@article {pmid43012510,
year = {2026},
author = {Crossen, AJ and Cohen, S and Manzer, HS and Zackular, JP and Ost, KS and Doran, KS},
title = {The BspC surface adhesin and gastrointestinal fungal colonization enhance group B streptococcal neonatal infection.},
journal = {mBio},
volume = {},
number = {},
pages = {e0256126},
doi = {10.1128/mbio.02561-26},
pmid = {43012510},
issn = {2150-7511},
abstract = {Group B Streptococcus (GBS) colonizes the gastrointestinal (GI) and female reproductive tracts of up to 30% of healthy adults, but during pregnancy can be transmitted to the newborn, causing neonatal sepsis, pneumonia, and meningitis. Neonatal GI colonization is an important precursor to invasive disease, yet the mechanisms governing GBS intestinal persistence and dissemination are still being elucidated. Given the predominance of hypervirulent sequence type 17 (ST-17) strains in neonatal invasive disease, we hypothesized that the ST-17-associated surface adhesin BspC contributes to gastrointestinal colonization and infection. Using a neonatal mouse model, we found that pups infected with wild-type GBS exhibited increased mortality and significantly higher bacterial burdens in the intestine, blood, spleen, and brain compared with pups infected with a ΔbspC mutant. We also observed that BspC promoted adherence to a 2D organoid model of the human infant colon and Caco-2 intestinal epithelial cells through its variable domain. Building on previous findings that Candida albicans interacts with BspC, we found that C. albicans enhanced GBS intestinal epithelial adherence in a BspC-dependent manner, and coinfection increased intestinal GBS burden and brain dissemination in neonatal mice. Finally, analysis of published human neonatal fecal microbiome data sets revealed higher GBS abundance in infants colonized with C. albicans or other Candida species. Together, these findings identify BspC as a key mediator of GBS intestinal colonization and invasive disease and suggest that fungal colonization of the neonatal GI promotes GBS pathogenesis.IMPORTANCEGroup B Streptococcus (GBS) is a leading cause of neonatal infection, which can result in fatality or long-term neurological morbidity in survivors. Intestinal colonization is an important precursor to invasive disease, yet the factors that promote GBS persistence in the neonatal gastrointestinal tract remain incompletely understood. Here, we identify the GBS surface adhesin BspC as a mediator of intestinal epithelial adherence, gastrointestinal colonization, and systemic dissemination. We further demonstrate that the common fungal pathobiont Candida albicans enhances GBS intestinal adherence and infection. Consistent with our experimental findings, analysis of human infant microbiome data sets revealed greater GBS abundance in infants colonized with Candida species. These findings identify BspC as a key mediator of this process and suggest that fungal colonization can enhance GBS disease.},
}

@article {pmid43012643,
year = {2026},
author = {Wheeler, M and Bakkeren, E},
title = {Erratum: Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001904},
pmid = {43012643},
issn = {2057-5858},
}

@article {pmid43012696,
year = {2026},
author = {Dong, KH and Zheng, ZQ and Shen, L and Ji, HF},
title = {Thyme Beyond Its Traditional Culinary Use: Bioactive Constituents as Potential Modulators of the Gut Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34545-34575},
doi = {10.1021/acs.jafc.6c07962},
pmid = {43012696},
issn = {1520-5118},
support = {ZR2023MH357//Natural Science Foundation of Shandong Province/ ; },
mesh = {*Thymus Plant/chemistry/metabolism ; Humans ; Animals ; *Plant Extracts/chemistry/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Bacteria/genetics/isolation & purification/classification/metabolism/drug effects ; Oils, Volatile/chemistry/pharmacology ; },
abstract = {Thyme, particularly Thymus vulgaris L., is a widely used culinary spice and a source of compounds with diverse reported pharmacological activities. This Review examines how thyme extracts, essential oils, and their major constituents, including characteristic monoterpenes, sesquiterpenes, triterpenes, phenolic acids, and flavonoids, interact with the gut microbiome. On the basis of structure-activity relationships, we evaluate how these constituents influence gut microbial composition and function and summarize the implicated mechanisms. Thyme preparations and individual compounds can influence intestinal availability, microbial transformation, and target selectivity, while microbiota-dependent and -independent pathways may contribute to changes in intestinal barrier function, metabolite profiles, and related signaling pathways. Interactions among multiple constituents may produce additive or synergistic effects, suggesting potential advantages of multicomponent thyme preparations, whereas studies of individual compounds can facilitate the target identification and mechanistic analysis. Future research should systematically address gaps in causal validation, formulation standardization, and human evidence to consolidate the translational foundations.},
}

*Thymus Plant/chemistry/metabolism
Humans
Animals
*Plant Extracts/chemistry/pharmacology/metabolism
*Gastrointestinal Microbiome/drug effects
Bacteria/genetics/isolation & purification/classification/metabolism/drug effects
Oils, Volatile/chemistry/pharmacology

@article {pmid43012714,
year = {2026},
author = {Lee, CC and Ashaolu, TJ},
title = {AI-Driven Prediction of Allergenicity and Toxicity in Novel Plant-Based Peptides.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34683-34700},
doi = {10.1021/acs.jafc.6c13356},
pmid = {43012714},
issn = {1520-5118},
mesh = {Humans ; *Allergens/immunology/chemistry/toxicity ; *Peptides/immunology/chemistry/toxicity ; *Artificial Intelligence ; *Plant Proteins/immunology/chemistry/toxicity ; Animals ; Prediction Algorithms ; *Plants/chemistry/immunology ; },
abstract = {Peptides from plant sources have antihypertensive, antioxidative, and antimicrobial properties but also entail a risk of allergic and toxic reactions that cannot be detected in conventional wet-lab assays. This review examines deep learning techniques and protein language models for their prediction, from linear motifs screening to transformers (BERT, ESM). The best-performing tools achieve high sensitivity (pLM4Alg 96.2%, ToxinPred3 95.8%) but low specificity and positive predictive value (pLM4Alg 92.8% and 81.7%), meaning that most predictions are false positives. There are four major constraints on the generalization capabilities of these tools: scoring of native peptides while proteolytic processing yields post-translational modifications and neoantigens; training samples correspond to IgE binding, not clinical manifestations, and are biased toward well-characterized organisms; T-cell immunity, microbiome, and organ-specific toxicity are scarcely modeled; and regulatory agencies do not consider in silico predictions sufficient. AI currently serves best as a prioritization filter, not a replacement for biological assays.},
}

Humans
*Allergens/immunology/chemistry/toxicity
*Peptides/immunology/chemistry/toxicity
*Artificial Intelligence
*Plant Proteins/immunology/chemistry/toxicity
Animals
Prediction Algorithms
*Plants/chemistry/immunology

@article {pmid43012717,
year = {2026},
author = {Lin, Z and Huang, R and Zhang, S and Wang, L and Fang, X and Du, R and Xiao, S and Pramono, H and Xu, Z},
title = {Metabolite-Mediated Rhizosphere-Endosphere Microbiome Shapes Genotype-Dependent Cadmium Accumulation via Coupled Chemical Immobilization and Microbial Detoxification.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {44},
pages = {34933-34947},
doi = {10.1021/acs.jafc.6c12601},
pmid = {43012717},
issn = {1520-5118},
support = {2022ZDJS019//Guangdong Province Key Construction Discipline Research Capacity Enhancement Project/ ; 2023ZDZX4016//Special Projects in Key Fields of Ordinary Universities in Guangdong Province/ ; 2024YFC3711903//National Basic Research Program of China (973 Program)/ ; 2024YFD1701304//National Basic Research Program of China (973 Program)/ ; 2026JJ40030//Natural Science Foundation of??Hunan Province/ ; 42577473//National Natural Science Foundation of China (NSFC)/ ; kq2502110//Changsha Natural Science Foundation Project/ ; NA//Changsha Natural Science Foundation Project/ ; NA//National Basic Research Program of China (973 Program)/ ; NA//National Natural Science Foundation of China (NSFC)/ ; NA//Natural Science Foundation of??Hunan Province/ ; NA//Special Projects in Key Fields of Ordinary Universities in Guangdong Province/ ; },
mesh = {*Cadmium/metabolism/analysis ; Rhizosphere ; *Microbiota ; Plant Roots/metabolism/microbiology/chemistry/genetics/growth & development ; *Amaranthus/metabolism/microbiology/genetics/chemistry/growth & development ; Genotype ; *Bacteria/isolation & purification/genetics/classification/metabolism ; *Soil Pollutants/metabolism/chemistry ; Soil Microbiology ; },
abstract = {Cadmium (Cd) contamination threatens food safety, yet genotype-dependent Cd accumulation at the soil-root interface remains poorly understood. We integrated physiological profiling, metabolomics, density functional theory (DFT), and 16S rRNA sequencing to compare two amaranth cultivars, Quanhong (QH, low-Cd) and Liuye (LY, high-Cd). QH showed greater shoot biomass (6.84 g/plant) and stronger Cd exclusion (root/shoot Cd: 0.12/0.08 mg/kg), whereas LY developed a larger root system (1.42 vs 0.71 g/plant) and accumulated more Cd (0.26/0.16 mg/kg). QH promoted conversion of exchangeable Cd into stable residual fractions and enriched humic-like dissolved organic matter and 9-Oxo-ODE, which showed strong predicted Cd2+ binding (-22.34 kcal/mol), supporting its potential role in Cd immobilization. QH showed stronger host-associated microbial selection, enriching Bacillus and Streptomyces associated with sulfur metabolism and thiol-mediated metal sequestration, together with greater diversity and stability of root endophytes. These findings indicate coordinated chemical and microbial regulation contributing to the low-Cd phenotype of QH.},
}

*Cadmium/metabolism/analysis
Rhizosphere
*Microbiota
Plant Roots/metabolism/microbiology/chemistry/genetics/growth & development
*Amaranthus/metabolism/microbiology/genetics/chemistry/growth & development
Genotype
*Bacteria/isolation & purification/genetics/classification/metabolism
*Soil Pollutants/metabolism/chemistry
Soil Microbiology

@article {pmid43012904,
year = {2026},
author = {Cai, Q and Li, H and Shen, Z and Wei, C},
title = {Wetland microbiomes: diversity, biogeochemical functions, climate feedbacks, and emerging frontiers.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {43012904},
issn = {1573-0972},
support = {20251705107//Medical and health research projects in Zibo/ ; 24DWYJ09//Social Science Planning Project of Shandong Province/ ; 2025QN08109//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; },
mesh = {*Wetlands ; Methane/metabolism ; *Microbiota/physiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Soil Microbiology ; Climate ; Biodiversity ; Oxidation-Reduction ; Ecosystem ; },
abstract = {Wetlands occupy roughly 6% of the Earth's surface yet store 20 to 30% of global soil carbon and emit an estimated 145 to 180 Tg of methane each year, fluxes that are controlled by microbial communities. This review synthesizes the past decade of research on wetland microbiomes across peatlands, mangroves, salt marshes, and constructed wetlands, and draws three main conclusions. First, community assembly is governed mainly by environmental filtering: salinity and pH are the strongest predictors, deterministic processes dominate steep gradients, and stochastic processes become important in hydrologically homogeneous settings. Second, the evidence linking microbial communities to biogeochemical fluxes is uneven in strength. Process-level measurements and meta-analyses support a well-constrained picture of methanogenesis, methane oxidation, and sulfate suppression of methanogenesis, whereas much of the evidence for cryptic sulfur cycling, anaerobic methane oxidation coupled to nitrogen species, and viral regulation rests on gene abundance, which reports functional potential rather than in situ activity. Third, in constructed wetlands, antibiotic removal does not necessarily reduce antimicrobial resistance risks, because antibiotic concentrations, resistance gene abundance, mobile genetic elements, and horizontal gene transfer respond to different environmental drivers. The most pressing unresolved questions are the controls on the N2O: N2 product ratio of denitrification, the scaling from gene abundance to ecosystem fluxes, and the joint response of greenhouse-gas emissions to interacting climate drivers. We close by identifying where multi-omics integration and standardized cross-site observation networks would most rapidly close these gaps.},
}

*Wetlands
Methane/metabolism
*Microbiota/physiology
Bacteria/classification/genetics/metabolism/isolation & purification
Soil Microbiology
Climate
Biodiversity
Oxidation-Reduction
Ecosystem

@article {pmid43012929,
year = {2026},
author = {Divya, S and Bag, TK and Makeshkumar, T and Jeeva, ML and Chouhan, V and Manirajan, BA and Veena, SS and Kumar, A},
title = {Comparative metabarcoding of the cassava rhizoplane bacteriome in wetland and upland fields reveals Bacillus-mediated suppression of stem and root rot.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {43012929},
issn = {1573-0972},
mesh = {*Manihot/microbiology ; Plant Roots/microbiology ; *Plant Diseases/microbiology/prevention & control ; RNA, Ribosomal, 16S/genetics ; Plant Stems/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Fusarium ; Wetlands ; *Bacillus/physiology/genetics/isolation & purification/classification ; Rhizosphere ; DNA Barcoding, Taxonomic ; Soil Microbiology ; Microbiota ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Cassava (Manihot esculenta Crantz) stem and root rot caused by Fusarium falciforme is a major constraint to cassava production. This study investigated rhizoplane bacteriome shifts across wetland and upland fields differing in disease incidence and evaluated potential microbial indicators and biocontrol agents using 16 S rRNA gene amplicon sequencing, culture-dependent isolation, and functional assays. Bacterial richness was highest in diseased wetlands (Chao1, 601.60 ± 10.37), followed by healthy wetlands (581.20 ± 14.39) and uplands (547.97 ± 5.74), whereas bacterial evenness was comparable among sites. Pseudomonadota dominated across all field types (63-92%). Bacteroidota, and Acidobacteriodota were relatively enriched in healthy wetlands but declined in diseased samples, whereas Verrucomicrobiota increased in diseased roots (7.35%). Pseudomonas was predominant in uplands (29.7%), while Aeromonas, Salmonella, and Devosia were associated with diseased sites. The core bacteriome comprised Aquicella, Enterobacter, Klebsiella, Sodalis, and Salmonella. A multiple-testing-corrected bacterial-fungal co-occurrence network was sparse, comprising only five inter-kingdom associations. Of 195 bacterial isolates recovered, Bacillus subtilis ULB-36 and Bacillus stercoris ULB-12 exhibited the strongest antagonistic activity against F. falciforme, inhibiting mycelial growth by 83.33% and 78.52%, respectively. In greenhouse assays, these strains reduced disease incidence to 0% and 20%, respectively, compared with 70% in the pathogen-inoculated control; Bacillus subtilis ULB-36 performed comparably to carbendazim. Overall, cassava stem and root rot was associated with distinct shifts in the rhizoplane bacteriome, including depletion of potentially beneficial bacterial taxa in diseased fields. The identified site-specific microbial signatures and native Bacillus strains provide valuable insights into cassava-microbe interactions and highlight their potential for biological management of cassava stem and root rot.},
}

*Manihot/microbiology
Plant Roots/microbiology
*Plant Diseases/microbiology/prevention & control
RNA, Ribosomal, 16S/genetics
Plant Stems/microbiology
*Bacteria/classification/genetics/isolation & purification
Fusarium
Wetlands
*Bacillus/physiology/genetics/isolation & purification/classification
Rhizosphere
DNA Barcoding, Taxonomic
Soil Microbiology
Microbiota
DNA, Bacterial/genetics
Phylogeny

@article {pmid43012953,
year = {2026},
author = {Okamoto, KE and Harris, EV and Juneau, WC and Harshman, R and Kovacs, J},
title = {Resilient but Unreliable: Cross-Generational Restructuring of the Tribolium castaneum Gut Microbiome Under Contrasting Nutritional Regimes.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {43012953},
issn = {1432-184X},
support = {2042735//National Science Foundation/ ; },
mesh = {Animals ; *Tribolium/microbiology/physiology ; *Gastrointestinal Microbiome ; Diet ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Microbial communities are frequently exposed to environmental disturbances, yet recovery does not always lead to a single, predictable outcome. Distinguishing resilience, the capacity to recover following perturbation, from reliability, the predictability of that recovery, is essential for understanding microbiome dynamics. Here, we investigated cross-generational gut microbiome responses in the red flour beetle, Tribolium castaneum, a globally significant stored-product pest exposed to frequent environmental and dietary shifts. Using a four-generation experimental design (G0-G3), we examined how gut microbial communities respond to a major environmental transition from commercial to laboratory rearing, followed by dietary perturbations. The shift to laboratory conditions produced the largest change in gut microbiome composition, occurring within a single generation and exceeding the effects of dietary shifts. Following this disturbance, microbial communities stabilized across subsequent generations, consistent with strong ecological resilience. However, recovery trajectories and endpoints differed among treatments, with replicate lineages stabilizing toward multiple, partially distinct community configurations rather than a single shared state, indicating low reliability. Diet influenced overall community composition and diversity trajectories, but these effects were smaller in magnitude than the dominant generational restructuring. Together, these results show that the T. castaneum gut microbiome is resilient but not strictly reliable, stabilizing after rapid reorganization toward multiple partially distinct community configurations associated with environmental history rather than a single shared state. These findings underscore the importance of environmental context in shaping host-associated microbiomes and suggest that the capacity for rapid microbiome restructuring may contribute to the ecological success of insect pests in variable environments.},
}

Animals
*Tribolium/microbiology/physiology
*Gastrointestinal Microbiome
Diet
*Bacteria/classification/genetics/isolation & purification

@article {pmid43013030,
year = {2026},
author = {Zhou, W and Zhu, H and Liu, Y and Li, H and Wu, M and Li, S and Qu, R and Liu, S and Qian, H and Xue, B and Cao, Y and Jiang, X and Zhen, X},
title = {Ultrasound-Driven Lysis of Tumor-Resident Bacteria Awakens Innate Immunity for Systemic Cancer Therapy.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {44},
pages = {48101-48115},
doi = {10.1021/jacs.6c14587},
pmid = {43013030},
issn = {1520-5126},
support = {BK20244003//Natural Science Foundation of Jiangsu Province/ ; 5431ZZXM2506//State Key Laboratory of Analytical Chemistry for Life Sciences/ ; 52333003//National Natural Science Foundation of China (NSFC)/ ; 52373141//National Natural Science Foundation of China (NSFC)/ ; 52573166//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Immunity, Innate ; Animals ; *Fusobacterium nucleatum/immunology/drug effects ; Mice ; *Immunotherapy ; *Ultrasonic Waves ; Humans ; *Ultrasonic Therapy ; *Neoplasms/therapy/immunology ; },
abstract = {Tumor-resident bacteria establish a profound immunosuppressive microenvironment that compromises cancer immunotherapy. While ablating these microbes holds therapeutic promise, broad-spectrum antibiotics can cause systemic dysbiosis, and the Gram-negative outer membrane can restrict the entry of conventional sonosensitizers, limiting the antibacterial efficacy of sonodynamic therapy (SDT). Here, we report an ultrasound-driven, bacteria-targeted immunotherapy utilizing polyarginine-functionalized peptide-sonosensitizer conjugates to achieve the in situ pulverization of the tumor Fusobacterium nucleatum (F. nucleatum), thereby eliciting potent innate antitumor immunity. The cationic conjugates electrostatically intercalate into Gram-negative bacterial membranes, inflicting a structural predisruption. Subsequent ultrasound irradiation synergizes localized sonochemical oxidation with mechanical shear forces to thoroughly shatter the bacteria. This targeted microbial fragmentation liberates massive quantities of pathogen-associated molecular patterns (PAMPs) that, unlike tumor-derived signals from conventional SDT, decisively reprogram macrophages toward an antitumor M1 phenotype to awaken innate immunity. Synchronized with tumor-specific antigens released via conjugate-induced immunogenic cell death, the liberated PAMPs synergistically amplify antigen presentation and optimally drive dendritic cell maturation. In a bacteria-colonized murine colorectal cancer model, this localized therapy markedly suppressed primary tumor growth and elicited both a pronounced abscopal effect against distant tumors and antitumor immune memory. By repurposing complicit bacteria into potent endogenous adjuvants, this ultrasound-driven strategy reverses bacteria-mediated immunosuppression, offering a transformative paradigm for treating microbiome-colonized solid tumors.},
}

*Immunity, Innate
Animals
*Fusobacterium nucleatum/immunology/drug effects
Mice
*Immunotherapy
*Ultrasonic Waves
Humans
*Ultrasonic Therapy
*Neoplasms/therapy/immunology

@article {pmid43013155,
year = {2026},
author = {Al-Zaidi, OSSH and Ali, AH},
title = {Gut microbiome in leukemia: emerging insights, mechanistic and clinical implications.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {43013155},
issn = {1573-4978},
mesh = {Humans ; *Leukemia/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Animals ; },
abstract = {Leukemia is a hematological malignancy that arises from complex interactions among environmental factors, immune dysregulation, and genetic mutations. The Human Microbiome Project has contributed to understanding the potential role of the gut microbiome in the health of patients with leukemia, and its impact on leukemia development, progression, and response to therapies. This review summarizes how the gut microbiome and its constituent microorganisms may influence development and the new therapeutic approaches against leukemia. Recent findings indicate that microorganisms might influence leukemia through multiple mechanisms, including chronic inflammation, homeostasis disruption, and genomic instability. Dysbiosis of the gut microbiome might increase the risk of infection, impair response to immunotherapy and chemotherapy and increase the risk of clinical complications. Probiotics, postbiotics, and fecal microbiota transplantation (FMT) have emerged as promising microbiome-modulating approaches. Despite the abundance of emerging data suggesting potential therapeutic benefits, most studies remain small and preliminary. Integrating gut microbiome science into medical practice may open up new and potentially more effective therapeutic avenues for managing leukemia.},
}

Humans
*Leukemia/microbiology/therapy
Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
Probiotics/therapeutic use
Animals

@article {pmid43013265,
year = {2026},
author = {Valk, LC and Ruigrok, RAAA and Timmerman, H and Björk, JR and Li, Q and Zhang, S and Meneses, R and Vázquez Castellanos, JF and de Wit, N and Raes, J and Weersma, RK and Kleerebezem, M and Vich-Vila, A and Boekhorst, J},
title = {Mapping the genetic landscape of microbial lipid transformation in the intestinal microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2756735},
doi = {10.1080/19490976.2026.2756735},
pmid = {43013265},
issn = {1949-0984},
mesh = {*Lipid Metabolism/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Colon/microbiology ; Metagenome ; Intestine, Small/microbiology ; Bile Acids and Salts/blood ; },
abstract = {Dietary lipids are a key component in our diet, and fats and their derivatives have been associated with both beneficial as well as adverse effects on host health. However, the contribution of the gut microbiome to lipid metabolism remains understudied. Recognizing the importance of this interplay, we conducted extensive literature reviews to identify key bacterial genes involved in lipid metabolism, and created 88 Hidden Markov Models to allow rapid and accurate identification of these genes in genome and metagenome data. We applied these models to over 1000 metagenomes representative of the small intestine and colon, from both population-based and disease cohorts (LLDeep, MetaCardis and 1000IBD) to determine their lipolytic capacity. We observed that microbiome community types (enterotypes) carry different lipolytic potential. Serum levels of conjugated and sulfonated secondary bile acids were significantly associated with increased abundance of sterol-sulfonation genes (cysC, cysD and BtSULT). Small-intestinal communities were enriched in lipid genes compared to the colonic microbiota, underscoring the importance of microbial lipid metabolism in the small intestine compared to the colon. Overall, we demonstrate the value of our lipid metabolism models for functional microbiome profiling. Additionally, our study suggests that microbial activity in the upper gut might play a direct role in shaping host lipid metabolism, with potential implications for cardiometabolic health.},
}

*Lipid Metabolism/genetics
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/genetics/metabolism/classification/isolation & purification
Colon/microbiology
Metagenome
Intestine, Small/microbiology
Bile Acids and Salts/blood

@article {pmid43013324,
year = {2026},
author = {Lee, HR and Kim, KN and Jung, S and Ju, S and Lee, YJ and Kang, MS and Joo, NS},
title = {Food-based resistant starch, metabolic outcomes and the gut microbiome in women with metabolic syndrome risk factors: a randomized, double-blind pilot trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo05525c},
pmid = {43013324},
issn = {2042-650X},
abstract = {Resistant starch (RS) has been widely studied for its metabolic effects; however, evidence regarding the physiological effects of RS when consumed within whole-food-based dietary patterns remains limited. In this 8-week, double-blind, randomized pilot trial, 30 women aged ≥40 years with at least two metabolic syndrome features were assigned 1 : 1 to High-RS or Control foods, resulting in mean total dietary RS intakes of 7.9 and 2.4 g day[-1], respectively. Primary outcomes were metabolic syndrome components and gut microbiome composition and diversity. Secondary outcomes included urinary organic acids, fecal calprotectin, and heart rate variability, while microbiome-metabolic associations were exploratory. Between-group effects were estimated using baseline-adjusted analyses with multiplicity correction. No significant between-group differences were observed in the primary metabolic outcomes, including systolic blood pressure (adjusted mean difference, -1.7 mmHg; 95% CI, -6.4 to 2.9; P = 0.456), in global gut microbiome diversity and composition, or in the secondary outcomes after multiplicity correction. In exploratory genus-level analysis, Veillonella showed the strongest signal, with higher week-8 CLR abundance in the High-RS group (adjusted difference, 3.24; 95% CI, 1.48-5.00; P < 0.001), although no genus remained significant after FDR correction (q = 0.070). The association between change in urinary lactate-to-pyruvate ratio (LPR), a redox-sensitive metabolic index, and fasting glucose differed nominally between groups (P for interaction = 0.010; q = 0.185), but this finding was attenuated after exclusion of one high-leverage observation. Overall, 8 weeks of RS intake within a food matrix at intakes in the upper habitual range produced no detectable short-term change in the primary metabolic or global gut microbiome outcomes in this pilot trial. The exploratory Veillonella finding and LPR-glucose association did not remain statistically significant after multiplicity correction and should therefore be considered hypothesis-generating. The clinical trial registry number is KCT0011082 (Clinical Research Information Service (CRIS), Republic of Korea).},
}

@article {pmid43013553,
year = {2026},
author = {Hanna, DA and Kumar, R and Ji, Y and Wong, HKA and Lyssiotis, CA and Jones, JW and Banerjee, R},
title = {Lipid droplets buffer hydrogen sulfide-induced redox imbalance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {46},
pages = {e2613433123},
doi = {10.1073/pnas.2613433123},
pmid = {43013553},
issn = {1091-6490},
support = {GM130183//HHS | NIH (NIH)/ ; F32GM140694//HHS | NIH (NIH)/ ; },
mesh = {Oxidation-Reduction/drug effects ; *Hydrogen Sulfide/metabolism/pharmacology ; Humans ; *Lipid Droplets/metabolism/drug effects ; NAD/metabolism ; Mitochondria/metabolism ; Ubiquinone/metabolism ; },
abstract = {The electron transport chain is a signaling hub for hydrogen sulfide (H2S) that serves both as a respiratory substrate and an inhibitor. While acute sulfide toxicity is well characterized, cellular adaptations to chronic H2S, particularly microbially-derived sulfide exposure in colon, is poorly understood. We report that chronic, low-level H2S exposure (4 to 20 µM) drives robust carbon sequestration in lipid droplets (LD) across several human cell lines, driven by a coordinated remodeling of redox and nucleotide metabolism. Specifically, H2S-induced reductive shifts in nicotinamide adenine dinucleotide (NAD) and coenzyme Q (CoQ) pools are accompanied by glycerol-3-phosphate accumulation and cytidine triphosphate (CTP) depletion. Lipidomic analysis reveals increased neutral lipid synthesis and triacylglyceride accumulation concomitant with decreased CTP-dependent synthesis of membrane phospholipids. Mitochondrial expression of a water-generating NADH oxidase attenuates LD accumulation and spatially confines the origin of H2S-induced reductive stress signaling to this compartment. Interestingly, LD abundance increases even after H2S withdrawal, continuing over 48 h, during which time the reductively-shifted NAD and CoQ pools slowly reoxidize. Inhibition of fatty acid synthesis during sulfide exposure impairs cellular recovery of respiration. These findings establish an active role for LDs in stress response and reveal that lipid biogenesis is a strategy for countering H2S-induced redox imbalance. The sulfide-LD-redox axis uncovered in this study has implications for understanding how gut-derived H2S, shaped by diet and microbiome, can influence metabolic health.},
}

Oxidation-Reduction/drug effects
*Hydrogen Sulfide/metabolism/pharmacology
Humans
*Lipid Droplets/metabolism/drug effects
NAD/metabolism
Mitochondria/metabolism
Ubiquinone/metabolism

@article {pmid43013631,
year = {2026},
author = {Ongaga, E and Neondo, JO and Muli, JK and Kamau, PK and Bii, C and Odari, E and Budambula, NLM},
title = {Genetic diversity of bacterial endophytes associated with Crotalaria (Rattlepods).},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362184},
pmid = {43013631},
issn = {1932-6203},
mesh = {*Crotalaria/microbiology ; *Endophytes/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Genetic Variation ; *Bacteria/genetics/classification ; Phylogeny ; Microbiota/genetics ; DNA, Bacterial/genetics ; Animals ; },
abstract = {Crotalaria is a diverse legume genus valued for its ecological and agronomic roles. However, its associated endophytic microbiome remains minimally characterized. This study examined the genetic diversity and community structure of bacterial endophytes inhabiting domesticated and wild Crotalaria species. Twenty-nine healthy Crotalaria plant samples were analyzed using the culture-independent 16S rRNA gene amplicon sequencing approach. Genomic DNA was extracted using the Phenol-Chloroform method from both domesticated and wild samples. Sequencing of 16S ribosomal RNA gene was performed using Illumina MiSeq to profile endophytic bacterial communities. The sequence data was imported into R and processed using Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline. In total, 1,546,153 high-quality sequence reads were obtained and grouped into 611 amplicon sequence variants (ASVs) at 97% sequence similarity threshold. Domesticated samples exhibited higher observed species richness (median of 39 ASVs) than wild samples (median of 36 ASVs), while wild samples showed greater microbial community evenness (median ~1.08) compared to domesticated samples (median ~0.93). Beta diversity analyses showed clear separation between domesticated and wild endophytic bacterial communities, with domestication status explaining most of the observed variations (PERMANOVA: Bray-Curtis R2 = 0.826; Jaccard R2 = 0.846), but PERMANOVA detected no statistically significant difference (Bray-Curtis and Jaccard; p = 0.067). Overall, five bacteria phyla were detected in the Crotalaria samples. Pseudomonadota was the dominant phylum (64.27%) followed by Cyanobacteriota (35.5%). Enterobacteriaceae was the most abundant family (81.06%) with Enterobacter emerging as the most abundant genus in both domesticated (38.3%) and wild (89.4%) accessions. Notably, Pseudomonas was relatively enriched in domesticated plants while several bacterial genera were restricted to either wild or cultivated hosts, indicating habitat-associated endophytic specialization. This study provides the first comprehensive assessment of endophytic bacterial diversity in Kenyan Crotalaria species and highlights wild germplasm as an important reservoir of microbial diversity with potential biotechnological value.},
}

*Crotalaria/microbiology
*Endophytes/genetics/classification
RNA, Ribosomal, 16S/genetics
*Genetic Variation
*Bacteria/genetics/classification
Phylogeny
Microbiota/genetics
DNA, Bacterial/genetics
Animals

@article {pmid43013737,
year = {2026},
author = {Silvey, S and Patel, N and O'Leary, JG and Bajaj, JS},
title = {Ascites fluid PMN counts below the SBP threshold predict 30-day mortality in a national hospitalized cirrhosis cohort.},
journal = {Hepatology communications},
volume = {10},
number = {12},
pages = {},
doi = {10.1097/HC9.0000000000001071},
pmid = {43013737},
issn = {2471-254X},
mesh = {Humans ; Male ; *Liver Cirrhosis/mortality/complications ; Aged ; *Ascitic Fluid/cytology ; Middle Aged ; *Neutrophils ; *Ascites/mortality ; Female ; Prognosis ; Leukocyte Count ; Hospitalization ; United States/epidemiology ; Veterans/statistics & numerical data ; Biomarkers ; Hypertension, Portal ; Predictive Value of Tests ; },
abstract = {BACKGROUND: Complications in patients with cirrhosis often result from bacterial and bacterial product translocation. This translocation can occur because of portal hypertension, alterations in the gut microbiome, and immune dysregulation. We aimed to re-evaluate admission ascites PMN/mm3 count as a biomarker of 30-day mortality.

METHODS: We identified veterans with cirrhosis using validated ICD-9/10 codes who had a paracentesis ≤24 hours of their index hospitalization in the Veterans Affairs Corporate Data Warehouse from 2009 to 2024. In multivariable analysis, we determined the prognostic significance of ascites PMN/mm3 <100, 100-249, and ≥250.

RESULTS: The 4111 veterans who met the inclusion criteria were mostly older (66 y) men (96.3%) with alcohol-associated liver disease (31.1%) who experienced 16.9% 30-day mortality. Most patients (~80%) had an ascites PMN/mm3 count <100. A roughly linear relationship between 30-day mortality was seen until the threshold of 100 PMN/mm3 was reached, when the relationship plateaued. The OR for 30-day mortality of a PMN/mm3 count 100-249 was 1.93 (95% CI: [1.55-2.38], p<0.001) after adjusting for age, CCI, liver disease etiology, admission lactulose use, SBP prophylaxis, serum WBC count, MELD-Na, and serum albumin. The 30-day mortality risk was not statistically different from the higher threshold of ≥250 PMN/mm3 (p=0.53).

CONCLUSIONS: Admission ascites PMN/mm3 count ≥100, compared with <100, independently predicts a doubling in 30-day mortality in a national cohort of hospitalized patients with cirrhosis. Larger prospective studies are needed to examine the optimal ascites fluid PMN (polymorphonuclear neutrophil) thresholds that increase mortality risk.},
}

Humans
Male
*Liver Cirrhosis/mortality/complications
Aged
*Ascitic Fluid/cytology
Middle Aged
*Neutrophils
*Ascites/mortality
Female
Prognosis
Leukocyte Count
Hospitalization
United States/epidemiology
Veterans/statistics & numerical data
Biomarkers
Hypertension, Portal
Predictive Value of Tests

@article {pmid43013741,
year = {2026},
author = {Barcena-Varela, M and Shang, J and Lozano, A and Mogno, I and Liebling, I and Mead, K and Li, Z and Grinspan, LT and Lindblad, KE and Ruiz de Galarreta, M and Donne, R and Gnjatic, S and Merad, M and Jun, T and Ang, C and Marron, TU and Faith, JJ and Lujambio, A},
title = {Bacteroidetes promote hepatocellular carcinoma progression and resistance to immunotherapy.},
journal = {Hepatology communications},
volume = {10},
number = {12},
pages = {},
pmid = {43013741},
issn = {2471-254X},
mesh = {Animals ; *Carcinoma, Hepatocellular/microbiology/immunology/therapy/pathology/drug therapy ; *Liver Neoplasms/microbiology/immunology/therapy/pathology/drug therapy ; Mice ; *Bacteroidetes ; Humans ; *Immunotherapy/methods ; Disease Progression ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Dysbiosis ; *Drug Resistance, Neoplasm ; Disease Models, Animal ; Tumor Microenvironment/immunology ; Male ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND AND AIMS: Growing evidence highlights the gut microbiome's critical role in tumorigenesis and immunotherapy response. However, the impact of gut microbes on hepatocellular carcinoma (HCC) progression and response to immune checkpoint blockade (ICB) remains unclear due to the lack of combined preclinical and clinical studies.

APPROACH AND RESULTS: We performed 16S rRNA sequencing of cross-cohort stool samples from 10 HCC responders (R) and 40 non-responders (NR) to ICB at baseline and on-treatment time points. We identified Bacteroidetes enrichment in NR. To study the microbiome's role in cancer immune response, we generated an immunogenic mouse model of HCC via hydrodynamic tail-vein injection (HDTVI) of DNA plasmids mimicking common HCC alterations and immunogenicity by expressing OVA model antigens (MYC-lucOS;CTNNB1 tumors). We found that antibiotic (ABX)-induced dysbiosis promoted a pro-tumorigenic effect in the MYC-lucOS;CTNNB1 HCC and reshaped the tumor immune microenvironment by reducing dendritic cells (DCs) through the expansion of the Bacteroidetes species, Parabacteroides distasonis. P. distasonis colonization in mice harboring MYC-lucOS;CTNNB1 liver tumors confirmed its pro-tumorigenic effect in vivo. Furthermore, fecal matter transplant of patient microbiotas into murine recipients demonstrated that microbiota from an NR donor enriched in Bacteroidetes promoted faster tumorigenesis compared with microbiota from an R donor with reduced Bacteroidetes. We isolated 6 Bacteroidetes species from the NR donor into a bacterial cocktail. After colonization with the Bacteroidetes cocktail, mice harboring MYC-lucOS;CTNNB1 HCC exhibited increased tumorigenesis, reduced survival, and impaired response to ICB.

CONCLUSIONS: This study identified Bacteroidetes enrichment as a potential biomarker of ICB resistance in HCC and, by using immunogenic mouse models, established that Bacteroidetes abundance influences tumor development and response to ICB.},
}

Animals
*Carcinoma, Hepatocellular/microbiology/immunology/therapy/pathology/drug therapy
*Liver Neoplasms/microbiology/immunology/therapy/pathology/drug therapy
Mice
*Bacteroidetes
Humans
*Immunotherapy/methods
Disease Progression
*Gastrointestinal Microbiome/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Dysbiosis
*Drug Resistance, Neoplasm
Disease Models, Animal
Tumor Microenvironment/immunology
Male
Mice, Inbred C57BL

@article {pmid43014061,
year = {2026},
author = {Li, H and Zhang, X and Liu, J and Chen, X and Liao, B and Zhang, Y and Li, W and Sun, B and Li, X},
title = {Microbiome evidence-guided construction of a defined microbial consortium for light-aroma Baijiu fermentation and flavor development.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112147},
doi = {10.1016/j.ijfoodmicro.2026.112147},
pmid = {43014061},
issn = {1879-3460},
abstract = {Natural fermentation systems harbor microbial resources, but translating microbiome information into cultivable and controllable defined communities remains challenging. We integrated 74 metagenomic datasets from light-aroma Baijiu-associated Daqu and fermented grains with metagenome-assembled genome (MAG) functional profiles and independent 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) amplicon time series to propose four candidate functional roles: substrate conversion, acid/acyl-precursor formation, alcoholic fermentation, and aroma formation. Metagenomic profiling revealed community heterogeneity, whereas MAG analysis showed widespread genetic potential for starch conversion and lactic- and acetic-acid-related metabolism. Amplicon data revealed genus-level temporal distributions of Bacillus, Weissella, Wickerhamomyces, and Saccharomyces. Bacillus amyloliquefaciens, Weissella confusa, Saccharomyces cerevisiae, and Wickerhamomyces anomalus were selected from the available laboratory culture collection as candidate representatives of these roles. A three-factor Box-Behnken design optimized the two bacterial inoculum volumes and the combined yeast volume, with the yeast ratio fixed at 1:1 (v/v). For 500 g of substrate, inoculation volumes were 7 mL for B. amyloliquefaciens, 20 mL for W. confusa, 41 mL for S. cerevisiae, and 41 mL for W. anomalus, yielding 2.28 ± 0.12 g/L ethyl acetate (HPLC). During 28 d of solid-state fermentation, starch, reducing sugars, acidity, and volatile profiles changed, with 51 volatile compounds detected. The final base Baijiu contained 33 volatile compounds, including 13 with odor activity values (OAVs) >1, of which 11 were also detected by gas chromatography-olfactometry (GC-O). These findings support a role-guided route from natural fermentation microbiome evidence to a defined consortium with measurable fermentation and flavor phenotypes.},
}

@article {pmid43014287,
year = {2026},
author = {Takeuchi, T},
title = {Beyond who is there: Industrialization shifts gut microbial ecology and evolution.},
journal = {Cell host & microbe},
volume = {34},
number = {11},
pages = {2065-2067},
doi = {10.1016/j.chom.2026.10.004},
pmid = {43014287},
issn = {1934-6069},
mesh = {Humans ; *Bacteria/genetics/classification/isolation & purification ; *Biological Evolution ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology ; Animals ; },
abstract = {The relationship between industrialization and the gut microbiome remains incompletely understood due to limitations in cohort design involving host physiology and bacterial isolates. Two recent studies from the Global Microbiome Conservancy link industrialization to lower microbiome diversity and stability, altered host immune markers, and gene gain in gut bacteria.},
}

Humans
*Bacteria/genetics/classification/isolation & purification
*Biological Evolution
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology
Animals

@article {pmid43014293,
year = {2026},
author = {Weber, AM and Spencer, SP},
title = {A microbial sugar tips the metabolic scales.},
journal = {Cell host & microbe},
volume = {34},
number = {11},
pages = {2081-2083},
doi = {10.1016/j.chom.2026.10.007},
pmid = {43014293},
issn = {1934-6069},
mesh = {*Clostridium/metabolism ; Humans ; Interleukin-22 ; *Interleukins/metabolism ; Animals ; Energy Metabolism ; Signal Transduction ; *Polysaccharides, Bacterial/metabolism ; Obesity/metabolism/microbiology ; },
abstract = {Obesity and metabolic disorders are linked to the microbiome, but the underlying pathways remain poorly defined. In this issue of Cell Host & Microbe, Tan et al. identify a Clostridium immunis-derived exopolysaccharide that reduces interleukin-22 signaling to reshape visceral adipose immunometabolism, and their findings link microbial chemistry to host energy balance.},
}

*Clostridium/metabolism
Humans
Interleukin-22
*Interleukins/metabolism
Animals
Energy Metabolism
Signal Transduction
*Polysaccharides, Bacterial/metabolism
Obesity/metabolism/microbiology

@article {pmid43014623,
year = {2026},
author = {Vlachakis, DP and Evangelou, K and Kittas, C and Gorgoulis, V and Chrousos, GP},
title = {Longevitomics as the Science of the Longevitome: Towards a Unified Systems Science of Healthy Longevity.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112271},
doi = {10.1016/j.mad.2026.112271},
pmid = {43014623},
issn = {1872-6216},
abstract = {The twenty-first century has transformed longevity research through genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome science, digital phenotyping and artificial intelligence. Yet healthy longevity remains difficult to explain because its determinants are commonly studied as separate molecular layers, mechanisms or biomarkers. Here, we introduce Longevitomics as an integrative systems framework for understanding, modeling and predicting healthy longevity and define the Longevitome inspired by the Latin expression vita longa (long life) as the dynamic architecture of biological, environmental and behavioral determinants that collectively shape psychosomatic resilience across the life course. We position this proposal in relation to the Hallmarks of Aging, geroscience, biological-age biomarkers, multi-omics and systems medicine. Longevitomics is not intended to replace these established frameworks or to constitute another molecular "ome." Rather, it provides a systems-level framework in which mechanistic hallmarks, multi-omic layers, physiological phenotypes, exposures and adaptive responses can be integrated longitudinally. We further consider how network analysis, causal inference, machine learning and digital-twin approaches may enable reconstruction of individual Longevitome trajectories and support a transition toward predictive and personalized longevity medicine.},
}

@article {pmid43014635,
year = {2026},
author = {Kim, E and Lawson, LP and Wilson, E and Chapman, WD and Zabeti, A and Kottyan, LC and Weirauch, MT},
title = {Genetic and environmental etiology of pediatric and adult-onset multiple sclerosis.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {104234},
doi = {10.1016/j.autrev.2026.104234},
pmid = {43014635},
issn = {1873-0183},
abstract = {Multiple sclerosis (MS) is a chronic demyelinating disease of the central nervous system with complex etiology shaped by both genetic susceptibility and environmental exposures. This review synthesizes classic and emerging literature to provide an integrated framework for understanding MS risk, with emphasis on gene-environment interactions and their contribution to disease. We compile a comprehensive linkage disequilibrium-expanded MS genetic risk variant set identified through genome-wide association studies, including annotation of risk alleles. We discuss insights obtained from functional genomics studies that illuminate genotype-dependent regulatory mechanisms. Environmentally, we assess evidence implicating infectious agents (most notably Epstein-Barr virus) as well as vitamin D insufficiency, obesity, smoking, heavy metal exposure, and the gut microbiome, highlighting epidemiologic associations and areas where mechanistic understanding remains limited. We highlight current knowledge on individuals with pediatric-onset MS (POMS), a population underrepresented in etiologic studies despite its distinct clinical and immunological features. We compare genetic burden, environmental exposures, and immunopathology between pediatric- and adult-onset MS, identifying shared determinants as well as age-specific risk modifiers. Finally, we propose important future directions, including improved ancestry and age-range representation, functional validation of risk loci, and the use of treatment-naïve, tissue-derived patient samples.},
}

@article {pmid43014869,
year = {2026},
author = {Lee, EC and Hirekatur, R},
title = {Gut Health and Integrative Primary Care.},
journal = {Primary care},
volume = {53},
number = {4},
pages = {625-638},
doi = {10.1016/j.pop.2026.07.011},
pmid = {43014869},
issn = {1558-299X},
mesh = {Female ; Humans ; Complementary Therapies ; *Gastrointestinal Diseases/therapy/diagnosis ; *Integrative Medicine ; *Primary Health Care/organization & administration ; },
abstract = {This article presents a case of a patient with gastrointestinal symptoms through an integrative lens. At the end of this article, primary care providers will identify relevant history to obtain, use high-yield evaluations, and develop a patient plan that maximizes lifestyle habits and integrative therapies to help patients with common gastrointestinal symptoms.},
}

Female
Humans
Complementary Therapies
*Gastrointestinal Diseases/therapy/diagnosis
*Integrative Medicine
*Primary Health Care/organization & administration

@article {pmid43014893,
year = {2026},
author = {Hua, G and Geng, L and Li, D and Zhao, Y and Gao, P and Sun, H and Yang, S and Zhao, Q and Xue, P and Liu, W},
title = {Cadmium/arsenic co-contamination drives delayed succession of root endosphere bacteria and aligns with the metal partitioning stage in maize.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {101-110},
doi = {10.1016/j.jes.2026.02.056},
pmid = {43014893},
issn = {1001-0742},
mesh = {*Zea mays/microbiology ; *Cadmium/toxicity/analysis/metabolism ; *Soil Pollutants/toxicity/analysis/metabolism ; Plant Roots/microbiology ; *Soil Microbiology ; *Arsenic/toxicity/analysis/metabolism ; Rhizosphere ; Bacteria ; },
abstract = {Root-associated microbiota have been shown to mediate cadmium (Cd) and arsenic (As) transfer from soil to crops, however, their temporal dynamics and linkage to metal accumulation in maize under different Cd-As co-contamination levels remain unclear. A field experiment was conducted with low (LS) or high (HS) Cd-As co-contamination levels to elucidate the dynamics of root-associated bacteria and metal accumulation across maize growth stages. The results revealed that while the rhizosphere community remained stable, the temporal succession of root endosphere bacteria was delayed by one growth stage under high contamination rather than merely showing a reduction in diversity. The peak diversity (Shannon) and richness (Chao) occurred at the tasselling stage (TS) in the LS condition but was delayed until the grain-filling stage (GS) in the HS condition. This delay was synchronized with a shift in metal partitioning that Cd was highly retained in roots at the TS, with the translocation factor (TF) decreasing by 33.73 %-238.61 % (HS) and 31.34 %-191.20 % (LS) compared with the other stages, while As following a similar pattern at the GS, with the TF decreasing by 36.36 %-272.24 % (HS) and 56.25 %-146.44 % (LS). This metal-specific patterning was associated with the stage-delayed enrichment of Actinobacteria. Specifically, enrichment of Streptomyces, Agromyces, and Microbacterium at the TS was linked to the inhibition of Cd translocation, whereas enrichment of Lechevalieria and Mycobacterium at the GS was corresponded to the restriction of As translocation. These findings provided a stage‑synchronized framework for microbiome‑based remediation in Cd-As co‑contaminated soils.},
}

*Zea mays/microbiology
*Cadmium/toxicity/analysis/metabolism
*Soil Pollutants/toxicity/analysis/metabolism
Plant Roots/microbiology
*Soil Microbiology
*Arsenic/toxicity/analysis/metabolism
Rhizosphere
Bacteria

@article {pmid43014940,
year = {2026},
author = {Liu, H and Luo, Y and Deng, G and Zhao, W and Chen, J and Jin, Z and Tang, N and Zhang, G},
title = {Bacterial airborne diversity in typical pharmaceutical wastewater treatment plants and preventive effect on Klebsiella pneumoniae induced pulmonary injury.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {582-594},
doi = {10.1016/j.jes.2026.04.057},
pmid = {43014940},
issn = {1001-0742},
mesh = {*Wastewater/microbiology ; Klebsiella pneumoniae/physiology ; *Waste Disposal, Fluid/methods ; *Air Microbiology ; *Lung Injury/prevention & control/microbiology ; Bacteria/classification ; Animals ; RNA, Ribosomal, 16S ; },
abstract = {Wastewater treatment plants have peculiar bioaerosol feature. However, limited research has focused on bacterial function in bioaerosols from pharmaceutical wastewater treatment plants (PWWTPs). Here, airborne bacterial communities of two PWWTPs were analyzed using culturable and 16S rRNA gene high-throughput sequencing. The results revealed the bacterial aerosols collected from the PWWTPs differed significantly owing to the treatment process. The genera Pseudocyanosarcina, Potamoosiphon and Sphingomonas were the dominant genera in the two plants. Bacillus velezensis strain PB131 (Laboratory designation) was screened based on inhibition of Klebsiella pneumoniae (Kp) in vitro and in vivo. This strain colonizes the lungs, intestines, and trachea, and its mechanism for alleviating Kp-induced inflammation was investigated through modulation of gut microbiota. Strain PB131 inhibited the maturation and release of interleukin-1β (Il-1β), interleukin-6 (Il-6), and tumor necrosis factor α (Tnf-α) in the Prevention group (1.35 ± 0.08, 1.26 ± 0.27 and 1.20 ± 0.10) compared with the Kp infection group (2.23 ± 0.21, 2.10 ± 0.18 and 1.49 ± 0.19). These change mechanisms were related to gut microbial composition and short-chain fatty acids (SCFAs) levels, such as affecting Limosilactobacillus, Duncaniella, Bifidobacterium, and butyric acid content. This study provides valuable insights from microbiome research that enable an assessment of gut colonization by probiotics. These findings could potentially lead to the use of in vitro-derived probiotics as an alternative method for preventing respiratory inflammation.},
}

*Wastewater/microbiology
Klebsiella pneumoniae/physiology
*Waste Disposal, Fluid/methods
*Air Microbiology
*Lung Injury/prevention & control/microbiology
Bacteria/classification
Animals
RNA, Ribosomal, 16S

@article {pmid43014959,
year = {2026},
author = {Huang, Y and Zhou, Q and He, M and Ma, J and Xue, L and Wu, X and Gu, W and Qin, Y and Du, G},
title = {Perfluorononanoic acid impairs intestinal barrier integrity and induces gut microbiome dysbiosis in zebrafish.},
journal = {Journal of environmental sciences (China)},
volume = {170},
number = {},
pages = {794-803},
doi = {10.1016/j.jes.2026.04.047},
pmid = {43014959},
issn = {1001-0742},
mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; Intestinal Barrier Function ; *Fluorocarbons/toxicity ; *Water Pollutants, Chemical/toxicity ; Male ; },
abstract = {Perfluorononanoic acid (PFNA) is a ubiquitous persistent organic pollutant, yet its impact on gut health and associated mechanisms remains poorly understood. Here, we used multi-omics approaches to explore PFNA-induced alterations in intestinal homeostasis. Adult male zebrafish were exposed for 28 days to a series of concentrations (0, 0.1, 10 µg/L) of PFNA. Comprehensive analyses revealed that PFNA caused physical barrier damage, characterized by intestinal villus vacuolation and decreased mucin secretion. Furthermore, PFNA altered gut microbial composition by reducing beneficial bacteria and promoting opportunistic pathogens. Transcriptome analysis implicated intestinal barrier dysfunction and abnormalities in lipid and inflammatory pathways. Correspondingly, metabolomic analysis revealed significant perturbations in glycerolipid, phospholipid, and amino acid metabolism. Integrated multi-omics established strong correlations among the observed dysbiosis, altered gene expression, and metabolic disruption. Our findings demonstrate that PFNA exposure compromises intestinal barrier integrity and induces gut dysbiosis, providing crucial mechanistic insights into the PFNA toxicity and informing human health risk assessment.},
}

Animals
*Zebrafish
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/chemically induced
Intestinal Barrier Function
*Fluorocarbons/toxicity
*Water Pollutants, Chemical/toxicity
Male

@article {pmid43015024,
year = {2026},
author = {Anderson, JL and Ljótsson, B and Burton-Murray, H and West, ML and Yao, CK and Basnayake, C and Van Oudenhove, L and Biesiekierski, JR},
title = {Exclude or expose in irritable bowel syndrome study: what works for whom and how? Protocol for a randomised controlled trial of internet-delivered FODMAP diet versus exposure-based cognitive behavioural therapy.},
journal = {BMJ open},
volume = {16},
number = {11},
pages = {e126664},
pmid = {43015024},
issn = {2044-6055},
abstract = {INTRODUCTION: Irritable bowel syndrome (IBS) is a disorder of gut-brain interaction characterised by abdominal pain and altered bowel habits and is associated with reduced quality of life. Although several treatments are effective at the group level, treatment responses vary substantially between individuals, highlighting the need for personalised approaches. This trial investigates moderators and mediators of treatment response to two established IBS interventions to determine for whom treatments are most effective and how they exert their effects.

METHODS AND ANALYSIS: This parallel-group randomised controlled trial will enrol 235 adults with IBS from community, primary and tertiary care across Australia and the US. Participants will be randomised to a 12 week online fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) diet intervention targeting reduction of fermentable carbohydrate intake or an exposure-based cognitive behavioural therapy (E-CBT) programme targeting symptom-related avoidance behaviours, each with therapist support (dietitian or psychologist, respectively). The primary objective is to assess moderators and mediators of treatment response on gastrointestinal symptom severity, measured using the Gastrointestinal Symptom Rating Scale (GSRS-IBS), assessed weekly from baseline to week 12. Pre-specified moderators and mediators include gastrointestinal-specific anxiety and avoidance behaviour and total FODMAP intake; treatment preference will also be examined as a moderator. Treatment expectancy and credibility and therapeutic alliance will be assessed as covariates accounting for non-specific treatment effects. Secondary outcomes, assessed at baseline, post-treatment (12 weeks) and 3- and 6-month post-intervention follow-up, include IBS-specific symptom severity (measured using the IBS-Symptom Severity Scale, IBS-SSS), IBS-related quality of life, eating-related symptoms, psychological symptoms, extraintestinal symptom distress, stool frequency and consistency and gut microbiome composition and function. We will also assess gastrointestinal symptom severity by the GSRS-IBS at 3- and 6-month follow-up to assess maintenance. Linear mixed-effects models will assess treatment effects and moderation. Latent growth curve modelling and time-lagged mixed-effects models will examine mediation.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the University of Melbourne Human Research Ethics Committee (Project ID: 31186). This manuscript is based on protocol V.4.0 (06–04-26). Recruitment is ongoing. Results will be disseminated via peer-reviewed publications and presentations at scientific meetings.

TRIAL REGISTRATION NUMBER: NCT06940596.},
}

@article {pmid43015393,
year = {2026},
author = {Neves, JM and Mil-Homens, M and Martins, M and Adão, H and Gutierrez-Patricio, S and Jiménez, PN and Osman, JR and Miller, AZ and Lobo-Arteaga, J},
title = {Bivalve Gut Microbiome Responses to Sediment Characteristics and Anthropogenic Activities in Cerastoderma edule (Linnaeus, 1758).},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {43015393},
issn = {1432-184X},
support = {UI/BD/150954/2021//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Geologic Sediments/chemistry/microbiology/analysis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Fungi/classification/genetics/isolation & purification ; Anthropogenic Effects ; *Microbiota ; Water Pollutants, Chemical/analysis ; Seasons ; Estuaries ; *Bivalvia/microbiology ; Ecosystem ; },
abstract = {Estuaries are dynamic ecosystems influenced by fluctuating environmental conditions and sediment-associated contamination, which may affect host-associated microbiomes. This study investigated the gut microbiome of the bivalve Cerastoderma edule across three estuarine sites differing in anthropogenic pressure. Bacterial 16S rRNA and fungal ITS metabarcoding data were integrated with sediment physicochemical parameters to assess spatial and seasonal variation in gut microbial diversity and composition. Bacterial communities showed clear differences among sites and seasons, with stronger variation in areas characterized by higher organic matter and trace metal concentrations. Fungal communities also varied among samples, although their interpretation was limited by the high proportion of unassigned ITS taxa. Multivariate analyses indicated associations between gut microbial composition and sediment parameters, including organic matter, salinity, and trace metals such as mercury (Hg), zinc (Zn), and lead (Pb). Putative bacterial functional profiles were inferred from taxonomic data using FAPROTAX, suggesting potential involvement in nitrogen, sulfur, and carbon cycling, as well as organic compound degradation. Nevertheless, it is important to note that these functional predictions should be interpreted as indicators of potential metabolic capacity rather than direct evidence of activity. Ultimately, these findings demonstrate that the C. edule gut microbiome has strong potential as a complementary tool for the assessment of estuarine environmental conditions and host-environment interactions.},
}

Animals
*Geologic Sediments/chemistry/microbiology/analysis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Fungi/classification/genetics/isolation & purification
Anthropogenic Effects
*Microbiota
Water Pollutants, Chemical/analysis
Seasons
Estuaries
*Bivalvia/microbiology
Ecosystem

@article {pmid43015415,
year = {2026},
author = {Sun, W and Zhang, B and Wang, Y},
title = {Exploring a potential link between protein kinase C zeta and gut microbiota in cervical cancer: a hypothesis-generating study.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {43015415},
issn = {2191-0855},
abstract = {Cervical cancer remains a leading cause of cancer-related death. Integrating TCGA/GTEx and GWAS, we identified PRKCZ as a risk factor (OR = 1.26, p = 0.008). PRKCZ was upregulated in tumors, and its knockdown inhibited SiHa and HeLa proliferation. Using gutMGene, we identified Escherichia coli as a microbe computationally predicted to be associated with PRKCZ based on literature-curated data. Public 16S rRNA data (45 patients vs. 30 controls) showed reduced gut microbial diversity and higher abundance of the genus Escherichia-Shigella (which includes Escherichia coli) in patients. Parallel trends of higher Escherichia-Shigella abundance and PRKCZ expression were observed in separate cohorts. Importantly, because the microbiome and transcriptomic data derive from independent, non‑paired cohorts, no direct microbiota-gene association was measured, and no causal or mechanistic relationship can be inferred. These hypothesis-generating observations suggest a hypothetical association among gut Escherichia coli, PRKCZ, and isoquercetin, warranting direct validation in paired multi‑omics cohorts and functional studies.},
}

@article {pmid43015433,
year = {2026},
author = {Kapono, C},
title = {How I balance my life as a professional surfer and a university researcher.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {43015433},
issn = {1476-4687},
}

@article {pmid43015450,
year = {2026},
author = {Jakimowicz, M and Napora-Rutkowski, Ł and Suchocki, T and Mirończuk, A and Urbanek, AK and Mielczarek, M and Brzoza, A and Kamińska-Gibas, T and Szyda, J},
title = {Does supplementation with effective microorganisms under recirculating aquaculture system conditions affect water and intestinal microbiome of common carp?.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {43015450},
issn = {2190-3883},
support = {2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; Mistrz//Uniwersytet Przyrodniczy we Wrocławiu/ ; },
abstract = {The efficacy of effective microorganism products in aquaculture covers multiple aspects that act directly on fish, such as improving resistance to fungal, bacterial, and viral infections, reproduction, feed efficiency, and overall growth performance, or indirectly through improved water quality. In this study, the application of two commercial water and two commercial food Effective Microorganism supplements was tested under recirculating aquaculture system conditions for their effect on the water and intestinal microbiome of common carp (Cyprinus carpio), as well as on carp growth performance. Neither the dynamics of alpha diversity nor the abundance of single genera followed a pattern related to the experimental setup defined by the supplementation. However, the effects of supplementation were clearly manifested by an increase in the final weight of the fish. The most consistent alteration was a significant increase in Lactococcus abundance in the intestinal microbiome compared to that in the control group, as observed in both experimental setups. We conclude that feed supplementation with Lactococcus enhances its intestinal abundance in fish and promotes improved growth performance, likely through mechanisms involving glucose absorption and metabolism, as demonstrated in previous studies.},
}

@article {pmid43015492,
year = {2026},
author = {Sarma, V and Sarma, SK and Sarma, D and Devi, M and Kumar, D and Choudhary, N and Kondaveeti, SB and Sarma, AD},
title = {Microbiome-derived Metabolites in Anti-inflammatory Therapy: from Mechanisms to Translational Potential.},
journal = {Inflammation},
volume = {49},
number = {1},
pages = {},
pmid = {43015492},
issn = {1573-2576},
mesh = {Humans ; *Anti-Inflammatory Agents/therapeutic use/metabolism/pharmacology ; *Microbiota/physiology/drug effects ; *Inflammation/drug therapy/metabolism/microbiology ; Animals ; *Translational Research, Biomedical/methods ; Fatty Acids, Volatile/metabolism ; },
abstract = {Chronic inflammation underlies autoimmune, metabolic, cardiovascular, and neurodegenerative disorders and remains difficult to manage because current anti-inflammatory therapies often have systemic adverse effects and variable clinical efficacy. This review synthesizes evidence on microbiome-associated metabolites relevant to inflammation, including short-chain fatty acids, microbial indole derivatives, secondary bile acids, polyamines, trimethylamine N-oxide, and selected host-microbe co-metabolites. These compounds regulate host immunity through G-protein-coupled receptors, nuclear receptors, epigenetic mechanisms, inflammasome regulation, and major inflammatory signaling pathways such as NF-kappaB, MAPK, and JAK-STAT. The translational potential of direct metabolite administration, prodrug design, microbiome engineering, dietary modulation, and targeted delivery systems is discussed alongside key limitations, including low bioavailability, context-dependent activity, interindividual microbiome variation, incomplete pharmacokinetic data, and the limited number of well-controlled human trials. Overall, microbiome-associated metabolites represent promising but still evolving therapeutic candidates; their clinical use requires stronger causal evidence, standardized formulations, safety evaluation, and disease-specific validation.},
}

Humans
*Anti-Inflammatory Agents/therapeutic use/metabolism/pharmacology
*Microbiota/physiology/drug effects
*Inflammation/drug therapy/metabolism/microbiology
Animals
*Translational Research, Biomedical/methods
Fatty Acids, Volatile/metabolism

@article {pmid43015589,
year = {2026},
author = {G R, SK and Vaithilingam, M},
title = {16S rRNA gene amplicon sequencing reveals lifestyle-associated gut microbiome variation among tribal, rural, and urban populations from North Arcot regions of Tamil Nadu, India.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015589},
issn = {1471-2180},
mesh = {India ; Humans ; *RNA, Ribosomal, 16S/genetics ; Rural Population ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Adult ; Urban Population ; Phylogeny ; Middle Aged ; *Life Style ; Female ; Sequence Analysis, DNA/methods ; Young Adult ; DNA, Bacterial/genetics ; Male ; Biodiversity ; },
abstract = {BACKGROUND: The gut microbiota in humans not only supports metabolism and immune function but also influences susceptibility to various diseases. Changes in lifestyle, diet, and environment are the major factors affecting the variety and capability of gut microbes. Despite the growing interest in microbiome research, there are still only a few comparative studies of the microbiomes of tribal, rural, and urban Indian populations, especially in terms of their potential pharmacological and therapeutic benefits. The present work was focused on investigating the gut microbiota profile, diversity, and inferred functional capabilities of three different populations of Tamil Nadu, India, tribal (Mulluvadi), rural (Odugathur), and urban (Vellore)with the aim of discovering microbiota features that could have pharmacological significance.

METHODS: Fecal samples (n = 75; Mulluvadi tribal n = 25, Vellore urban n = 25, Odugathur rural n = 25; age 20-60 years) were analysed using 16S rRNA gene sequencing (V3-V4 region, Illumina MiSeq). Sequence data were processed using QIIME2 and DADA2, and taxonomic classification was performed against the SILVA 138 database. Microbial diversity was assessed using Chao1, Shannon, Simpson, and Fisher indices, while beta diversity was evaluated using BrayCurtis dissimilarity and principal coordinate analysis (PCoA). Functional profiles of microbial communities were predicted using PICRUSt2 and mapped to KEGG metabolic pathways.

RESULTS: We found distinct microbial diversity patterns to characterize the three populations. Differences in microbial diversity were observed among the three populations, with variations in both species-richness and community evenness. Across groups, major phyla were Firmicutes, Bacteroidota, Actinobacteria, and Proteobacteria. In this study, the tribal microbiome showed characteristics consistent with fiber degradation and potential short-chain fatty acid production, likely associated with Prevotella/Segatella-dominated taxa. Functional prediction of the microbiomes of the three groups suggests an abundance of carbohydrate and amino acid metabolic pathways in the tribal microbiome, and membrane transport and xenobiotic metabolism pathways predominate urban microbiome.

CONCLUSION: In summary, our study has revealed a lifestyle impact on gut microbial composition and metabolic potential differences among tribal, rural and urban populations of Tamil Nadu. The tribal microbiome showed enrichment of fiber-associated genera with predicted SCFA-related metabolic pathways. These findings are exploratory and require validation through individual-level sampling and functional analyses.},
}

India
Humans
*RNA, Ribosomal, 16S/genetics
Rural Population
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Adult
Urban Population
Phylogeny
Middle Aged
*Life Style
Female
Sequence Analysis, DNA/methods
Young Adult
DNA, Bacterial/genetics
Male
Biodiversity

@article {pmid43015590,
year = {2026},
author = {Sahu, S and Kaushik, SR and Chaudhary, S and Mohapatra, AK and Kupa, RU and Kapfo, W and Saha, S and Das, R and Bhalla, N and Kaur, M and Sivaji, Y and Das, B and Das, A and Khamo, V and Nanda, RK},
title = {Gut microbiome dysbiosis and associated metabolome changes in tuberculosis patients resolve partially post-therapy.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015590},
issn = {1471-2180},
support = {NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; NER//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Feces/microbiology ; *Metabolome ; *Gastrointestinal Microbiome/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; *Tuberculosis/microbiology/drug therapy ; Antitubercular Agents/therapeutic use ; Female ; Male ; Longitudinal Studies ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Mycobacterium tuberculosis/drug effects ; },
abstract = {BACKGROUND: Mycobacterium tuberculosis (Mtb) infection in the host and subsequent treatment with anti-tuberculosis drugs impact lung pathophysiology and influence the lung and gut microbiome. Elucidating the role of the gut microbiome and its metabolites in the perturbed metabolic and immune functions observed in tuberculosis (TB) might help design corrective prebiotic and probiotic mixtures.

METHODOLOGY: In this study, fecal samples (n = 107) of drug-naïve active TB patients (ATB) and controls (other respiratory disease: NTB and healthy) from the two clinical sites were analyzed for microbiota composition (16S rRNA sequencing), metabolites (GC-TOF-MS), and their correlation. In addition, a longitudinal follow-up study was conducted to understand the dynamics of the microbiota and metabolites during anti-TB treatment in a small cohort (n = 10).

RESULTS: Gut microbiota showed site-specificity; however, an overall reduction in alpha diversity was observed in disease states compared with healthy subjects. Underrepresentation of gut commensals (Faecalibacterium, Ligilactobacillus and Romboustia) and overrepresentation of Thomasclavelia and Clostridioides were observed among active TB patients. The longitudinally followed-up ATB subjects undergoing treatment showed a time-dependent increase in beta-diversity variance. Over time, the beta diversity of follow-up subjects was almost similar to that of healthy controls. Decrease in the abundance of Streptococcus occurred after anti-TB treatment, with higher levels of opportunistic pathogens, such as Escherichia and Stenotrophomonas. Similarly, specific fecal metabolites also returned to pretreatment levels in relative abundance at later time points.

CONCLUSIONS: The gut microbiota of TB patients showed dysbiosis at the time of case presentation and partially resolved upon complete therapeutic interventions. Partial recovery of microbiota observed during treatment is also reflected in the fecal metabolome, indicating the possible use of microbiome and metabolites as adjunct therapeutics in TB.},
}

Humans
*Dysbiosis/microbiology
Feces/microbiology
*Metabolome
*Gastrointestinal Microbiome/drug effects/genetics
RNA, Ribosomal, 16S/genetics
*Tuberculosis/microbiology/drug therapy
Antitubercular Agents/therapeutic use
Female
Male
Longitudinal Studies
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Mycobacterium tuberculosis/drug effects

@article {pmid43015619,
year = {2026},
author = {Djodjeu Kamega, LC and Foko Kouam, EM and Tchabou Tientcheu, ML and Hall, LJ and Kaktcham, PM},
title = {Genomic and phenotypic assessment of functional and safety properties of Lacticaseibacillus rhamnosus PMK4 isolated from Cameroonian infant faeces.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015619},
issn = {1471-2180},
mesh = {Humans ; Cameroon ; *Lacticaseibacillus rhamnosus/genetics/isolation & purification/physiology/classification ; *Feces/microbiology ; Infant ; *Probiotics ; Genome, Bacterial ; Phenotype ; Whole Genome Sequencing ; Bacterial Adhesion ; Genomics ; },
abstract = {The gut microbiota is a complex community of microorganisms that plays a crucial role in maintaining short- and long-term health. However, a perturbed microbial ecosystem is associated with a range of diseases, including increased risk of infections. Probiotic-based strategies may help restore microbiome function, but candidate strains require robust functional and safety evaluation. Here, we performed integrated genomic and phenotypic characterisation of beneficial properties of Lacticaseibacillus rhamnosus PMK4, isolated from the stool of a healthy Cameroonian infant. Whole-genome sequencing and comparative pangenomic analysis against 13 L. rhamnosus genomes were used to infer functional potential, with in silico safety screening conducted using ResFinder, CARD and VFDB. Beneficial-relevant phenotypes were assessed through tolerance to simulated gastrointestinal conditions, adhesion-associated traits (hydrophobicity, aggregation), antimicrobial activity, nutrients utilisation profiling and safety-related assays. The L. rhamnosus PMK4 genome (2,935,039 bp), contains strain-specific loci predicted to support acid stress tolerance and epithelial adhesion. Functional annotation indicated the presence of genetic potential for carbohydrate metabolism, stress response, adhesion-related functions, and biosynthesis of secondary metabolites including acids, terpenes and vitamins. No acquired antibiotic resistance determinants or virulence genes were detected. Consistent with genomic predictions, PMK4 showed high survival under simulated gastrointestinal conditions, strong auto-aggregation capacity, moderate hydrophobicity and co-aggregation, and broad antagonistic activity against a range of enteropathogens. The strain also utilised a wide range of substrates, including complex carbohydrates and proteins, suggesting metabolic versatility relevant to microbe-microbe and microbe-host interactions in the gut. Together, these data support L. rhamnosus PMK4 as a promising indigenous probiotic candidate with a favourable safety profile and functional potential.},
}

Humans
Cameroon
*Lacticaseibacillus rhamnosus/genetics/isolation & purification/physiology/classification
*Feces/microbiology
Infant
*Probiotics
Genome, Bacterial
Phenotype
Whole Genome Sequencing
Bacterial Adhesion
Genomics

@article {pmid43015622,
year = {2026},
author = {Zhang, P and Jiang, L and Ge, C and Yang, J and Shi, Z and Liang, X and Fan, Z},
title = {The gut-inflammation-hearing axis in diabetic patients aged 30-55: exploring microbiome-mediated pathways to auditory complications.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015622},
issn = {1471-2180},
support = {XY21BS36//Boshi Foundation of Heze University/ ; ZR2023QC302//Natural Science Foundation of Shandong Province/ ; ZR2021QB188//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; Middle Aged ; Adult ; Male ; Female ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/complications/microbiology ; Biomarkers/blood ; Cross-Sectional Studies ; *Dysbiosis/microbiology ; *Inflammation/microbiology ; RNA, Ribosomal, 16S/genetics ; *Hearing Loss/microbiology/etiology ; Lipopolysaccharide-Binding Protein ; Bacteria/classification/genetics/isolation & purification ; Tumor Necrosis Factor-alpha/blood ; Acute-Phase Proteins ; Interleukin-6/blood ; Carrier Proteins/blood ; },
abstract = {BACKGROUND/OBJECTIVES: Hearing impairment is an underrecognized yet prevalent complication of type 2 diabetes mellitus (T2DM), but the underlying mechanisms remain poorly understood. This study investigated whether gut microbiota dysbiosis contributes to diabetic hearing loss through systemic inflammatory pathways, and evaluated the potential of microbiota-inflammation biomarkers for early risk identification.

METHODS: We conducted a cross-sectional study of 100 T2DM patients aged 30-55 years. Hearing function was assessed using pure-tone audiometry. Gut microbiota composition was analyzed by 16 S rRNA gene sequencing. Plasma inflammatory biomarkers including tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), high-sensitivity C-reactive protein (hs-CRP), and lipopolysaccharide-binding protein (LBP) were measured by ELISA. Mediation analyses with bootstrapping (5,000 resamples) examined whether inflammatory markers mediated the relationship between gut dysbiosis and hearing impairment. Receiver operating characteristic curves evaluated biomarker discriminatory ability.

RESULTS: Hearing impairment was present in 43% of participants. Patients with hearing impairment exhibited significant gut dysbiosis characterized by depletion of anti-inflammatory bacteria (Faecalibacterium: 6.2% vs. 9.8%, P < 0.001; Roseburia; Akkermansia) and enrichment of pro-inflammatory taxa (Escherichia-Shigella: 3.8% vs. 1.4%, P < 0.001; Klebsiella; Desulfovibrio). Inflammatory markers were significantly elevated, particularly LBP (18.6 vs. 12.4 µg/mL, P < 0.001), TNF-α (4.82 vs. 3.21 pg/mL, P < 0.001), and IL-6 (5.67 vs. 3.45 pg/mL, P < 0.001). Mediation analyses revealed that inflammatory pathways, predominantly through LBP-mediated gut barrier dysfunction, accounted for 48.7-56.3% of the total effect of microbiota alterations on hearing impairment (all P < 0.001). An integrated biomarker panel combining microbial taxa (Faecalibacterium, Escherichia-Shigella, Shannon diversity) and LBP achieved excellent discrimination for identifying hearing impairment (AUC = 0.921, 95% CI: 0.869-0.973; sensitivity 88.4%, specificity 87.7%).

CONCLUSIONS: This study establishes a novel gut-inflammation-hearing axis in type 2 diabetes, wherein microbiota dysbiosis characterized by loss of beneficial bacteria and expansion of pathogenic taxa promotes hearing impairment through systemic inflammation mediated by intestinal barrier dysfunction and metabolic endotoxemia. These findings identify gut barrier integrity and associated inflammatory pathways as potential therapeutic targets, and demonstrate that integrated microbiota-inflammation biomarker panels can serve as non-invasive tools for early identification of hearing impairment risk in diabetic patients, enabling targeted preventive interventions.},
}

Humans
Middle Aged
Adult
Male
Female
*Gastrointestinal Microbiome
*Diabetes Mellitus, Type 2/complications/microbiology
Biomarkers/blood
Cross-Sectional Studies
*Dysbiosis/microbiology
*Inflammation/microbiology
RNA, Ribosomal, 16S/genetics
*Hearing Loss/microbiology/etiology
Lipopolysaccharide-Binding Protein
Bacteria/classification/genetics/isolation & purification
Tumor Necrosis Factor-alpha/blood
Acute-Phase Proteins
Interleukin-6/blood
Carrier Proteins/blood

@article {pmid43015632,
year = {2026},
author = {Guo, Y and Zhang, J and Zhang, B and Yang, M and Zhao, J and Chen, G and Shi, G},
title = {Longitudinal gut microbiome dynamics in neurosurgical ICU patients: Enterococcus expansion as a feature of microbial restructuring.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43015632},
issn = {1471-2180},
support = {FYD202607//2026 Incubation Fund (Category D), Beijing Tiantan Hospital/ ; L2602077//Beijing Natural Science Foundation/ ; 82000510//National Natural Science Foundation of China/ ; ZYLX202109//Beijing Hospital Authority "Sailing Plan" Key Medical Specialty Program/ ; },
mesh = {Humans ; *Enterococcus/genetics/isolation & purification/classification ; *Intensive Care Units ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Critical Illness ; },
abstract = {BACKGROUND: Gut microbiota alterations are commonly observed in critical illness, but their temporal dynamics in neurosurgical ICU patients remain insufficiently characterized. This study aimed to describe postoperative microbial trajectories and their clinical context during ICU stay.

METHODS: We conducted a longitudinal study of 39 postoperative neurosurgical ICU patients, with 101 rectal swab samples collected on ICU Days 1, 7, and 14. Microbiota profiles were generated using 16S rRNA sequencing. Temporal shifts and configurations were analyzed using diversity analyses, PERMANOVA, and OTU-level clustering. Clinical features associated with Enterococcus (OTU502) abundance were examined using regression models, and microbiota-clinical relationships were further explored using redundancy and variance partitioning analyses.

RESULTS: Patients were stratified into short-stay (< 14 days) and long-stay (≥ 14 days) groups. Alpha diversity showed a mild, non-significant decline by Day 7 with a slight increase at Day 14 in long-stay patients, while beta diversity demonstrated significant temporal restructuring. Genus-level analyses revealed stay-dependent changes: short-stay patients showed early loss of anaerobic genera and enrichment of Enterococcus by Day 7, whereas long-stay patients exhibited persistent anaerobe depletion and later emergence of Enterococcus. OTU clustering identified two profiles dominated by Enterococcus (OTU502) or Escherichia-Shigella (OTU967). Higher OTU502 abundance at Day 7 was more frequently observed in patients with greater illness severity and lower GCS scores. Prolonged probiotic use showed a non-significant trend toward a lower likelihood of high OTU502 abundance. Measured clinical variables accounted for a limited proportion of observed microbial variance (3-7%).

CONCLUSIONS: Neurosurgical ICU patients displayed time-stratified microbial trajectories. Enterococcus (OTU502) enrichment represents a consistent feature of microbiota restructuring during ICU stay. These findings provide a descriptive framework for understanding microbiome dynamics in neurosurgical ICU patients.

TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR2000031760). Registered on 9 April 2020.},
}

Humans
*Enterococcus/genetics/isolation & purification/classification
*Intensive Care Units
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Female
Male
Middle Aged
Aged
*Bacteria/classification/genetics/isolation & purification
Critical Illness

@article {pmid43015659,
year = {2026},
author = {Chen, Y and Huang, C and Qin, Y and Jian, Y and Li, L and Li, J and Meng, Z and Kang, M},
title = {Microbial dysbiosis and treatment-related gastrointestinal adverse events in locoregionally advanced nasopharyngeal carcinoma: an exploratory study of the oral and gut microbiome.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {},
pmid = {43015659},
issn = {1471-2407},
support = {2020//Guangxi Medical University First Affiliated Hospital Specialised and Innovative Teams Project/ ; 2020//the Second Batch of Guangxi High-Level Mid-Career and Young Academic Backbone Projects/ ; 2022//the Guangxi Medical University High-Level Innovative Team and Xinghu Scholars Programme/ ; 2022//Key Research Project of the CSCO/ ; 2025//the Guangxi Medical University Young Leading Talent Programme/ ; },
mesh = {Humans ; Female ; Male ; *Dysbiosis/microbiology/etiology ; *Nasopharyngeal Carcinoma/therapy/microbiology/pathology ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Nasopharyngeal Neoplasms/therapy/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Diseases/etiology/microbiology ; *Mouth/microbiology ; Aged ; Feces/microbiology ; },
abstract = {BACKGROUND: Gastrointestinal adverse events are frequent during treatment for locoregionally advanced nasopharyngeal carcinoma (LA-NPC) and can impair nutritional status and treatment tolerance. Radiotherapy and chemotherapy may disrupt microbial communities, but whether oral and gut microbiota are associated with treatment-related gastrointestinal adverse events remains unclear.

MATERIALS AND METHODS: Oral swab and stool samples from 80 patients with LA-NPC were analyzed using 16S rRNA gene sequencing. Associations between treatment-related gastrointestinal adverse events and oral microbial composition were evaluated, together with analyses of microbial functions and gut microbial profiles. Oral microbiota features were then used to develop machine learning models for distinguishing patients with gastrointestinal adverse events.

RESULTS: Among 80 patients with LA-NPC, nausea, vomiting, diarrhea, and constipation occurred in 72.5%, 51.3%, 46.3%, and 67.5%, respectively. Oral microbiota analysis showed enrichment of Alloprevotella, Fusobacterium, and Campylobacter in patients with gastrointestinal adverse events or a high symptom burden, whereas Rothia and Streptococcus were enriched in those without events or with a low burden. Predicted oral microbial functions involved propanoate metabolism, lipoic acid metabolism, retinol metabolism, glycan degradation, sphingolipid metabolism, calcium signaling, and lipopolysaccharide biosynthesis. Alterations in specific gut genera, including Helicobacter, Parasutterella, and Anaerotruncus, were also observed.

CONCLUSIONS: This study identified oral and gut microbial features associated with treatment-related gastrointestinal adverse events in patients with LA-NPC. Oral microbial features showed potential value for classifying gastrointestinal adverse event status during treatment.},
}

Humans
Female
Male
*Dysbiosis/microbiology/etiology
*Nasopharyngeal Carcinoma/therapy/microbiology/pathology
Middle Aged
*Gastrointestinal Microbiome/drug effects
*Nasopharyngeal Neoplasms/therapy/microbiology/pathology
Adult
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Diseases/etiology/microbiology
*Mouth/microbiology
Aged
Feces/microbiology

@article {pmid43015841,
year = {2026},
author = {Sun, J and Song, S and Luo, S and Fan, Q and Li, X and Liu, H and Wu, G},
title = {The intratumoral microbiome as an emerging hub in cancer pathogenesis and precision oncology.},
journal = {Molecular cancer},
volume = {25},
number = {1},
pages = {},
pmid = {43015841},
issn = {1476-4598},
mesh = {Humans ; *Microbiota ; *Neoplasms/etiology/microbiology/pathology/metabolism/therapy ; Tumor Microenvironment/immunology ; Animals ; *Precision Medicine/methods ; Biomarkers, Tumor ; },
abstract = {Over the past decade, the number of microbial communities identified within tumors has increased by 400%. Notably, the intratumoral microbiome, which includes bacteria, fungi, viruses, and other microorganisms within tumor tissues, was first discovered more than a century ago. Based on the updated framework of cancer characteristics, we propose that the immune microenvironment is a fundamental and variable microbial feature in cancer. Numerous studies have demonstrated that the intratumoral microbiome constitutes a critical component of the tumor microenvironment. However, due to its low biomass, characterizing its functional mechanisms remains a significant challenge. To summarize current research on the intratumoral microbiome in oncology, we first examine its establishment, homeostasis, and heterogeneity across different cancer types, followed by a comprehensive exploration of its multifaceted roles in tumor initiation and progression. Furthermore, we discuss the critical implications of the intratumoral microbiome in cancer biomarkers, antitumor therapies, and novel microbe-based anticancer strategies. In summary, this review highlights the intratumoral microbiome as an emerging therapeutic target, offering new perspectives for deciphering the complex mechanisms of cancer.},
}

Humans
*Microbiota
*Neoplasms/etiology/microbiology/pathology/metabolism/therapy
Tumor Microenvironment/immunology
Animals
*Precision Medicine/methods
Biomarkers, Tumor

@article {pmid43015880,
year = {2026},
author = {Schrieke, H and Trouche, B and Kerrigan, D and Pondeville, E and Reveillaud, J},
title = {Optimizing bacterial enrichment procedures to improve mosquito midgut microbiome research.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {43015880},
issn = {2524-4671},
support = {MC_UU_00034/8/MRC_/Medical Research Council/United Kingdom ; 948135/ERC_/European Research Council/International ; },
abstract = {Mosquitoes are major vectors of infectious diseases, with their midgut microbiota playing a crucial role in host development, reproduction, and pathogen interactions. However, characterizing midgut microbial communities remains challenging because host DNA often dominates metagenomic libraries, reducing the resolution of bacterial community profiling and hindering the recovery of microbial genomes. To evaluate strategies for bacterial DNA enrichment in this context, we compared three DNA extraction protocols applied to pooled Aedes aegypti midguts: (i) the QIAGEN DNeasy Blood and Tissue kit without filtration (DNeasy NF), (ii) the same kit preceded by a 5 μm filtration step to reduce eukaryotic material (DNeasy F), and (iii) the QIAGEN QIAamp Microbiome kit, which combines differential host cell lysis and enzymatic DNA depletion. Each method was assessed using qPCR-based quantification of bacterial and host DNA, SSU rRNA-based taxonomic profiling of metagenomic reads, and Metagenome-Assembled Genomes (MAGs) reconstruction using advanced binning approaches. Our results show that while the Microbiome kit provided the highest bacterial enrichment and captured a large fraction (> 85%) of the bacterial taxa detected with the other kits, it yielded a higher relative abundance of Gammaproteobacteria. This occurred without a loss of overall diversity, suggesting improved recovery of microbial taxa rather than a compositional bias. The filtration step associated with the DNeasy kit significantly reduced host DNA but also lowered bacterial material, allowing MAG reconstruction, though less efficiently than the Microbiome kit. Despite this, the DNeasy methods allowed recovering a broader range of bacterial phyla with a more even distribution across taxa, while each extraction method also detected a unique set of NTUs. Overall, a combination of DNA extraction methods may be necessary to optimize microbiome analysis in mosquito midguts, facilitating a more comprehensive understanding of microbial diversity and its potential applications in vector control strategies.},
}

@article {pmid43015910,
year = {2026},
author = {Weerasingha, S and Yan, A and Butcher, J and Mack, DR and Stintzi, A},
title = {Relative abundance of a gut-derived Lancefieldella parvula strain is associated with severe inflammation in IBD.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {43015910},
issn = {1757-4749},
support = {OGI-149//Genome Canada and the Ontario Genomics Institute/ ; ECD-144627/CAPMC/CIHR/Canada ; Project 13440//Ontario Ministry of Economic Development and Innovation/ ; },
abstract = {BACKGROUND: Lancefieldella parvula (previously known as Atopobium parvulum) has been associated with inflammatory bowel disease (IBD); however, prior in vivo studies relied on an oral-derived reference strain rather than intestinal clinical isolates, limiting interpretation of its role in gut inflammation. To address this gap, we isolated a clinical strain of L. parvula (designated L. parvula TI19E08) from a mucosal luminal aspirate of an ulcerative colitis (UC) participant. We developed a strain-specific quantitative PCR assay to quantify its abundance across anatomical sites in treatment-naïve pediatric IBD participant (UC and Crohn's disease (CD)) and examined its relationship with site-specific endoscopic inflammation severity.

RESULTS: We demonstrated that the relative abundance of L. parvula TI19E08 increased with increasing local inflammation severity. In UC, both strain-specific and total L. parvula levels were strongly correlated with inflammation severity, particularly in the proximal colon. In CD patients, strain-level associations were most pronounced in the terminal ileum, which is consistent with the disease distribution.

CONCLUSION: This study characterizes an intestinal L. parvula isolate and demonstrates that strain-level expansion correlates with disease severity across IBD subtypes and anatomical regions. These findings identify L. parvula TI19E08 as a candidate mucosal marker of inflammation severity in IBD patients.},
}

@article {pmid43015979,
year = {2026},
author = {Avnet, S and D'Amico, F and Falzetti, L and Di Pompo, G and Pasquarelli, A and Longhi, A and Errani, C and Brigidi, P and Turroni, S and Baldini, N},
title = {Association of Gut Microbiome Dynamics With Systemic Inflammation and Disease-Free Survival in Osteosarcoma Patients.},
journal = {Cancer medicine},
volume = {15},
number = {11},
pages = {},
pmid = {43015979},
issn = {2045-7634},
support = {RF-2019-12368819//Ministero della Salute/ ; },
mesh = {Humans ; *Osteosarcoma/microbiology/mortality/drug therapy/pathology ; Female ; Male ; *Gastrointestinal Microbiome ; *Inflammation/microbiology ; *Bone Neoplasms/microbiology/mortality/drug therapy ; Adolescent ; Child ; Disease-Free Survival ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {Gut microbiota (GM) is increasingly recognised as a key modulator of cancer development, progression, and treatment response. However, clinical studies remain limited, especially in osteosarcoma (OS), the most common bone cancer in children and adolescents. In this study, we analysed GM diversity, composition, and predicted function in a small OS cohort (n = 18) using 16S rRNA gene sequencing of stool samples collected at diagnosis, during chemotherapy, and post-treatment. Microbial profiles were compared to healthy controls. Alpha diversity was assessed via ASVs, Shannon, inverse Simpson, and Faith's index; beta diversity via Bray-Curtis and UniFrac distances. We examined associations between GM profiles and clinical variables (age, gender, BMI, tumour volume, outcome) and systemic inflammation (e.g., C-reactive protein, CRP) using PERMANOVA, LEfSe, and Kaplan-Meier analysis. At diagnosis, OS patients showed reduced diversity and a distinct GM signature-depletion of anti-inflammatory genera (Blautia, Faecalibacterium, Roseburia) and enrichment of potentially pro-tumorigenic taxa (Collinsella, Streptococcus), which correlated with elevated CRP. Baseline GM composition stratified patients by long-term outcome, with specific taxa and predicted pathways linked to event-free survival. Chemotherapy induced transient dysbiosis, notably affecting Lactobacillus and Enterococcus, with partial recovery post-treatment. This is the first study to track GM alterations in OS patients across the disease course, extending current knowledge beyond preclinical models. As one of the few longitudinal microbiota studies in oncology, it highlights GM's potential as a biomarker, shedding light on the mechanisms underlying OS pathogenesis, though findings require validation in larger cohorts.},
}

Humans
*Osteosarcoma/microbiology/mortality/drug therapy/pathology
Female
Male
*Gastrointestinal Microbiome
*Inflammation/microbiology
*Bone Neoplasms/microbiology/mortality/drug therapy
Adolescent
Child
Disease-Free Survival
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid43016293,
year = {2026},
author = {Negi, A and Borah, A and Chen, JY},
title = {Modulation of the teleost gut-microbiome-immunity axis in Nile tilapia Oreochromis niloticus following intestinal delivery of a microencapsulated deep-sea Lactococcus lactis strain.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag279},
pmid = {43016293},
issn = {1365-2672},
abstract = {AIMS: This study investigated the applied biotechnological delivery, viable intestinal recovery, and associated mucosal microbiome and transcriptomic profiles of a deep-sea bacterial isolate, Lactococcus lactis L25_4, within the freshwater landscape of Nile tilapia (Oreochromis niloticus). The objective was to decode how this marine-derived isolate influence host responses along the teleost gut-microbiome-immunity axis to stabilize mucosal environments.

METHODS AND RESULTS: To ensure gastric survival, L. lactis L25_4 was microencapsulated using a double-layer chitosan-alginate (C/A)2 coating. While uncoated bacteria failed to survive transit, the microencapsulated strain achieved robust colonization (106 CFU/g midgut; 107 CFU/g hindgut). Following a 30-day feeding trial, PacBio Full-Length 16S sequencing revealed that probiotic administration structurally overhauled the gut ecosystem, introducing 661 unique taxonomic features and expanding beneficial genera (Lactobacillus, Akkermansia, Bacillus). Host transcriptomic profiling identified 2,411 differentially expressed genes. Major upregulation centered on epithelial barrier reinforcement (Zonadhesin-like, Integrin α2) and cellular energy optimization via an 8.51 log2FC increase in the creatine synthesis enzyme Gatm. Crucially, the probiotic profoundly suppressed systemic inflammatory markers, notably Serum Amyloid P-component (-9.28 log2FC) and IL-17A, alongside downregulating MHC class II pathways.

CONCLUSIONS: Integrative analysis suggests that L. lactis L25_4 facilitates a physiological trade-off, where a reinforced physical mucosal barrier allows the freshwater host to downregulate energetically expensive immune responses in favor of reduced inflammatory gene expression. Encapsulated deep-sea bacterium can trigger cross-ecosystem homeostatic recalibration, providing a robust framework for microbiota-driven modulation along the vertebrate gut-microbiome-immunity axis.},
}

@article {pmid43016307,
year = {2026},
author = {Li, J and Duplouy, A and Sun, L},
title = {Meta2Data: Automated data processing for large scale microbiome data re-analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag828},
pmid = {43016307},
issn = {1367-4811},
abstract = {UNLABELLED: Meta2Data is a modular, largely automated pipeline implemented in Python and Bash for the retrieval, standardization, and processing of public microbiome sequencing data. It retrieves metadata from major public repositories, including INSDC and CNCB, using user-provided keywords or BioProject/BioSample identifiers. Retrieved metadata are standardized using a synonym dictionary and then subjected to manual curation. Based on the curated metadata, Meta2Data downloads the corresponding raw sequencing data and processes them using standardized workflows based on DADA2 or VSEARCH. The pipeline supports both single- and multiple-target-region datasets and produces integrated feature tables, taxonomic assignments, and phylogenetic trees for downstream microbial community analyses.

AVAILABILITY: Meta2Data is freely available at https://github.com/LinyangSun/Meta2Data and archived on Zenodo at https://doi.org/10.5281/zenodo.20670433.

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

@article {pmid43016444,
year = {2026},
author = {Ji, B},
title = {Microalgal-bacterial granular sludge: bridging the gap between laboratory discovery and engineering reality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1967626},
pmid = {43016444},
issn = {1664-302X},
abstract = {Microalgal-bacterial granular sludge (MBGS) has been extensively studied as a promising process for energy-efficient and carbon-neutral wastewater treatment. The self-sustaining synergy of this process has been validated under laboratory conditions, and CO2 supplementation has been shown to push the system toward carbon-negative operation. However, the technology remains largely confined to laboratory benchtops, with most studies conducted under constant conditions using synthetic wastewater. Existing reviews have mainly summarized performance or individual operational factors, but have not translated these findings into a coherent engineering framework for scalable deployment. Based on a comprehensive synthesis of past review articles and experimental studies, this Perspective proposes seven testable and, where possible, quantifiable engineering perspectives: dynamic diel carbon management for net greenhouse gas removal, active microbiome engineering for targeted pollutant degradation, multi-layer stacked photobioreactors with integrated light-guide systems, self-cleaning reactor walls to overcome biofouling, integrated design strategies for simultaneous shear delivery and light utilization in a single reactor, hydrocyclone-based physical selection for long-term stability, and tiered biorefinery with integrated life-cycle assessment. The key advance is not the individual concepts themselves, but their integration into a coordinated, hypothesis-driven framework that shifts the focus from laboratory feasibility to scalable engineering implementation. These perspectives are grounded in established knowledge and offered as testable hypotheses to guide the next generation of research and development toward full-scale deployment.},
}

@article {pmid43016472,
year = {2026},
author = {Amorin de Hegedus, R and Panke-Buisse, K and Deiss, TC and McClure, JC},
title = {Impact of rumen microbiome sample handling and extraction procedures on downstream long-read sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907783},
pmid = {43016472},
issn = {2235-2988},
mesh = {Animals ; *Rumen/microbiology ; Cattle ; *Specimen Handling/methods ; DNA, Bacterial/isolation & purification/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Female ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; },
abstract = {The rumen microbiome is a complex microbial ecosystem central to ruminant nutrition and productivity. Long-read sequencing technologies, such as Oxford Nanopore, have greatly improved resolution of strain-level diversity and enabled assembly of near-complete genomes, but these benefits depend on the integrity and purity of input DNA, which can be affected by sample preservation and extraction methods. This study evaluated multiple DNA extraction protocols to best maximize high-molecular-weight DNA recovery for long-read sequencing and whether flash freezing or freezing and thawing samples biased read length, microbial composition, or the recovery of different taxa. We also used simulated datasets to assess how read length influences taxonomic classification accuracy. Rumen fluid samples of equal volume from four lactating Holstein cows were preserved using two different methods: 1. Pelleting 1 ml of rumen fluid then flash freezing; and 2. bulk freezing 15ml aliquots, thawing, then pelleting 1 ml of rumen fluid. DNA was extracted using four modified Zymo Quick-DNA HMW MagBead protocols (0BB, 3BB, DDZ, PREC) incorporating different lysis and purification strategies, then sequenced on Oxford Nanopore PromethION flow cells. Read length, yield, and microbial composition were analyzed using nonparametric statistics, while synthetic long-read datasets (400-7600 bp) generated with Nano Sim evaluated classification accuracy with Kaiju. The precipitation method produced the highest DNA yields and maintained fragment integrity, whereas bead-based methods yielded less DNA due to high-molecular-weight DNA-selective binding. Preservation of DNA quality was identified in FF over FT samples with longer reads and higher archaeal and Gram-positive abundances. Read lengths were reduced in FT samples for both Gram-positive and Gram-negative taxa, with Gram-negative bacteria showing the greatest loss. Simulations confirmed that longer reads improve taxonomic classification, underscoring the need to optimize upstream protocols for high-resolution rumen microbiome profiling.},
}

Animals
*Rumen/microbiology
Cattle
*Specimen Handling/methods
DNA, Bacterial/isolation & purification/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Female
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics

@article {pmid43016562,
year = {2026},
author = {Morampudi, V},
title = {Editorial: Advancing enteric disease treatments: probiotics and antimicrobial strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2023428},
pmid = {43016562},
issn = {1664-3224},
}

@article {pmid43016569,
year = {2026},
author = {Mei, Y and Shi, L and He, S and Liu, C and Liu, M and Hou, Y},
title = {Reduced classical probiotic-associated butyrate biosynthetic potential predicts early primary resistance to anti-PD-1 therapy in advanced non-small cell lung cancer: a shotgun metagenomic study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1975315},
pmid = {43016569},
issn = {2235-2988},
mesh = {Humans ; *Probiotics ; *Butyrates/metabolism ; Metagenomics ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology ; *Lung Neoplasms/drug therapy/microbiology ; Female ; *Drug Resistance, Neoplasm ; Feces/microbiology ; Microbiota ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Male ; Coenzyme A-Transferases/genetics ; Metagenome ; },
abstract = {BACKGROUND: Early primary resistance to anti-PD-1 therapy is common in advanced non-small cell lung cancer (NSCLC). Existing microbiome biomarkers largely rely on individual species and lack stability across populations.

OBJECTIVE: The aim of this study was to construct the classical probiotic-butyrate axis score (PBAS), perform external validation, and evaluate its value for risk stratification of 90-day early primary resistance and PFS.

METHODS: This study adopted a dual-cohort, patient-level secondary analysis design and reanalyzed pretreatment fecal shotgun metagenomic data from two public cohorts, including 70 and 40 patients in the discovery and external validation cohorts, respectively. An equally weighted PBAS was constructed based on predefined classical probiotic-associated taxa and the butyryl-CoA:acetate CoA-transferase (but) and the butyrate kinase (buk) genes. ANCOM-BC2 was used for differential analysis, Firth logistic regression for association analysis of early primary resistance, 2,000 patient-level bootstrap resampling for internal validation, and Cox proportional hazards models for PFS analysis.

RESULTS: Early primary resistance occurred in 41/70 and 23/40 patients in the two cohorts, respectively. Classical probiotic-associated taxa, the butyrate functional subscore, and PBAS were lower in the resistant group than in the nonresistant group, whereas buk and Akkermansia muciniphila showed no significant differences. After adjustment for age, sex, and BMI, acetyl-CoA pathway potential was also reduced. For each 1-SD increase in PBAS, the OR for early primary resistance was 0.39 and 0.37 after adjustment for clinical variables. The bootstrap-corrected area under the receiver operating characteristic curve (AUC) was 0.733, and the external validation AUC was 0.726 (95% CI: 0.559-0.894). Increased PBAS was associated with a lower risk of progression or death, with HRs of 0.54 and 0.61 in the two cohorts, respectively (both p < 0.001).

CONCLUSION: Combined reductions in pretreatment classical probiotic-associated ecology and butyrate biosynthetic potential indicate a high risk of early primary resistance to anti-PD-1 therapy in advanced NSCLC and support PBAS as an exploratory outcome risk marker for cross-cohort risk stratification among patients receiving anti-PD-1 therapy, without establishing treatment-specific predictive value.},
}

Humans
*Probiotics
*Butyrates/metabolism
Metagenomics
*Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology
*Lung Neoplasms/drug therapy/microbiology
Female
*Drug Resistance, Neoplasm
Feces/microbiology
Microbiota
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Male
Coenzyme A-Transferases/genetics
Metagenome

@article {pmid43016601,
year = {2026},
author = {Zai, K},
title = {The bidirectional interface between oral drug and the gut microbiome: Implications for drug delivery.},
journal = {Pharmaceutical science advances},
volume = {4},
number = {},
pages = {100112},
pmid = {43016601},
issn = {2773-2169},
abstract = {Oral administration remains the preferred route for systemic therapy, yet achieving consistent drug exposure is often hindered by interindividual variability. The gut microbiome is increasingly recognized as a key determinant in this variability, capable of transforming, inactivating, or degrading drugs through microbial enzymatic activity. Conversely, advanced oral delivery systems, comprising polymeric matrices, lipid vesicles, hydrogels, and nanocarriers, can reshape microbial composition and function, either unintentionally or as part of a deliberate formulation strategy. This review examines the bidirectional interactions between oral drug delivery systems and the gut microbiome, emphasizing their implications for drug exposure, therapeutic predictability, and safety. We discuss delivery system-microbe interactions that govern drug stability, transport, and activation, alongside emerging microbiome-responsive formulation designs that leverage microbial cues for site-specific release. Advanced experimental and analytical tools, including gut-on-chip platforms, humanized and gnotobiotic animal models, and integrated pharma-co-microbiomics approaches, are highlighted as enablers of rational formulation development. Finally, we propose a formulation-oriented framework for microbiome-aware oral drug delivery, outlining strategies to protect drugs from microbial degradation, harness microbial metabolism, or reshape the microbiome to support precision and safer therapeutics.},
}

@article {pmid43016668,
year = {2026},
author = {Rodrigues, JT and Batista, ACS and Lima, JPMS and De Magalhães, MTQ},
title = {Evolutionary divergence of uric acid catabolic enzymes: structure-function constraints and genomic innovations across taxa.},
journal = {Biophysical reviews},
volume = {18},
number = {5},
pages = {1189-1211},
pmid = {43016668},
issn = {1867-2450},
abstract = {Uric acid degradation is a model for understanding how gene duplication, loss, and functional divergence drive metabolic evolution. In hominoids and uricotelic animals, uric acid is the terminal purine catabolite, whereas most other taxa further degrade it to allantoin and beyond. Comparative genomics and structural analyses reveal recurrent duplication and repurposing of key enzymes. 5-Hydroxyisourate hydrolase (HIUase) and transthyretin (TTR) share a common ancestral hydrolase, later diverging through neofunctionalization, while independent gene fusions reshaped the pathway, notably the gene fusion of Urah (HIUase) and Urad (2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, or OHCUd) into single-chain allantoin synthases in plants, diatoms, and bacteria. Elastic network modeling this gene fusion shows uncorrelated motions between the catalytic domains, suggesting its advantage stems from fixed stoichiometry and spatial proximity rather than conformational coupling. Further divergence is seen in enzyme families with complementary substrate specificities, and gene clustering in bacteria and yeast reflects regulatory optimization under nitrogen limitation, paralleling the ureide pathway in legumes. In hominoids, pseudogenization of urate oxidase relaxed constraints on downstream enzymes, elevating serum uric acid, an ancestral adaptation now linked to hyperuricemia. Gut microbiome-mediated degradation and links between Urad variants and cancer risk underscore the pathway's continuing relevance. Mammalian Urad orthologs show strong sequence conservation. Molecular modeling of the human ortholog demonstrated a conserved fold, consistent with a predominantly α-helical secondary structure content supported by circular dichroism, whereas kinetic characterization revealed the absence of detectable catalytic activity. Building on these principles, evolution-guided protein engineering achieved partial functional interconversion between transthyretins and HIUases without disrupting the ancestral scaffold, revealing purine catabolism's plasticity as a model for enzyme innovation and the metabolism-disease-protein design interface.},
}

@article {pmid43016752,
year = {2026},
author = {Li, VY and González-Pech, R and Lera-Lozano, D and Román-Reyna, V and Medina, M},
title = {Evaluation of full-length 16S rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes.},
journal = {Access microbiology},
volume = {8},
number = {11},
pages = {},
pmid = {43016752},
issn = {2516-8290},
abstract = {The use of long-read sequencing is becoming increasingly popular in the study of host-associated microbiomes. However, its application has not yet been optimized for characterizing understudied microbiomes, such as those in marine environments. We evaluated the accuracy and consistency of long-read sequencing of full-length 16S rRNA genes for diversity surveys of symbiotic dinoflagellate (family Symbiodiniaceae) microbiomes. When comparing long-read amplicon sequencing of the full-length bacterial 16S rRNA gene with short-read sequencing of the V4 hypervariable gene region using a known microbial community, the former recapitulated the bacterial taxonomic composition more accurately. Long-read sequencing performed using Oxford Nanopore Technologies was also highly consistent between sequencing runs and flow cells. Long-read sequencing technologies enable microbiome surveys using the full-length 16S rRNA gene, achieving higher accuracy and resolution. This work validates long-read sequencing as a robust approach for resolving microbiome composition in understudied marine systems, thereby supporting ecological and evolutionary investigations of host-microbe associations.},
}

@article {pmid43016947,
year = {2026},
author = {Aziz, T and Alahmari, LA and Siddig, NH and Almsaud, MM and Al-Asmari, F and Alqahtani, HA and Alonaizan, R and Mengue Ngadena, YS},
title = {Short-chain fatty acids (SCFAs) mediated gut breast crosstalk in breast cancer: integrative network analysis of molecular signaling, immune infiltration and prognostic biomarkers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1969874},
pmid = {43016947},
issn = {1664-3224},
mesh = {Humans ; *Breast Neoplasms/immunology/metabolism/genetics/mortality ; Female ; *Fatty Acids, Volatile/metabolism ; Prognosis ; Tumor Microenvironment/immunology ; Signal Transduction ; *Biomarkers, Tumor/metabolism ; Protein Interaction Maps ; *Gastrointestinal Microbiome/immunology ; STAT3 Transcription Factor/metabolism/genetics ; Gene Expression Regulation, Neoplastic ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics/metabolism ; Gene Regulatory Networks ; },
abstract = {INTRODUCTION: Breast cancer is a heterogeneous malignancy in which metabolic dysregulation, immune remodelling, and complex host microbiota interactions contribute to disease progression and therapeutic response. Emerging evidence suggests that gut microbiota-derived short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate, may act as important molecular mediators linking the gut microbiome to systemic immune and tumor-associated signalling. However, the molecular networks through which SCFA-mediated signalling may influence breast cancer progression and the tumor immune microenvironment remains poorly characterized. This study aimed to investigate the potential regulatory mechanisms underlying the gut-breast axis by integrating SCFA host interaction networks in breast cancer transcriptomic, prognostic, immune infiltration, and drug gene interaction analyses.

METHODS: The SCFA-host interactome was constructed from the combination of HMDB and PubChem data in a protein-protein interaction network. The identification of hub genes was conducted through topological analysis, followed by validation using TCGA-BRCA RNA-seq data, Kaplan-Meier Survival Analysis, TIMER2.0 immune analysis, and DGIdb repurposing analysis.

RESULTS: The findings indicated that the genes STAT3, HIF1A, and IL6 served as key nodes connecting SCFA signalling and cancer formation. Selected SCFAs, such as propionate, have direct experimental evidence of involvement in the modulation of the JAK2/STAT3 pathway in breast cancer models, while butyrate has been associated with several breast cancer-related signalling and epigenetic mechanisms. Associations were most strongly identified in acetate which was mainly related to metabolic and immune regulatory pathways. This computational analysis did not give a quantitative ranking of the strength of interaction between SCFA and hub genes. In exploratory survival analysis without multiple-testing correction, increased STAT3 and HIF1A expression was associated with unfavourable relapse-free survival. SCFA-associated immune targets showed positive correlations with CD8+ T-cell infiltration.

DISCUSSION: This study identifies the SCFA-host interactome as an essential regulatory network in breast cancer. Uncovering metabolic and signalling chokepoints such as STAT3 leads to the discovery of new biomarkers for prognosis and drug targets. This highlights the possibility of exploiting the gut-breast axis to increase immune cell penetration.},
}

Humans
*Breast Neoplasms/immunology/metabolism/genetics/mortality
Female
*Fatty Acids, Volatile/metabolism
Prognosis
Tumor Microenvironment/immunology
Signal Transduction
*Biomarkers, Tumor/metabolism
Protein Interaction Maps
*Gastrointestinal Microbiome/immunology
STAT3 Transcription Factor/metabolism/genetics
Gene Expression Regulation, Neoplastic
Hypoxia-Inducible Factor 1, alpha Subunit/genetics/metabolism
Gene Regulatory Networks

@article {pmid43016949,
year = {2026},
author = {Matarrese, P and Percoco, G and Patatian, A and Guéré, C and Fitoussi, R and Vié, K and Poulet, V and Ngari, C and Seyer, D},
title = {Assessment of microbiome-UV interactions in a physiological ex vivo human skin model.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1922638},
pmid = {43016949},
issn = {1664-302X},
abstract = {INTRODUCTION: The cutaneous microbiome is increasingly recognized as a modulator of skin physiology and UV responses, yet mechanistic studies in human models remain limited by the lack of model systems that preserve physiologically relevant skin architecture and microbial communities.

METHODS: We used the physiological Perfex ex vivo human skin explant system to assess microbiome-UV interactions. Abdominal skin explants from three donors were inoculated with donor-specific cheek microbiomes or vehicle, and, after 24 h, exposed or not to a single UV irradiation. Assessments were performed 48 h after inoculation. Bacterial survival and transfer were evaluated by culture-based CFU enumeration and 16S rRNA gene sequencing. Cutaneous responses were assessed by RT-qPCR for 29 genes involved in oxidative stress, inflammation, skin hydration, barrier function, and epidermal differentiation. Cyclobutane pyrimidine dimers (CPDs), 8-hydroxy-2'-deoxyguanosine (8-OHdG), oxidized proteins, and NRF2 were quantified by immunohistochemistry.

RESULTS: Perfex explants supported short-term persistence of donor-derived skin microbiota for up to 48 h, although cultivable bacteria decreased by approximately 90% over this period, including upon UV irradiation. 16S profiles confirmed donor-specific microbiome transfer but also revealed residual bacterial DNA in uninoculated controls, limiting interpretation of UV effects on microbial composition. Assessing expression changes in 29 epidermal genes examined, four-GPX1, IVL, LOR, and KRT1-exhibited UV-induced expression patterns that differed according to the presence or absence of the microbiome. By contrast, microbiome inoculation markedly attenuated UV-induced CPDs, 8-OHdG, protein oxidation, and NRF2 induction.

DISCUSSION: Despite substantial limitations in microbial engraftment, viability, and temporal resolution, the Perfex system provides a physiologically relevant ex vivo platform in which a transplanted human skin microbiome could modulate UV-induced oxidative and genotoxic damage. These proof-of-concept data support further refinement of this model for mechanistic microbiome-UV studies.},
}

@article {pmid43016950,
year = {2026},
author = {Arunkumar, P},
title = {Microbiome-guided rhizosphere engineering for sustainable remediation of agricultural soil contaminants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1994433},
pmid = {43016950},
issn = {1664-302X},
abstract = {Agricultural soils increasingly carry mixtures of pesticide residues, heavy metals, petroleum hydrocarbons and microplastics, and conventional phytoremediation is too slow and too contaminant-specific to address them. Rhizosphere engineering, the deliberate manipulation of root-associated microbial communities, is widely proposed as the alternative, but the literature reports laboratory, pot and field results in a single register, so a reader cannot easily tell which approaches are deployable. This mini-review stratifies that evidence rather than surveying it. Every approach examined is assigned to one of three tiers: field-validated, emerging at pot or microcosm scale, or conceptual. Only two domains prove to be field-validated, namely metal immobilization and phytoextraction through bioaugmentation and bulk amendment, and hydrocarbon rhizoremediation by defined consortia; both rest on cultured isolates rather than engineered organisms. Microplastic rhizoremediation has not been demonstrated in soil, and we separate interception, adsorption, weathering, transformation and mineralization to show why reported removal is usually not degradation. Synthetic biology, CRISPR-based community editing and computational design remain conceptual, and we set out the horizontal gene transfer, containment, non-target and regulatory obstacles that stand between them and field use. We identify the measurements that would move an approach from one tier to the next, and argue that the principal deficit in this field is not technical capability but field-scale evidence reported to a common standard.},
}

@article {pmid43016980,
year = {2026},
author = {Khan, A and Tareen, A and Farid, AAM and Amin, A and Khan, HN and Hadi, DK and Khan, SR and Raza, A},
title = {The microbiome-metabolome axis in colorectal cancer therapy resistance: mechanisms, mediators, and therapeutic opportunities.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1985675},
pmid = {43016980},
issn = {2234-943X},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, with therapeutic resistance representing a significant barrier to improved patient outcomes. Although tumor-intrinsic genetic alterations are important determinants of treatment resistance, emerging evidence suggests that the gut microbiome and its metabolites may also influence responses to chemotherapy, targeted therapy, and immunotherapy. The microbiome and metabolome function as an interconnected axis that can influence host immunity, microbial drug metabolism, epithelial homeostasis, and tumor-associated signaling pathways, thereby contributing to variation in therapeutic response. Despite advances in microbiome research, the mechanisms by which the microbiome-metabolome axis promotes therapy resistance are not fully elucidated, and clinical translation is limited by the absence of standardized biomarkers and validated therapeutic strategies. This review synthesizes current evidence on the molecular mechanisms through which the microbiome-metabolome axis contributes to CRC therapy resistance, with emphasis on microbial dysbiosis, bacterial metabolites, and host-microbial interactions in modulating treatment efficacy. Emerging microbiome-directed therapeutic approaches, including fecal microbiota transplantation, defined microbial consortia, dietary interventions, microbial metabolites, and engineered microbial therapies, are examined, along with the methodological and translational challenges that must be addressed before their integration into routine clinical practice.},
}

@article {pmid43016998,
year = {2026},
author = {Saeed, AF and Ashraf, MN and Iqbal, MZ},
title = {Tumor-associated macrophage reprogramming in cancer: recent advances in resistance mechanisms and therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1920004},
pmid = {43016998},
issn = {1664-3224},
mesh = {Humans ; *Tumor-Associated Macrophages/immunology/metabolism ; *Neoplasms/immunology/therapy/pathology/metabolism ; Animals ; Tumor Microenvironment/immunology ; *Cellular Reprogramming/immunology ; *Drug Resistance, Neoplasm ; Signal Transduction ; Efferocytosis ; },
abstract = {Tumor-associated macrophages (TAMs) are abundant, heterogeneous, and spatially organized immune cells that regulate cancer progression, immune evasion, metastasis, and therapeutic resistance. Single-cell and spatial technologies have revealed diverse TAM states shaped by ontogeny, tumor type, disease stage, cytokines, hypoxia, metabolism, epigenetic remodeling, extracellular matrix architecture, stromal interactions, extracellular vesicles, microbiome-derived signals, and therapy-induced damage. Bidirectional cancer-TAM crosstalk evolves from tumor initiation through progression and recurrence, generating tumor-specific resistance programs that suppress lymphocytes, impair antigen presentation and phagocytosis, promote angiogenesis and metabolic restriction, remodel stroma, mediate tolerogenic efferocytosis, and sustain stem-cell, metastatic, dormancy, and regenerative niches. Therapeutic strategies include blocking macrophage recruitment or survival, activating CD40/TLR/STING signaling, targeting PI3Kγ and STAT pathways, restoring phagocytosis, modulating efferocytosis, and applying metabolic, epigenetic, stromal, vascular, nanoparticle, RNA-based, microbiome-directed, and engineered-macrophage approaches. Randomized trials have established the efficacy of CSF1R inhibition in selected CSF1-driven, macrophage-dependent tumors, whereas most other TAM- or myeloid-directed strategies in conventional solid tumors have demonstrated only preliminary clinical activity or pharmacodynamic modulation without consistent durable benefit. Off-target toxicity, spatial heterogeneity, dynamic plasticity, preclinical-clinical discordance, and combination-treatment optimization remain major barriers. Biomarker-guided patient selection, longitudinal monitoring, tumor-specific targeting, and rationally sequenced combinations will be essential for converting tumor-supportive TAMs into durable antitumor effectors.},
}

Humans
*Tumor-Associated Macrophages/immunology/metabolism
*Neoplasms/immunology/therapy/pathology/metabolism
Animals
Tumor Microenvironment/immunology
*Cellular Reprogramming/immunology
*Drug Resistance, Neoplasm
Signal Transduction
Efferocytosis

@article {pmid43017044,
year = {2026},
author = {Roselli, GE and Smart, KA and Crow, M and Powell, CD},
title = {The microbiome of draught no- and low-alcohol beer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1966818},
pmid = {43017044},
issn = {1664-302X},
abstract = {The microbiological ecosystem of commercially available draught dispensed no- and low-alcohol beers was evaluated, with a focus on identifying predominant microorganisms with spoilage potential and characterizing variation in community structure. More than 50 samples, representing 20 no- and low- alcohol beers (7 different beer styles: lager, India pale ale, pale ale, wheat, radler, pilsner and amber ale; and 17 brands) were collected for analysis across 12 different public houses (accounts) in Nottingham, UK. Bacterial and fungal identification was achieved via third generation sequencing technologies, using amplicon-based nanopore sequencing (Oxford Nanopore Technologies). Analysis of samples indicated that species of Acetobacter, Brettanomyces and Saccharomyces were core microbiome members. The account from which a beer was sampled was shown to harbor distinct microbial communities and was the dominant factor in determining microbial community structure, explaining 72.6% of variation. This is the first study to apply third-generation sequencing technology for the analysis of draught no- and low-alcohol beers. The findings underscore the vulnerability of draught products to microbial spoilage, and highlight the importance of implementing strict hygiene control focused on draught lines, taps, keg couplers and nozzles, especially when dispensing microbiologically sensitive no- and low-alcohol beverages.},
}

@article {pmid43017136,
year = {2026},
author = {Piroozmand, F and Kaushik, R and Kawashima, H and Yamaguchi, T and Mizuguchi, K and Mohammadipanah, F and Re, S},
title = {Structure-based binding pocket conservation analysis identifies 9-OH urolithin dehydroxylase candidates across phylogenetically diverse bacteria.},
journal = {Biochemistry and biophysics reports},
volume = {48},
number = {},
pages = {102871},
pmid = {43017136},
issn = {2405-5808},
abstract = {Urolithins are polyphenolic compounds produced by gut microbiota from dietary ellagitannins and ellagic acid, with urolithin A being the most bioactive and associated with a range of pharmaceutical activities like anti-aging and anti-inflammatory effects. Despite these benefits, the number of known urolithin A-producing bacteria and their corresponding enzymes is very limited. In this study, we combined conventional sequence-based homology search with structural modeling to identify novel bacteria potentially harboring 9-OH urolithin dehydroxylases, primarily characterized in the Enterocloster genus, that catalyze a key dehydroxylation step essential for urolithin A production. Using three Enterocloster references, a sequence database search coupled with subunit co-occurrence screening was performed. AlphaFold 3 was then employed to model the three-dimensional structures of the candidate multi-subunit complexes. Based on these models, comparative analysis was conducted to screen for candidate enzymes that share closely conserved three-dimensional structural characteristics and conserved core residue architectures within their active-site pockets. The resulting non-Enterocloster candidates, including Aromatoleum sp. and Dehalobacter restrictus, exhibited high predicted functional similarity to the reference enzymes based on conserved binding pocket architectures. This study demonstrates that binding pocket structural signatures help the identification of novel potential urolithin dehydroxylases and previously unrecognized urolithin A-producing bacteria.},
}

@article {pmid43017153,
year = {2026},
author = {Feng, Y and Sha, Y and Xu, L and Tian, J and Gao, Y and Zhou, R and Liu, G},
title = {Integrated gut microbiome and fecal metabolome profiling identifies taurine-associated microbial dysbiosis across the Alzheimer's disease clinical spectrum.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1981076},
pmid = {43017153},
issn = {1663-4365},
abstract = {BACKGROUND: Gut microbiome alterations have been associated with Alzheimer's disease (AD), but how microbial composition, fecal metabolites, and cognitive function relate across the cognitive impairment spectrum-from subjective cognitive decline (SCD) through mild cognitive impairment (MCI) to AD-remains unclear. We integrated microbiome and metabolome profiles across this clinical spectrum.

METHODS: Fecal samples from 84 participants [10 healthy controls (HC), 22 SCD, 23 MCI, 29 AD] underwent 16S rRNA V3-V4 sequencing and untargeted LC-MS metabolomics. Profiles were integrated via Procrustes analysis, sparse canonical correlation, MIMOSA2 community-metabolism modeling, and mediation analysis. Differential abundance was assessed by Kruskal-Wallis, ANCOM-BC2, and LinDA.

RESULTS: Microbial composition differed across groups (ANOSIM R = 0.111, p = 0.001; Adonis R [2] = 0.070, p = 0.002). Cross-method validation confirmed 8 differentially abundant genera in AD vs. HC with 100% directional concordance between ANCOM-BC2 and LinDA, including depletion of butyrate-producing Lachnospiraceae (Blautia, Dorea, Fusicatenibacter) and enrichment of opportunistic pathobionts (Klebsiella, Escherichia-Shigella). Taurine showed the highest MIMOSA2 community-prediction R [2] (0.129; n = 62) and was positively associated with MMSE scores (r = 0.45, BH-FDR Q = 0.0005). A multi-omic random forest model (5 genera + 5 metabolites + age + sex) discriminated AD-clinical spectrum participants from HC with AUC = 0.86 (95% CI 0.82-0.90), although pairwise differences from the age + sex baseline (AUC = 0.75) did not reach statistical significance. Statistical mediation analysis was consistent with a Blautia → taurine → MMSE statistical mediation [ACME = 0.21, p = 0.008; 54% proportion mediated, bootstrap 95% CI (9%, 58%)].

CONCLUSION: Integrated multi-omic profiling reveals coordinated microbiome-metabolome dysregulation across the AD clinical spectrum, with taurine as a candidate microbial-metabolic node linking gut dysbiosis to cognitive performance. Microbial and metabolic alterations are detectable at the SCD stage, before objective cognitive impairment. These findings warrant validation in larger, age-matched cohorts and higher-resolution metagenomic studies.},
}

@article {pmid43017163,
year = {2026},
author = {Liu, M and Yan, L and Lai, J and Xu, X and Cheng, S},
title = {Effects of different concentrations of exogenous methyl jasmonate on tuber metabolism and rhizosphere bacterial community dynamics in Polygonatum cyrtonema Hua.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1950448},
pmid = {43017163},
issn = {1664-462X},
abstract = {Polygonatum cyrtonema Hua is a traditional medicinal and edible plant valued for its tubers, which are rich in bioactive components such as polysaccharides, flavonoids, and saponins. The phytohormone methyl jasmonate (MeJA) regulates plant secondary metabolism and stress responses, promoting the accumulation of medicinal compounds in P. cyrtonema. However, the temporal dynamics of the rhizosphere microbiome and its association with the tuber metabolism under different MeJA concentrations remain poorly understood. In this study, three-year-old P. cyrtonema plants were treated with rhizosphere sprays of 200 μmol L[-1] and 400 μmol L[-1] MeJA. Plants were sampled at 7, 14, 21, and 28 days post-treatment to evaluate tuber physiology and metabolite profiles, and metagenomic sequencing was used to characterize the structure and function of the rhizosphere bacterial community. Application of 200 μmol L[-1] MeJA significantly enhanced tuber peroxidase (POD) activity, which peaked at 2.29 times that of the control on day 14 (P < 0.05), and increased total flavonoid and saponin contents by 22.58% and 13.85%, respectively (P < 0.05). In contrast, 400 μmol L[-1] MeJA mainly inhibited antioxidant enzyme activities and delayed the induction of secondary metabolism. Metagenomic analysis revealed that the two MeJA concentrations shared the same dominant bacterial phyla but showed concentration-dependent differences in relative abundance dynamics, alpha diversity trajectories, and temporal patterns of community structure. The 200 μmol L[-1] MeJA group exhibited a directional temporal shift (PERMANOVA R[2] = 0.79, P = 0.003) and continuously rising alpha diversity, whereas the 400 μmol L[-1] treatment showed nonspecific stress fluctuations, with reduced alpha diversity, a weaker temporal gradient in community structure, and increased community homogenization. At the functional level, the 200 μmol L[-1] MeJA group had higher relative abundances of microbial genes associated with nitrogen, carbon, and secondary metabolic pathways. In contrast, the 400 μmol L[-1] MeJA group showed disrupted coordination among functional genes and persistently higher abundances of genes involved in antioxidant pathways. Correlation analysis identified associations between specific phyla and host traits: Nitrospirota was positively correlated with POD activity (r = 0.48, P < 0.05); Methylomirabilota was positively correlated with total flavonoid and saponin contents (r ≥ 0.41, P < 0.05); and Verrucomicrobiota was negatively correlated with these components (r < -0.55, P < 0.01). These findings suggest that 200 μmol L[-1] MeJA promotes the accumulation of bioactive metabolites in P. cyrtonema through two proposed ways: the direct activation of host metabolism and the indirect association with shifts in potentially beneficial rhizosphere microbial taxa. This study provides a practical foundation for selective MeJA concentrations in medicinal plant cultivation.},
}

@article {pmid43017210,
year = {2026},
author = {Li, R and Tang, J and Zhou, M and Yang, B and Zhang, X and Jing, F},
title = {Bidirectional Microbiota-Gut-Brain Communication in Anorexia Nervosa: Mechanistic Insights and Therapeutic Perspectives.},
journal = {Neuropsychiatric disease and treatment},
volume = {22},
number = {},
pages = {643705},
pmid = {43017210},
issn = {1176-6328},
abstract = {The gut-brain axis (GBA), particularly communication between the gut microbiota (GM) and the brain, has become a major focus in neuropsychiatric research because of its role in appetite regulation, energy metabolism, immune function, and behavior. Anorexia nervosa (AN) is a severe eating disorder with high morbidity and mortality, but the contribution of GBA dysfunction to its pathogenesis remains incompletely defined. This review synthesizes evidence linking GM dysbiosis with AN and organizes the current literature around neural, endocrine, immune, and metabolic pathways. It also summarizes altered brain regions and circuits implicated in AN and discusses how peripheral microbial changes may interact with central regulatory systems. Current evidence supports a multidirectional model in which GM alterations, intestinal barrier function, vagal signaling, hypothalamic-pituitary-adrenal (HPA) axis activity, immune activation, microbial metabolites, and neurocircuit dysfunction may reinforce disordered appetite and weight regulation. Microbiota-targeted strategies, including probiotics, prebiotics, fermented foods, dietary modulation, and lifestyle interventions, may offer adjunctive therapeutic potential, but clinical evidence remains preliminary. Future studies should use longitudinal multi-omics designs, mechanistic animal models, and rigorously controlled clinical trials to determine whether microbiome changes are drivers, consequences, or modifiers of AN.},
}

@article {pmid43017261,
year = {2026},
author = {Kim, DDH and Pagano, FS and Costa, SK and Germann, DA and Belenky, P and Tang, JX},
title = {A cyclic swarming assay produces genetically and phenotypically distinctive variants of Enterobacter sp. SM3.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1968333},
pmid = {43017261},
issn = {1664-302X},
abstract = {INTRODUCTION: Swarming motility, the collective migration of bacteria across semi-solid surfaces, is often associated with cell elongation and increased flagella number or strength. Enterobacter sp. SM3 is a strain originally isolated from murine gut and previously shown to mitigate colitis in mice.

METHODS: To investigate phenotypic and genomic correlates of enhanced surface motility, we derived hyper-swarming variants of SM3 through serial passage from a single clonal isolate, generating five independent lineages collectively termed "Swarmium."

RESULTS: Optical microscopy revealed that Swarmium populations contained cells that were two to three times longer than the parental strain. Motility analysis showed similar swimming speed and tumble duration, but longer run times and reduced tumble angles. Whole-genome sequencing (mean coverage 634×; range 571-845×) identified population-level sequence variants affecting loci annotated for functions including flagellar regulation (rcsB), cell division (ftsL), translation machinery (ribosomal RNA operons and EF-Tu), and Type VI secretion-associated loci (including PAAR-adjacent regions and DUF6531-containing proteins).

DISCUSSION: These findings identify candidate genes associated with the hyper-swarming phenotype, although their functional significance remains unclear. This study identifies genetic changes in populations selected based on swarm expansion rate and provides useful leads for future functional and mechanistic investigations of bacterial swarm motility.},
}

@article {pmid43017398,
year = {2026},
author = {Yang, J and Cui, S and Li, W and Liu, J},
title = {Host immunometabolic reprogramming in paediatric refractory mycoplasma pneumoniae pneumonia: cellular circuits, multi-omics signatures, and translational opportunities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1954451},
pmid = {43017398},
issn = {2235-2988},
mesh = {Humans ; *Mycoplasma pneumoniae/immunology ; Multiomics ; *Pneumonia, Mycoplasma/immunology/metabolism/microbiology ; Metabolic Reprogramming ; Child ; *Host-Pathogen Interactions/immunology ; Epithelial Cells/immunology/microbiology ; Metabolomics ; Macrophages/immunology ; Neutrophils/immunology ; },
abstract = {Paediatric refractory Mycoplasma pneumoniae pneumonia (RMPP) is a heterogeneous syndrome in which persistent microbial stimulation, dysregulated host immunity and evolving airway injury may coexist despite macrolide treatment. This review integrates clinical, experimental and multi-omics evidence to examine RMPP through an immunometabolic framework. Mycoplasma pneumoniae reprograms airway epithelial cells, macrophages and neutrophils by altering glycolysis, mitochondrial and redox signalling, autophagy and lipid and amino-acid metabolism. These responses can support early antimicrobial defence yet become maladaptive when inflammatory output is uncoupled from bacterial clearance. Epithelial ATP-dependent signalling, macrophage inflammasome activation, neutrophil aconitate decarboxylase 1 (ACOD1; historically termed immune-responsive gene 1 [IRG1])-itaconate activity and extracellular trap accumulation illustrate this context-dependent transition. Adaptive immune remodelling, compartment-specific Th17-regulatory T-cell imbalance and incomplete mucosal antibody protection may further sustain disease. Emerging metabolomic, lipidomic, microbiome and single-cell studies support biological heterogeneity but remain predominantly cross-sectional and cannot distinguish causal drivers from consequences of severe disease or treatment. Current mechanistic evidence is strongest for epithelial glycolysis and the neutrophil ACOD1-itaconate axis in experimental M. pneumoniae systems, whereas direct cell-resolved functional validation in paediatric RMPP remains limited, and ferroptosis and several proposed therapeutic targets remain provisional. We therefore present immunometabolic states as a hypothesis-generating framework rather than as validated endotypes. Future studies should determine whether dynamic combinations of pathogen burden, cell-specific metabolic function, inflammatory activity and anatomical injury reproducibly identify biological states that precede progression and predict differential treatment response. Longitudinal, cell-resolved studies integrating metabolic flux, pathogen trajectories, treatment exposure and anatomical evolution are required before these candidate states can support mechanism-informed clinical stratification.},
}

Humans
*Mycoplasma pneumoniae/immunology
Multiomics
*Pneumonia, Mycoplasma/immunology/metabolism/microbiology
Metabolic Reprogramming
Child
*Host-Pathogen Interactions/immunology
Epithelial Cells/immunology/microbiology
Metabolomics
Macrophages/immunology
Neutrophils/immunology

@article {pmid43017476,
year = {2026},
author = {Swaney, MH and Steidl, OR and Tackett, A and Fye, S and Lee, KE and Ong, IM and Bendixsen, C and Spicer, G and DeLine, J and Gern, JE and Lucey, J and Seroogy, CM and Kalan, LR and Singh, AM},
title = {Farm exposure is associated with human milk immune profile and microbiota.},
journal = {iScience},
volume = {29},
number = {11},
pages = {118038},
pmid = {43017476},
issn = {2589-0042},
abstract = {Prenatal and early-life farm exposure and breastfeeding are associated with protection from allergic diseases. We hypothesize that farm exposure influences the human milk microbiota and immune proteins. The immune protein profiles and microbial communities of 152 human milk samples were compared among three maternal farm exposure groups (traditional agrarian, farm, and non-farm) in rural Wisconsin to identify signatures associated with farm status and atopic disease. We found significant differences between farm groups for 23 immune proteins (p adj<0.05), microbial diversity (p = 2.2E-05), and microbial richness (p = 8.0e-06). Traditional agrarian human milk had the highest immune protein levels and microbial diversity and richness, followed by farm and non-farm human milk. Furthermore, Gram-positive bacterial species correlated with IL-23 mediated signaling events (p adj<1.0E-05). These data suggest that increased farm exposures promote human milk that is more microbially diverse and rich in immune-associated proteins, ultimately influencing immune development in the infant.},
}

@article {pmid43017556,
year = {2026},
author = {Huang, X and Zhang, X and Zhu, Q},
title = {Microbiome-targeted strategies for Alzheimer's disease: multi-omics signatures, mechanistic links, and intervention evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828118},
pmid = {43017556},
issn = {1664-302X},
abstract = {Alzheimer's disease (AD) is increasingly studied in relation to gut microbial mechanisms because microbial metabolism, mucosal barrier function, and peripheral immune activation may influence neuroinflammation and host metabolic stress. This review evaluates microbiome-linked evidence in AD with emphasis on studies that combine metagenomics, metabolomics, inflammatory markers, neuroimaging, cerebrospinal fluid or blood biomarkers, and cognitive phenotyping. Current data support several recurring but not yet causal axes, including bile acid transformation, short-chain fatty acid (SCFA) production, trimethylamine N-oxide (TMAO), bacterial product-related inflammatory signaling, and barrier dysfunction. We also review microbiome-targeted interventions, including diet and prebiotics, strain-specified probiotics and synbiotics, oligosaccharide-based agents, gut-restricted antimicrobials, and fecal microbiota transplantation (FMT). The strength of evidence differs substantially across these strategies: sodium oligomannate has been tested in a phase 3 trial, whereas many probiotic, antimicrobial, and FMT approaches remain early clinical, preclinical, or mechanism-generating. Future trials should define a priori microbial, metabolite, immune, and brain biomarker endpoints; control diet, medication, and comorbidity confounding; and validate candidate signatures across independent cohorts before using microbiome profiles for screening or treatment selection.},
}

@article {pmid43017565,
year = {2026},
author = {Fiori, L and Lin, Y and Gu, S and Sánchez-Contreras, GJ and Walker, K and Orbach, DN},
title = {Water chlorination and environmental factors are associated with dolphin skin microbiome diversity and composition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934395},
pmid = {43017565},
issn = {1664-302X},
abstract = {Dolphin skin microbiome is constantly exposed to a microorganism-rich medium and represents the first line of defense from environmental stressors and potential pathogens. While some bacteria cause skin diseases and ulcerating wounds, high water temperature, salinity, and pH seem to lower dolphin wound rates and promote accelerated scar healing. Despite its importance in host health, interactions of dolphin skin microbiome with physical and chemical characteristics of habitats remain poorly understood. Using 16S rRNA metabarcoding, we characterized and compared the skin bacteria communities of 87 common bottlenose dolphins (Tursiops truncatus) and 4 rough-toothed dolphins (Steno bredanensis) living in chlorinated tanks, enclosed lagoons, or open bays. Dolphins living in enclosed lagoons and open bays had skin microbiomes dominated by Enhydrobacter, a bacteria genus found on cetacean skin that occurred at low relative abundance in dolphins in chlorinated tanks. The skin microbiome of dolphins in chlorinated tanks was the most diverse and showed a significant increase of Staphylococcus relative abundance and prevalence when compared to enclosed lagoons and open bay specimens. Among dolphins sampled in open bays across seasons, summer conditions (higher temperature and pH) were associated with up to 10-fold lower Mycobacterium relative abundance, as well as a significant decrease of Streptococcus prevalence, genera associated with slow healing of cutaneous wounds in dolphins. Our results reveal novel insights into the association of physical/chemical environmental factors with dolphin skin microbiome composition. We highlight how the relative abundance and prevalence of potentially opportunistic bacteria on dolphins may vary across human-managed and wild habitats, providing crucial information for the improvement of dolphin husbandry practices and conservation.},
}

@article {pmid43017629,
year = {2026},
author = {Gatarayiha, A and Ubuzima, P and Nshimiyimana, E and Uwayezu, D and Mutesa, L},
title = {Oral health, dysbiotic oral microbiome, and hypertension in Sub-Saharan Africa: a scoping review of current evidence.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {11},
pages = {7421-7431},
pmid = {43017629},
issn = {2049-0801},
abstract = {BACKGROUND: Hypertension (HTN) is a significant public health concern globally, with Sub-Saharan Africa (SSA) bearing a considerable burden. Dysbiosis of the oral microbiome may play a role in the pathogenesis of HTN, with a scarcity of evidence in SSA. The aim of this review was to explore the existing literature on the influence of oral health and dysbiotic oral microbiomes on the development of HTN in SSA countries.

METHODS: A comprehensive search across electronic databases, including PubMed, Google Scholar, Scopus, ScienceDirect, and Web of Science, was conducted from 2000 up to December 2025. Studies involving SSA populations and addressing the role of the oral microbiome in HTN were included.

RESULTS: The review identified 12 studies investigating oral microbiota dysbiosis and its association with HTN in six SSA countries (South Africa, Nigeria, Tanzania, Senegal, Ghana, and Cameroon). Of these, 10 studies assessed periodontal diseases using clinical indices as a proxy for dysbiosis, 1 study assessed dental caries, while only a single study performed direct microbial analysis (using 16S rRNA gene sequencing). Eight studies reported quantitative effect estimates: odds ratios for the association between periodontal disease or gingivitis and HTN ranged from 1.5 to 4.30 (all P < 0.05), while one study reported an association between dental caries and HTN (odds ratio, 0.72-0.73). The reported prevalence of HTN ranged between 19.7 and 91.8%.

CONCLUSION: This scoping review finds that most available evidence from SSA supports an association between periodontal disease and HTN. However, direct evidence regarding the oral microbiome itself remains very limited, with only one study performing species-level microbial analysis.},
}

@article {pmid43017741,
year = {2026},
author = {Moldakozhayev, A and Eames, AW and Mitchell, W and Tskhay, A and de Magalhães, CG and Alba-Linares, JJ and Ying, K and Zhang, B and Zhang, S and Iqbal, S and Yucel, AD and Tyshkovskiy, A and Van Raamsdonk, JM and Gladyshev, VN},
title = {Ageing begins early: developmental origins of ageing trajectories.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1963},
pages = {},
pmid = {43017741},
issn = {1471-2970},
support = {//National Institute on Aging (NIA)/ ; //Longevity Impetus Grant from Norn Group/ ; },
mesh = {*Aging/physiology ; Animals ; *Longevity ; Reproduction ; Humans ; Energy Metabolism ; },
abstract = {Ageing has traditionally been viewed as a process of late-life organismal deterioration, with interventions aimed at slowing ageing being administered after the ageing process has already begun. However, recent advances in quantifying ageing indicate that the process of molecular ageing starts as early as the end of gastrulation. Further, growing evidence suggests that the foundations of how different systems of an organism age are established during prenatal and postnatal development. Herein, we review the impact of early-life environmental conditions on disease susceptibility, adaptation, energy metabolism, microbiome and neurodevelopmental processes to ascertain how changes early in life can affect ageing-related features late in life. We also link growth, reproductive capacity and ageing by providing examples when the balance between longevity and reproduction is shifted towards a longer life through the growth axis at a cost of fecundity across species. We encourage researchers to investigate interventions aimed at mitigating ageing during the developmental period of life, with the important note that such interventions must be assessed with extra caution, given that many life-extending strategies may attenuate growth and reproduction, which may be detrimental for the organism during development. This article is part of the theme issue 'Developmental circuits in ageing'.},
}

*Aging/physiology
Animals
*Longevity
Reproduction
Humans
Energy Metabolism

@article {pmid43017757,
year = {2026},
author = {Liu, X and Wang, J and Li, J and Hu, Y and Hu, C and Tan, Q and Sun, X and Wu, S},
title = {Targeted rewiring of the rhizosphere metabolite-microbe axis restores phosphorus acquisition in inefficient citrus rootstock.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71743},
pmid = {43017757},
issn = {1469-8137},
support = {CARS-24//the Modern Citrus Industry Technology System of China/ ; 2024YFD2300801//the Key Technologies Research and Development Program/ ; },
abstract = {Low phosphorus (P) availability limits citrus production, while genotypic determinants governing rhizosphere P mobilization remain elusive. Here, we investigated P-acquisition strategies in citrus rootstocks. We performed a systematic screening of citrus rootstocks under P-deficient conditions and identified two contrasting genotypes: P-efficient Citrus tangerina and P-inefficient Citrus junos. Comparative metabolomics, microbiome profiling, targeted strain isolation, and inoculation assays were combined to unravel metabolic and microbial drivers governing P mobilization. The superior P acquisition of C. tangerina stemmed from a unique root-exudate profile enriched in 2-hydroxyflavanone, scopoletin, raffinose, and gallic acid. These metabolites selectively enriched Methylobacterium sp. strain HA110, a robust P-solubilizing bacterium. Exogenous exudate application enhanced C. junos P acquisition, yet this beneficial effect was abolished under soil sterilization, demonstrating an essential role of microbiota. Combined supplementation of the metabolites and strain HA110 enhanced rhizosphere P activation, which in turn strengthened the P-acquisition capacity of C. junos and consequently stimulated its growth. Collectively, these findings uncover a novel metabolite-microbe axis: P-efficient rootstocks reshape their rhizosphere microbiome through specific exudates. This axis is amenable to rational reconfiguration to restore P acquisition in P-inefficient genotypes, laying a theoretical basis for exudate-derived biofertilizers to boost P-use efficiency in sustainable citriculture.},
}

@article {pmid43017913,
year = {2026},
author = {Toh, TS and Ding, HX and Khairul Anuar, AN and Zulhaimi, NS and Hor, JW and Pang, YC and Kong, IX and Zulkefli, J and Tay, YW and Lit, LC and Lim, SY and Tan, AH},
title = {Plasma LBP and sCD14 levels in Parkinson's disease with Asian LRRK2 risk variants: Associations with systemic inflammation and clinical severity.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261499246},
doi = {10.1177/1877718X261499246},
pmid = {43017913},
issn = {1877-718X},
abstract = {LRRK2 is implicated in the Parkinson's disease (PD) microbiome-gut-brain axis. We compared plasma lipopolysaccharide-binding protein (LBP) and soluble CD14 (sCD14), markers of gut permeability and endotoxin exposure, in PD patients with/without LRRK2 p.G2385R and/or p.R1628P and controls, and examined their associations with systemic inflammation and clinical severity. Neither marker differed between groups. Among PD patients, LBP correlated with higher IL-6, TNF-α, and worse motor function, while sCD14 correlated with higher IL-6, CCL5, and worse constipation, with no LRRK2 risk variant-specific associations. Further prospective longitudinal studies are warranted to determine the clinical significance of these associations.},
}

@article {pmid43005491,
year = {2026},
author = {Fijabi, O and Morenikeji, OB and Ivey, SL and Loest, C and Idowu, M and Ashley, R and Ogunade, IM and Taiwo, G},
title = {Feed additives as systems-level modulators of the ruminant host-microbiome interaction: a multi-omics perspective on efficiency, resistance, and reproduction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1995937},
pmid = {43005491},
issn = {1664-302X},
abstract = {Ruminant livestock face converging pressures from climatic variation, antimicrobial agents, and the imperative for sustainable intensification. However, the molecular imprints through which nutritional interventions modulate host-microbiome interactions across physiological contexts remain fragmented across disciplinary themes. Here, we synthesize evidence from metagenomics, metatranscriptomics, metabolomics, and host transcriptomics to propose that feed additives operate as systems-level modulators of a functionally integrated rumen-liver-immune-reproductive axis, rather than acting on isolated metabolic pathways. Prevotella, Butyrivibrio, Ruminococcus, and Fibrobacter recurrently emerged across studies to be associated with feed efficiency, immune modulation, resistome dynamics, and reproductive fitness. However, their relationship is context dependent and not causal. Furthermore, hepatic transcriptomic and microRNA (miRNA)-mediated regulatory networks could serve as a molecular bridge connecting ruminal fermentation events to systemic phenotypic outcomes. The ruminant resistome may also represent a potential interface with public health rather than an isolated ecological phenomenon, given the capacity for horizontal gene transfer through mobile genetic elements, although the extent of transmission to humans remains to be quantified. Early-life microbial programming and reproductive tract microbiome composition also represent tractable intervention windows for precision management. This integrated framework could reframe feed additive research from a single pathway to a systems-level perspective, offering a basis for precision ruminant production.},
}

@article {pmid43005495,
year = {2026},
author = {Sanabria, FMLS},
title = {From Prebiotics to Mitochondrial Response: A Critical Narrative Review of Microbiota-Host Metabolic Interactions and Their Implications for Child Neurodevelopment.},
journal = {Cureus},
volume = {18},
number = {11},
pages = {e119347},
pmid = {43005495},
issn = {2168-8184},
abstract = {Prebiotics can modify intestinal microbial fermentation and short-chain fatty acid (SCFA) production, but whether these changes improve mitochondrial bioenergetics or neurodevelopmental outcomes in children remains uncertain. This critical narrative review examines the relationships among prebiotic substrates, microbial metabolism, SCFA availability, host metabolic processing, mitochondrial function, and pediatric clinical outcomes. Literature was identified through PubMed/MEDLINE, journal and publisher websites, and citation tracking, with literature identification completed before October 15, 2026. Evidence was organized by intervention or exposure, biological system, and measured endpoint, distinguishing direct microbial metabolite exposure from oral prebiotic supplementation. Experimental studies show that butyrate supports oxidative energy metabolism in colonocytes and that mitochondrial responses to microbial metabolites vary with concentration, tissue, redox state, and individual metabolic capacity. Increased intestinal fermentation does not necessarily establish greater systemic metabolite availability, enhanced mitochondrial ATP synthesis, or improved neuronal function. Pediatric galactooligosaccharide trials have documented microbial changes without directly measuring mitochondrial ATP production or establishing consistent between-group improvements in behavioral or overall gastrointestinal outcomes. Findings from combined probiotic, prebiotic, and synbiotic interventions cannot establish prebiotic-specific efficacy. A hypothesis-generating framework termed fermentation-bioenergetic response uncoupling is proposed, comprising five potential points of divergence: substrate accessibility, microbial transformation, host exposure, metabolic processing, and mitochondrial functional response. Clinical outcomes are assessed separately. Missing downstream measurements indicate an evidence gap rather than demonstrated biological uncoupling. Future pediatric research should integrate chemically defined nutritional interventions, functional microbiome profiling, metabolomics, validated mitochondrial measurements, and prespecified clinically relevant outcomes. Current evidence does not establish prebiotics as treatments for mitochondrial dysfunction or core neurodevelopmental features; potential gastrointestinal benefits require evaluation for specific clinical indications.},
}

@article {pmid43005677,
year = {2026},
author = {Li, GL and Zhang, ZC and Lyu, XM and Li, MX and Lin, PY and Yu, HS and Zhu, YY and Zhang, GH and Duan, CG and Cheung, Y and Li, W and Zhang, ZJ and Xu, TS and Chen, F and Huang, MW},
title = {Current research status of risk assessment models for oral squamous cell carcinoma based on microbiome databases.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1894946},
pmid = {43005677},
issn = {1664-302X},
abstract = {Oral squamous cell carcinoma (OSCC) is one of the most common oral malignancies. Due to insidious early symptoms, high invasiveness, and frequent cervical lymph node metastasis, patient survival remains poor. Recent studies demonstrate significant associations between oral dysbiosis and OSCC. To address limited early screening and suboptimal survival rates, this review systematically summarizes OSCC microbiome research and disease risk assessment applications. Studies reveal marked oral dysbiosis in patients with OSCC, characterized by enrichment of Fusobacterium and Porphyromonas, reduced Neisseria abundance, and altered community stability. These promote tumorigenesis through chronic pro-inflammatory signaling, the production of carcinogenic metabolites, and direct oncogenic pathway interference. Consequently, the oral microbiome offers non-invasive, sensitive biomarkers for early detection. We identify and distinguish four categories of predictive models in the current literature: (1) detection/discrimination of prevalent OSCC, (2) prediction of malignant transformation from oral potentially malignant disorders, (3) prediction of recurrence or metastasis after treatment, and (4) prognostic models for survival prediction. Existing databases include comprehensive and OSCC-specific collections with multi-omics integration. Risk assessment models encompass traditional statistics, machine learning, deep learning, and multimodal fusion, and have shown promising performance in retrospective cohorts. However, standardized databases are lacking, and existing models face confounding interference, limited generalizability, and insufficient interpretability. Furthermore, current predictive models are predominantly based on 16S rRNA sequencing (bacteriome-centric), whereas comprehensive risk assessment requires integrating interkingdom entities, including fungi, viruses, and archaea, through metagenomic and virome profiling. Critically, the distinction between promising retrospective discrimination and validated prospective clinical utility remains a major translational barrier. Future directions include developing standardized longitudinal databases, integrating multi-omics, using explainable artificial intelligence, and conducting prospective validation studies to achieve personalized precision treatment.},
}

@article {pmid43005720,
year = {2026},
author = {Shree, S and Chaudhary, A and Kumar, S and Singh, K and Dubey, N},
title = {Beneficial microbes in plant salt stress tolerance: mechanisms, antioxidant defense, and multi-omics insights.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1965097},
pmid = {43005720},
issn = {1664-302X},
abstract = {Salinity stress represents a significant environmental challenge that affects plant growth, resulting in adverse impacts on crop productivity and overall yield. Salt accumulation in plants affects cellular homeostasis and provokes osmotic and ionic imbalance. It stimulates higher reactive oxygen species (ROS) production leading to oxidative stress damage and eventual cellular dysfunction. Beneficial microorganisms like plant growth-promoting rhizobacteria, arbuscular mycorrhizal fungi, endophytic fungi, and rhizosphere-associated microbes have recently emerged as resources for sustainable solutions to enhance plant resiliency against salinity stress. Their effects can involve osmotic adjustment, ion sequestration, oxidative-stress mitigation, phytohormone regulation, and rhizosphere-mediated stress buffering. The mechanisms to impart such benefits may include improved nutrients acquisition, assist in osmotic regulation, modulation of phytohormones signaling, and maintenance of cellular ion homeostasis. Often, beneficial microorganisms carry the potential to trigger both enzymatic and non-enzymatic antioxidant defense mechanisms. These responses contribute to oxidative-stress mitigation, yet, their interpretation requires contemplation of fine balance between oxidative damage and plant responses. For example, selected microbial inoculation studies have reported changes in the activity of crucial antioxidant enzymes, like superoxide dismutase, ascorbate peroxidase, catalase, and glutathione reductase. However, the magnitude and the direction of these responses are context dependent. Multi-omics approaches, including amplicon and shotgun metagenomics, metatranscriptomics, host transcriptomics, proteomics, and metabolomics, have expanded our understanding of the taxa, genes, transcripts, proteins, and metabolites associated with plant-microbe interactions under salinity. Therefore, here an effort has been made to present the evidential support for reported microbial effects and their proposed mechanisms of salt tolerance, with a focus on enzymatic and non-enzymatic defense mechanisms and the learnings of multi-omics studies. Frontier integrative mechanisms, including microbiome engineering, synthetic microbial consortia, and systems biology frameworks, are discussed for cultivating climate-resilient crops and sustainable agricultural systems in the salt-affected environments.},
}

@article {pmid43005796,
year = {2026},
author = {Wu, C and Liu, R},
title = {Gut microbiota-host co-metabolism in sepsis and critical illness: source, compartment, immune state, and host defense.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1975307},
pmid = {43005796},
issn = {1664-302X},
abstract = {Critical illness can profoundly disturb the intestinal microbiota-metabolite-host immune axis through the combined effects of shock, hypoxia, altered nutritional intake, antimicrobial exposure, organ dysfunction, and impaired epithelial barrier integrity. These changes can reshape microbial metabolic capacity, host co-metabolism, and systemic metabolite exposure, while the host may simultaneously exhibit overlapping features of hyperinflammation, immune tolerance, lymphocyte dysfunction, impaired antimicrobial defense, and tissue repair. Metabolites generated through microbial metabolism or shared microbial-host pathways may therefore contribute to immune reprogramming, although their effects are highly context dependent and cannot be regarded as uniformly beneficial or detrimental. This narrative review examines short-chain fatty acids, tryptophan-derived indoles, secondary bile acids, succinate, lactate, trimethylamine N-oxide, polyamines, and aromatic metabolites, with particular attention to source attribution, anatomical compartment, host co-metabolism, receptor signaling, and their potential influence on antimicrobial immunity. These metabolites may act through G-protein-coupled receptors, AhR, PXR, FXR, TGR5, VDR, HIF-1α, inflammasome pathways, mitochondrial signaling, and epigenetic mechanisms to modulate macrophages, neutrophils, dendritic cells, innate lymphoid cells, T lymphocytes, epithelial barriers, and endothelial responses. The direction and magnitude of these effects are likely to vary according to timing, concentration, anatomical compartment, immune-cell state, pathogen burden, and renal or hepatic clearance. Within this framework, attenuation of inflammatory signaling may help limit early collateral tissue injury, yet the same response could become disadvantageous when antimicrobial competence is already impaired. Similarly, succinate and lactate may reflect or contribute to distinct inflammatory, regulatory, or reparative programs depending on whether they arise from microbial or host metabolism and whether they act within intracellular or extracellular compartments. Human studies in critically ill populations have linked dysbiosis and metabolomic alterations with secondary infection, prolonged organ support, and mortality; however, most have not been able to resolve microbial source attribution or establish causal mediation. Future work would therefore benefit from integrating longitudinal microbiome, metabolome, immune-function, and organ-clearance measurements with source-resolved approaches, including isotope tracing, as well as state-specific and trajectory-informed clinical endpoints. Microbiome-directed interventions may be most appropriately investigated as context-dependent modulators of host defense rather than as broadly anti-inflammatory strategies.},
}

@article {pmid43005894,
year = {2026},
author = {Wu, L and Yao, HY and Fu, ZJ and Luo, RH and Zhou, S},
title = {The "gut-immune-bone axis": quantitative MRI reveals the microbial-immune-bone metabolic interplay in osteoporosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1909663},
pmid = {43005894},
issn = {1664-3224},
mesh = {Humans ; *Osteoporosis/metabolism/immunology/diagnostic imaging/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Bone and Bones/metabolism/immunology/diagnostic imaging ; *Magnetic Resonance Imaging/methods ; Bone Remodeling/immunology ; },
abstract = {Osteoporosis is a systemic skeletal disorder, whose pathogenesis is related to abnormalities in bone metabolism, as well as gut microbiota and immune system dysregulations. This structured narrative review synthesizes recent evidence on the "gut-immune-bone axis" in osteoporosis, with emphasis on studies published from 2020 to 2025 and selected later studies incorporated during manuscript revision when directly relevant. This article first outlines the direct and indirect regulatory roles of gut microbiota and its products (short-chain fatty acids, tryptophan catabolites, etc.) in bone metabolism. It then focuses on immune cells that participate in bone remodeling, including the Th17/Treg balance, B cells, and macrophages, and their interactions with the gut microbiota. The review further discusses recent developments in quantitative magnetic resonance imaging for quantifying bone microarchitecture, marrow composition, and metabolic status and considers how these measures may serve as downstream phenotyping tools in studies of the gut-immune-bone axis. Finally, an integrative model of the microbial-immune-bone metabolic network is proposed and translational strategies, including microbiome-directed interventions, immunomodulatory therapies, and multi-omics approaches, are critically discussed.},
}

Humans
*Osteoporosis/metabolism/immunology/diagnostic imaging/microbiology
Animals
*Gastrointestinal Microbiome/immunology
*Bone and Bones/metabolism/immunology/diagnostic imaging
*Magnetic Resonance Imaging/methods
Bone Remodeling/immunology

@article {pmid43005955,
year = {2026},
author = {Thomson, T and Fusi, M and Prinz, N and Cary, SC and Pilditch, CA and Ellis, JI},
title = {Nutrient enrichment shapes depth-resolved bacterial community assembly in mangrove sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag298},
pmid = {43005955},
issn = {2730-6151},
abstract = {Microbial communities in mangrove sediments are critical for carbon and nutrient cycling; yet despite their importance, responses to eutrophication-a pervasive global threat to coastal ecosystems-remain poorly understood. Here, we tested whether nutrient enrichment restructures mangrove sediment bacterial communities more strongly in the subsurface than at the sediment surface. We assessed bacterial community responses to an in-situ slow-release NPK (Osmocote®) enrichment experiment in a temperate mangrove (Avicennia marina subsp. australasica) forest in Aotearoa New Zealand. Using 16S rRNA gene sequencing, we compared surface (0-2 cm) and subsurface (5-7 cm) community diversity and functional potential, 4.5 months after enrichment. Differences in porewater nutrient concentrations between ambient and enriched plots were subtle and spatially heterogeneous; however, bacterial communities exhibited significant shifts relative to controls. Community shifts in subsurface samples were stronger compared to the surface, with enrichment reducing diversity and altering community composition to Proteobacteria and Bacteroidota favoured communities. Conversely, taxa from Desulfobacterota, Chloroflexi, and Nitrospirota were more abundant in controls. Similarly, shifts in inferred functional potential in the surface remained limited, while the subsurface showed strong, selective changes: a proportional decline of sulphur-cycling and hydrogen-oxidizing taxa and a relative increase of heterotrophic guilds. Community assembly was more deterministic in subsurface compared to surface sediments, and under nutrient addition subsurface assembly shifted, mainly through reduced dispersal limitation, to more closely resemble the surface communities. These results underscore the need to better understand and integrate microbial responses at relevant spatial scales into predictions of ecosystem resilience under increasing anthropogenic pressures.},
}

@article {pmid43005997,
year = {2026},
author = {Benchea, MS and Neamtu, AA and Solomon, CN and Cuc, EA and Pantor, M and Pop, O},
title = {Adjunctive Oral Treatment Improves Helicobacter pylori Eradication Without Evidence of a Dose-Response Gradient: An Updated Meta-Analysis Challenging the Oral Reservoir Hypothesis.},
journal = {Cureus},
volume = {18},
number = {10},
pages = {e117737},
pmid = {43005997},
issn = {2168-8184},
abstract = {Standard antibiotic regimens for Helicobacter pylori are failing more often as resistance rises, and the oral cavity has long been proposed as an extragastric reservoir that seeds gastric recolonization. If so, treating the mouth should improve gastric eradication, a testable clinical claim rather than a correlation. We therefore pooled the randomized evidence on adjunctive periodontal and oral hygiene treatment identified through our search strategy and tested the reservoir hypothesis rather than assuming it. We included randomized and quasi-randomized controlled trials in which adults or children receiving standard eradication therapy for confirmed gastric H. pylori infection were allocated to receive, or not receive, an adjunctive periodontal or oral hygiene intervention. Trials were identified by citation searching of three previous syntheses and by targeted searches for trials published after August 2015, without language restriction. The primary outcome was eradication confirmed at the first post-treatment assessment, at least four weeks after therapy; the co-primary outcome was absence of recurrence at six months or later. We pooled odds ratios and risk ratios using random-effects models with the Hartung-Knapp adjustment, assessed risk of bias with the second version of the Cochrane risk-of-bias tool, and rated certainty using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Subgroup analyses by intervention intensity, region, publication period, and source verifiability were prespecified, and small-study effects were examined by funnel plot, Egger and Begg tests, and trim-and-fill. Eleven trials contributed data. For eradication, 10 trials, including 1,575 participants, gave a pooled odds ratio of 2.84 (95% confidence interval 1.84 to 4.39; p = 0.0004) with modest heterogeneity (I-squared 34.4%, prediction interval 1.18 to 6.87), corresponding to eradication in 87.1% versus 72.0% and a number needed to treat of six. For recurrence, four trials including 999 participants gave a pooled odds ratio for remaining free of infection of 4.64 (95% confidence interval 2.06 to 10.45); the same trials pooled as risk ratios gave 1.63 (95% confidence interval 0.86 to 3.09), and both are reported with equal prominence because the finding does not survive the change of scale. There was no evidence of small-study effects (Egger p = 0.51; none imputed by trim-and-fill). No gradient with intervention intensity was detected: an antiseptic mouthrinse alone performed at least as well as full-mouth scaling and root planing (test for subgroup differences p = 0.19), although the stratum-level confidence intervals were wide, and the largest single effect in the dataset came from a placebo-controlled trial of an antiseptic mouthrinse with no mechanical component. No trial was at low overall risk of bias. Adjunctive oral treatment is consistently associated with better eradication, but no evidence of a dose-response gradient was detected, which does not support simple mechanical removal of an oral reservoir as the explanation. Certainty was moderate for eradication, downgraded for risk of bias, and low for recurrence, downgraded for risk of bias and imprecision.},
}

@article {pmid43006147,
year = {2026},
author = {Zubairi, I},
title = {Comment on: "Oral Leukoplakia Microbiome Predicts the Degree of Dysplasia and Is Shaped by Smoking and Tooth Loss".},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70579},
pmid = {43006147},
issn = {1601-0825},
}

@article {pmid43006633,
year = {2026},
author = {Gutmann, F and Börschel, CS and Markó, L and Löber, U and Bartolomaeus, TUP and Jovanovic, N and Zeller, T and Nauck, M and Friedrich, N and Henning, AK and Forslund-Startceva, SK and Schnabel, RB},
title = {Distinct Gut Microbial and Metabolic Biomarkers Related to Atrial Fibrillation in Low-Risk Patients.},
journal = {Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/europace/euag302},
pmid = {43006633},
issn = {1532-2092},
}

@article {pmid43006873,
year = {2026},
author = {Rebeck, ON and Zhang, A and Mahmud, B and Wallace, MA and Nickel, KB and Johnson, C and Habrock-Bach, T and Zahrah, D and Liao, J and Myckatyn, TM and Tenenbaum, MM and Brandt, KE and Burnham, C-AD and Olsen, MA and Dantas, G},
title = {Comparative genomics of the skin microbiome and associated isolates of patients undergoing mastectomy with immediate breast reconstruction.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0053126},
doi = {10.1128/msphere.00531-26},
pmid = {43006873},
issn = {2379-5042},
abstract = {Mastectomy with immediate breast implant reconstruction (IBIR) is an increasingly common component of breast cancer treatment; however, these procedures carry a substantial risk of surgical site infections (SSIs) and noninfectious wound complications (NIWCs). We hypothesized that the local skin microbiota may contribute to the development of post-operative complications, in part by serving as a reservoir for pathobionts, such as Staphylococcus epidermidis and Cutibacterium acnes. We collected skin and intraoperative samples from 60 patients undergoing mastectomy with IBIR. To evaluate longitudinal shifts in community composition, we performed 16S rRNA gene sequencing of 151 breast and axilla skin swabs collected at pre- and post-operative time points. Using a comprehensive culture approach, we recovered diverse cultivable organisms and selected 232 S. epidermidis and 130 C. acnes isolates from skin swabs, implant swabs, and seroma fluid for whole-genome sequencing and comparative genomic analysis. We observed perturbations to community structure in the breast and axilla following mastectomy. These shifts were characterized by a significant and persistent depletion of Corynebacterium spp., which did not resolve in patients who subsequently developed an SSI. We also uncovered outcome-specific genomic signatures in S. epidermidis isolates, which may offer mechanistic insight into the role of this species in SSI and NIWC development. Importantly, we also identified genomic signatures detectable prior to mastectomy and infection diagnosis that may offer clinical utility toward predicting post-operative complications. Together, these findings illustrate the importance of the skin microbiome in SSI and NIWC development following mastectomy with IBIR.IMPORTANCEAn improved understanding of the relationship between surgical sites and adjacent resident skin microbiota can help identify which patients are at increased risk for developing surgical site infections and noninfectious wound complications. By characterizing bacterial communities before mastectomy with immediate breast reconstruction and during subsequent healing, we sought to evaluate how changes in community composition may contribute to the development of post-operative complications. We also performed in-depth genomic analyses of Staphylococcus epidermidis and Cutibacterium acnes isolates recovered from patients to identify genetic components that may determine whether an isolate protects or predisposes patients toward development of post-operative complications. Last, we identified genomic signatures detectable prior to surgery and infection diagnosis that are correlated with patient outcome, which may serve as informative biomarkers to inform patient care.},
}

@article {pmid43006913,
year = {2026},
author = {Atoom, AM and Allela, OQB and Nayak, PP and Arora, V and Singla, S and Athab, ZH and Urazbaeva, D and Usmanov, R},
title = {Epigenome, Microbiome, and Metabolites: Unraveling the Complex Pathogenesis of Celiac Disease.},
journal = {Cell biology international},
volume = {50},
number = {11},
pages = {},
doi = {10.1002/cbin.70231},
pmid = {43006913},
issn = {1095-8355},
mesh = {Humans ; *Celiac Disease/genetics/microbiology/metabolism ; *Epigenesis, Genetic ; *Epigenome ; *Gastrointestinal Microbiome ; *Microbiota ; Genetic Predisposition to Disease ; Diet, Gluten-Free ; Animals ; DNA Methylation ; HLA-DQ Antigens/genetics ; },
abstract = {Celiac disease (CeD) is a chronic autoimmune disease triggered by gluten consumption in genetically susceptible individuals, primarily those with HLA-DQ2 or HLA-DQ8 haplotypes. Although these genetic factors are responsible for a substantial portion of disease risk, they do not fully explain disease heritability or the rising incidence observed worldwide. Recent clinical studies highlight epigenetic modifications-including DNA methylation, histone modifications, non-coding RNA regulation, and RNA methylation-as critical mediators bridging genetic susceptibility and environmental influences, such as gut microbiota dysbiosis, dietary patterns, early-life exposures, infections, and pharmaceutical interventions. These epigenetic mechanisms modulate immune responses, intestinal barrier function, and inflammatory pathways, contributing to the loss of gluten tolerance and perpetuation of mucosal damage. Key players, including tissue transglutaminase 2 (TG2) and interferon-gamma (IFN-γ), form amplifying feedback loops that exacerbate pathogenesis. Bacterial metabolites and lifestyle factors further influence epigenetic landscapes, offering reversible targets for intervention. This review synthesizes current evidence on epigenetic alterations in CeD, emphasizing their interplay with microbiota and metabolites, tissue-specific patterns, and potential as biomarkers. It also explores implications for novel therapeutic strategies beyond the gluten-free diet, including epigenetic modulators and microbiota-targeted approaches, to advance personalized prevention and management of CeD.},
}

Humans
*Celiac Disease/genetics/microbiology/metabolism
*Epigenesis, Genetic
*Epigenome
*Gastrointestinal Microbiome
*Microbiota
Genetic Predisposition to Disease
Diet, Gluten-Free
Animals
DNA Methylation
HLA-DQ Antigens/genetics

@article {pmid43006985,
year = {2026},
author = {Wang, Q and Fu, D and Ma, Y and Cheng, C and Xu, Y and Agathokleous, E and Feng, Z},
title = {Elevated ozone reshapes wheat root-associated microbiomes through coordinated plant responses and rhizosphere environmental filtering.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0185826},
doi = {10.1128/aem.01858-26},
pmid = {43006985},
issn = {1098-5336},
abstract = {Elevated tropospheric ozone (O3) threatens crop productivity, but how O3-induced changes in plant responses influence root-associated microbiomes remains unclear. We investigated the responses of microbial communities inhabiting the rhizosphere and root endosphere to elevated O3 using four cultivars grown under ambient and 1.5-fold ambient O3 in a field-based free-air O3-concentration enrichment (FACE) system. Plant traits, root-released organic carbon (ROC), rhizosphere properties, extracellular enzyme activities, and bacterial and fungal communities were jointly analyzed. Elevated O3 reduced yield and root biomass, with cultivar-dependent changes in ROC. Elevated O3 consistently increased rhizosphere pH and altered microbial resource allocation, increasing ecoenzymatic vector length by 4.1% and decreasing vector angle by 4.6%. Bacterial communities showed a stronger response than fungal taxonomic communities, particularly in the rhizosphere. However, variation partitioning indicated that soil properties, especially pH, rather than O3 treatment alone, provided the strongest independent explanation for bacterial community variation. Fungal communities showed limited taxonomic turnover but exhibited shifts in predicted trophic guilds, including increased pathotroph- and saprotroph-associated groups and decreased symbiotroph-containing guilds under elevated O3. These results demonstrate that elevated O3 reshapes the wheat root-associated microbiome through coordinated changes in plant performance, rhizosphere environmental filtering, and microbial functional strategies, highlighting the importance of plant-mediated processes in regulating belowground responses to atmospheric change.IMPORTANCEElevated tropospheric O3 is an increasing threat to crop production, but its effects on belowground microbial processes remain poorly understood. This study demonstrates that O3-induced root-associated microbiome changes are closely linked with altered plant carbon allocation and rhizosphere environmental conditions rather than O3 exposure also. By integrating plant traits, soil properties, extracellular enzyme allocation, and microbial community analyses, we reveal a compartment-specific plant-soil-microbiome response to elevated O3. These findings improve our understanding of how atmospheric pollution may reshape crop-associated microbial functions and soil ecological processes under future climate change.},
}

@article {pmid43007215,
year = {2026},
author = {Chakraborty, D and Vanderhyde, M and Camuy-Velez, L and Saha, B and Fayshal, MA and Elvers, R and Dragt, H and Rodriguez, S and Xu, J and Iskander, SM and Banerjee, S},
title = {Longitudinal Multiomics Reveals Core Microbiome Disruption and Potential Keystone-Associated Recovery Following Pesticide Exposure.},
journal = {Environmental science & technology},
volume = {60},
number = {44},
pages = {32021-32033},
doi = {10.1021/acs.est.6c07798},
pmid = {43007215},
issn = {1520-5851},
support = {37000-7690-02442-FARG006387//NDSU Development Foundation/ ; },
mesh = {*Microbiota/drug effects ; *Pesticides ; Multiomics ; Soil Microbiology ; Bacteria ; Fungi ; },
abstract = {Pesticides have become indispensable in modern agriculture, serving as a primary tool to minimize crop loss amid increasing human population pressures. While the negative effects of pesticides on the soil microbiome have been reported, the temporal dynamics of soil microorganisms under pesticide use remain underexplored. Specifically, limited knowledge exists regarding how the soil microbiome responds to pesticides before and after the manufacturer-labeled 'safe period' of 21 days after application. We conducted a longitudinal microcosm study to investigate the temporal impacts of herbicide, fungicide, and insecticide on soil microbial diversity, composition, network complexity, and functional pathways across five time points. Our results show that soil microbial communities are negatively impacted by pesticide applications, but there is a trend of recovery after 21 days. We found a significant impact of the temporal persistence of pesticides on both bacterial and fungal community composition, with a stronger effect on fungi. Network analysis revealed that core microbiome networks were negatively impacted by pesticide applications, with the core microbial nodes, raw associations, and modularity declining in pesticide-treated soils, and this negative effect was particularly strong for pyrethroid insecticides. We identified several differentially abundant taxa, including Xanthobacteraceae and Vicinamibacteriales among bacteria, and Mortierella, Mytilinidales among fungi, which could serve as useful biomarkers for pesticide-affected soils. Results from microbial co-occurrence network analysis revealed that one ASV assigned to the Methyloligellaceae family consistently emerged as a keystone taxon in pesticide-treated soils. Using genome-resolved metagenomics, we assembled the genomes (MAGs) of Methyloligellaceae members and found these taxa harbor putative genes associated with pesticide degradation and antimicrobial resistance, suggesting their possible role in community recovery. Given the remarkably dynamic nature of soil microbial communities, our findings bridge an important knowledge gap regarding the short-term dynamics of microbial structures and functional pathways in response to major pesticides.},
}

*Microbiota/drug effects
*Pesticides
Multiomics
Soil Microbiology
Bacteria
Fungi

@article {pmid43007386,
year = {2026},
author = {Vashishth, S and Ambasta, RK and Kumar, P},
title = {Mechanistic role of functional bacterial amyloids (FuBAs) in inflammatory responses, ubiquitin proteasome system (UPS) impairment, and cross-seedings with host amyloids.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {43007386},
issn = {1573-4978},
mesh = {Humans ; *Proteasome Endopeptidase Complex/metabolism ; *Ubiquitin/metabolism ; *Amyloid/metabolism ; *Inflammation/metabolism ; Animals ; Neurodegenerative Diseases/metabolism/microbiology ; *Bacterial Proteins/metabolism ; Amyloid beta-Peptides/metabolism ; alpha-Synuclein/metabolism ; Bacteria/metabolism ; Proteotoxic Stress ; },
abstract = {Neurodegenerative diseases are characterized by disruption of protein homeostasis, aggregation, inflammation, and neuronal resilience, with age affecting disease susceptibility. Bacterial amyloids, such as curli, Fap, TasA, and phenol-soluble modulins, are functional amyloids that aid in biofilm formation and potentially interact with host proteins and innate immune pathways. They are cross-β-sheet proteins that interact with other proteins from different species, and experimental data show that some bacterial amyloids promote the aggregation of amyloid-β and α-synuclein. Various fuBA effects along the gut-brain axis depend on microbial production, retention in the gut, barrier integrity, clearance from the system, immune status, and tissue susceptibility. The activation of innate immune mechanisms, such as Toll-like receptor signaling, by FuBAs or related microbial signals could lead to inflammation and oxidative stress. The ubiquitin-proteasome system (UPS) is another aspect of cellular protein quality control that could be further compromised by increased amyloid burden. To date, direct FuBA-mediated proteasome inhibition remains poorly established. To this end, this review separates direct evidence, indirect effects of aggregation/inflammatory stress, and mechanistic precedents from studies on human amyloid. Structural biology, immunology, and proteostasis research will be combined, and FuBAs will be investigated as potential upstream modulators of the neurodegenerative proteinopathies. We assess whether FuBAs directly influence UPS function in intestinal, peripheral, or neural compartments, and discuss possible therapeutic strategies, including microbiome modulation, barrier repair, immunomodulation, and proteasome stimulation. FuBAs can alter neuronal proteostasis in both amyloid-related disorders and other neurodegenerative processes, but not necessarily act as triggers of these processes.},
}

Humans
*Proteasome Endopeptidase Complex/metabolism
*Ubiquitin/metabolism
*Amyloid/metabolism
*Inflammation/metabolism
Animals
Neurodegenerative Diseases/metabolism/microbiology
*Bacterial Proteins/metabolism
Amyloid beta-Peptides/metabolism
alpha-Synuclein/metabolism
Bacteria/metabolism
Proteotoxic Stress

@article {pmid43007660,
year = {2026},
author = {Pandia, B and Vasudevan, S and Regati, D and Rathod, N and Sankar, S and Sowdhamini, R and Chandra, N},
title = {CAcnesDB: a database of Cutibacterium acnes with integrated functional insights derived from multi-modal genome annotation.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {43007660},
issn = {1758-0463},
support = {BT/PR40186/BTIS/137/3/2020//Department of Biotechnology/ ; BT/PR40316/BTIS/137/83/2023//Department of Biotechnology/ ; },
mesh = {*Molecular Sequence Annotation ; *Genome, Bacterial ; *Databases, Genetic ; *Bacterial Proteins/genetics/metabolism/chemistry ; *Propionibacterium acnes/genetics/metabolism ; Biocuration ; Proteome/genetics/metabolism ; Humans ; },
abstract = {Cutibacterium acnes is a predominant member of the human skin microbiome, generally as a beneficial or a benign inhabitant, which under specific conditions transforms into a pathogen, causing acne and associated inflammatory responses. While there is a wealth of data on the microbiology and genomics of the microbe, there is a lack of comprehensive annotation of the proteins coded by the genome, slowing progress in understanding its unique metabolic versatility and survival in host hypoxic sebaceous niches. We configured an integrated pipeline for functional annotation of the C. acnes genome, combining gene calling, domain and ontology mapping, KEGG pathways assignment, proteome-scale structural modeling, predicting pockets and associating the small-molecule metabolites based on binding site similarity to facilitate structure-to-function annotation. Structural predictions using ColabFold covered nearly the full proteome, with 83.7% of models showing high confidence. To infer protein function, ligand-binding sites in the C. acnes modeled proteome were predicted using a consensus of three independent algorithms, PocketDepth, SiteHound, and Fpocket. Small molecule ligands were mapped to the resulting pockets through structural comparison of the pockets with known small-molecule binding sites in PDB where there was direct or indirect evidence for such binding, resulting in the C. acnes predicted ligandome (CApL) comprising 693 protein-ligand pairs across 534 proteins. CAcnesDB is a comprehensive database of the C. acnes genome, hosting functional annotation from multiple levels of input and analyses, covering 2297 protein-coding genes.},
}

*Molecular Sequence Annotation
*Genome, Bacterial
*Databases, Genetic
*Bacterial Proteins/genetics/metabolism/chemistry
*Propionibacterium acnes/genetics/metabolism
Biocuration
Proteome/genetics/metabolism
Humans

@article {pmid43007723,
year = {2026},
author = {Kugelmann, D and García-Ponce, A and Thielemann, N and Radeva, MY and Anders, M and Kang, DE and Siadjeu, C and Burkard, N and Horn, AK and Neubauer, J and Hiermaier, M and Egu, DT and Schmitz, C and Kurzai, O and Vuopala, KS and Kuismin, O and Schlegel, N and Waschke, J},
title = {Dsg2 truncation causes a severe intestinal epithelial barrier breakdown and alters microbiome and immune response.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.183554},
pmid = {43007723},
issn = {2379-3708},
abstract = {Inflammatory bowel diseases (IBD) including Crohn's disease (CD) are characterized by impaired intestinal epithelial barrier (IEB) function. Alterations in the desmosomal cadherin desmoglein 2 (Dsg2) have been linked to loss of IEB and intestinal inflammation in IBD. We investigated the pathogenic impact of a cytoplasmatic-truncating mutation in the desmosomal cadherin desmoglein 2 gene (DSG2) in an IBD patient. Genetic analysis of a CD patient revealed a likely pathogenic DSG2 mutation leading to a truncated protein lacking part of the intracellular domain. Generation of an enterocyte-specific mouse model to recapitulate the human mutation resulted in a lethal intestinal barrier defect which was evident in homozygous but not in heterozygous mice. In vitro, barrier defects correlated with changes in Dsg2 mobility and upregulation of pore-forming tight junction protein claudin-2. Organoids derived from heterozygous Dsg2 truncated mice exhibited increased epithelial susceptibility to proinflammatory cytokines. Bulk RNAseq followed by gene ontology analysis in homozygous mice revealed a skewed IL17/IL23 response overlapping with transcriptional changes in patients with CD. Furthermore, 16S rRNA sequencing revealed alterations in microbiome composition in animals that carried the Dsg2 truncation. In summary, a patient-derived mutation in the DSG2 gene causing cytoplasmic truncation in homozygous state induced a lethal intestinal barrier breakdown in mice paralleled by altered gut microbiota and intestinal immune response.},
}

@article {pmid43008459,
year = {2026},
author = {Sun, J and Zhao, X and Yan, WJ and Li, WT and Sun, WL and Zhang, PD},
title = {Roots through time: dynamics of the rhizosphere microbiome and its nutrient-cycling potential in Zostera marina meadows with implications for microbiome-based restoration.},
journal = {Marine environmental research},
volume = {223},
number = {},
pages = {108529},
doi = {10.1016/j.marenvres.2026.108529},
pmid = {43008459},
issn = {1879-0291},
abstract = {The seagrass rhizosphere microbiome is critical for sedimentary nutrient turnover, yet the spatiotemporal dynamics of carbon, nitrogen, phosphorus, and sulfur cycling across Zostera marina developmental stages remain poorly understood. Leveraging metagenomic sequencing and 147 metagenome-assembled genomes (MAGs), we resolved functional gene profiles in rhizosphere and bulk sediments across three discrete developmental stage (vegetative, reproductive and dormant). Temporal variation (i.e., sampling period) explained 48.1-57.4% of the variance in nutrient-cycling-associated microbial community composition, whereas spatial partitioning between rhizosphere and bulk compartments accounted for 11.6-20.0%. Carbon fixation genes were significantly enriched in the rhizosphere during reproduction but reached peak abundance in bulk sediments during dormancy. Nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA) genes were enriched in the rhizosphere during both vegetative and dormant stages. Phosphorus mobilization-associated genes displayed parallel enrichment patterns, with the regulatory two-component system gene phoR broadly conserved across MAGs. Sulfur oxidation genes were enriched in the rhizosphere during vegetative and dormant stages, yet exhibited higher relative abundance in bulk sediments during reproduction. Critically, multiple Desulfobacterota MAGs co-occurred with nitrogen fixation and sulfate reduction genes, and the alkaline phosphatase gene phoD was identified in several of these genomes. Together, these findings reveal developmentally orchestrated shifts in microbial nutrient-cycling potential, underscoring the importance of protecting the native rhizosphere microbiome in eelgrass restoration, while considering site-specific biogeochemical constraints, particularly nutrient availability and sulfide conditions.},
}

@article {pmid43008658,
year = {2026},
author = {Sun, M and Li, B and Li, T and Li, D and Qin, B and Song, W and Li, X},
title = {Neighbor effects of companion cropping on microbial assembly and potential functions in phthalate-contaminated soils.},
journal = {Journal of environmental management},
volume = {420},
number = {},
pages = {131306},
doi = {10.1016/j.jenvman.2026.131306},
pmid = {43008658},
issn = {1095-8630},
abstract = {Di(2-ethylhexyl) phthalate (DEHP) has emerged as a major contributor to global soil pollution, endangering plant vitality and altering microbial ecosystem balance. However, the ecological mechanisms underlying plant-microbe interactions in response to phthalate stress remain poorly understood. We investigated how interspecific interactions between maize and wheat influence rhizosphere microbial community under varying DEHP concentrations (20, 60, and 100 mg/kg). By analyzing 16S rRNA and ITS amplicon data from soil samples, we explored the mechanisms by which bacteria and fungi contribute to the ecological remediation of DEHP contaminated soils. Here, we found that interspecific planting altered wheat responses to DEHP stress and was associated with shifts in rhizosphere microbial community composition in contaminated soils. The companion crop (maize) played a key role in stabilizing the rhizosphere environment and enriching functional microbial taxa, particularly under high DEHP exposure. Interspecific interactions enhanced the contribution of stochastic processes to the bacterial community in wheat, thereby inducing changes in the core hubs of the bacterial-fungal multi-kingdom network and increasing the potential functional capacity related to DEHP degradation. Hence, interspecific diversity can drive beneficial microbial reorganization, supporting both plant health and pollutant mitigation. Our findings highlight the pivotal role of plant-microbe interactions in restoring DEHP-contaminated soils, demonstrating that intercropping can foster resilient microbial communities and support long-term ecological recovery. This approach offers a promising, nature-based solution for sustainable agriculture.},
}

@article {pmid43008738,
year = {2026},
author = {Schwartz, DJ and Wong, GG and Wardenburg, KE and Erickson, IR and Tung, J and Ning, J and Zhao, L and Shalon, N and D'Souza, AW and Ferreiro, A and Silverstein, RB and Crofts, TS and Hall-Moore, C and Wallace, MA and Robinson, JI and Henderson, JP and Burnham, CD and Warner, BB and Tarr, PI and Dantas, G},
title = {Microbiome-antibiotic-immune interactions influence mortality in preterm infant gut microbiota-humanized gnotobiotic mice.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103161},
doi = {10.1016/j.xcrm.2026.103161},
pmid = {43008738},
issn = {2666-3791},
abstract = {Infants born preterm are treated with antibiotics when bacterial infection is suspected. Antibiotics disrupt the gut microbiota, leading to unfavorable immune and infectious consequences. However, the impact of specific antibiotics on gut microbial and immune responses is largely unknown. We develop a humanized gnotobiotic mouse model where we gavage preterm infant stool into germ-free dams. We treat microbiota-humanized pups with subcutaneous antibiotics with probenecid to model empiric sepsis treatment regimens. Pups humanized with microbiota including ampicillin-resistant Enterobacteriaceae die during ampicillin with probenecid treatment with increased gut permeability and systemic microbial spread. Conversely, pups with microbiota containing gelatinase-expressing Enterococcus faecalis die during meropenem with probenecid treatment with increased gut E. faecalis and systemic immune dysregulation. Gut E. faecalis, especially strains containing gelE and fsr, increase in human preterm infant gut microbiomes after meropenem. These data raise concerns about the unintended consequences of antibiotic treatment and provide a framework for understanding microbiome-antibiotic-immune interplay.},
}

@article {pmid43009102,
year = {2026},
author = {Bouzid, YY and Oliver, A and Blecksmith, SE and Wilson, SMG and Alkan, Z and Huang, L and Bennett, BJ and Kable, ME and Stephensen, CB and Lemay, DG},
title = {Cross-Sectional Association between Fiber Intake and Gastrointestinal Inflammation is Dependent on FUT2 Secretor Status in Healthy Adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101938},
doi = {10.1016/j.tjnut.2026.101938},
pmid = {43009102},
issn = {1541-6100},
abstract = {BACKGROUND: Gut microbes consume mucins in the absence of dietary fermentable fiber. People with non-secretor alpha-1-2-L-fucosyltransferase 2 (FUT2) genotypes produce gastrointestinal (GI) mucins that lack terminal fucose and have increased risk for inflammatory bowel disease.

OBJECTIVES: This study aimed to determine whether associations between fiber intake and subclinical GI inflammation and/or microbiome function are modified by FUT2 genotype in healthy adults.

METHODS: We assessed interactions between fiber intake, FUT2 genotype, and GI inflammation markers in a cross-sectional observational study of healthy adults. Participants with 24-h dietary recalls and food frequency questionnaires to characterize recent and habitual diet, respectively, and fecal samples, plasma samples and/or shotgun metagenomes (n=297) were included in this analysis. Differences in microbiome composition between secretors and non-secretors were analyzed using PERMANOVA and machine learning. A custom-designed TaqMan[TM] probe was used to genotype a single nucleotide polymorphism (rs601338) to determine secretor status. ELISA was used to measure fecal calprotectin, myeloperoxidase, and neopterin, as well as plasma lipopolysaccharide binding protein. Short-chain fatty acids (SCFAs) were measured in fecal samples. Relationships between fiber intake, FUT2 genotype and outcomes were analyzed using linear mixed effect models.

RESULTS: Higher energy-adjusted total recent fiber, total habitual fiber, and soluble fiber intake was associated with lower calprotectin levels in secretors, but not in non-secretors. Overall microbiome composition did not differ by secretor status. However, the ratio of mucin-degrading to plant-degrading enzymes, Muc2Plant, in the gut microbiome was positively associated with increased fecal calprotectin in secretors, but not in non-secretors. There was no interaction between dietary fiber intake, the FUT2 genotype, and fecal SCFAs.

CONCLUSION: The association of higher dietary fiber intake with lower subclinical GI inflammation and lower mucin-degrading enzymes was observed in secretors, but not in non-secretors. Clinical trials in nutrition are needed to determine if non-secretors are less responsive to dietary fiber.},
}

@article {pmid43009116,
year = {2026},
author = {Zhao, X and Sun, Y and Ding, J and Fei, F and Gu, W and Qu, X and Wang, B and Jiang, X},
title = {Herbicide-based control of Spartina alterniflora disrupts microbial functional potential in a coastal wetland.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129508},
doi = {10.1016/j.envpol.2026.129508},
pmid = {43009116},
issn = {1873-6424},
abstract = {Herbicide-based control of invasive plants is increasingly implemented in coastal wetlands, yet the ecological consequences of herbicide residues for sediment microbiome-mediated biogeochemical functioning remain poorly understood. Here, we investigated how herbicide exposure associated with Spartina alterniflora management reshapes sediment microbial communities and biogeochemical potentials in Hangzhou Bay, China. Using metagenomic sequencing and a microbe-based Index of Functional Integrity (M-IFI), we quantified alterations in microbial potentials involved in methane, nitrogen, phosphorus, and sulfur cycling. Higher concentrations of haloxyfop and imazapyr were detected in areas subjected to herbicide-based management. Treated sediments exhibited lower α-diversity of methane-cycling genes, and more than 65% of reconstructed biogeochemical pathways had lower relative abundances, with reductions in methanogenesis-associated genes. Nitrogen and sulfur cycling pathways underwent extensive restructuring, whereas phosphorus acquisition, transport, and utilization potentials were broadly impaired. Genome-resolved analyses recovered 300 metagenome-assembled genomes and revealed distinct patterns of functional specialization and metabolic complementarity among microbial populations. Complete methane, nitrogen, and sulfur cycling potentials were sustained through community-level metabolic cooperation, whereas phosphorus cycling was disproportionately supported by a limited number of metabolically versatile populations. Herbicide exposure markedly decreased M-IFI values, with over 70% of treated sediments classified as moderately or severely disturbed. Collectively, our findings reveal that chemical control of invasive plants can impose hidden belowground ecological costs by disrupting microbiome-supported biogeochemical networks and reducing microbial functional integrity, highlighting the need to incorporate microbiome-based indicators into sustainable coastal wetland management.},
}

@article {pmid43009122,
year = {2026},
author = {Hu, SL and Yu, XW and Xue, R and Li, M and Zhou, XZ and Xu, JY and Gong, LK and Li, J and Peng, JJ and Juhasz, AL and Li, HB and Xue, XM},
title = {Arsenic Metabolism and Gut Microbiome Responses Following a Single Meal of Seaweeds in Humans.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129493},
doi = {10.1016/j.envpol.2026.129493},
pmid = {43009122},
issn = {1873-6424},
abstract = {Seaweeds are increasingly consumed as sustainable foods but contain high concentrations of organoarsenicals. However, their excretion kinetics, metabolic fate, and oral bioavailability in humans remain poorly understood. We conducted a four-day study with 54 volunteers on standardized diets supplemented with a single meal of either nori (Pyropia haitanensis) or kelp (Saccharina japonica). Total arsenic concentrations and arsenic species in urine and feces, gut microbiota composition, and carbohydrate-active enzyme genes were analyzed. Following seaweed consumption, urinary and fecal arsenic concentrations increased markedly during Days 1-2 and declined by Day 3, with urinary arsenic peaking approximately 14-30 h after ingestion. The urinary excretion factor of arsenic from nori was 6.3-fold higher than that from kelp. Phosphate arsenosugar from nori underwent extensive gastrointestinal transformation, with arsenobetaine accounting for 74.0-90.2% of fecal arsenic species. In contrast, sulfonate arsenosugar from kelp was less extensively transformed, with oxo- and thio-sulfonate arsenosugars remaining the predominant fecal arsenic species. This study offers valuable insights into the excretion kinetics, metabolism, and bioavailability of organoarsenicals from seaweeds.},
}

@article {pmid43009128,
year = {2026},
author = {Kain, V and Upadhyay, G and Suraksha, K and Li, S and Sundaraswamy, PM and Jayaprakash, J and Gowda, D and Chainani, N and Krishna, N and Ghobrial, M and Fouad, A and Hui, SP and Mishra, SP and Hall, N and Tan, Z and Soto, NH and Liu, R and Jain, S and Gowda, SGB and Yadav, H and Halade, GV},
title = {Multi-omics analyses of HFpEF progression and regression reveals multi-organ-specific metabolic dysregulation and impaired inflammation resolution.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {156838},
doi = {10.1016/j.metabol.2026.156838},
pmid = {43009128},
issn = {1532-8600},
abstract = {BACKGROUND: Heart failure with preserved ejection fraction (HFpEF) is a complex cardiometabolic syndrome with limited effective therapies. Given its heterogeneity, whether withdrawal of cardiometabolic stress reverses HFpEF-associated inflammatory, metabolic, and molecular remodeling remains unclear.

OBJECTIVES: To characterize multi-organ metabolic, molecular, and bioactive-lipid remodeling in an obesity-hypertension HFpEF model and determine the extent of recovery during an 8-week combined high-fat diet withdrawal and L-NAME cessation protocol using parallel multi-omics profiling.

METHODS: HFpEF was induced in C57BL/6 mice using a high-fat diet plus nitric oxide synthase inhibition(H + L). A regression cohort(R-H + L) underwent simultaneous return to standard chow and L-NAME cessation for 8 weeks. Multi-omics profiling included targeted and untargeted lipidomics, cardiac transcriptomics, metabolomics, fecal microbiome, and plasma short-chain fatty acid analyses, with detailed assessment of the left ventricle.

RESULTS: H + L mice developed an obesity-hypertension HFpEF phenotype characterized by predominant diastolic dysfunction, concentric remodeling, hypertension, and increased fat mass. The combined regression of H + L protocol attenuated these phenotypic abnormalities but did not restore all measures to control levels. H + L was associated with multi-organ remodeling marked by altered arachidonic acid-derived oxylipid pathways, depletion of triacylglycerols and phospholipids, and enrichment of diacylglycerols and lysophospholipids, consistent with altered resolution-related lipid signaling. Cardiac transcriptomics revealed changes in immune, circadian, vascular, and mitochondrial gene programs, whereas metabolomics revealed altered energy, arginine, and redox metabolism. H + L was also associated with reduced microbial diversity and altered short-chain fatty acids, particularly acetate and propionate. Within the 8-week recovery window, partial reprogramming occurred, but differences remained in lipid signaling, metabolic stress responses, and microbiome-associated measures.

CONCLUSIONS: The HFD/L-NAME model is accompanied by extensive multi-organ metabolic and molecular remodeling. Combined withdrawal of HFD/L-NAME attenuates the HFpEF phenotype however did not fully normalize molecular profiles within the 8-week recovery period. Persistent lipid-remodeling and metabolic dysregulation may represent potential therapeutic targets thus warrants pathway specific investigation.},
}

@article {pmid43009395,
year = {2026},
author = {Einarsson, GG and Elborn, JS and Sherrard, LJ and Carson, JP and Vardy, N and Adler, FR and Tunney, MM and Liou, TG and , },
title = {Airway microbial-inflammatory endotypes are associated with disease severity and predicted survival in cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.11.005},
pmid = {43009395},
issn = {1873-5010},
abstract = {BACKGROUND: The airway microbiome and host inflammatory response synergistically drive cystic fibrosis (CF) lung disease. We hypothesized that integrating airway microbial community structures with inflammatory biomarker profiles would reveal distinct ecological-inflammatory endotypes associated with clinical outcome measures.

METHODS: We performed a cross-sectional secondary analysis of 112 clinically stable people with CF. Baseline sputum microbial communities were profiled via 16S rRNA sequencing, clustered using partitioning around medoids and linked with previously quantified inflammatory biomarker data. Co-occurrence network analyses assessed microbial community organisation. Associations with time-to-next pulmonary exacerbation (PEx) and 5-year prognostic survival scores were evaluated utilizing Cox proportional hazards models and multivariable regression.

RESULTS: Two distinct ecological-inflammatory endotypes were identified. Endotype 1 (n = 65) exhibited higher microbial diversity, enrichment of oral-associated commensals (e.g., Prevotella, Veillonella), a highly interconnected co-occurrence network, and a moderated inflammatory milieu. Endotype 2 (n = 47) was characterized by Pseudomonas dominance, elevated neutrophilic inflammation (e.g., neutrophil elastase, IL-1β), and more advanced lung disease. The two-cluster solution was highly stable under repeated subsampling. Higher microbial diversity was independently associated with a more favourable 5-year prognostic survival score, including after adjustment for endotype membership. Endotype membership itself was not associated with time to subsequent PEx, and associations between ecological measures and PEx were attenuated after additional adjustment for baseline lung function.

CONCLUSIONS: Distinct ecological-inflammatory endotypes in the CF airway reflect differences in microbial community structure, inflammatory state and underlying disease severity. Longitudinal studies are required to determine the stability of these states and their relationship with subsequent clinical disease.},
}

@article {pmid43009614,
year = {2026},
author = {Wu, J and Li, L and Lai, Y and Li, J and Asthana, P and Zhai, L and Chen, L and Chen, M and Chen, B and Gurung, S and Lyu, J and Zhang, Y and Lu, L and Huang, S and Kuang, W and Shi, H and Luo, Y and Gou, Z and Kong, X and Wong, SH and Chan, KM and Yuan, S and Kwan, HY and Yuan, X and Huang, W and Ruan, Y and Lu, H and Wong, CC and Su, Y and Koohi-Moghadam, M and Lyu, A and Bian, Z and Ren, Y and Hu, X and Ma, Y and Wong, HLX},
title = {Microbiota-based modulation of intratumoral cholesterol metabolism for colorectal cancer treatment.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {43009614},
issn = {2522-5812},
support = {12102020//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 08793626//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; ITS/058/22MS//Innovation and Technology Commission (ITF)/ ; 32322091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070535//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82370601//National Natural Science Foundation of China (National Science Foundation of China)/ ; RC-RSRG/23-24/SCM/01//Hong Kong Baptist University (HKBU)/ ; RC-SFCRG/23-24/R2/SCM/01//Hong Kong Baptist University (HKBU)/ ; 2022A1515011302//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
abstract = {Excess cholesterol accumulates in colorectal cancer (CRC) and promotes its progression, yet systemic cholesterol-lowering has limited benefits and safety concerns. Here we show that redirecting intestinal cholesterol metabolism through the gut microbiota generates a metabolite, 4-cholesten-3-one (4-C-3), which suppresses CRC growth. A screen of microbial cholesterol metabolites showed that 4-C-3 is depleted in faecal and tumour samples from patients with CRC. 4-C-3 suppresses tumour growth in CRC cell lines, patient-derived organoids and xenografts. Mechanistically, 4-C-3 suppresses two major oncogenic drivers of CRC by inhibiting epidermal growth-factor receptor activation and stabilizing mutant oncogenic KRAS in an inactive state, thereby overcoming KRAS-driven resistance to anti-epidermal growth-factor receptor therapy. As proof of concept, restoring 4-C-3 using either Oscillibacter ruminantium, a natural 4-C-3 producer reduced in CRC, or a non-pathogenic Escherichia coli engineered to convert intestinal cholesterol into 4-C-3, lowered intratumoral cholesterol and induced tumour regression in preclinical models without overt toxicity. These findings uncover a microbiota-cholesterol metabolic pathway that can be harnessed through microbiome engineering to selectively target CRC and overcome therapy resistance.},
}

@article {pmid43009621,
year = {2026},
author = {Nachman, EJ and Wozniak, KJ and Danhof, HA and Di Rienzi, SC and Britton, RA},
title = {The small intestine microbiome: composition, host interactions and therapeutic potential.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {43009621},
issn = {1740-1534},
abstract = {The human microbiome, the collection of microorganisms that inhabit the human body, has been extensively studied over the past two decades and has been shown to play a critical part in health and disease. These research efforts renewed interest in developing microbial therapeutics to promote human health and treat disease. However, the vast majority of human gut microbiome research has been focused on fecal microbial strains and communities, leaving most of the gastrointestinal tract understudied. The dynamic environment of the small intestine provides distinct opportunities for microorganisms to interact with the host and diet. In this Review, we discuss the current state of research on the microbiome of the small intestine, how interactions between the small intestine and its microbiome influence host physiology, and we posit that small intestinal microorganisms are a unique source of novel therapeutics for treating human disease. Next-generation microbial therapeutics that emerge from the small intestinal microbiome are anticipated to be relevant to improving small intestinal diseases as well as systemic human health.},
}

@article {pmid43009709,
year = {2026},
author = {Damgaard, F and Justesen, US},
title = {Metagenomic evidence for persistent gut colonization of colibactin-producing Escherichia coli in colorectal cancer patients.},
journal = {Cancer causes & control : CCC},
volume = {37},
number = {12},
pages = {},
pmid = {43009709},
issn = {1573-7225},
mesh = {Humans ; *Polyketides/metabolism ; *Colorectal Neoplasms/microbiology ; *Escherichia coli/genetics/metabolism ; *Peptides/metabolism ; Female ; Male ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Escherichia coli Infections/microbiology ; Middle Aged ; Aged ; },
abstract = {Colibactin-producing Escherichia coli (pks[+] E. coli) has been linked to colorectal cancer (CRC) through double-strand DNA breaks and distinct mutational signatures. Whether gut colonization by pks[+] E. coli is persistent and has direct implications for whether it represents a modifiable risk factor in diagnosed patients. Based on whole-genome metagenomic sequencing data from 638 individuals it was found that pks[+] E. coli was significantly more prevalent in CRC patients (34.7%) than in controls (17.2%; OR = 2.76, 95% CI 1.86-4.09, p < 0.001). These findings indicate that colonization by pks[+] E. coli might not be confined to early carcinogenesis but may persist in a substantial proportion of CRC patients.},
}

Humans
*Polyketides/metabolism
*Colorectal Neoplasms/microbiology
*Escherichia coli/genetics/metabolism
*Peptides/metabolism
Female
Male
Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Escherichia coli Infections/microbiology
Middle Aged
Aged

@article {pmid43009760,
year = {2026},
author = {Li, S and Yu, Z and Jin, Y and Ma, K and Sha, L and Qian, M and Chen, X and Han, S},
title = {Gut microbiome and metabolite profiling in term SGA infants: a multi-omics approach to physical development.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43009760},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; Female ; Male ; Multiomics ; Infant, Newborn ; Case-Control Studies ; Prospective Studies ; *Infant, Small for Gestational Age/growth & development/metabolism ; Infant ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; },
abstract = {INTRODUCTION: Early-life gut microbial composition and fecal metabolic profiles may be altered in infants born small for gestational age (SGA), but evidence specifically concerning term SGA infants remains limited.

OBJECTIVES: To characterize gut microbial composition, predicted microbial functions, and fecal metabolite profiles in term SGA infants and explore their associations with early growth.

METHODS: This prospective nested case-control study included 62 term infants (31 SGA and 31 appropriate for gestational age [AGA]). Fecal samples were collected at 3 months. Untargeted metabolomics was performed in the full cohort, and shotgun metagenomic sequencing was conducted in a nested subset of 20 infants (10 SGA and 10 AGA). Differential taxa, KEGG orthologs (KOs), metabolites, and cross-omics correlations were analyzed.

RESULTS: Alpha diversity did not differ significantly between groups, whereas microbial composition and species-level abundance patterns differed between SGA and AGA infants. Functional analysis identified 135 differential KOs, including 36 with higher and 99 with lower abundance in the SGA group. These KOs were mapped to 25 metabolic pathways, including galactose, butanoate, D-amino acid, aromatic amino acid, fructose-mannose, pyruvate, propanoate, and lipid metabolism. Twelve fecal metabolite features differed between groups, including 5'-methylthioadenosine, taurocholate, β-alanine, and 17α-hydroxypregnanolone. Exploratory integration identified connections among microbial species, KOs, and metabolites. Several microbial and metabolite features showed nominal associations with 6-month growth indices, but most cross-omics and metabolite-growth associations did not remain significant after false discovery rate correction.

CONCLUSIONS: Term SGA infants showed differences in gut microbial composition, predicted metabolic potential, and fecal metabolite profiles at 3 months. Associations with subsequent growth were exploratory and require validation in larger longitudinal studies.},
}

Humans
*Gastrointestinal Microbiome
Feces/microbiology/chemistry
Female
Male
Multiomics
Infant, Newborn
Case-Control Studies
Prospective Studies
*Infant, Small for Gestational Age/growth & development/metabolism
Infant
*Bacteria/classification/genetics/isolation & purification/metabolism
*Metabolome
Metabolomics/methods
Metagenomics/methods

@article {pmid43009769,
year = {2026},
author = {Li, Y and Chen, Y and Pu, R and Zhu, Z and Wang, T and Li, Y and Liu, J},
title = {Machine learning-based analysis of behavioral and dental plaque microbiome features associated with dental caries in 5-year-old children from urban and rural Yunnan.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {43009769},
issn = {1471-2180},
support = {2022QN001//Youth Research Fund of Yunnan Provincial Clinical Research Center for Oral Diseases/ ; XDYC-YLWS-2023-0047//Xingdian Talent Support Plan of Yunnan Province-Medical and Health Talents Special Project/ ; },
mesh = {Humans ; *Dental Caries/microbiology/epidemiology ; Child, Preschool ; *Dental Plaque/microbiology ; *Machine Learning ; China/epidemiology ; *Microbiota ; Female ; Rural Population/statistics & numerical data ; Male ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Urban Population ; Surveys and Questionnaires ; Oral Hygiene ; Feeding Behavior ; },
abstract = {BACKGROUND: This study aimed to integrate questionnaire-based oral health behavior data with dental plaque microbiome profiles to identify behavioral and microbiological factors associated with dental caries among 5-year-old children from urban and rural areas of Yunnan Province. It also evaluated the performance of these features in machine learning classification models.

METHODS: This study included children from Fengqing County (rural) and Hongta District (urban) in Yunnan Province, who were categorized into a caries-free (CF) group and a dental caries (DC) group based on their caries status. Dietary habits, oral hygiene practices, and regional background data were collected using a questionnaire. Dental plaque samples were collected simultaneously for 16 S rRNA gene sequencing. Based on the relative abundances of the microbial community at the phylum and genus levels, differences in microbial profiles were compared between children with different caries statuses and across regions. Random forest, least absolute shrinkage and selection operator (LASSO), and other machine learning models were employed to identify key microbial features and evaluate the performance of these features, together with relevant behavioral variables, in classifying caries status.

RESULTS: Questionnaire analysis revealed significant differences between the DC and CF groups in location, frequency of dessert consumption, and nighttime post-brushing sugar intake (NPSI). By location, Fengqing County and Hongta District differed significantly in NPSI and use of fluoridated toothpaste. Plaque microbiome analysis revealed significant phylum-level differences between the DC and CF groups, particularly in Bacteroidetes, Fusobacteria, and Proteobacteria. A phylum-level diagnostic model identified Fusobacteria as a key discriminative variable (area under the curve [AUC] = 0.737). LASSO analysis identified three genera-Capnocytophaga, Haemophilus, and Comamonas-with Capnocytophaga contributing to diagnostic performance (AUC = 0.720). Incorporating location, dessert consumption, and NPSI further improved model performance (AUC = 1.000).

CONCLUSION: Behavioral factors, regional background, and dental plaque microbial characteristics are jointly associated with the risk of dental caries in 5-year-old children, suggesting that regional differences may partially reflect underlying socioeconomic conditions. However, as these findings are correlational, further validation is required.},
}

Humans
*Dental Caries/microbiology/epidemiology
Child, Preschool
*Dental Plaque/microbiology
*Machine Learning
China/epidemiology
*Microbiota
Female
Rural Population/statistics & numerical data
Male
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Urban Population
Surveys and Questionnaires
Oral Hygiene
Feeding Behavior

@article {pmid43009984,
year = {2026},
author = {Lu, Q and Zhou, D and Yang, R and Ban, Y and Gao, C and Li, P and Wang, J and Dai, Y and Yang, Y and Chen, R and Xie, S and Tian, X},
title = {Effects of different feeding regimes on growth performance, antioxidant activity, rumen fermentation, rumen microbiota and rumen metabolism in beef cattle.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {43009984},
issn = {1746-6148},
support = {Qiankehe Foundation [2024] Youth 106//Basic Research Program (Natural Science) Youth Guidance Project of Guizhou Province/ ; Qianjiaoji [2024] 33//Youth Science and Technology Talent Development Project of Guizhou Province/ ; none//the Agriculture and Rural Affairs Department Project of Guizhou Province (Exploration and Utilization of Excellent Germplasm Resources of Guanling Cattle)/ ; Qiankexie KJLYRC-[2026] 078//Science and Technology Project of Guizhou Province/ ; 32260849 and 32302779//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology/metabolism/physiology ; *Rumen/microbiology/metabolism ; *Antioxidants/metabolism ; Fermentation ; *Diet/veterinary ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Male ; Animal Nutritional Physiological Phenomena ; },
abstract = {BACKGROUND: The feeding regime significantly impacts on the production performance, ruminal fluid microbiota, and metabolites of ruminants. However, studies comparing the microbial metagenomics and metabolites in ruminal fluid of beef cattle fed pasture-based grazing and housed total mixed ration (TMR) feeding regimes have rarely been reported.

METHODS: Forty healthy Guanling beef cattle were divided into two equal groups according to a randomized complete block design. The pasture-based grazing group (BG) was allowed to the grazing period was 08:00-18:00 at a natural ranch. The housed TMR feeding group (BB) was reared under a housed feeding system and fed a TMR diet. Each treatment consisted of 20 beef cattle, and the experimental period lasted for 90 d. The metagenomics and metabolomics were used analysis ruminal fluid microbiota and metabolism.

RESULTS: The results indicated that the BB group showed significantly higher levels of average daily gain, total antioxidant capacity, catalase, 2,2-diphenyl-1-picrylhydrazyl scavenging activity, ammonia nitrogen, and volatile fatty acid (P < 0.05), whereas it had significantly lower levels of malondialdehyde and hydroxyl free radical relative to the BG group (P < 0.05). Compared with the BB group, the BG group exhibited a significantly increased (P < 0.05) abundance of Bacillota at the phylum level but a significantly decreased (P < 0.05) abundance of Prevotella at the genus level. The modules associated with these relative abundance levels (Reductive citrate cycle (Arnon-Buchanan cycle), and Guanine ribonucleotide degradation, GMP = > Urate) were significantly more important in the BG group (P < 0.05) than in the BB group. Glycosyltransferase 2_Glycos_transf_2 was significantly enriched in the BB group, whereas glycoside hydrolase (GH)3, GH78, and GH36 were significantly enriched in the BG group. Metabolomic analysis revealed that linoleic acid metabolism was the dominant pathway in the rumen.

CONCLUSION: Overall, the housed TMR-fed cattle enhanced growth performance, antioxidant activity, rumen fermentation, and Prevotella abundance, whereas the pasture-based grazing fed cattle enhanced Bacillota abundance and linoleic acid metabolism.},
}

Animals
Cattle/growth & development/microbiology/metabolism/physiology
*Rumen/microbiology/metabolism
*Antioxidants/metabolism
Fermentation
*Diet/veterinary
Animal Feed/analysis
*Gastrointestinal Microbiome
Male
Animal Nutritional Physiological Phenomena