693-8839},
}

@article {pmid42904512,
year = {2026},
author = {Zhou, Y and Fuentes, D and Merchant, A and Kaiser, BN and Alemneh, AA and Toh, R and Li, J and Wei, Y and Denton, MD},
title = {Benzoic Acid Secreted From the Chickpea Root Promotes Persistent Colonisation by Specific Soil Microbes.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70990},
pmid = {42904512},
issn = {1365-3040},
support = {IH140100013//Australian Research Council/ ; LP200200813//Australian Research Council/ ; //Grains Research and Development Corporation/ ; //Government of South Australia/ ; 2024SFQZX007//National Sustainable Development Agenda Innovation Demonstration Area/ ; 2024GH15//Innovation Pilot Project of Integration of Science, Education, and Industry of Shandong Academy of Sciences/ ; },
abstract = {The plant root tip is highly sensitive to environmental cues and exerts sensory, chemical and movement responses. However, the microbial diversification at the root tip, and the nature of root-selection for microbes, are poorly understood. This study investigated root exudation and microbiome colonisation in the chickpea (Cicer arietinum L.) root tip and root base, in diverse soils. For the endosphere microbiome, deterministic effects were more important than stochastic processes in shaping the root tip microbiome, indicated by the stable endophyte composition independent of the soil microbiota background. A genotype with high secretion of benzoic acid (BA), was consistently colonised by 3 core ASV (Amplicon Sequence Variant) from the Burkholderia clade. Two of 98 isolated strains were confirmed as the culturable candidates of the core ASV, both of which were characterised by superior BA tolerance and the ability to utilise BA as a sole carbon source, demonstrated through high expression of BA degradation genes. Additionally, one IAA-producing coloniser specifically promoted the growth of its original host genotype across different soils, but provided no consistent benefits for other genotypes. Our results reveal the mechanisms by which soil microbes interact with root exudates of a host genotype to establish colonisation.},
}

@article {pmid42904632,
year = {2026},
author = {Geng, T and Yang, H and Liu, Y and Zhao, J and Zhou, Y},
title = {Transcriptomic, untargeted metabolomic, and gut microbiota studies on the anticoccidial activity of the combination formula in broilers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0341024},
doi = {10.1128/spectrum.03410-24},
pmid = {42904632},
issn = {2165-0497},
abstract = {UNLABELLED: Coccidiosis, a devastating intracellular parasitic disease, poses a significant threat to the poultry industry. Traditional control methods, which involve the inclusion of anticoccidial drugs in feed, have raised concerns over veterinary drug residues. Consequently, there is a pressing need to identify suitable alternatives or complementary strategies to anticoccidial drugs, with plant-derived natural products emerging as a promising candidate. Our laboratory has previously identified a combination formula that demonstrates good anticoccidial activity. However, the underlying mechanisms remain elusive. This study aims to elucidate the mechanism of action of this formula using a multi-omics approach, including transcriptomics, untargeted metabolomics, and gut microbiota analysis. Cecal transcriptomic analysis revealed significant enrichment in pathways, such as lysosomes, ribosomes, oxidative phosphorylation, and sphingolipid metabolism following treatment with the combination formula. Untargeted metabolomic profiling indicated a pronounced enrichment in the gut IgA generation immune network pathway, with retinoic acid identified as a key differential metabolite. Gut microbiota sequencing analysis suggested that the combination formula modulates the gut microbiota of infected broilers towards a composition resembling that of healthy broilers. Collectively, these results suggest that the combination formula exerts its anticoccidial effects through the regulation of differential gene clusters, metabolites, and microbiota. The results of this study have provided us with a deeper understanding of the good anticoccidial effects of the combination formula.

IMPORTANCE: Eimeria tenella is a significant parasitic protozoan that poses a substantial threat to the development of the poultry industry. The combination formula, a synergistic blend of plant-derived natural products, has been identified in our laboratory for its good anticoccidial effects. In this study, we employed non-targeted metabolomics, transcriptomics, and gut microbiome sequencing to elucidate the mechanism of action against coccidiosis. Our results revealed a multitude of differential gene clusters and metabolites. Furthermore, the gut microbiota structure of the cecal content in the treated group more closely resembled that of the healthy control group.},
}

@article {pmid42904669,
year = {2026},
author = {Maulen, M and Pezoa-Soto, I and León, D and Dominguez, EM and Martin, AJM and Díaz-Vásquez, WA},
title = {SARS-CoV-2 variant-dependent alterations in nasopharyngeal microbiota and host inflammatory response.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093026},
doi = {10.1128/spectrum.00930-26},
pmid = {42904669},
issn = {2165-0497},
abstract = {The SARS-CoV-2 pandemic saw multiple outbreaks occur over short periods. This was linked to the virus's high infectivity and rapid mutation rate, which hindered the development of effective treatments and a comprehensive understanding of COVID-19 pathophysiology. The nasopharyngeal tract, the main entry site of SARS-CoV-2, interacts with angiotensin-converting enzyme 2 receptors via the viral spike glycoprotein, triggering pro-inflammatory responses that affect both tissue integrity and the resident microbiota. Viral infection induces dysbiosis by modulating microbiome diversity. Although distinct variants produce independent symptoms and viral loads, their impact on the nasopharyngeal microbiota and host inflammatory profile remains poorly understood. To address this, we analyzed nasopharyngeal samples from Chilean individuals collected during different phases of the pandemic. The microbiota was characterized by 16S rRNA gene sequencing (V3-V4 region), and cytokine expression was quantified by RT-qPCR. Finally, applied rigorous data processing and machine-learning models, Random Forest and K-Nearest Neighbors, to identify associations between SARS-CoV-2 variants, inflammatory markers, and opportunistic bacterial genera. Our results reveal that SARS-CoV-2 infection is associated with distinct immunomicrobial signatures marked by increased TNF-α expression and the expansion of opportunistic taxa. These variant-dependent alterations indicate that host inflammatory responses and microbial dysbiosis are closely intertwined in the nasopharyngeal environment. This study provides a comprehensive framework integrating microbial and host factors to better understand the mechanisms underlying COVID-19 pathogenesis and highlights the potential of combining microbiome and cytokine profiling with machine-learning approaches to differentiate infection outcomes across viral variants.IMPORTANCEUnderstanding how SARS-CoV-2 infection alters the upper respiratory microbiota and host immune responses is essential to uncover the mechanisms underlying COVID-19 severity. In this study, we integrate bacterial 16S rRNA sequencing, inflammatory markers, and machine learning to identify key descriptors of infection such as TNF-α, Acinetobacter, Prevotella, and Staphylococcus. These markers define a conserved immunomicrobial signature across viral variants, linking inflammatory activation with microbial dysbiosis in the nasopharyngeal environment. Our findings highlight the value of the correct and robust application of machine learning models and nested cross-validation strategies in high-dimensional (wide) data sets to improve variant discrimination, reveal host-microbe interactions, and support the development of therapeutic strategies for respiratory viral infections.},
}

@article {pmid42904670,
year = {2026},
author = {Wen, X and Han, S and Wu, M and Show, PL and Liao, B and Cai, Z and Zhou, J},
title = {Functional convergence despite taxonomic turnover across coral-associated microbiomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240126},
doi = {10.1128/spectrum.02401-26},
pmid = {42904670},
issn = {2165-0497},
abstract = {Coral-associated microbiomes are fundamental to holobiont health and resilience, yet their community structures often demonstrate high taxonomic variability across host species. Whether such variability results in functional instability or reflects pervasive metabolic redundancy remains unclear. Here, we investigated microbial taxonomic structure, functional potential, and community assembly mechanisms across 15 coral species using 16S rRNA gene sequencing and shotgun metagenomics. These communities exhibited extreme taxonomic heterogeneity, high beta-diversity, and the absence of a universally shared core genus, indicating strong host-specific filtering that dictates microbial membership. In contrast, Kyoto Encyclopedia of Genes and Genomes pathway-based functional profiles exhibited striking convergence across hosts, revealing a conserved metabolic landscape despite extensive taxonomic turnover. Mantel and Procrustes analyses identified a weak but significant correspondence between taxonomic composition and functional potential, a pattern consistent with functional redundancy across coral-associated microbiomes. Null model-based assembly analyses further revealed a decoupling between taxonomic and functional organization. Taxonomic structure was shaped by a host-dependent balance of stochastic and deterministic processes, whereas functional profiles were predominantly assembled through stochastic processes, maintaining consistently high functional redundancy across hosts. Metagenomic profiling uncovered a two-tier functional architecture underlying this stability: a conserved, high-abundance metabolic core enriched in carbon and phosphorus cycling and stress response functions that support microbial persistence in the coral microenvironment, together with lower-abundance host-specific metabolic modules involved in nitrogen and sulfur transformations that enable niche adaptation. Thus, functional requirements primarily govern the coral-associated microbiome rather than taxonomic identity. This synergy between conserved survival traits and flexible metabolic capacities maintains holobiont homeostasis despite extensive taxonomic turnover.IMPORTANCECoral reefs rely on complex partnerships between corals and their associated microorganisms to maintain health and withstand environmental stress. However, it remains unclear whether changes in microbial communities across different coral species lead to loss of important functions. In this study, we examined microorganisms associated with 15 coral species from the South China Sea and found that coral species hosted highly different microbial communities, while maintaining similar microbial functions. Our findings reveal that different microbial groups can perform similar ecological roles, allowing coral-associated communities to remain functionally stable despite changes in microbial membership. This functional flexibility may help corals maintain biological balance under changing environmental conditions and provides new insights into how coral holobionts preserve resilience in the face of ecological disturbances.},
}

@article {pmid42904697,
year = {2026},
author = {Westcott, SL and Schloss, PD},
title = {rchime: an R package for detecting chimeras in amplicon sequencing data.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0104826},
doi = {10.1128/mra.01048-26},
pmid = {42904697},
issn = {2576-098X},
abstract = {A longstanding challenge in analyzing amplicon sequencing data is the presence of chimeras, which are PCR products that are formed by two or more templates. rchime is an R package that implements the UCHIME algorithm, which efficiently screens amplicon sequence collections for chimeras.},
}

@article {pmid42905002,
year = {2026},
author = {Chu, Z and Zhang, X and Zhu, B and Liu, Q and Zeng, Y and Zhou, Y and Hu, Z and Luo, F},
title = {Protective Effects of Narirutin Against Exercise-Induced Fatigue in Mice: Insights from Integrated Microbiome, Metabolome, and Transcriptome Analysis.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {41},
pages = {32426-32447},
doi = {10.1021/acs.jafc.6c11203},
pmid = {42905002},
issn = {1520-5118},
support = {25B0319//Education Department of Hunan Province/ ; 32603353//National Natural Science Foundation of China/ ; 2022YFF1100200//National Key Research and Development Program of China/ ; 2024YJ006//Central South University of Forestry and Technology/ ; 2025QT-40//Hunan Province 2025 Furong Plan Youth Talent Project/ ; },
mesh = {Animals ; Mice ; *Fatigue/microbiology/metabolism/drug therapy/genetics/etiology/prevention & control ; Male ; *Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Physical Conditioning, Animal/adverse effects ; Humans ; Multiomics ; Bacteria/genetics/isolation & purification/classification/drug effects/metabolism ; Mice, Inbred C57BL ; Transcriptome/drug effects ; *Protective Agents/administration & dosage ; Gene Expression Profiling ; },
abstract = {Exercise-induced fatigue is linked to oxidative stress, inflammation and intestinal dysbiosis. Narirutin (NAR), a natural flavonoid, lacks systematic evidence and mechanistic clarification against exercise fatigue. Herein, a forced exercise fatigue mouse model was constructed, and behavioral, biochemical, histological and multiomics analyses including 16S rRNA sequencing, untargeted metabolomics, transcriptomics and RT-qPCR were performed. Fecal microbiota transplantation (FMT) and antibiotic-mediated microbiota depletion further verified the causal role of gut microbiota. NAR dose-dependently improved exercise endurance, muscle strength, glycogen storage, oxidative status and inflammatory profiles. It restored gut microbial diversity, remodelled microbial composition and altered metabolic signatures. Multiomics integration indicated NAR regulated immune genes via the gut microbiota-metabolite-gene axis. FMT reproduced antifatigue effects, whereas antibiotic treatment eliminated NAR protection. This study demonstrates that NAR alleviates exercise-induced fatigue largely relying on intact gut microbiota, although microbiota-independent peripheral effects cannot be fully excluded. These findings support its exploitation as a natural antifatigue functional component.},
}

Animals
Mice
*Fatigue/microbiology/metabolism/drug therapy/genetics/etiology/prevention & control
Male
*Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Physical Conditioning, Animal/adverse effects
Humans
Multiomics
Bacteria/genetics/isolation & purification/classification/drug effects/metabolism
Mice, Inbred C57BL
Transcriptome/drug effects
*Protective Agents/administration & dosage
Gene Expression Profiling

@article {pmid42905044,
year = {2026},
author = {Zhang, Y and Chen, M and Zhang, F},
title = {Multivariate Genome-Wide Analysis Delineates Shared Genetic Determinants Across Periodontal and Oral Microbial Phenotypes.},
journal = {Oral health & preventive dentistry},
volume = {24},
number = {},
pages = {1029-1038},
doi = {10.3290/j.ohpd.c_2823},
pmid = {42905044},
issn = {1757-9996},
mesh = {*Genome-Wide Association Study ; Humans ; Phenotype ; *Periodontitis/genetics/microbiology ; Polymorphism, Single Nucleotide ; *Microbiota/genetics ; Genetic Predisposition to Disease ; },
abstract = {BACKGROUND: Periodontitis affects approximately 10% of the global population, posing a serious threat to tooth retention and quality of life. The disease emerges from bidirectional host-microbiome interactions that can shift from homeostasis to dysbiosis and chronic inflammation, yet conventional single-phenotype analyses cannot resolve pleiotropic loci acting across interrelated periodontal and microbial traits. We aimed to jointly model the shared genetic structure of six periodontitis-related phenotypes and to prioritise pleiotropic loci with translational relevance.

METHODS AND MATERIALS: We harmonised European-ancestry genome-wide association studies (GWAS) summary statistics for six traits representing host periodontal phenotypes (gingivitis, chronic periodontitis, periapical abscess, dental calculus) and oral microbial composition (genus Porphyromonas, order Bacteroidales). A common genetic factor was estimated using genomic structural equation modelling (genomic SEM), and factor-level genome-wide association analysis was conducted on 4,899,781 SNPs. The resulting signals were annotated through locus discovery and novelty assessment (FUMA), fine-mapping (SuSiE and FINEMAP), gene-level testing (MAGMA), and transcriptome-wide association with Bayesian gene prioritisation (FUSION and FOCUS). Heritability was partitioned across functional annotations (stratified LD score regression), and cell types (CELLECT); spatial enrichment was assessed using gsMap, and a polygenic risk score was constructed with PRS-CS.

RESULTS: A single-factor model provided adequate fit (CFI = 1.0). Factor-level GWAS identified 127 genome-wide significant SNPs consolidating into 56 independent lead variants, all uniquely identified at the factor level. MAGMA prioritised RASAL2 and C5orf27. Fine-mapping yielded 56 variants with posterior inclusion probabilities exceeding 0.95. Transcriptome-wide association and FOCUS converged on the long non-coding RNA RP11-563N4.1 (PIP = 1). Cell-type enrichment highlighted a vascular-stromal axis led by hepatic sinusoidal endothelial cells, with additional signals in pericytes, cardiac and smooth muscle cells, endocardium, and lung stroma. Spatial mapping localised the strongest aggregate signal to lung tissue, consistent with an oral-lung mucosal axis. Polygenic risk was distributed unevenly across chromosomes.

CONCLUSIONS: These analyses delineate a vascular-matrix-centred genetic architecture shared across periodontal and oral microbial traits. The prioritised loci and effector genes provide genetically informed candidates for risk stratification and for targeted investigation of periodontal pathobiology. Clinically, these genetically informed candidates may aid in identifying individuals at elevated risk and in guiding mechanism-based preventive and therapeutic strategies for periodontitis.},
}

*Genome-Wide Association Study
Humans
Phenotype
*Periodontitis/genetics/microbiology
Polymorphism, Single Nucleotide
*Microbiota/genetics
Genetic Predisposition to Disease

@article {pmid42905123,
year = {2026},
author = {Darawshy, F and Tsay, JJ and Sanchez, E and Jin, DM and Kim, Y and Li, Q and Chung, M and Becker, AS and Sulaiman, I and Barnett, C and Wu, BG and Pillai, R and Kwok, B and Wong, KK and Kugler, MC and Li, Y and Schluger, R and Collazo, D and Kyeremateng, Y and Bain, A and Chang, M and Bessich, JL and DeMaio, A and Laniado, I and O'Neill, DK and Shum, E and Chachoua, A and Hall, JJ and Sanders, J and Thurston, G and Goncalves, MD and Dantas, EC and Vanguri, RS and Wong, KK and Sterman, DH and Tsirigos, A and Morton, J and Li, H and Ghedin, E and Segal, LN},
title = {Lower airway microbiome transcriptional and metabolic activities influence responsiveness to immunotherapy in NSCLC.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {},
doi = {10.1158/2326-6066.CIR-26-0433},
pmid = {42905123},
issn = {2326-6074},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed the treatment of advanced non-small cell lung cancer (NSCLC), yet a large proportion of patients do not respond. The lung microbiome is a key modulator of antitumor immunity, however, the functional contribution of active microbial communities and their interaction with host transcriptional programs in shaping ICI outcomes remain poorly defined. Here, we prospectively analyzed bronchoalveolar lavage (BAL) samples from 71 NSCLC patients prior to ICI initiation. We profiled the microbiome and host transcriptome in the BAL to look for microbial and host signatures in the lower airways associated with treatment response. We found that enrichment of the lower airway microbiome with oral commensals was associated with disease progression and worse prognosis of patients treated with ICI. Metatranscriptomics-derived microbial clustering revealed distinct functional profiles. The microbial cluster enriched with oral commensals, which was only present among patients with poor response to ICI, had differential regulation of pathways involved in the metabolism of short-chain fatty acids, methane, and pyruvate. This cluster also correlated with host immune pathways including upregulation of interferon signaling, neutrophil degranulation, and mitophagy, all of which could contribute to the poor response to immunotherapy. In a preclinical murine model of lung cancer with dysbiosis, inoculating lung tumor-bearing mice with oral commensals increased intratumoral neutrophils and Th17 responses and impaired ICI efficacy. Our findings support the concept that microbial communities in the lower airways influence tumor-immune interactions via defined metabolic-immune axes.},
}

@article {pmid42899159,
year = {2026},
author = {Bogdon, R and Roark, K and Busbee, PB},
title = {The aryl hydrocarbon receptor and kynurenine pathway: connecting inflammatory bowel disease and depression via the microbiota gut brain axis.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1851943},
pmid = {42899159},
issn = {1662-4548},
abstract = {Inflammatory bowel disease (IBD) is a disorder characterized by chronic inflammation in the gastrointestinal (GI) tract. This disease has a complex etiology with major contributing factors including genetics, host-microbiome interactions, dysregulation of the immune response, and various environmental triggers. The negative impacts of IBD are not limited to the GI tract however, as IBD patients also develop extraintestinal manifestations involving multiple organs and organ systems. In support of this, IBD patients have increased incidence of mood and behavioral disorders, such as depression, which are often attributed to the concept known as the microbiota gut brain axis (MGBA). This concept refers to the bidirectional communication between the GI tract and central nervous system (CNS) via key components. While it is clear IBD and depression often manifest together, it remains unclear what major mechanisms drive this relationship. Growing evidence suggests that the aryl hydrocarbon receptor (AhR) impacts disease severity in both IBD and behavioral disorders. The purpose of this review is to summarize IBD and depression with emphasis on the potential role AhR plays in both disorders. In addition, evidence of the kynurenine pathway (KP) in IBD and depression will be discussed with particular focus on how this biochemical pathway is linked to both the activation of AhR and its regulation, thus making it an interesting connection requiring further investigation. This review will also summarize key mechanisms of the MGBA implicated in the comorbidity of IBD and depression highlighting the impact, if any, AhR and KP play in these factors. Lastly, the review will discuss limitations of this current topic and any potential future directions to better understand the roles of AhR and KP in comorbid IBD and depression.},
}

@article {pmid42899285,
year = {2026},
author = {Fernandes, KE and Levina, A and Frost, EA and Carter, DA},
title = {Spatially organized chemical defences shape microbial communities in honey bee colonies.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag247},
pmid = {42899285},
issn = {2730-6151},
abstract = {The success of social insects relies on dense colony living, but these conditions also favour pathogen transmission. Colonies mitigate this risk through social immunity, a coordinated system of behavioural, chemical, and immunological defences. Here, we investigate how chemical defences contribute to colony-level immunity using the European honey bee (Apis mellifera) as a model system. Integrating microbiome profiling, antimicrobial assays, and chemical characterization across hive components, we show that antimicrobial activity exhibits clear distance decay across compartments, closely paralleling shifts in microbial communities. This spatial pattern is most pronounced for bacterial communities and hive-associated pathogenic taxa, indicating selective suppression of harmful microbes while permitting neutral or beneficial species. Chemical analyses identify mediators including H2O2 in honey, flavonoids in propolis and wax, and polar aliphatics in pollen as drivers of this structured immunity. Variation in antimicrobial activity and chemical composition correlates with environmental and colony-level factors, such as apiary location, hive health, and pest exposure, highlighting the ecological sensitivity of these defences. Collectively, these results demonstrate that chemical social immunity is a coordinated, spatially organized system that shapes microbial communities and supports colony function, offering a framework to link chemical defence, microbiome dynamics, and resilience of social insects under environmental and pathogen pressures.},
}

@article {pmid42899387,
year = {2026},
author = {Shan, S and George, I and Kinkel, LL and Lankau, RA},
title = {Regionally Divergent Relationships Between Microbial Communities and Environmental Gradients in Potato Production Systems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70437},
pmid = {42899387},
issn = {1758-2229},
support = {SCMP1701//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; *Solanum tuberosum/growth & development ; *Bacteria/classification/isolation & purification/genetics ; *Microbiota ; Soil/chemistry ; Agriculture ; Fungi/classification/isolation & purification/genetics ; Biodiversity ; },
abstract = {Using soil microbiome data as indicators of soil health remains a challenging task in agriculture research. Microbiome data are complex and exhibit strong spatiotemporal variation and diverse responses to environmental factors. As a result, measurements of microbiota often are difficult to interpret and do not provide credible inferences about soil health status. In this study, we evaluated the distributions of soil microbial communities in three distinct potato growing regions of the Upper Midwest of the USA and compared their relationships with soil chemistry and management factors across regions. A total of 1270 soil samples were collected and analysed for microbial properties, including bacterial and fungal abundance, taxonomic and functional diversity and composition. We found substantial variation in the microbial community properties across spatial scales. Environmental factors were more strongly associated with community diversity at the class level than at finer taxonomic levels. Soil pH, soil organic matter (SOM), crop rotation schemes and fumigation correlated with different aspects of microbial properties, while most of the relationships were region-specific. Our results suggest that the microbiological component of soil health includes multiple aspects of the community properties, and region-specific recommendations are needed for developing soil health promoting practices.},
}

*Soil Microbiology
*Solanum tuberosum/growth & development
*Bacteria/classification/isolation & purification/genetics
*Microbiota
Soil/chemistry
Agriculture
Fungi/classification/isolation & purification/genetics
Biodiversity

@article {pmid42899598,
year = {2026},
author = {Hitchings, R and Ghosh, A and Arcinas, AJ and Almo, SC and Kelly, L and Ryan, A},
title = {Ligand Binding Remodels the Oligomeric State and Active Site of Klebsiella pneumoniae Azoreductase.},
journal = {Biochemistry},
volume = {65},
number = {20},
pages = {3236-3246},
doi = {10.1021/acs.biochem.6c00568},
pmid = {42899598},
issn = {1520-4995},
support = {CA013330/CA/NCI NIH HHS/United States ; },
mesh = {*Klebsiella pneumoniae/enzymology ; Nitroreductases ; *NADH, NADPH Oxidoreductases/chemistry/metabolism/genetics ; Catalytic Domain ; Ligands ; Azo Compounds/metabolism/chemistry ; Models, Molecular ; Protein Binding ; *Bacterial Proteins/chemistry/metabolism/genetics ; Protein Multimerization ; },
abstract = {Azo dyes are widespread in the environment, and humans ingest a range of these dyes present in food and drugs. The human gut microbiome significantly impacts the fate of ingested azo dyes primarily through the reduction of the azo bond (R-N = N-R'). Flavin-dependent azoreductases have been considered the key enzymatic drivers of this process. To challenge this paradigm, we constructed a sequence similarity network of known azoreductases and focused on AzoA of Klebsiella pneumoniae, a central representative within the gut microbiome cluster. Unexpectedly, K. pneumoniae AzoA displayed relatively low in vitro activity against a range of azo compounds. While the physiological implications remain unclear, these findings are consistent with the possibility that nonenzymatic mechanisms contribute substantially to azo compound reduction in the gut. Furthermore, structural characterization of AzoA, as a holoenzyme and in its ligand-bound state, revealed a previously unrecognized ligand-coupled mechanism involving remodeling of the active site and oligomeric state.},
}

*Klebsiella pneumoniae/enzymology
Nitroreductases
*NADH, NADPH Oxidoreductases/chemistry/metabolism/genetics
Catalytic Domain
Ligands
Azo Compounds/metabolism/chemistry
Models, Molecular
Protein Binding
*Bacterial Proteins/chemistry/metabolism/genetics
Protein Multimerization

@article {pmid42899660,
year = {2026},
author = {Zeng, BH and Li, P and Liu, B and Li, T and Yin, H and Sun, L and Liu, L and Li, ZH},
title = {Enrofloxacin Disrupts Microbiota-Gut-Brain Axes in Marine Medaka: Mechanistic Insights from Multiomics and Germ-Free Models.},
journal = {Environmental science & technology},
volume = {60},
number = {41},
pages = {29299-29312},
doi = {10.1021/acs.est.6c06063},
pmid = {42899660},
issn = {1520-5851},
support = {42677347,42277269//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Oryzias/microbiology ; *Enrofloxacin ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; *Brain/drug effects ; Anti-Bacterial Agents ; },
abstract = {The widespread use of antibiotics has resulted in their frequent occurrence in marine environments, yet their ecological risks remain poorly understood. Enrofloxacin (ENR) is one of the most frequently detected antibiotics in aquatic ecosystems. However, its toxicological mechanisms in marine fish remain unclear. Here, multiomics, Vibrio parahemolyticus infection, short chain fatty acid supplementation and germ-free fish models were integrated to investigate ENR induced neurotoxicity and the role of gut microbiota. The results showed that ENR exposure impaired intestinal function in marine medaka (Oryzias melastigma), accompanied by behavioral abnormalities, neurotoxicity, and liver injury. ENR also induced gut microbiome dysbiosis and altered SCFAs levels. Furthermore, SCFAs supplementation and germ-free fish experiments provided complementary and supportive evidence that gut microbial dysbiosis and altered SCFAs levels may be involved in ENR neurotoxic responses. Moreover, ENR pretreated fish showed increased susceptibility to V. parahemolyticus challenge, which further disrupted the gut microbiome and aggravated neurological dysfunction. Collectively, these findings suggest that ENR induced neurotoxicity is linked to disruption of the microbiome-gut-brain axis and increased susceptibility to subsequent pathogenic stress. This study provides new insights into antibiotic toxicity in marine fish and supports ecological risk assessment of ENR in marine aquaculture.},
}

Animals
*Oryzias/microbiology
*Enrofloxacin
Multiomics
*Gastrointestinal Microbiome/drug effects
*Brain/drug effects
Anti-Bacterial Agents

@article {pmid42894768,
year = {2026},
author = {Powell, AM and Jones-Beatty, K and Ensign, LM and Delong, KM and Burd, I},
title = {Impact of Short-Term Fluoride Supplementation in Pregnancy on the Maternal Microbiome, Pregnancy, and Neonatal Outcomes: A Pilot Randomized Controlled Trial.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e116487},
pmid = {42894768},
issn = {2168-8184},
abstract = {Introduction This report presents secondary, exploratory analyses of a double-blind randomized trial originally designed to determine whether fluoride supplementation during pregnancy reduced preterm birth (PTB). The trial was terminated early because of enrollment difficulties and was not powered for its original clinical endpoint. We therefore examined whether randomized fluoride supplementation was associated with oral or vaginal microbiome composition and descriptively evaluated gestational and neonatal outcomes. Methodology In the original double-blind randomized controlled trial, pregnant participants at 10-20 weeks of gestation were assigned to a daily capsule containing 3 mg fluoride or an otherwise comparable prenatal vitamin. Of 319 screened individuals, 47 were eligible, and 30 participants completed follow-up through delivery. Maternal urine, oral swabs, and vaginal swabs were collected during the second and third trimesters and at delivery. The V3-V4 region of the bacterial 16S rRNA gene was sequenced from oral and vaginal specimens. The present secondary analyses compared microbiome composition and diversity by treatment assignment and descriptively examined gestational and neonatal outcomes. Results Urine fluoride concentration differed between groups at the second-trimester assessment but not at later assessments. No differences in vaginal microbiome richness or diversity were observed between treatment groups. Several oral taxa, including Actinomyces, Actinomycetaceae, and Rothia mucilaginosa, had nominally different abundances by treatment assignment; however, these exploratory comparisons were not adjusted for multiple testing. Overall oral alpha- and beta-diversity did not consistently differ by treatment group or visit. Eight positive correlations were observed between oral and vaginal taxa. Clinical outcomes did not show a consistent pattern by treatment assignment, and the study was not powered to assess maternal or neonatal efficacy or safety. Conclusions In this early-terminated pilot trial, prenatal fluoride supplementation was not associated with detectable differences in vaginal microbiome diversity and was not consistently associated with oral microbiome diversity. Nominal taxonomic and clinical differences should be considered hypothesis-generating because of the small sample size and multiple unadjusted comparisons. These data do not establish clinical benefit or harm from fluoride supplementation during pregnancy.},
}

@article {pmid42894949,
year = {2026},
author = {Algul, S and Beyhan, YE and Ozcelik, O},
title = {Microplastics as Microbiota Modulators: Rewiring the Gut Metabolism Immune Axis.},
journal = {Toxicology mechanisms and methods},
volume = {},
number = {},
pages = {1-49},
doi = {10.1080/15376516.2026.2749674},
pmid = {42894949},
issn = {1537-6524},
abstract = {Microplastics (MPs) have emerged as pervasive environmental contaminants with increasing relevance to human health. Beyond their role as inert particulate pollutants, accumulating evidence suggests that MPs may act as biologically active modulators of the gastrointestinal ecosystem. The gut represents a major interface for MP exposure, where ingested particles interact with intestinal epithelial cells, mucus layers, immune components, and resident microbial communities. This review summarizes current evidence on MPs' capacity to alter gut microbiota composition, impair intestinal barrier integrity, disrupt microbial metabolite production, and promote inflammatory and metabolic disturbances.Experimental studies indicate that MP exposure may reduce microbial diversity, shift the abundance of key bacterial taxa, impair tight junction proteins, and increase intestinal permeability. These changes may facilitate the translocation of bacterial products such as lipopolysaccharide, thereby activating inflammatory pathways including TLR4/NF-κB signaling. In parallel, MP-associated dysbiosis may alter short-chain fatty acids, bile acid metabolism, and tryptophan-derived metabolites, suggesting plausible biological pathways relevant to insulin resistance, hepatic lipid dysregulation, cardiometabolic risk, and gut-brain axis disruption. However, most available evidence is derived from animal and in vitro models, and causal relationships in humans remain insufficiently established. Major limitations include heterogeneous exposure protocols, non-standardized particle characterization, limited human longitudinal data, and difficulty separating particle-specific effects from those of associated chemical contaminants.Future studies integrating environmentally realistic exposure models, standardized microbiome analyses, multi-omics approaches, and human cohort designs are needed. Overall, the gut microbiota may represent a critical biological interface through which MPs interact with host physiology; however, further evidence is required before definitive conclusions can be drawn regarding their role in human chronic disease susceptibility.},
}

@article {pmid42895069,
year = {2026},
author = {Fan, X and Mei, L},
title = {Bacteria-nanomaterial co-delivery systems for precision therapy: interfacial design, transport behavior, and translational barriers.},
journal = {Therapeutic delivery},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/20415990.2026.2750073},
pmid = {42895069},
issn = {2041-6008},
abstract = {A literature search was conducted using ProQuest and PubMed, covering publications from August 2016 to August 2026. Older references were included as appropriate.},
}

@article {pmid42895104,
year = {2026},
author = {Giorgio, CM and Licata, G and Argenziano, G},
title = {Why does classic scabies spare the adult scalp? A site-specific barrier hypothesis.},
journal = {Dermatology reports},
volume = {},
number = {},
pages = {},
doi = {10.4081/dr.2026.10955},
pmid = {42895104},
issn = {2036-7392},
abstract = {Dear Editor, The relative sparing of the scalp and face in immunocompetent adults with classic scabies is clinically familiar, whereas these sites may be involved in infants, older adults, immunocompromised patients, and crusted scabies. This distribution is commonly used as a diagnostic clue, but its biological basis remains incompletely explained. [...].},
}

@article {pmid42895105,
year = {2026},
author = {Mushii, O and Lukianova, Y and Bazas, V},
title = {Intratumoral Microbiome-Tumor Microenvironment Crosstalk in Breast Cancer Aggressiveness.},
journal = {The breast journal},
volume = {2026},
number = {1},
pages = {e1508684},
pmid = {42895105},
issn = {1524-4741},
mesh = {Humans ; *Tumor Microenvironment ; *Breast Neoplasms/microbiology/pathology ; Female ; *Microbiota ; },
abstract = {Breast cancer (BC) remains the most common malignancy among women worldwide, with incidence and mortality rates continuing to rise. Alongside tumor heterogeneity and diverse clinical outcomes, increasing attention has been directed toward the role of the intratumoral microbiome as a regulator of breast tumorigenesis. Recent evidence demonstrates that breast tissue harbors one of the most diverse microbial communities compared with other cancer types, with marked differences between normobiota and malignant tissue. Intratumoral microorganisms are potentially associated with BC progression through multiple mechanisms, including modulation of inflammation, steroid hormone metabolism, and extracellular matrix remodeling. Specific taxa, including Staphylococcus, Bacillus, Fusobacterium, and Paenibacillus, have been associated with tumor aggressiveness, molecular subtypes, and patient prognosis. Moreover, the microbiome actively shapes the tumor microenvironment by altering immune infiltration, inducing resistance to anticancer therapy, and regulating immune checkpoint signaling, including PD-1/PD-L1 pathways. Microbial proteases and bacterial analogs of matrix metalloproteinases further contribute to extracellular matrix degradation and stromal remodeling, enhancing metastatic potential. Despite rapid advances, the clinical utility of intratumoral microbial signatures as predictive biomarkers of BC aggressiveness remains under investigation. Comprehensive characterization of microbial profiles across clinical and molecular subgroups may offer novel diagnostic, prognostic, and therapeutic opportunities in BC management.},
}

Humans
*Tumor Microenvironment
*Breast Neoplasms/microbiology/pathology
Female
*Microbiota

@article {pmid42895354,
year = {2026},
author = {Goethals, V and Vanwinsen, N and Mermans, F and De Gand, S and Boon, N and Van de Wiele, T and De Paepe, K},
title = {An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting, and extraction bias in sorted microbial communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0071226},
doi = {10.1128/spectrum.00712-26},
pmid = {42895354},
issn = {2165-0497},
abstract = {Fluorescence-activated cell sorting (FACS) followed by metataxonomics is commonly used to probe the composition of microbial subpopulations with a functionality of interest. Metataxonomic analysis of sorted low-microbial-biomass samples is prone to contamination and bias introduced during sorting and DNA extraction. To improve metataxonomic accuracy, the DNA yield obtained by the DNeasy PowerSoil Pro kit was first maximized. FACS-sequencing using the optimized DNA extraction method distorted the composition of sorted microbiota by introducing sheath fluid contaminants, termed the FACSome. Since FACSome contaminants were experiment-specific, a standardized, applicable in silico decontamination method was developed to characterize and remove FACSome contamination in PacBio and Illumina metataxonomic sequencing data based on carefully selected controls. The optimized DNA extraction and decontamination methods were validated in soil, water, feces, saliva, gut reactor, and mock microbial communities. Metataxonomic profiles of non-selectively sorted and unsorted samples derived from these ecosystems did not perfectly match due to relic DNA depletion during FACS. Effective (97%) relic DNA depletion was confirmed with a spike-in experiment and is desirable since naturally present relic DNA can interfere with function-driven FACS-sequencing. A nuclease-based digest further enhanced relic DNA depletion. Since FACS depleted relic DNA, the preservation of intact cells prior to sorting is essential for activity- or viability-targeted FACS. Intact cells were best preserved during long-term -80°C storage of fecal samples that were not amended with glycerol-1× Tris-EDTA cryoprotectant.IMPORTANCEBulk meta-omics fail to provide sufficient resolution to gain mechanistic insights in microbial ecosystems. Function-driven microbiome research requires high-throughput profiling of active microbial subpopulations. These can be singled out through fluorescence-activated cell sorting (FACS) combined with function-, activity-, or viability-based labeling. The resulting low-biomass sorted samples present a currently overlooked challenge for accurate 16S rRNA gene profiling. We systematically identified all potential sources of interference to enable decontamination of 16S rRNA gene sequences from sorted microbiota. While this study focused on metataxonomic read-outs, our optimized extraction and decontamination workflow can advance other sequencing-based omics analyses of sorted microbial communities. Our optimized FACS-sequencing workflow is thus imperative to unlock the full potential of single-cell labeling and FACS, in turn enabling mode-of-action studies that will broaden our understanding of microbe-environment interactions.},
}

@article {pmid42895480,
year = {2026},
author = {Malcomson, FC and O'Connell, CP and Farhat, Z and Buchanan, DD and Frone, MN and Hatton, JN and Katki, HA and Kim, J and Le Marchand, L and Phipps, AI and Potter, JD and Sinha, R and Stewart, DR and Vogtmann, E and Jenkins, MA and Loftfield, E},
title = {Gut microbiome-related plasma metabolites and risk of colorectal cancer.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-26-0718},
pmid = {42895480},
issn = {1538-7755},
abstract = {BACKGROUND: Perturbations in gut microbiome composition and altered levels of related metabolites may be related to colorectal cancer (CRC). This study assessed whether pre-diagnostic, circulating, microbiome-related metabolite concentrations were associated with CRC risk.

METHODS: We undertook a nested case-control study of 739 participants in the Colon Cancer Family Registry Cohort (312 cases, 427 controls). Median follow-up time from blood draw to diagnosis was 7 years. Pre-diagnostic plasma concentrations of 70 metabolites were quantified by targeted liquid chromatography-tandem mass spectrometry. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated for metabolite concentrations and CRC risk using multivariable conditional logistic regression models. Stratified analyses were conducted by sex, Lynch syndrome diagnosis, and age at tumor onset.

RESULTS: The primary bile acids, cholate and chenodeoxycholate, were positively associated with CRC incidence, overall and among females. The odds of CRC were higher in individuals in the highest compared with the lowest quartiles of cholate (ORQ4vQ1=1.61, 95% CI=1.05-2.49) and chenodeoxycholate (ORQ4vQ1=1.60, 95% CI=1.03-2.50). Two short-chain fatty acids (caproate, valerate) and three metabolites involved in phenylalanine and tyrosine metabolism (cinnamoylglycine, phenylpropionate, 4-ethylphenylsulfate) were suggested to be associated, positively and negatively, respectively, with incident CRC but these associations did not withstand correction for multiple comparisons. In stratified analyses, some differences were observed according to sex, Lynch syndrome diagnosis, and age at tumor onset.

CONCLUSIONS: Circulating microbiome-related metabolites, including bile acids and short-chain fatty acids, may be associated with CRC risk.

IMPACT: These findings provide insight into potential pathways linking the gut microbiome to colorectal carcinogenesis.},
}

@article {pmid42895608,
year = {2026},
author = {Hosseinzadeh, N and Bazdar, M and Hashemi, N and Ashkezary, MR and Mehrabi, A and Kazemi, N and Sarabi-Aghdam, V and Abbasi, A and Kazemi, S},
title = {Nutritional Innovations in Functional Foods: Exploring Postbiotics for Gut and Vascular Health Enhancement.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42895608},
issn = {1867-1314},
abstract = {The exploration of microbiome-targeted interventions in functional foods has accelerated, with postbiotics emerging as a compelling alternative to probiotics. Defined as non-viable microbial cells or their metabolic products, postbiotics demonstrate diverse bioactivities, including anti-inflammatory, antioxidant, and immunomodulatory effects. These attributes enable modulation of the gut-vascular axis, a critical interface influencing systemic inflammation and cardiovascular risk. Short-chain fatty acids (SCFAs), bioactive peptides, and microbial enzymes are among the most studied postbiotics with profound effects on gut integrity and vascular function. Mineral-enriched postbiotics, particularly those supplemented with zinc and selenium, offer further promise in managing metabolic syndrome and cardiovascular disorders. This review critically evaluates the molecular mechanisms through which postbiotics modulate the gut-vascular axis. We discuss the pathways associated with the improvement or eradication of gut-vascular axis-related diseases, focusing on their impact on intestinal integrity, immune regulation, and vascular function. Furthermore, we highlight the potential of postbiotics as functional food ingredients and therapeutic agents for chronic disease management, particularly in metabolic syndrome and cardiovascular disorders.},
}

@article {pmid42895709,
year = {2026},
author = {Sage, SA and Abbott, SJ and Korczak, R and Williams, NC},
title = {Prebiotics in sport and exercise: current evidence, practical applications, and methodological considerations.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2748763},
doi = {10.1080/15502783.2026.2748763},
pmid = {42895709},
issn = {1550-2783},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Sports Nutritional Physiological Phenomena ; Athletic Performance/physiology ; *Exercise/physiology ; Gastrointestinal Microbiome ; Sleep ; Gastrointestinal Tract/physiology/microbiology ; Post-Exercise Recovery ; *Sports ; Athletes ; Affect ; },
abstract = {BACKGROUND: Prebiotics are selectively utilized by the host microbiota and can confer health and/or performance benefits, in part through increasing the abundance of beneficial gut microorganisms and their metabolites. While several studies have shown promising initial findings, high-quality scientific evidence examining the effects of prebiotics on athlete performance, health and wellbeing remains limited.

METHODS: This narrative review summarizes the current available evidence on prebiotic intake in athletic populations, including effects on gastrointestinal structure and function, immune responses, recovery, sleep, wellness, mood and exercise performance. In areas where there is limited evidence in athletic cohorts, but a physiological rationale for a benefit, findings from sedentary and/or clinical populations are evaluated, and the potential relevance of these findings to athletes are discussed. Finally, considerations for practitioners around the use of prebiotics with athletes are provided, and recommendations for designing future prebiotic-based research are explored.

RESULTS: Despite the limited existing literature around prebiotic use in athletes, there are several studies that indicate their potential to improve gut barrier integrity and reduce the incidence/severity of gastrointestinal symptoms. Data also indicates that prebiotics can increase salivary Immunoglobulin A secretion rate and reduce the duration and/or severity of upper respiratory symptoms in trained individuals. Other areas with emerging evidence that warrant further investigation in athletic populations include prebiotics' ability to support exercise adaptation and recovery, promote sleep improvements and enhance mood and cognitive function. The interpretation of current studies is limited by the lack of gut microbiome and metabolome measures and the absence of robust performance measures following a period of prebiotic supplementation. Well-controlled, adequately powered studies incorporating these outcomes are needed to determine the contexts in which prebiotic intake can meaningfully improve health and performance metrics, and to elucidate the underlying physiological mechanisms of any beneficial effects.

CONCLUSION: Prebiotic intake represents a promising intervention to attenuate exercise-induced disturbances to the intestinal epithelium, reduce exercise-associated gastrointestinal symptoms, and lower the duration/severity of upper respiratory symptoms in athletes. Future studies should prioritize high-quality performance assessments, alongside comprehensive microbiome and metabolome profiling, to elucidate mechanistic effects. Areas with limited current evidence such as recovery, sleep, mood, cognitive function, bone health and nutrient absorption in athlete cohorts should also be further explored.},
}

Humans
*Prebiotics/administration & dosage
*Sports Nutritional Physiological Phenomena
Athletic Performance/physiology
*Exercise/physiology
Gastrointestinal Microbiome
Sleep
Gastrointestinal Tract/physiology/microbiology
Post-Exercise Recovery
*Sports
Athletes
Affect

@article {pmid42895782,
year = {2026},
author = {Manninen, JA and Jääskeläinen, E and Johansson, P and Björkroth, J},
title = {Latilactobacillus parafuchuensis sp. nov., isolated from marinated rainbow trout.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {10},
pages = {},
doi = {10.1099/ijsem.0.007322},
pmid = {42895782},
issn = {1466-5034},
mesh = {Animals ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; *Oncorhynchus mykiss/microbiology ; Sequence Analysis, DNA ; Nucleic Acid Hybridization ; Base Composition ; Fatty Acids/chemistry ; },
abstract = {While studying the spoilage microbiome of commercially manufactured marinated rainbow trout (Oncorhynchus mykiss), two strains, Mkasi1-1[T] and Mkahm2-6, that could not be identified as any known species of the family Lactobacillaceae by MALDI Biotyper MSP Identification Standard Method 1.1 analysis were isolated. In phylogenetic analyses, the two strains were positioned closest to Latilactobacillus (L.) fuchuensis. Genetically, Mkasi1-1[T] and Mkahm2-6 were highly similar to each other, having 100% average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) identities. The ANI and dDDH pair values of both Mkasi1-1[T] and Mkahm2-6 with the L. fuchuensis type strain DSM14340[T] were 94.9 and 59.8%, respectively, suggesting that they represent a novel species distinct from L. fuchuensis. Phenotypic properties of Mkasi1-1[T] and Mkahm2-6 were quite similar to those of L. fuchuensis type strain DSM14340[T], differing only in the utilization of fewer carbon sources. Due to the close relation of Mkasi1-1[T] and Mkahm2-6 to L. fuchuensis, we propose the name Latilactobacillus parafuchuensis sp. nov. for this novel species. The type strain is Mkasi1-1[T] (=LMG 34323[T]=DSM 121188[T]), and a second strain is Mkahm2-6 (=LMG 34324=DSM 121189).},
}

Animals
*Phylogeny
RNA, Ribosomal, 16S/genetics
Bacterial Typing Techniques
DNA, Bacterial/genetics
*Oncorhynchus mykiss/microbiology
Sequence Analysis, DNA
Nucleic Acid Hybridization
Base Composition
Fatty Acids/chemistry

@article {pmid42896052,
year = {2026},
author = {Leite Montalvão, AP and Murray, KD and Bezrukov, I and Betz, N and Henry, LP and Duran, P and Boppert, P and Kolb, M and , and Roux, F and Bergelson, J and Weigel, D and Yuan, W},
title = {Biotic response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {43},
pages = {e2611539123},
doi = {10.1073/pnas.2611539123},
pmid = {42896052},
issn = {1091-6490},
support = {951444//EC | European Research Council (ERC)/ ; NONE//Charles H. Revson Foundation (CHRF)/ ; 101028577//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; SFI-PD-Grant-01308072//Simons Foundation (SF)/ ; CMFI//Deutsche Forschungsgemeinschaft (DFG)/ ; Novozymes Prize//Novo Nordisk Fonden (NNF)/ ; NONE//Max-Planck-Gesellschaft (MPG)/ ; },
mesh = {*Arabidopsis/genetics ; *Transcriptome/genetics ; Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; Stress, Physiological/genetics ; Europe ; Gene Expression Profiling ; North America ; },
abstract = {Extensive laboratory experimentation has revealed conserved molecular pathways controlling growth and stress responses in plants, yet how these programs operate in natural settings remains poorly understood. We have investigated the organization of the transcriptome in wild populations of Arabidopsis thaliana by sampling plants across 60 natural sites in Europe and North America over two seasons. Transcriptomes varied extensively among individuals and were only weakly structured by geography or season. No groups of plants stood out due to clear biotic or abiotic stress signatures known from the laboratory. While only a small portion of transcriptome variance was explained by disease symptoms or environmental and phenotypic variables, infection-associated signals accounted for the largest share of the explainable fraction. Biotic-response networks identified in controlled laboratory conditions were well conserved in wild transcriptomes, while other networks, including abiotic-response networks were substantially reorganized in wild plants. Together, these results indicate that while certain transcriptional modules are easily reidentified when moving from the wild to controlled conditions, many regulatory relationships differ in these two contexts, highlighting how ecological complexity shapes transcriptome organization in natural populations.},
}

*Arabidopsis/genetics
*Transcriptome/genetics
Gene Expression Regulation, Plant
*Gene Regulatory Networks
Stress, Physiological/genetics
Europe
Gene Expression Profiling
North America

@article {pmid42896091,
year = {2026},
author = {Frame, LA},
title = {Diet and the microbiome-gut-brain axis: implications for clinical neuropsychology.},
journal = {Archives of clinical neuropsychology : the official journal of the National Academy of Neuropsychologists},
volume = {41},
number = {7},
pages = {},
doi = {10.1093/arclin/acag083},
pmid = {42896091},
issn = {1873-5843},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/physiology/metabolism ; *Diet ; *Neuropsychology ; },
abstract = {OBJECTIVE: To synthesize current evidence on the microbiome-gut-brain axis, with a specific focus on dietary modulation, and to outline its relevance and practical implications for clinical neuropsychology.

METHOD: This narrative review synthesizes literature on mechanistic pathways linking diet, the gut microbiome, and brain health, including interoception and vagal signaling, immune education within the gut-associated lymphoid tissue, microbial metabolites such as short-chain fatty acids, and hypothalamic-pituitary-adrenal axis regulation. Content is based on the author's invited National Academy of Neuropsychology lecture and considers methodological limitations of the field, including variability in sequencing pipelines, reliance on preclinical models, and limited clinical translation.

RESULTS: The gut microbiome plays a critical role in bidirectional communication between the gastrointestinal tract and central nervous system, influencing cognition, mood, behavior, and neurodegenerative processes. Diet is one of the most powerful and modifiable determinants of gut microbiome composition and function, with downstream effects on immune regulation, neuroendocrine signaling, and neural activity relevant to brain health.

CONCLUSIONS: Diet represents a foundational, adjunctive strategy for supporting brain health and cognitive resilience across the lifespan. Neuropsychologists can meaningfully incorporate evidence-based dietary discussion into assessment, patient education, and interdisciplinary care coordination, reinforcing established public health guidance rather than providing individualized medical nutrition therapy.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain/physiology/metabolism
*Diet
*Neuropsychology

@article {pmid42896243,
year = {2026},
author = {Wang, X and Zheng, B and Sun, Y and Liu, L and Li, C},
title = {2'-Fucosyllactose enhances indole-3-lactic acid production by Bifidobacterium bifidum DNG-08 and alleviates colitis-associated bone loss: Associations with microbiota remodeling and intestinal AHR-related responses.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128781},
doi = {10.1016/j.micres.2026.128781},
pmid = {42896243},
issn = {1618-0623},
abstract = {Inflammatory bowel disease is frequently associated with an imbalance in bone remodeling and a decline in bone mass, however, there is a lack of systematic research on microbiome-based intervention strategies targeting colitis-associated bone loss. In this study, Bifidobacterium bifidum DNG-08 (DNG-08) was selected from four candidate strains based on its favorable 2'-fucosyllactose (2'-FL) utilization and indole-3-lactic acid (ILA) production. Genomic annotation revealed that DNG-08 harbors functional genes related to fucosylated oligosaccharide utilization and the conversion of tryptophan to ILA. In a dextran sulfate sodium (DSS)-induced mouse model, combined intervention with DNG-08 and 2'-FL significantly alleviated colitis-associated phenotypes, and reduced pro-inflammatory cytokine levels by 13.33%-58.69%, while increasing IL-10-1.23 times that of the DSS group. Simultaneously, the combined intervention improved trabecular bone microstructure, increasing the bone formation marker procollagen type I N-terminal propeptide (PINP) by 14.61%-56.37%, decreasing the bone resorption marker C-terminal telopeptide of type I collagen (CTX-I) by 17.03%-21.77%, and upregulating the expression of Wnt3a, β-catenin, and Runx2. Gut microbiota analysis showed that combined intervention could partially reverse DSS-induced dysbiosis, enriching potentially beneficial bacterial taxa while reducing inflammation-associated genera. Notably, combined treatment group exhibited elevated serum ILA levels, increased colonic aryl hydrocarbon receptor (AHR) fluorescence, and upregulatied CYP1A1 expression. Correlation analysis identified significant associations among serum ILA, AHR-related indicators, selected bacterial genera, and bone remodeling parameters. This study highlights that strain-substrate matching may serve as a precise synbiotic strategy to improve inflammation-related gut-bone axis dysfunction.},
}

@article {pmid42896370,
year = {2026},
author = {Liu, C and Li, J and Zhu, K and Liu, G and Liu, J and Zou, J and Huang, G},
title = {Mulberry-soybean intercropping reshapes rhizosphere metabolites and microbiota alongside enhanced soybean nodulation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111866},
doi = {10.1016/j.plaphy.2026.111866},
pmid = {42896370},
issn = {1873-2690},
abstract = {Woody perennial-legume intercropping may improve nitrogen-use efficiency, but the belowground links among root-zone configuration, soybean nodulation, rhizosphere chemistry, microbial assembly and nitrogen movement remain unclear. We conducted a greenhouse pot experiment with soybean monoculture (Mono-S), mulberry monoculture (Mono-M), full-contact mulberry-soybean intercropping (Int), and root-separated intercropping with a 30 μm nylon-mesh barrier (Int + B). Physiological and N-related traits were assessed with six pot-level biological replicates, whereas untargeted rhizosphere metabolomics, bacterial full-length 16S rRNA profiling and fungal full-length ITS profiling used three pot-level replicates per treatment-plant component. Relative to Mono-S, Int increased soybean total nodule number by 12.3%, nitrogenase activity by 21.6%, whole-plant N accumulation by 9.1% and shoot dry weight by 26.5%. GmNIN and GmENOD40 transcript abundance was 2.60- and 2.22-fold higher, respectively, in Int-S than in Mono-S. Metabolomics revealed broad, host-specific treatment-associated shifts across multiple chemical classes, while selected putatively annotated soybean isoflavonoids and mulberry flavonoids showed contrasting response patterns. Host-specific PERMANOVA revealed significant differences in bacterial and fungal community composition. [15]N label applied to soybean-side soil was recovered in mulberry roots, stems and leaves under both intercropping configurations, indicating recovery of soil-applied [15]N label in mulberry. Mean land equivalent ratios exceeded 1 in both treatments and differed significantly. Cross-omics associations were largely treatment-structured, highlighting the need for targeted validation of specific metabolite-microbe relationships. Overall, full root-zone continuity was associated with the strongest coordinated soybean symbiotic and growth responses, while both intercropping configurations produced distinct rhizosphere restructuring. These findings provide a framework for understanding rhizosphere-mediated interactions in woody perennial-legume intercropping systems.},
}

@article {pmid42896437,
year = {2026},
author = {Duckett, SK and Udoka, ANS and Iheanacho, GC and Cornett, AH and Bible, JD and May, JB and Powell, RR and Bruce, TF and Klotz, JL},
title = {5-hydroxytryptophan mitigation of ergot alkaloid-induced vasoconstriction in pregnant ewes on blood metabolites, placental and fetal growth, and maternal microbiome.},
journal = {Domestic animal endocrinology},
volume = {98},
number = {},
pages = {107060},
doi = {10.1016/j.domaniend.2026.107060},
pmid = {42896437},
issn = {1879-0054},
abstract = {Twin bearing ewes were randomly assigned and individually fed one of three treatments: 1) total mixed ration (TMR) (CON, n = 10), 2) 5-hydroxytryptophan (5-HTP, 2.5 mg/kg BW) and toxic tall fescue seed containing 1.77 mg ewe[-1]d[-1] ergovaline/ergovalinine (E+) in TMR (E[+]/5-HTP, n = 10), or 3) E+ tall fescue seed in TMR (E[+], n = 10) from gestational day (gd) 86 to 110. At terminal necropsy (gd111), placental and fetal growth measurements were collected and analyzed as a completely randomized design. Maternal blood samples were collected over time and samples of rumen microbiome and fetal blood were collected at necropsy. Feeding E+ fescue seed reduced (P < 0.05) total fetal weight per ewe by 20% compared to CON with E[+]/5-HTP being intermediate. Supplementation of 5-HTP increased (P < 0.05) circulating 5-HTP and 5-HIAA but not 5-HT. Ergovaline was detected in the maternal and fetal blood samples collected at necropsy from E[+] and E[+]/5-HTP fed ewes. Serum non-esterified fatty acid concentrations were greater (P < 0.05) in CON at the end of the study; however, serum glucose and plasma insulin concentrations did not differ. Individual caruncle and cotyledon weights differed by treatment and placentome type. Ewe rumen microbiome diversity was greater with E[+]/5-HTP compared to E[+]. Feeding E[+] tall fescue seed to ewes from gd 86 to 110 reduced fetal growth; however, supplementation of 5-HTP partially mitigated the negative effects of E[+]. Further research is needed at higher dose levels of 5-HTP to fully mitigate the negative effects of E+ on fetal growth.},
}

@article {pmid42896552,
year = {2026},
author = {Li, M and Kuang, J and Chen, T and Ding, K and Chen, Y and Jiao, F and Li, Y and Luo, P and Xia, L and Zhang, H and Wang, J and Zheng, D and Zhao, M and Sun, T and Chao, X and Guo, Y and Zhu, M and Sun, Y and Xia, X and Ge, K and Qu, C and Yao, C and Xie, G and Zhou, K and Louca, P and Menni, C and Zhao, A and Guo, Q and Wan, X and Zhang, L and Ji, G and Zhou, J and Hu, C and Jia, W and Zheng, X and Jia, W},
title = {A microbiome-bile acid axis mediates protection from chronic liver disease in females.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.048},
pmid = {42896552},
issn = {1097-4172},
abstract = {Sex-based differences in chronic liver disease (CLD) incidence and progression are well documented, yet the mechanistic basis of this sexual disparity remains elusive. Here, leveraging a large-scale metabolomics database comprising 9,254 individuals, we identify the endogenous bile acid, isoursodeoxycholic acid (isoUDCA), as a candidate mediator of female-associated hepatoprotection. We trace the origin of isoUDCA to a bacterial consortium, which is selectively enriched by estrogen through shaping a specialized intestinal microenvironment. Mechanistically, isoUDCA promotes the nuclear accumulation of SREBP2. This upregulates the intracellular transporter STARD4 and its functionally coupled downstream enzyme CYP7B1, thereby facilitating intracellular cholesterol handling and metabolic conversion. Collectively, our findings support a microbiome-bile acid-liver axis that may contribute to sex differences in CLD susceptibility and support further evaluation of isoUDCA as a potential therapeutic intervention.},
}

@article {pmid42896616,
year = {2026},
author = {Demir, M and Weglage, J and Sigal, M},
title = {Rethinking Pathogenesis of Primary Sclerosing Cholangitis.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2983-6480},
pmid = {42896616},
issn = {1098-8971},
abstract = {Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease characterized by progressive fibroinflammatory injury of intrahepatic and extrahepatic bile ducts that may lead to cirrhosis, hepatobiliary malignancy, and death, with liver transplantation representing the only effective intervention in end-stage disease. Rather than a single dominant pathomechanism, the data support a model in which four axes - bile acid metabolism, the intestinal microbiome and gut barrier, biliary epithelial dysfunction, and Th17-skewed immune dysregulation - are reciprocally coupled and converge on a shared periductal fibrogenic output dominated by TGF-beta signaling. This review summarizes key mechanistic advances from genetic, epigenomic, single-cell, spatial transcriptomic, and microbiome studies. These investigations implicate antigen presentation pathways, Th17-skewed immune responses, cholangiocyte senescence and profibrotic signaling, and disrupted gut-liver communication as central drivers of chronic biliary injury. Emerging spatial and multi-omics approaches further reveal complex cellular crosstalk among cholangiocytes, immune cells, macrophages, and mesenchymal populations within portal inflammatory niches. We discuss evolving biomarkers and recent clinical trial data targeting bile acid metabolism, fibrosis, the microbiome, and immune pathways. In conclusion, research data suggests viewing PSC as a network disease, which provides a unifying framework for disease pathogenesis and may enable biomarker-guided patient stratification and mechanism-based therapy development targeting distinct pathogenic pathways.},
}

@article {pmid42896712,
year = {2026},
author = {Hou, L and Zhang, X and Huang, K and Wu, W and Xing, L and Shen, W and Zhang, Y and Dong, Z},
title = {Composition-aware and leakage-controlled sparse log-ratio learning for mortality classification from respiratory microbiome profiles.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107758},
doi = {10.1016/j.mimet.2026.107758},
pmid = {42896712},
issn = {1872-8359},
abstract = {BACKGROUND: Respiratory microbiome profiles contain compositional information that may complement clinical variables for mortality classification in hospitalized patients with COVID-19. However, microbiome-based classifiers remain vulnerable to compositional artifacts, patient-level leakage, and cohort-specific feature construction.

OBJECTIVE: To develop and externally evaluate a leakage-controlled sparse log-ratio learning framework for mortality classification using respiratory microbiome profiles.

METHODS: This retrospective secondary analysis used three public COVID-19 respiratory microbiome cohorts. The Sparse Log-Ratio Risk Network (SLRRN) was developed using patient-level nested validation, with genus filtering, zero replacement, balance construction, model tuning, and threshold selection restricted to training partitions. The model learned 16 signed genus balances and integrated four clinical covariates available at the first eligible respiratory sampling landmark. The final specification and threshold were frozen before external evaluation.

RESULTS: The development cohort included 82 patients (20 deaths) from PRJNA678105 and PRJNA683617, and frozen external evaluation included 76 independent patients (38 fatal and 38 severe nonfatal cases) from PRJNA726205. Internal AUROC was 0.838 (95% CI, 0.765-0.911), and AUPRC was 0.674 (0.577-0.771). The paired AUROC difference versus XGBoost was 0.041 (0.009-0.073). Without refitting or threshold revision, external AUROC was 0.821 (0.738-0.904), with sensitivity of 0.816 and specificity of 0.842 at the frozen threshold of 0.37. In the outcome-enriched external cohort, the Brier score was 0.166 and the ECE was 0.065; these estimates describe the selected study sample.

CONCLUSION: SLRRN provides a composition-aware and leakage-controlled framework for respiratory microbiome-based mortality classification. The findings support further prospective evaluation with standardized sampling and direct comparison with established clinical models before clinical translation.},
}

@article {pmid42896802,
year = {2026},
author = {Fang, L and Zeng, H and Zhang, H and Liu, W and Shangguan, W and Huang, M and Di, S and Su, X and Xiao, R and Deng, Y},
title = {Enantiomer-specific effects of metconazole disrupt soil microbiota, gut homeostasis, and genomic responses of Eisenia fetida.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125975},
doi = {10.1016/j.envres.2026.125975},
pmid = {42896802},
issn = {1096-0953},
abstract = {The selective use of highly active, low-risk enantiomers in place of racemic fungicides represents a sustainable approach to balancing agricultural productivity with environmental safety. Little is known about the enantioselective toxicity and environmental disturbances of the chiral triazole fungicide metconazole (MEZ) on the soil ecosystem. This study revealed that rac-MEZ dissipated faster than cis-MEZs in soil, but rac-MEZ induced a greater decrease in bacterial diversity and network complexity. The longer persistence of cis-MEZs possibly led to greater bioaccumulation in earthworms (Eisenia fetida). Enantioselectivity was observed for two cis-MEZs; cis-1R,5S-MEZ exhibited more severe acute toxicity in earthworms than cis-1S,5R-MEZ. This may be attributed to the potential detoxifying protein (CYP4V), which binds weakly with cis-1R, 5S-MEZ. This weaker detoxification capacity potentially resulted in oxidative stress response system collapse in earthworms, leading to excess reactive oxygen species (ROS) accumulation and disturbance of antioxidant and detoxification enzymes (such as CAT, SOD, and GST). The ROS dysregulation caused by cis-1R, 5S-MEZ induced severe ecotoxicity, including DNA damage, heme metabolism disruption, and downregulation of transcriptional ovo-spermathecal apparatus development and genomic diversification, possibly resulting in higher ipotoxicity, genotoxicity, and reproductive toxicity. Therefore, cis-1R,5S-MEZ is more toxic to earthworms and their ecological functions, suggesting a less favorable environmental risk profile for potential agricultural use.},
}

@article {pmid42896808,
year = {2026},
author = {Zeyaullah, M and Ahmad, MF},
title = {The Childhood Estrobolome: A Missing Link in Early Puberty Onset.},
journal = {Endocrine practice : official journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eprac.2026.10.008},
pmid = {42896808},
issn = {1530-891X},
abstract = {Precocious puberty, defined as the onset of secondary sexual characteristics before age 8 in girls, is rising globally with most cases lacking a clearly identifiable cause. The biome is increasingly recognized as a regulator of hormonal homeostasis, yet its role in childhood hormonal programming remains largely unexplored. The estrobolome - the collection of gut bacteria encoding β-glucuronidase (β-GUS) enzymes - controls enterohepatic estrogen recycling in adult women but has never been systematically characterized in prepubertal girls. This narrative review proposes and synthesizes evidence supporting the hypothesis that early-life dysregulation of the childhood estrobolome may prime the hypothalamic-pituitary-gonadal (HPG) axis for premature activation, contributing to early puberty onset in girls. Elevated fecal β-GUS activity has been documented in girls with central precocious puberty (CPP), consistent with altered estrobolome activity during pubertal development. Early-life exposures - including antibiotics, high-fat diet, cesarean delivery, formula feeding, and endocrine-disrupting chemicals - modulate the childhood microbiome in ways that enrich β-GUS-producing taxa. The resulting increase in enterohepatic estrogen reabsorption may provide a chronic low-level estrogenic signal sufficient to sensitize kisspeptin neurons and initiate premature GnRH pulsatility. Overall, the childhood estrobolome represents a compelling but entirely uncharacterized mechanistic bridge between gut dysbiosis and early puberty. Direct characterization of β-GUS activity in healthy prepubertal girls and longitudinal cohort studies are urgently needed. Microbiome-targeted interventions including probiotics, dietary modification, and antibiotic stewardship may hold promise as preventive strategies.},
}

@article {pmid42896859,
year = {2026},
author = {Bao, Z and Jiao, M and Zhao, M and Huang, FY and Liu, Y and Wang, S},
title = {Effects of Protein Intake on Gut Microbiota in Physically Active Individuals: A Systematic Review and Meta-Analysis.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag156},
pmid = {42896859},
issn = {1753-4887},
abstract = {CONTEXT: Protein (PRO) intake supports exercise adaptation and recovery, but its effects on gut microbiota (GM) in physically active individuals remain inconsistent across doses, PRO sources, and exercise conditions.

OBJECTIVE: To systematically evaluate and meta-analyze the effects of PRO intake on GM in physically active individuals.

DATA SOURCES: The PubMed, EBSCOhost, the Cochrane Library, and Web of Science databases were searched through June 2026. Reference lists of relevant studies and reviews were also examined.

DATA EXTRACTION: Two reviewers independently screened records and extracted study, participant, intervention, and outcome data. Eligible studies quantified PRO intake, included an exercise or physical-activity component, and reported extractable GM outcomes. Risk of bias and evidence certainty were assessed using the Cochrane Risk of Bias 2.0 tool and Grading of Recommendations, Assessment, Development and Evaluation approach, respectively.

DATA ANALYSIS: Random-effects meta-analyses using Hedges' g, subgroup analyses, and meta-regression were performed. Eighteen studies (n = 819 participants) were included. Protein intake significantly increased the Shannon and Chao1 indices but not the Simpson index or observed operational taxonomic units (OTUs). A significant U-shaped association was observed between PRO dose and the α-diversity effect size, with the fitted curve reaching its lowest point at 1.5-2.0 g kg-1 d-1. Protein intake significantly decreased populations of Actinobacteria, Bifidobacterium, and Firmicutes, and the Firmicutes to Bacteroidetes ratio, and increased Bacteroidetes numbers. Subgroup findings suggested that age, body mass index, intervention duration, PRO dose, and exercise modality and intensity moderated the effects on Shannon diversity and Bifidobacterium abundance.

CONCLUSIONS: Protein intake appears to improve gut microbial diversity in physically active individuals but may also induce notable shifts in beneficial taxa, particularly reductions in Bifidobacterium. Future studies should prioritize individualized microbiome-informed strategies, evaluate long-term safety, and clarify the ecological impact of different PRO sources to optimize exercise nutrition interventions.

PROSPERO registration No. CRD420261288197.},
}

@article {pmid42897051,
year = {2026},
author = {Li, YR and Chen, Y and Yeh, S and Yuen, T and Yang, L},
title = {MAIT cells in gastrointestinal cancer: immunity to therapy.},
journal = {Trends in cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trecan.2026.09.009},
pmid = {42897051},
issn = {2405-8025},
abstract = {Mucosal-associated invariant T (MAIT) cells are emerging as important regulators of immunity in gastrointestinal (GI) cancers. Enriched in mucosal and hepatic tissues, MAIT cells recognize microbial-derived metabolites presented by MHC class I-related molecule (MR1) and rapidly exert effector functions, including cytokine production and cytotoxicity. Across GI malignancies, including hepatocellular carcinoma, cholangiocarcinoma, colorectal, gastric, pancreatic, and esophageal cancers, MAIT cells display context-dependent roles shaped by the tumor microenvironment, microbiome, and immune signaling pathways. While they can mediate antitumor immunity, they frequently exhibit functional exhaustion or adopt pro-tumorigenic phenotypes. Therapeutic strategies aim to enhance MAIT cell activity, reverse dysfunction, and integrate them into combinatorial immunotherapy approaches. Understanding MAIT cell biology may enable their exploitation as biomarkers and therapeutic targets in GI cancers.},
}

@article {pmid42897152,
year = {2026},
author = {Zhang, T and Zhang, C and Yuan, S and Wang, Y and Zhang, M and Dai, K and Yu, Y and Zhang, L and Cao, L and Zhang, M and Su, Y},
title = {Role of cervicovaginal microbiome and metabolome in ALA-PDT-mediated HPV clearance in patients with cervical HSIL.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42897152},
issn = {2055-5008},
support = {LHGJ20220381//Henan Provincial Medical Science and Technology Joint Construction Project/ ; 222102310196//Henan Provincial Science and Technology Research Project/ ; 242102310283//Henan Provincial Science and Technology Research Project/ ; 25A320031//Henan Provincial Key Scientific Research Project Plan of Higher Education Institutions/ ; },
mesh = {Female ; Humans ; *Microbiota/drug effects ; *Metabolome ; *Aminolevulinic Acid/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Vagina/microbiology ; *Human Papillomavirus Viruses/drug effects ; *Cervix Uteri/microbiology/virology ; *Photochemotherapy/methods ; *Papillomavirus Infections/drug therapy/virology ; *Uterine Cervical Dysplasia/virology/drug therapy/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; },
abstract = {The cervicovaginal microbiome and its associated metabolites play a pivotal role in the persistence of human papillomavirus (HPV) infection. Here, we investigated the contribution of the cervicovaginal microbiome and metabolome to 5-aminolevulinic acid photodynamic therapy (ALA-PDT)-mediated HPV clearance in patients with cervical high-grade squamous intraepithelial lesions (HSIL). 16S ribosomal RNA sequencing analysis identified significant differences in cervicovaginal microbiota before ALA-PDT between the HPV clearance and non-clearance groups. The HPV non-clearance group exhibited higher abundances of Anaerococcus and Gemella. ALA-PDT exerted a more substantial impact on cervicovaginal microbiota diversity in the HPV clearance group, characterized by increased abundances of Finegoldia, Corynebacterium, Lancefieldella, and Winkia, and a decreased abundance of Anaeroglobus following treatment. Global untargeted metabolomics analysis further revealed distinct cervicovaginal metabolic profiles before ALA-PDT between the two groups. The pathways of mineral absorption and valine, leucine, and isoleucine biosynthesis were significantly enriched in the HPV clearance group. Alterations in cervicovaginal metabolic profiles following ALA-PDT were also observed. Moreover, several key differential metabolites were observed to be significantly correlated with Anaeroglobus. Our findings underscore the critical involvement of the cervicovaginal microbiome and metabolome in ALA-PDT-mediated HPV clearance, providing valuable clues for predicting and improving the effect of HPV clearance following ALA-PDT.},
}

Female
Humans
*Microbiota/drug effects
*Metabolome
*Aminolevulinic Acid/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
*Vagina/microbiology
*Human Papillomavirus Viruses/drug effects
*Cervix Uteri/microbiology/virology
*Photochemotherapy/methods
*Papillomavirus Infections/drug therapy/virology
*Uterine Cervical Dysplasia/virology/drug therapy/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification

@article {pmid42897181,
year = {2026},
author = {Gu, Z and Gao, H and Guo, H and Fan, Z and Zhang, W and Xing, D and Zhou, X and Yu, H and Zhao, T and Wu, J and Li, C},
title = {Mosquito repellency mediated by skin commensal Bacillus species via volatile metabolite reprogramming.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42897181},
issn = {2041-1723},
mesh = {Animals ; Skin Microbiome ; *Bacillus/metabolism/physiology ; *Skin/microbiology ; Humans ; *Insect Repellents/pharmacology/metabolism ; Female ; Cresols/metabolism ; *Volatile Organic Compounds/metabolism ; Decanoic Acids/metabolism ; *Culicidae ; Mosquito-Borne Diseases ; Symbiosis ; },
abstract = {Individual variation in human attractiveness to mosquitoes critically influences vector-borne disease transmission, and this phenomenon arises from multiple underlying factors. This study integrated human skin microbiome profiling, non-human primate in situ intervention, and volatilomics to uncover a microbial-mediated mechanism underlying host-specific mosquito repellency. Bacillus species were identified as a microbial signature associated with reduced mosquito attraction in humans. Targeted Intervention of B. licheniformis and B. paralicheniformis on primate skin was sufficient to significantly reduce mosquito attraction, thereby establishing a causal microbial contribution beyond descriptive correlations. Mechanistic analyses revealed that Bacillus enrichment reprogrammed the skin volatilome, specifically increasing the abundance of aromatic and fatty acid-derived effectors, such as p-Cresol and decanoic acid, which are associated with repellency phenotypes. Together, these findings revealed a potential role of skin commensals in shaping mosquito host-seeking behavior, providing a molecular basis for microbiome-informed and bio-inspired strategies for mosquito disease control.},
}

Animals
Skin Microbiome
*Bacillus/metabolism/physiology
*Skin/microbiology
Humans
*Insect Repellents/pharmacology/metabolism
Female
Cresols/metabolism
*Volatile Organic Compounds/metabolism
Decanoic Acids/metabolism
*Culicidae
Mosquito-Borne Diseases
Symbiosis

@article {pmid42897260,
year = {2026},
author = {Xu, X and Wang, F and Liu, W and Li, H and Wang, Y and Li, Y and Wang, B and Liu, M and Li, Y},
title = {An integrated single-cell transcriptomic and microbiome dataset of orbital adipose tissue in thyroid eye disease.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42897260},
issn = {2052-4463},
support = {7252093//Natural Science Foundation of Beijing Municipality/ ; 82571806//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Graves Ophthalmopathy/microbiology/genetics/immunology ; *Adipose Tissue/microbiology ; *Microbiota ; *Transcriptome ; RNA, Ribosomal, 16S/genetics ; *Orbit/microbiology ; Single-Cell Analysis ; Multiomics ; },
abstract = {Thyroid eye disease (TED), also historically referred to as thyroid-associated ophthalmopathy (TAO) or Graves' orbitopathy (GO), is an autoimmune ophthalmopathy characterized by inflammation and adipogenesis within orbital adipose (OA) tissue. While the contribution of immune cell infiltration and fibroblast activation is recognized, the cellular heterogeneity and the potential role of local microbial dysbiosis in the orbital microenvironment remain poorly defined. Here, we present a multi-omics dataset derived from OA of patients with TED and healthy controls collected at Beijing Tongren Hospital. The dataset comprises single-cell RNA sequencing (scRNA-seq) data generated from human orbital adipose tissue and subcutaneous fat. Following quality control filtering and doublet removal, a total of 61,302 high-quality singlet cells were retained for downstream analyses, capturing the transcriptomic landscape of orbital fibroblasts, immune subsets, and vascular cells. In parallel, 16S rRNA gene sequencing was performed on orbital adipose tissue samples collected from the integrated study cohort, alongside environmental samples for contamination assessment, to characterize the low-biomass orbital microbiome DNA signatures. Raw sequencing reads, quality-controlled gene-expression matrices, and contamination-corrected microbial feature tables are provided. Our dataset provides an opportunity to investigate the crosstalk between host cellular immunity and potential local microbiome signatures, facilitating hypothesis generation regarding host-microbiome crosstalk and the exploration of novel therapeutic targets for TED.},
}

Humans
*Graves Ophthalmopathy/microbiology/genetics/immunology
*Adipose Tissue/microbiology
*Microbiota
*Transcriptome
RNA, Ribosomal, 16S/genetics
*Orbit/microbiology
Single-Cell Analysis
Multiomics

@article {pmid42897631,
year = {2026},
author = {Mao, J and Zhang, C and Wang, L and Wang, Z and Xue, B and Peng, Q and Hu, R and Xiao, J},
title = {Differences in rumen microbiome protein metabolism are associated with individual variation in rumen bloating on high-concentrate diets.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42897631},
issn = {2524-4671},
support = {2025ZNSFSC0284//Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2025-13//Sichuan Beef Cattle Innovation Group/ ; 24ZDYF0020//Ya'an Municipal-University Cooperation Project/ ; },
abstract = {BACKGROUND: This study primarily investigated the differences in rumen microbial composition and functional profiles among goats with varying degrees of rumen bloat under a high-concentrate diets (HCDs) feeding condition. Forty Nubian goats fed a HCDs were selected as experimental animals and subjected to rumen bloating (RB) scoring. From these, six goats with high bloat scores (HB group) and six goats without obvious bloat (NB group) were selected. Rumen content samples were collected via oral stomach tubes. Rumen fluid foaming characteristics and pH values were measured, and metatranscriptome sequencing was conducted to analyze microbial functions.

RESULTS: The results demonstrated that compared to the NB group, the HB group exhibited significantly higher foaming capacity, foam stability, and viscosity of ruminal fluid, along with a significantly lower pH value (P < 0.05). Additionally, α-diversity indices (Chao1, ACE, and observed_species) were significantly elevated in the HB group (P < 0.05). Annotation of rumen microbial species showed that the relative abundance of Ascomycota, Basidiomycota, Dialister, and Dialister sp. CAG:486 was significantly higher in the HB group, whereas Bacteroidetes, Proteobacteria, Spirochaetes, Prevotella, Bacteroides, Treponema, Lactobacillus, Leptotrichia hofstadii and Prevotella oralis were significantly reduced (P < 0.05). Functional analysis of differentially expressed genes (DEGs) revealed significant enrichment in several biological processes. In the Gene Ontology (GO) database, DEGs were predominantly associated with cellular protein modification, protein maturation, and ribosome biogenesis. According to KEGG pathway analysis, DEGs were mainly enriched in pathways related to endocytosis, ubiquitin-mediated proteolysis, and protein processing in the endoplasmic reticulum.

CONCLUSION: In summary, under uniform feeding conditions, individual variations in goat rumen microbiota functions are associated with differences in microbial community structure and gene expression patterns. Alterations in the protein metabolism function of the rumen microbiome are associated with the presence of foaming proteins, which in turn are linked to individual differences in rumen foam production capacity. Ultimately, these associations may result in differing susceptibility and severity of RB among animals.},
}

@article {pmid42897671,
year = {2026},
author = {Chung, M and Barnett, CR and Hunger, L and Sulaiman, I and Wu, BG and Li, Y and Tsay, JJ and Brosnahan, SB and Chung, CJ and Angel, L and Silverman, GJ and Morton, JT and Segal, LN and Ghedin, E},
title = {Immunosuppression is associated with loss of airway microbiome resilience in severe COVID-19.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42897671},
issn = {2049-2618},
mesh = {Humans ; *Microbiota/immunology ; *COVID-19/immunology/microbiology/mortality ; SARS-CoV-2 ; *Immunocompromised Host ; Female ; *Respiratory System/microbiology ; Male ; Respiration, Artificial ; *Immunosuppression Therapy ; Middle Aged ; Longitudinal Studies ; Staphylococcus aureus/isolation & purification ; Aged ; },
abstract = {BACKGROUND: The role of the lower airway microbiome in COVID-19-associated mortality remains poorly understood despite evidence implicating secondary pathogens and non-airway commensals. The influence of prior immunosuppression on the lower airway microbiome and its contribution to mortality in mechanically ventilated patients has been largely unexplored. Given that host-microbiome interactions are dynamic, we assessed longitudinal patterns in the respiratory microbiome associated with mortality and immunosuppression status.

RESULTS: We conducted longitudinal forecasting, differential abundance, and comparative network analyses of metatranscriptomic data from 604 upper and lower airway samples collected from 243 mechanically ventilated COVID-19 patients to profile key microbial factors associated with immunosuppression and clinical outcome. SARS-CoV-2 was enriched over time in immunosuppressed patients and in both immunosuppressed and immunocompetent patients who died, highlighting the need for aggressive viral infection control early in the disease course. Using longitudinal forecasting and differential abundance analyses, we observed a progressive increase in opportunistic pathogens, such as Staphylococcus aureus and Escherichia coli, among the taxa most predictive of mortality. Concurrently, immunosuppressed individuals exhibited a significant decrease in typical airway commensals alongside a restructuring and marked destabilization of the microbial community compared with their immunocompetent counterparts.

CONCLUSIONS: These findings indicate that loss of airway microbiome stability in immunosuppressed patients constitutes an independent factor contributing to increased susceptibility to opportunistic pathogens and poor clinical outcomes. Video Abstract.},
}

Humans
*Microbiota/immunology
*COVID-19/immunology/microbiology/mortality
SARS-CoV-2
*Immunocompromised Host
Female
*Respiratory System/microbiology
Male
Respiration, Artificial
*Immunosuppression Therapy
Middle Aged
Longitudinal Studies
Staphylococcus aureus/isolation & purification
Aged

@article {pmid42898056,
year = {2026},
author = {Hosseinikia, M and Beaver, LM and Wong, CP and Ho, E},
title = {Beneficial Effects of Nuts on Cardiovascular and Metabolic Health: An Insight into the Gut-Cardiometabolic Axis.},
journal = {Current developments in nutrition},
volume = {10},
number = {10},
pages = {109535},
pmid = {42898056},
issn = {2475-2991},
abstract = {Cardiometabolic diseases (CMDs) are major contributors to global morbidity and mortality. Emerging evidence suggests that the gut microbiota plays a central role in the pathogenesis and progression of CMDs by regulating cardiometabolic endpoints, including lipid profiles, glucose homeostasis, immunity, inflammation, and oxidative stress. Nuts are nutrient-dense foods rich in unsaturated fatty acids, dietary fiber, polyphenols, vitamins, and minerals that interact with the gut microbiota. Additionally, nut intake has been associated with improved cardiometabolic health outcomes. This review examines current evidence on the effects of tree nut consumption on the gut-cardiometabolic axis, with an emphasis on clinical and mechanistic studies across different types of tree nuts. Clinical evidence of the capacity of nut consumption to affect CMDs is summarized. The bidirectional interaction between nut-derived microbial metabolites, including short-chain fatty acids, urolithins, phenolic acids, valerolactones, and gut microbiota, is highlighted. In addition, mechanisms by which changes in the nut-associated gut microbiome affect the CMDs via regulating lipids, glucose, energy homeostasis, and immunity modulation are discussed. The available evidence, although mostly associative, supports the potential favorable effects of nuts in modulating gut microbial composition and function in ways that may improve cardiometabolic health. However, future studies are needed to address limitations in current studies, including substantial heterogeneity across studies, the lack of established causal mechanisms, long-term clinical outcomes, and to investigate personalized responses to nut consumption given interindividual variability in gut microbiota.},
}

@article {pmid42898143,
year = {2026},
author = {Li, Q and Zu, Y and Liao, H and Huang, H and Lu, K and Lan, L and Wei, X and Yang, S},
title = {Integrated metabolomics and microbiome analyses reveal nutritional differences between yellow and white maize (Zea mays L.) kernels.},
journal = {Food chemistry: X},
volume = {39},
number = {},
pages = {104596},
pmid = {42898143},
issn = {2590-1575},
abstract = {Maize (Zea mays L.) is a globally significant cereal crop that exhibits wide phenotypic and nutritional diversity. Yellow maize is highly valued for its accumulation of health-promoting carotenoids, whereas the functional profile of white maize is characterized by distinct classes of secondary metabolites. However, the complex interplay among host genetics, the kernel endophytic microbiome, and the associated metabolic profiles remains poorly understood. In this study, we employed an integrated approach combining targeted carotenoid quantification, 16S rRNA and ITS amplicon sequencing, and untargeted metabolomics to comparatively analyze the internal microenvironments of yellow and white maize kernels. Phenotypic analysis confirmed that yellow maize kernels accumulated substantially higher concentrations of lutein (up to 5.45 μg/g) and zeaxanthin (up to 15.30 μg/g) relative to the trace amounts detected in white maize. Microbiome profiling revealed that host genotype profoundly shaped endophytic community assembly: although bacterial alpha diversity was comparable between the two groups, yellow maize harbored significantly higher fungal alpha diversity. Taxonomic analysis identified distinct microbial biomarkers, with Fusarium being identified as a fungal biomarker enriched in yellow maize, whereas Aspergillus was enriched in white maize and Pseudomonas dominated its bacterial community. Furthermore, untargeted metabolomics identified 313 differentially accumulated metabolites, predominantly comprising lipids, organic acids, and phenylpropanoids. KEGG enrichment analysis demonstrated that pathways related to phenylalanine, tyrosine, and tryptophan biosynthesis, plant hormone signal transduction, and ABC transporters were significantly enriched, indicating divergent metabolic profiles between the two cultivar groups. Collectively, these findings reveal consistent associations between host secondary metabolism and selectively enriched endophytic microbiomes, providing novel metabolic and microbial targets for future precision breeding and nutritional biofortification in maize.},
}

@article {pmid42898302,
year = {2026},
author = {Xiang, Q and Yang, Y and Gao, X and Zhang, H and Gui, R and Li, K and Li, Y},
title = {Comparative transcriptomic and rhizosphere microbiome profiling and cross-omics association analysis of wild and cultivated Panax japonicus var. major.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1961578},
pmid = {42898302},
issn = {1664-462X},
abstract = {INTRODUCTION: Panax japonicus var. major is an important medicinal plant endemic to China and is rich in terpenoid saponins with diverse pharmacological activities. Excessive harvesting of wild resources has accelerated the transition toward cultivation, raising questions about differences between wild and cultivated populations.

METHODS: Transcriptomic and rhizosphere microbiome analyses were conducted in sampled wild and cultivated populations, followed by an exploratory cross-omics association analysis.

RESULTS: Transcriptome comparisons identified 10,416, 8,782, and 5,441 differentially expressed unigenes in roots, rhizomes, and leaves, respectively. Functional enrichment analyses showed differences in plant hormone signal transduction, MAPK signaling, plant-pathogen interaction, phenylpropanoid biosynthesis, and terpenoid biosynthesis pathways. Several terpenoid biosynthesis-related genes, including AACT, HMGS, HMGR, DXS, and TPS, had higher transcript levels in wild plants. Rhizosphere microbiome analyses showed differences in bacterial and fungal community composition among the sampled groups. Exploratory cross-omics analysis identified candidate associations between several microbial taxa and terpenoid biosynthesis-related genes.

DISCUSSION: These taxonomic assignments do not establish the functional roles of the detected microorganisms. Because terpenoid and saponin concentrations were not measured, the transcriptomic differences do not demonstrate greater metabolite accumulation or improved medicinal quality. Moreover, because the populations were sampled from different sites and the microbiome data lacked independent biological replication within each sampling group, the observed patterns do not establish effects of cultivation status or habitat, nor do they demonstrate causal plant-microbe interactions. The results provide hypotheses for future controlled studies of P. japonicus var. major.},
}

@article {pmid42898479,
year = {2026},
author = {Nardone, GG and Rosso, LE and Santin, A and Spedicati, B and Cappellani, S and Concas, MP and Zito, G and Romano, F and Di Lorenzo, G and Zanotta, N and Campisciano, G and Ricci, G and Comar, M and Girotto, G},
title = {Connecting gut microbiome composition to symptom severity and host genetics in endometriosis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1873766},
pmid = {42898479},
issn = {1664-302X},
abstract = {BACKGROUND: Endometriosis (EM) is a multifactorial, estrogen-dependent inflammatory disease characterized by high clinical variability. Growing evidence is highlighting the role of gut microbiome dysbiosis in EM pathophysiology; however, associations between microbiome, symptom severity, and host genetics remain poorly characterized. Extra-oral taste receptor genes (TGs), expressed in both the gastrointestinal and female reproductive systems, may represent novel mediators of gut-reproductive tract axis crosstalk.

METHODS: A total of 50 women with surgically confirmed EM were deeply clinically characterized, including the evaluation of EM-symptoms and their severity. Microbiome profiles were obtained by 16S rRNA gene sequencing of rectal swabs. Genetic variants within four TGs (TAS2R3, TAS2R4, TAS2R5, and TAS2R14) were assessed using SNP-array genotyping. Microbiome composition was investigated through the evaluation of alpha and beta diversity, as well as enterotype classification analyses. Associations between EM-related features, bacterial taxa and TG-SNPs were investigated using regression models.

RESULTS: Three distinct gut microbiome community types were identified, dominated by Bacteroides, Prevotella, and Escherichia-Shigella. While microbiome composition did not differ significantly across EM stages, beta diversity was associated with dysmenorrhea (R[2] = 0.13) and disease stage (R[2] = 0.12). Regarding TGs, SNPs within TAS2R14 gene showed significant associations with alpha and beta diversity indices. Reduced abundance of short-chain fatty acid-producing taxa, including members of the Lachnospiraceae and Ruminococcaceae families, was associated with dysmenorrhea, whereas increased abundance of Prevotella and Mobiluncus with dysuria and infertility, respectively. Finally, an increased premenstrual pain severity was associated with a reduced relative abundance of taxa within the order Burkholderiales (β = -2.265) and the family Sutterellaceae (β = -1.563); high postmenstrual pain severity was associated with a lower abundance of Bifidobacteriales (β = -4.932) and Bifidobacteriaceae (β = -4.134).

CONCLUSION: This case-only study elucidated the complex relationship between gut microbiome composition, EM-related symptoms, and host genetic variation. In particular, extra-oral taste receptor genes emerged as novel risk factors to host-microbiome interactions, supporting their potential role in the microbiota-endometriosis axis and opening new perspectives on EM pathogenesis.},
}

@article {pmid42898499,
year = {2026},
author = {Li, K and Jiang, S and Huang, P and Guo, S and Ge, S and Li, J and Wang, S and Huang, L},
title = {Oliceridine and morphine differentially modulate the gut microbiota-intestinal barrier axis in a rat postoperative pain model.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1907666},
pmid = {42898499},
issn = {1663-9812},
abstract = {BACKGROUND: Oliceridine is a novel G protein-biased μ-opioid receptor agonist with potentially improved gastrointestinal tolerability compared with conventional opioids. However, its impact on postoperative intestinal homeostasis-specifically the gut microbiota and intestinal barrier-remains poorly understood.

METHODS: A postoperative pain model was established in male Sprague-Dawley rats using the Brennan plantar incision method. Animals were randomly assigned to four groups: non-incision control (CON), plantar incision plus normal saline, plantar incision plus oliceridine (OLI, 1 mg/kg subcutaneous bolus followed by continuous infusion at 1 mg/kg/day for 72 h), and plantar incision plus morphine (MF, 5 mg/kg subcutaneous bolus followed by continuous infusion at 5 mg/kg/day for 72 h). Analgesic efficacy was assessed by mechanical withdrawal threshold (MWT) and area under the curve (AUC). Intestinal morphology, epithelial Claudin-1 expression by immunofluorescence (n = 4 per group), gut microbiota composition (16S rRNA gene sequencing, n = 6 per group), and host ileal transcriptomic profiles (RNA-seq, n = 3 per group) were evaluated.

RESULTS: Oliceridine and morphine produced comparable analgesia, as reflected by MWT AUC (P < 0.0001 vs. NS; OLI vs. MF: P = 0.8770). Both opioids alleviated postoperative mechanical hypersensitivity. Compared with NS, opioid treatment increased the relative abundance of Limosilactobacillus and Lactobacillus and decreased Streptococcus. Exploratory microbiome analysis identified a potential Lactobacillus-related signal, but no genus-level difference between the OLI and MF groups remained significant after multiple-testing correction. Transcriptomic analysis revealed distinct ileal gene-expression profiles between the OLI and MF groups. Relative to MF, OLI was associated with higher expression of genes related to epithelial barrier integrity and brush border function and lower expression of genes involved in immune-related pathways. Histologically, both opioids attenuated intestinal injury compared with NS, with no significant difference between OLI and MF. In contrast, relative Claudin-1 fluorescence intensity was significantly higher in the OLI group than in the MF group (P = 0.036), providing protein-level support for the barrier-related transcriptomic findings. Integrated correlation analysis identified associations between Lactobacillus-related taxa and host genes linked to barrier function and metabolism (|r| > 0.6, P < 0.01).

CONCLUSION: Oliceridine and morphine produced comparable analgesia. Exploratory microbiome analysis identified a potential Lactobacillus-related signal, but no genus-level differences remained significant after multiple-testing correction. Oliceridine was associated with a distinct ileal transcriptomic profile and higher Claudin-1 fluorescence intensity than morphine, although histological injury did not differ between the two groups. The functional significance of these molecular differences requires further investigation.},
}

@article {pmid42898526,
year = {2026},
author = {Ke, Y and Jia, P and Gao, X and Liu, E and Wang, K and Chai, Z},
title = {Effects of exogenous microbial fertilizer and in situ green manure management on soil microbial community structure and predicted functional potential in Korla fragrant pear orchards.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1941612},
pmid = {42898526},
issn = {1664-302X},
abstract = {Long-term chemical fertilizer overuse has degraded soil quality in Korla fragrant pear orchards of Xinjiang, causing reduced organic matter accumulation, nutrient imbalance, and microbial community shifts. However, the effects of exogenous microbial fertilizers and endogenous green manure, particularly under different planting densities, on soil microbiome regulation in sandy orchards of southern Xinjiang remain unclear. Here, a 7-8-year-old Korla fragrant pear orchard was subjected to six fertilization treatments: conventional fertilization (CK), microbial fertilizer (JF), low- and high-density *Melilotus officinalis* (CM1 and CM2), and low- and high-density sunflower (*Helianthus annuus*) (DK1 and DK2). Soil physicochemical properties, 16S rRNA and ITS amplicon sequencing, and PICRUSt2-based functional prediction were integrated to evaluate treatment effects on soil properties, microbial communities, and predicted functional potential. Organic fertilization generally reduced electrical conductivity (EC) and improved organic matter and available nutrients. Among treatments, CM1 showed relatively favorable soil improvement, reducing EC by 19.20% and increasing alkali-hydrolyzable nitrogen and total nitrogen by 36.20 and 36.83%, respectively. JF significantly increased fungal diversity, with the Chao1 index rising by 48.6%, while green manure species and planting density strongly influenced bacterial and fungal community structures. All organic fertilization treatments reduced the relative abundance of *Fusarium*, with CM1 showing the greatest decrease (29.8-60.0%). Functional prediction revealed distinct microbial responses: JF enhanced pathways related to fatty acid β-oxidation and lysine fermentation, with associated gene abundances increasing by 11.86 and 203.32%, respectively; CM1 increased butyrate fermentation-related predicted functions and reduced several denitrification-related predicted functions; DK1 mainly enhanced glycolysis and the tricarboxylic acid cycle, whereas DK2 showed greater potential in nitrogen cycling and phosphorus transformation-related functions. RDA indicated that bacterial functional profiles were associated with soil available potassium, alkali-hydrolyzable nitrogen, and total nitrogen. Under the conditions of this experiment, different fertilization strategies altered soil microbial communities by modifying environmental conditions and microbial assembly patterns. CM1 showed relatively strong potential for improving soil properties and regulating microbial communities, while microbial fertilizer and sunflower treatments exhibited distinct functional responses. These findings provide insights into green manure and microbial fertilizer management in arid-region pear orchards of southern Xinjiang.},
}

@article {pmid42898560,
year = {2026},
author = {Shao, T and Li, M and Li, S and Pu, J and Li, C and Guo, C},
title = {Gut microbiome-shaped chemotherapy responses across cancer types: mechanisms of resistance, biomarkers, and targeted interventions.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1945287},
pmid = {42898560},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Drug Resistance, Neoplasm ; *Neoplasms/drug therapy/microbiology/metabolism/immunology ; Animals ; *Antineoplastic Agents/therapeutic use ; Biomarkers, Tumor/metabolism ; },
abstract = {Cytotoxic chemotherapy remains an important component of multimodal treatment for many solid tumors, but resistance and dose-limiting toxicities continue to constrain clinical benefit. The gut microbiome can influence chemotherapy response through microbial drug biotransformation, metabolite signaling, intestinal-barrier integrity, systemic immune regulation, and tumor-cell stress and death pathways. Across solid tumors, the evidence is strongest in colorectal cancer, where clinical associations are supported by increasingly detailed mechanistic and interventional studies; evidence in many extraintestinal cancers remains less mature and is dominated by smaller observational cohorts and selected preclinical models. Importantly, gut-derived systemic effects should be distinguished from local or tumor-associated microbial mechanisms, and direct tumor-cell resistance should be separated from altered drug exposure and toxicity-mediated reductions in relative dose intensity. Microbiota-associated and metabolic biomarkers and microbiota-targeted interventions show potential for treatment stratification, toxicity prediction, and therapeutic modulation, but clinical translation remains limited by heterogeneous cohorts, incomplete causal validation, variable engraftment and strain specificity, and safety and standardization requirements. Overall, the microbiome is best viewed as a cancer- and regimen-specific modifier of chemotherapy rather than a universal determinant of response. Prospective, mechanism-matched studies are needed to establish whether microbiome-guided strategies can improve treatment efficacy, tolerance, and completion.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Drug Resistance, Neoplasm
*Neoplasms/drug therapy/microbiology/metabolism/immunology
Animals
*Antineoplastic Agents/therapeutic use
Biomarkers, Tumor/metabolism

@article {pmid42898582,
year = {2026},
author = {Keum, GB and Cho, J and Song, M and Choi, Y and Kang, J and Doo, H and Kwak, J and Kim, H and Chae, Y and Yang, H and Lee, S and Kim, ES and Kim, S and Kim, HB},
title = {Effects of fructooligosaccharides and inulin on growth performance, immunity and the gut microbiome in weaned piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {5},
pages = {1444-1459},
pmid = {42898582},
issn = {2055-0391},
abstract = {Prebiotics such as fructooligosaccharides and inulin are biological activators that selectively stimulate the growth and activity of beneficial bacteria in the gastrointestinal tract. However, their specific effects when applied during the weaning period in piglets remains limited. Therefore, this study evaluated the effects of fructooligosaccharides and inulin supplementation in weaned piglets on growth performance, nutrient digestibility, immune response, and gut microbiota composition with the aim of exploring their potential benefits for piglet health during the weaning transition. A total of 72 weaned piglets (28 days of age) were allocated to three dietary groups: CON (basal diet), FOS (CON + 0.3% fructooligosaccharides), and INU (CON + 3% inulin) to investigate the effects of fructan supplementation. Growth performance, nutrient digestibility, blood profiles, immune responses, and fecal microbiota were evaluated. Although fructan supplementation did not induce significant changes in growth performance or nutrient digestibility, it significantly increased serum immunoglobulin A levels. Furthermore, the fecal microbiota of the fructan supplemented piglets was enriched with short-chain fatty acid-producing bacteria, including Phascolarctobacterium, Agathobacter, Clostridium sensu stricto, and Flavonifractor. Fructan supplementation in the diets of weaned piglets positively influenced immune response and gut microbiota composition, suggesting its potential to enhance gut health during the weaning period.},
}

@article {pmid42898607,
year = {2026},
author = {Park, NH and Lim, B and Lim, C and Seo, YJ and Lee, JY and Lee, SH and Yang, J and Lee, M and Park, KI and Kyoung, H and Song, M and Kim, JM},
title = {A multi-omics characterization of the gut microbiota of weaned piglets in response to Lactobacillus plantarum supplementation.},
journal = {Journal of animal science and technology},
volume = {68},
number = {5},
pages = {1567-1585},
pmid = {42898607},
issn = {2055-0391},
abstract = {Weaning is a critical developmental stage in piglets and is frequently associated with intestinal dysfunction, diarrhea, and growth retardation due to abrupt dietary and environmental changes. Probiotics have been explored as antibiotic alternatives to alleviate postweaning stress, and Lactobacillus plantarum has shown potential for modulating the gut microbiota and improving intestinal health. However, most previous studies have relied on single-omics approaches, limiting mechanistic understanding of host-microbiome interactions. This study employed an integrated multi-omics approach combining ileal transcriptomics, fecal microbiomics, and metabolomics to investigate the effects of dietary L. plantarum supplementation in weaned piglets. Six piglets were assigned to either a control or L. plantarum-supplemented group for two weeks. RNA sequencing, 16S rRNA gene sequencing, and gas chromatography mass spectrometry based metabolomics were conducted, followed by integrative analysis using MIMOSA2 and MetaboAnalyst. Transcriptomic analysis identified 1,229 differentially expressed genes enriched in immune-related pathways, including NF-κB and IgA signaling, as well as epithelial barrier regulation. Microbiome profiling revealed increased microbial diversity, enrichment of Lactobacillus, and reduced abundance of Shigella. Functional prediction suggested enhanced innate immune responsiveness. Integrated metabolome-transcriptome analysis highlighted lipid and amino acid metabolic pathways linking microbial metabolites with host gene expression. Overall, L. plantarum supplementation induced coordinated host-microbiome adaptations associated with reduced oxidative stress, improved intestinal barrier stability, and enhanced immune resilience. These findings provide mechanistic evidence supporting L. plantarum as a promising nutritional strategy to mitigate postweaning stress and improve piglet intestinal health.},
}

@article {pmid42898634,
year = {2026},
author = {Han, JL and Lu, XD and Du, JJ},
title = {The role of microbiota on thyroid cancer: from carcinogenicity, treatment and predictability.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1912576},
pmid = {42898634},
issn = {1664-3224},
mesh = {Humans ; *Thyroid Neoplasms/therapy/microbiology/immunology/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Probiotics/therapeutic use ; Carcinogenesis ; Prebiotics ; },
abstract = {In recent years, more and more attention has been paid to the mechanism of microbiota in thyroid cancer (TC). Gut microbiota (GM) and its metabolites can regulate the immune system and affect thyroid function through the gut-thyroid axis. When the GM is dysregulated, the intestinal barrier function is impaired, resulting in immune dysfunction, chronic inflammation, oncogene activation, and eventually leading to the occurrence of TC. In addition, intratumoral microbiota (ITM) is also directly involved in the occurrence, progression and invasion of TC. However, the mechanism of action between the microbiome and TC is still under exploration, and the research results in this field will have a major impact on disease cognition and clinical intervention. Chemotherapy, radiation, and immunotherapy are the main non-surgical treatments for TC. Furthermore, gut microbiota modulators, including probiotics and prebiotics, represent a potential therapeutic strategy for TC, offering new avenues for individualized treatment. In addition, the differences of microbiota in patients with TC can be used to predict tumor subtype, invasion, lymph node metastasis, and the efficacy of [131]I treatment. This review will integrate the existing research results to explore the role of microbiota in the occurrence, development, treatment and prediction of TC, so as to provide important reference for clinical research and treatment.},
}

Humans
*Thyroid Neoplasms/therapy/microbiology/immunology/etiology
*Gastrointestinal Microbiome/immunology
Animals
Probiotics/therapeutic use
Carcinogenesis
Prebiotics

@article {pmid42898640,
year = {2026},
author = {Zeng, L and Wei, S and Chen, N and Xie, X},
title = {Why only 3 months? Immunological constraints on CAR-T therapy in gastrointestinal cancers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1942381},
pmid = {42898640},
issn = {1664-3224},
mesh = {Humans ; *Immunotherapy, Adoptive/methods/adverse effects ; *Gastrointestinal Neoplasms/therapy/immunology/mortality ; *Receptors, Chimeric Antigen/immunology ; Tumor Microenvironment/immunology ; Claudins/immunology ; Animals ; },
abstract = {In June 2026, satri-cel/CT041, a chimeric antigen receptor (CAR) T-cell product targeting Claudin18.2, received approval from China's National Medical Products Administration for the treatment of Claudin18.2-positive, HER2-negative advanced gastric/gastroesophageal junction adenocarcinoma after failure of at least two prior lines of therapy. This marks the first CAR-T product approved worldwide for solid tumours. The approval ends the long-standing debate over whether CAR-T cells can be effective against solid malignancies, yet it simultaneously raises a more pointed issue: in its pivotal randomised controlled trial, median progression-free survival was 3.25 months (95% CI 2.86-4.53) with satri-cel against 1.77 months (95% CI 1.61-2.04) with treatment of physician's choice, giving a hazard ratio of 0.37 (95% CI 0.24-0.56). The two medians differ by 1.48 months; that figure marks where each survival distribution is cut in half and is not the benefit any individual patient can expect, and approval does not equate to a cure. Taking this as a starting point, this review systematically dissects the immunological bottlenecks that constrain CAR-T efficacy in gastrointestinal tumours. We first trace the evidence chain from phase I studies through the randomised controlled trial to exploratory adjuvant-therapy settings and then integrate the landscape of targets-Claudin18.2, glypican-3, carcinoembryonic antigen, mesothelin, and CDH17-within a target-tumour matrix encompassing gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic cancer. The core section focuses on four intertwined immunological constraints: spatiotemporal heterogeneity and escape at the antigen level; a therapeutic window shaped jointly by epitope masking within tight junctions and immune privilege of the gastric mucosal stem cell niche-this mechanism not only explains why Claudin18.2-directed CAR-T cells exhibit an acceptable safety profile despite target expression on normal tissues but also provides a paradigm for rational selection of next-generation targets; a suppressive microenvironment composed of regulatory T cells, myeloid-derived suppressor cells, tumour-associated macrophages, transforming growth factor-β, adenosine, and a hypoxic and acidotic metabolic milieu; and CAR-T exhaustion driven by chronic antigen stimulation. We particularly emphasise that metabolic stress and exhaustion are not two parallel obstacles. We put forward a mechanistic model in which persistent antigen stimulation combined with intratumoral hypoxia acts as a "double hit": through mitochondrial dysfunction and reactive oxygen species accumulation, the two inputs raise nuclear factor of activated T-cell (NFAT) activity and so drive the TOX/NR4A-dominated exhaustion program. This model is assembled from chronic-infection and mouse tumour systems and has not been tested in human CAR-T cells or in satri-cel-treated patients. We advance it as a framework for organising the four bottlenecks and for explaining why single-point interventions struggle to lift the efficacy ceiling, not as a demonstrated account. On this basis, we discuss strategies such as armouring, logic gating, transcription factor engineering, gene editing, and chemokine receptor modification, along with combination regimens involving checkpoint inhibition, oncolytic viruses, locoregional administration, and microbiome modulation, and we evaluate alternative platforms including CAR-macrophages, CAR-NK cells, and in vivo CAR-T generation. The watershed has been crossed, but the work of turning 3 months into 30 has only just begun.},
}

Humans
*Immunotherapy, Adoptive/methods/adverse effects
*Gastrointestinal Neoplasms/therapy/immunology/mortality
*Receptors, Chimeric Antigen/immunology
Tumor Microenvironment/immunology
Claudins/immunology
Animals

@article {pmid42898644,
year = {2026},
author = {Nong, Q and Liang, Q and Huang, X and Lin, L and Solanki, AC and Malviya, MK and Solanki, MK and Verma, KK and Li, C},
title = {Unlocking associative nitrogen fixation in Poaceae: molecular mechanisms, regulatory constraints, and pathways to sustainable productivity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1922705},
pmid = {42898644},
issn = {1664-302X},
abstract = {Biological nitrogen fixation (BNF) is a sustainable and environmentally friendly approach to nitrogen assimilation that extends beyond leguminous plants, where efficient nitrogen fixation occurs. Poaceae crops can also obtain nitrogen through associative nitrogen fixation (ANF) mediated by endophytic and rhizospheric diazotrophs, which typically contributes 10-30 kg N ha[-1] yr.[-1] to cereal crops, i.e., wheat, maize, rice, though certain tropical grasses, such as sugarcane may achieve up to 40-50 kg N ha[-1] yr.[-1] under optimal conditions. This review synthesizes recent advancements of ANF research across Poaceae crops, providing comprehensive analysis of their functional mechanisms. It explores the underlying mechanisms regulating ANF and assesses key factors influencing nitrogenase activity, including oxygen sensitivity, external nitrogen availability, and energy constraints. Furthermore, it discusses advanced strategies, such as genetic engineering of nitrogen-fixing microbes, host plant metabolic modifications, and optimized agronomic strategies to enhance nitrogen fixation efficacy. This review establishes a robust framework for sustainable crop production and long-term agricultural productivity by integrating molecular, physiological, and ecological perspectives. The major challenges of climate change, regional fertilizer restrictions, and achieving sustainable agricultural intensification collectively underscore the urgent need for biologically based nitrogen management strategies in cereal cropping systems.},
}

@article {pmid42898728,
year = {2026},
author = {Foley, M and Barrangou, R},
title = {Recombination-mediated gene-specific sweeps in motion across the human gut microbiome.},
journal = {Microbiome research reports},
volume = {5},
number = {3},
pages = {22},
pmid = {42898728},
issn = {2771-5965},
}

@article {pmid42898787,
year = {2026},
author = {Fan, W and Xu, H and Wu, Y and Peng, Y},
title = {Beyond combination: sequencing priming modalities before immune checkpoint inhibitors to convert immunologically cold tumors toward an ICI-responsive phenotype.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1947737},
pmid = {42898787},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; Tumor Microenvironment/immunology/drug effects ; *Neoplasms/immunology/therapy ; Animals ; Phenotype ; Immunotherapy/methods ; Combined Modality Therapy ; Neoadjuvant Therapy/methods ; },
abstract = {Immune checkpoint inhibitors have transformed oncology but largely spare immunologically "cold" tumors, those with sparse T-cell infiltration, low PD-L1 expression, and an immunosuppressive microenvironment. The prevailing response has been a combination: adding a priming modality to a checkpoint inhibitor, most often concurrently. We argue that this "addition" paradigm has plateaued in cold disease because it treats combination as arithmetic rather than as a temporally ordered program, and that timing, the order and interval of interventions, may govern outcome as much as the choice of agents. We first define what makes a tumor immunologically cold and why simultaneous stacking reaches a ceiling. We then assemble the clinical evidence that timing already shapes outcomes: most maturely in the scheduling of radiotherapy relative to checkpoint blockade and, strikingly, in neoadjuvant-versus-adjuvant immunotherapy, where the same agent changes outcome according to when it is given. We synthesize the temporal immunobiology that makes ordering matter-antigen release and dendritic-cell priming kinetics, the vascular-normalization window, compensatory adaptive-resistance windows, and the slow dynamics of the gut microbiome-and review, mechanism by mechanism, the timing evidence for microenvironment priming, checkpoint inhibition, and microbiome modulation, emphasizing that mistiming can be harmful rather than merely ineffective. We describe how several groups are translating this principle into integrated, time-sequenced strategies and set out, as one concrete and falsifiable instantiation, a three-axis schema, which we term TMEp-CI-M, illustrated by cross-tumor proof-of-concept experience and framed as hypothesis-generating rather than validated. A therapy built on timing will require dynamic biomarkers of window state and adaptive, biomarker-driven trials. For cold tumors, re-sequencing the agents we already have, rather than adding new ones, may be among the highest-yield and lowest-cost hypotheses in immuno-oncology and one that can be tested now.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
Tumor Microenvironment/immunology/drug effects
*Neoplasms/immunology/therapy
Animals
Phenotype
Immunotherapy/methods
Combined Modality Therapy
Neoadjuvant Therapy/methods

@article {pmid42898857,
year = {2026},
author = {Kang, R and Yu, C and Gwon, Y and Lee, S and Yang, J and Jeong, J and Kim, G and Lee, W and Jo, W and Oh, MG and Jang, C and Tilahun, M and Oh, J and Park, T},
title = {Meta-analysis with batch-effect adjustment reveals breed-specific ruminal microbiome variation of beef cattle and its implications for meat quality and productivity.},
journal = {Journal of animal science and technology},
volume = {68},
number = {5},
pages = {1544-1566},
pmid = {42898857},
issn = {2055-0391},
abstract = {Various beef cattle breeds are raised in different countries. Hanwoo and Wagyu breeds are primarily raised in Korea and Japan, respectively, whereas Angus breed is one of the most widely bred beef cattle breed worldwide. Although microbiome studies have been conducted for each breed, comparative analyses of the ruminal microbiome and their functions across breeds remain limited. Moreover, the potential links between the ruminal microbiome and animal traits related to meat quality and productivity have not been studied. Based on 13 studies comprising 954 samples (Hanwoo: 384, Angus: 246, Wagyu: 324) with the application of an optimal batch-effect adjustment tool, this meta-analysis aimed to compare the ruminal microbiome across Hanwoo, Angus, and Wagyu and explore potential associations between breed-specific microbiome profiles and key phenotypic traits, such as meat quality and production performance. The overall microbial composition at the phylum, genus, and Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog levels was effectively adjusted batch-effect using the selected adjustment tool (ConQuR). Subsequent analyses were conducted using batch-effect adjusted microbiome data to investigate the breed-specific differences. Cellulolytic bacteria such as Bacteroides, Fibrobacter, Lacrimispora, and Ruminococcus were dominant in Angus, whereas saccharolytic bacteria such as Selenomonas, Olsenella, Sporomusa, Streptococcus, and Bifidobacterium were relatively abundant in Wagyu. Predicted KEGG modules revealed that ubiquinone and biotin biosynthesis pathways were enriched in Angus, whereas amino acid biosynthesis was enriched in Wagyu. Hanwoo exhibited intermediate traits at both the phylum and genus taxonomic levels. In the comparative network analysis, Prevotella and Dialister were the keystone genera in Angus, Mogibacterium in Wagyu, and Streptococcus in Hanwoo. In archaeal microbiome comparisons, methane metabolism-related KEGG modules were enriched in Angus. KEGG modules and taxa previously known as high average daily gain-related were relatively enriched in Angus, whereas Wagyu was characterized by those related to high intramuscular fat. Hanwoo exhibited intermediate traits in both productivity and meat quality, and the microbiome features were between those of Angus and Wagyu. These findings suggest a potential link between the ruminal microbiome and meat quality- and productivity-related traits in beef cattle.},
}

@article {pmid42898902,
year = {2026},
author = {Velázquez-Ochoa, R and Li, VY and Krämer, WE and Medina, M and Enríquez, S},
title = {Microbial community dynamics mediate rapid biomass loss and phosphorus recycling in pelagic Sargassum.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1918885},
pmid = {42898902},
issn = {1664-462X},
abstract = {Sargassum blooms in the tropical North Atlantic have surged to unprecedented levels, causing massive algal tides that severely impact coastal ecosystems. To improve the current understanding of Sargassum biomass dynamics and the contribution of this productive algal bloom to carbon and nutrient fluxes between the Atlantic and the Caribbean, we characterized the growth and decomposition rates of this pelagic alga, nutrient release rates during litter decay, and the bacterial microbiome at several stages of this decay. The analysis revealed no exceptional growth under increased nutrient availability but a rapid biomass mineralization with a litter half-life of 16 days, comparable to phytoplankton. This fast decomposition triggers swift nutrient release, notably phosphorus, which fuels coastal eutrophication and may help explain oxygen depletion and toxic gas emission during massive beaching events. A microbial succession involving chemoheterotrophic and nitrogen-fixing bacteria predicts functions involved in the biomineralization of nitrogen and phosphorus-containing compounds that may facilitate such efficient phosphorus mineralization, supporting similar patterns in marine debris to terrestrial plant litter, where nutrients drive stage-specific patterns in microbial community succession during litter decomposition. Our results underscore the pivotal role of microbial communities in enhancing algal resilience to nutrient deprivation-through the establishment of mutualistic associations with their host-and in mediating global carbon and nutrient fluxes, an aspect of particular relevance to the marine phosphorus cycle. Ultimately, this study emphasizes the severe ecological threat that massive Sargassum tides pose to marine health and public safety at the coast.},
}