@article {pmid41742032,
year = {2026},
author = {Zhang, J and Dai, Y and Mustafa, A and Li, L and Li, Y and Sun, T and Chen, M and Yang, H and Ma, J},
title = {Terracing influences soil microbial assembly in citrus orchards: stochastic processes dominate community dynamics in a karst sloping land.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41742032},
issn = {1471-2180},
support = {GUIKE AB22080071//Guangxi Key Research and Development Program/ ; AA20161002//Science and Technology Major Project of Guangxi/ ; },
abstract = {BACKGROUND: Terracing is a key soil conservation practice in karst citrus orchards, yet its long-term effects on rhizosphere microbial community assembly remain poorly understood, especially the relative influence of deterministic (e.g., environmental filtering) versus stochastic processes (e.g., dispersal limitation).

RESULTS: We investigated rhizosphere soil microbial communities along a terrace chronosequence (0–12 years) in the Lijiang River Basin using MiSeq sequencing and metabolomics, with null model analysis employed to assess community assembly processes. Terrace age did not significantly affect microbial α-diversity, but was associated with subtle changes in community composition: Proteobacteria, a copiotrophic group, decreased slightly, while Chloroflexi, an oligotrophic group, increased modestly. These shifts suggest a weak trend toward lower soil nutrient availability rather than a clear successional reorganization. Microbial diversity and structure were significantly correlated with soil stoichiometric ratios and available phosphorus (p < 0.05). Terracing also affected microbial network complexity and potential function. Potential functional profiling and metabolome data revealed that L-glutamine, a key nitrogen source, was negatively correlated with potential catabolic nitrate reduction (p < 0.05). This relationship was most pronounced at the Y5 phase (peak diversity/network complexity), suggesting accelerated L-glutamine utilization tightly coupled with enhanced potential for dissimilatory nitrate reduction to maximize nitrogen-use efficiency during the successional climax. Notably, stochastic processes explained over 96% of the microbial assembly. Bacterial communities were primarily driven by homogenizing dispersal, while fungal communities followed undominated processes.

CONCLUSION: The prominence of stochasticity in our results complements current understanding of agricultural microbiome assembly, particularly emphasizing its vital role in fragile karst environments. We propose that optimizing terrace rotation intervals (e.g., every 5-year) could be a practical strategy to enhance nitrogen-cycling efficiency and support sustainable nutrient management in karst citrus cultivation.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04811-4.},
}

@article {pmid41749104,
year = {2026},
author = {Baz, L},
title = {Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41749104},
issn = {1471-2164},
abstract = {BACKGROUND: Archaea are a major domain of life that inhabit diverse and often extreme environments, contributing to biogeochemical cycles and participating in nutrient cycling within plant rhizospheric soils. This study applies metagenomic whole-genome shotgun sequencing to characterize the archaeal component of the rhizospheric microbiome associated with the wild plant species Moringa oleifera in Saudi Arabia.

RESULTS: Based on KEGG-annotated enzymes, Thaumarchaeota and Euryarchaeota emerged as the predominant archaeal phyla in the rhizosphere, with higher abundance than in bulk soil. The most abundant archaeal enzymes were assigned to metabolic pathways related to nitrogen and sulfur metabolism, carbon transformations, and responses to oxidative stress, indicating a putative contribution to nutrient turnover and stress-related functions. Network analysis further identified archaeal chemotaxis-related regulators and two-component sensor kinases linked to the root–soil interface. Key enzymes detected included urease, glutamine synthetase, thiosulfate sulfurtransferase, and catalase-peroxidase.

CONCLUSIONS: These findings suggest that archaeal communities form a distinct functional module within the M. oleifera rhizosphere, potentially influencing soil nutrient dynamics and plant performance. The chief limitation is reliance on DNA-based metagenomic data from a single site and time point, without multi-omics or detailed soil characterization, restricting temporal and ecological generalization. Nonetheless, the dataset provides a genome-scale view of archaeal functional potential and offers testable directions for future experimental and process-oriented studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12700-3.},
}

@article {pmid41896654,
year = {2026},
author = {Li, Y and Fu, W and Xiang, Z and Zhao, M and Xie, X and Guo, W and Zhou, Y and Zheng, M and Yang, J},
title = {Characteristics of gut microbiota and metabolites in patients with metabolic dysfunction-associated steatotic liver disease and colorectal adenoma.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41896654},
issn = {2045-2322},
support = {2021J0252//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2025J0270//Scientific Research Fund Project of Yunnan Provincial Department of Education/ ; 2024B010//Innovation Fund for Postgraduate Education of Kunming Medical University/ ; 202501AY070001-088//Science and Technology Plan Project of Yunnan Provincial Department of Science and Technology/ ; 82160106//National Natural Science Foundation of China/ ; },
abstract = {UNLABELLED: Metabolic dysfunction-associated steatotic liver disease (MASLD) has become one of the most prevalent chronic liver conditions worldwide, with its incidence steadily rising. However, the underlying mechanisms linking MASLD to colorectal adenoma remain unclear, and the role of gut microbiota and metabolites in this association requires further investigation. This study aims to characterise the gut microbiota and metabolites in patients with MASLD and colorectal adenoma. A cohort of 58 MASLD patients was enrolled and stratified into two groups based on colorectal adenoma status: the MASLD with colorectal adenoma group (M-CA group, n = 30) and the MASLD without colorectal adenoma group (M-NCA group, n = 28). The gut microbial ecosystem in the M-CA group showed significant dysregulation, evidenced by a decreased Gut Microbiome Health Index (GMHI) and significantly increased Microbiome Dysbiosis Index (MDI). Linear Discriminant Analysis Effect Size (LEfSe) identified 75 differentially abundant microbial taxa between groups, with Bacteroides vulgatus, Bacteroides ovatus, uncultured bacterium of norank genus of Muribaculaceae family, Muribaculaceae, and norank of Muribaculaceae family being significantly enriched in the M-CA group, representing potential microbial biomarkers for this cohort. Partial Least Squares Discriminant Analysis (PLS-DA) screened 116 differential metabolites. When combined with Random Forest (RF), Support Vector Machine (SVM) and Least Absolute Shrinkage and Selection Operator (LASSO) machine learning algorithms, 16 significantly identified biomarkers were discovered. The joint analysis of both omics revealed that variations in differential metabolite levels were associated with changes in specific microbiota abundances. Kyoto encyclopedia of genes and genomes (KEGG) functional prediction analysis indicated that the coordinated alterations in metabolites and microbiota may collectively influence multiple metabolic pathways, including lipid metabolism, xenobiotics biodegradation and metabolism, amino acid metabolism, carbohydrate metabolism, biosynthesis of other secondary metabolites and nucleotide metabolism. This study revealed that patients with MASLD and colorectal adenoma exhibited significant alterations in the gut microbiota composition and metabolic profile, indicating potential impacts on associated metabolic pathways. These findings provided novel insights and a foundation for future research into potential intervention strategies for this clinical complication.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45782-w.},
}

@article {pmid41915463,
year = {2026},
author = {Yasavoli-Sharahi, H and Shahbazi, R and Alsadi, N and Sahebi, NB and Cuenin, C and Cahais, V and Chung, FF and Herceg, Z and Matar, C},
title = {Lentinula edodes Cultured Extract Intake at Puberty Mitigates Inflammatory Signals at the Mammary Glands by the Involvement of Epigenetic Mechanisms in BALB/c Mice.},
journal = {The breast journal},
volume = {2026},
number = {1},
pages = {e2122220},
doi = {10.1155/tbj/2122220},
pmid = {41915463},
issn = {1524-4741},
support = {532223-18//Natural Sciences and Engineering Research Council of Canada/ ; 2019-01497//AHCC Research Association, and New Frontiers in Research Fund-Exploration (NFRF/ ; //University of Ottawa/ ; },
mesh = {Animals ; Female ; Mice ; Mice, Inbred BALB C ; *Epigenesis, Genetic/drug effects ; DNA Methylation/drug effects ; *Mammary Glands, Animal/drug effects/metabolism ; Lipopolysaccharides ; *Shiitake Mushrooms/chemistry ; Sexual Maturation ; MicroRNAs/metabolism ; *Inflammation ; },
abstract = {Exposure to immune stress or lipopolysaccharide (LPS) during critical developmental stages like puberty may lead to gut microbiome dysbiosis and epigenetic dysregulation in mammary glands, affecting gene expression and potentially elevating breast cancer susceptibility in adulthood. Although LPS's adverse impacts on intestinal and brain functions are well-documented, its effects on mammary glands remain underexplored. Using an immunocompetent BALB/c mouse model, we administered an acute LPS dose (1.5 mg/kg body weight) during puberty. The study evaluated the long-term consequences of LPS exposure alone and combined with AHCC (Lentinula edodes cultured extract, 2 g/kg body weight/day) on DNA methylation patterns, cytokine profiles, and microRNA expression in mammary glands at 9 weeks of age. Analyses included DNA methylation sequencing, multiplex immunoassays, quantitative PCR, and image processing. Pubertal LPS exposure produced persistent molecular dysregulation in mammary glands, including differential DNA methylation (> 5% change vs. control; FDR-adjusted p < 0.05), elevated inflammatory mediators, and altered microRNA expression. Differentially methylated regions were enriched in regulatory features, with decreased methylation at transcription start sites, promoters, and 5' UTRs of genes implicated in mammary development and oncogenic signaling (including Vav3, Pdgfa, Pdgfc, Jag2, Hras, Ksr1, Il2rb, Il17b, and Il17rb) in the LPS group, whereas the AHCC + LPS group exhibited a shift toward hypermethylation at these loci (approximately 5%-10% decrease). Inflammatory profiling showed increased IL-17A/F (∼2-fold vs. control; p < 0.05), while microRNA analyses indicated reduced let-7a/c (∼30% vs. control; p < 0.05). Notably, miR-130a and miR-34a increased ∼1.5-fold across all treatment groups relative to control. Pubertal LPS exposure induces enduring epigenetic and inflammatory changes in mammary glands that may heighten breast cancer risk. AHCC's mitigating role indicates potential for dietary interventions to counteract these effects.},
}

Animals
Female
Mice
Mice, Inbred BALB C
*Epigenesis, Genetic/drug effects
DNA Methylation/drug effects
*Mammary Glands, Animal/drug effects/metabolism
Lipopolysaccharides
*Shiitake Mushrooms/chemistry
Sexual Maturation
MicroRNAs/metabolism
*Inflammation

@article {pmid41915473,
year = {2026},
author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C},
title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117166},
doi = {10.1016/j.celrep.2026.117166},
pmid = {41915473},
issn = {2211-1247},
abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.},
}

@article {pmid41915616,
year = {2026},
author = {Wei, Y and Ji, X and Mao, Y and Liu, Y and Li, Y},
title = {Gut Microbiome, Immune Cells, and Heart Failure: A Multi-Omics Mendelian Randomization Study.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000550655},
pmid = {41915616},
issn = {1421-9751},
abstract = {INTRODUCTION: The global burden of heart failure is escalating, marked by persistently rising prevalence, incidence, and mortality. The emerging hypothesis that the gut microbiome, as a modifiable factor, influences HF pathogenesis through immune modulation.

METHODS: To examine the causal relationship, we conducted two-sample Mendelian randomization (MR) analyses using summary genetic data, which was obtained from genome-wide association studies (GWASs) of gut microbial taxa, immune cells, and HF. Single-cell RNA sequencing data and single-nucleus RNA sequencing from chronic heart failure and healthy samples were extracted for investigation. Expression quantitative trait loci (eQTL) MR analysis was used to integrate HF GWAS with eQTL from heart to confirm potential genes. We performed functional enrichment analysis to enrich their functions.

RESULTS: The analysis revealed that genus Blautia (p = 0.0287), genus Corynebactrium (p = 0.022), genus Demequina (p = 0.0064), genus Enterococcus (p = 0.0307), genus Eubacterium (p = 0.0234), genus F0482 (p = 0.0107), genus Leclercia (p = 0.0026), genus Prevotellamassilia (p = 0.0444), and genus Ruminococcus were causally linked to a higher risk of HF, while genus CAG-125 (p = 0.0443), genus CAG-245 (p = 0.0116), genus Fournierella (p = 0.0326), genus Roseibacillus (p = 0.028) protective factors for HF. Among differential microflora, genus Leclercia was significantly related to higher level of HVEM on terminally differentiated CD4+T-cell count (p = 0.0058). Moreover, HF patients underwent obviously increased NK/T cells. We identified positive association of EIF3A, RPL5, SLC25A51, HERC5, SUSD3, ZNF292, ZNF655, and DNAJC9 with increased risk of HF, whereas the expression of RMC1, CAMK2G, RPS26, ATP5PO displayed protective effect against HF by eQTL MR analysis; they were mainly enriched in myc-Targets-V1, IFN-γ-response, IFN-α-response, PI3K/AKT/mTOR signaling, TGF-beta signaling, allograft rejection, notch signaling pathways, angiogenesis, epithelial mesenchymal transition, UV-response-DN, hedgehog signaling, myogenesis.

CONCLUSION: Our multi-omics MR study uncovered the causality of gut microbiome on immune cells and HF. Genus Leclercia-related changes in T cells may present as a viable focus for HF. This offers new insights into mechanisms and therapy of gut microbiome-mediated HF.},
}

@article {pmid41915730,
year = {2026},
author = {Negahban, M and Msaada, K},
title = {Beyond the crop: the role of medicinal and aromatic plants in soil carbon sequestration and nitrogen cycling.},
journal = {International journal of environmental health research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/09603123.2026.2653197},
pmid = {41915730},
issn = {1369-1619},
abstract = {Medicinal and aromatic plants (MAPs) play a critical yet underexplored role in enhancing soil functionality through their unique phytochemical interactions and ecological adaptability. This review synthesizes current research on how MAPs influence soil carbon sequestration and nitrogen cycling, positioning them as multifunctional agents in sustainable agroecosystems. Unlike conventional crops, MAPs release complex secondary metabolites, such as flavonoids, alkaloids, terpenoids, and phenolics, which modulate microbial diversity, enzymatic activity, and nutrient transformation. These compounds shape the rhizosphere microbial communities, facilitate nitrogen fixation and mineralization, and contribute to soil organic matter (SOM) stabilization through rhizosphere priming and humus formation. Integrated approaches, such as intercropping, agroforestry, and organic amendments, enhance these benefits, while mitigating allelopathic effects and improving carbon and nitrogen fluxes. This review further explores technological innovations including remote sensing (RS), biochar applications, and nanotechnology, which support MAP-based climate-resilient agriculture. Case studies across diverse geographies demonstrate MAPs' potential to restore degraded soils, reduce greenhouse gas emissions, and improve phytochemical yields. Overall, MAPs offer a promising model for regenerative, low-input farming systems that align ecological integrity with economic viability. By actively engineering the soil environment, MAPs emerge not only as botanical resources but also as ecological catalysts in the transition to sustainable agriculture.},
}

@article {pmid41916054,
year = {2026},
author = {Pongmanee, K and Rassmidatta, K and Lee, TY and Lin, JS and Chaosap, C and Adeyemi, KD and Ruangpanit, Y},
title = {Influence of synbiotic supplementation on performance, fecal consistency, cecal microbiome, and egg quality of hens during late laying phase.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106851},
doi = {10.1016/j.psj.2026.106851},
pmid = {41916054},
issn = {1525-3171},
abstract = {Hens in the late laying phase often experience age-related physiological constraints that may reduce production efficiency, eggshell quality, and welfare. This study evaluated the effects of dietary synbiotic supplementation on laying performance, egg quality, fecal characteristics, and the cecal microbiome of late-phase laying hens. A total of 240 Lohmann Brown hens (50 weeks old) were distributed into 20 replicates and randomly assigned to a corn-soybean control diet or the same diet supplemented with 100 mg/kg synbiotic (SYNLAC Prime®) for 22 weeks. Synbiotic supplementation did not affect egg production or egg mass but significantly reduced feed intake (P = 0.036). It also improved eggshell quality by decreasing the proportion of cracked eggs (P = 0.014) and increasing eggshell weight (P = 0.049) and shell thickness (P = 0.031). Fecal score and moisture content were not affected; however, synbiotic-fed hens showed lower fecal ammonia concentration (P = 0.033). Synbiotic supplementation increased both alpha and beta microbial diversity in the cecum. While microbial composition at higher taxonomic levels was largely unchanged, the relative abundances of Ruminococcaceae and Lachnospiraceae increased, whereas those of Bacteroidaceae and Clostridiaceae decreased. At the genus level, synbiotic supplementation increased Faecalibacterium, Ruminococcus, and Lactobacillus, while reducing Bacteroides and Alistipes. Functional prediction analysis indicated that synbiotic supplementation upregulated 12 cecal metabolic pathways and downregulated two pathways. Overall, synbiotic supplementation improved eggshell quality, promoted beneficial gut microbial populations, and reduced fecal ammonia emissions, suggesting its potential as a dietary strategy to support productivity and gut health in hens during the late laying phase.},
}

@article {pmid41916081,
year = {2026},
author = {Machado, P and Mazahery, H and Black, LJ and Tremlett, H and Daly, A and Pham, NM and Tessema, GA and Zhu, F and Banwell, B and Bar-Or, A and Marrie, RA and Bernstein, CN and Mirza, AI and Yeh, EA and Waubant, E and O'Mahony, J and Dunlop, E and , },
title = {Higher ultra-processed food consumption is associated with higher likelihood of paediatric-onset multiple sclerosis.},
journal = {Multiple sclerosis and related disorders},
volume = {109},
number = {},
pages = {107159},
doi = {10.1016/j.msard.2026.107159},
pmid = {41916081},
issn = {2211-0356},
abstract = {BACKGROUND: Diets are increasingly dominated by ultra-processed foods, which have been linked to several chronic diseases. Emerging evidence suggests an association between ultra-processed food consumption and inflammatory diseases, including multiple sclerosis (MS).

OBJECTIVE: To assess associations between consumption of ultra-processed foods and paediatric-onset MS (PoMS).

METHODS: We used data from the microbiome sub-study of the Canadian Pediatric Demyelinating Disease Network Study for PoMS cases (symptom onset aged <18 years) and unaffected controls. Data on consumption of ultra-processed foods (defined within the Nova system) were derived from dietary intake data collected using the Block Kids Food Screener. Dietary contribution of ultra-processed foods (% of total grams consumed per day) was estimated. Logistic regression models were used to examine associations between ultra-processed food consumption (continuous and tertiles) and likelihood of PoMS. Models were adjusted for age at dietary data collection, sex, race, region of residence, and total energy intake.

RESULTS: Dietary data were collected from PoMS participants (females=57, males=23) aged 5-28 years and controls (females=30, males=16) aged 8-26 years. Each additional 10% in ultra-processed food consumption was associated with a 35% higher odds of being a PoMS participant (adjusted odds ratio [aOR]=1.35, 95% CI 1.05, 1.73). Participants in the highest (versus lowest) tertile for ultra-processed food consumption had over five times higher odds of being a PoMS participant (aOR=5.30, 95% CI 1.36, 20.70).

CONCLUSION: Participants with PoMS reported greater consumption of ultra-processed foods compared to unaffected peers. More comprehensive longitudinal dietary histories are required to better understand this observation.},
}

@article {pmid41916092,
year = {2026},
author = {Qiu, C and Jie, W and Qian, Y and Lu, X and Chen, Y and Si, M},
title = {Ageing of the Oral Mucosa: Mechanisms and Consequences.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109482},
doi = {10.1016/j.identj.2026.109482},
pmid = {41916092},
issn = {1875-595X},
abstract = {Oral mucosal ageing represents a fundamental reprogramming of the tissue microenvironment, a dynamic process that underlies the functional decline and heightened disease susceptibility observed in the elderly. This review synthesises current evidence to reconceptualise oral mucosal ageing as an active reprogramming of the tissue microenvironment, delineating the interplay between structural, molecular, and immunological changes, and exploring how these alterations drive functional decline and increase susceptibility to age-related oral diseases. Through a comprehensive analysis of experimental and clinical studies from human and animal models, we demonstrate that the ageing process fundamentally transforms the oral mucosa. Key findings include structural changes such as epithelial atrophy, extracellular matrix remodelling, and salivary gland degeneration, driven molecularly by genomic instability, accumulation of proinflammatory senescent cells, stem cell exhaustion, and dysregulated stress responses. These are compounded by an immunological state of 'inflammaging' and functional decline in innate and adaptive immunity, further exacerbated by shifts in the oral microbiome. Collectively, these deficits lead to impaired regeneration, diminished sensory function, and reduced salivary secretion, creating a permissive landscape for chronic oral diseases. In conclusion, oral mucosal ageing is a dynamic process of microenvironmental reprogramming driven by cellular senescence, immunosenescence, and structural decay. This actively underpins the heightened vulnerability to oral disease in the elderly, providing a mechanistic foundation for developing targeted interventions to preserve oral health in ageing populations.},
}

@article {pmid41916240,
year = {2026},
author = {Wen, S and Liu, J and Lin, B and Li, N and Diao, X},
title = {Aging enhances the ecological toxicity of polyethylene microplastics to marine medaka larvae (Oryzias melastigma).},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129493},
doi = {10.1016/j.jenvman.2026.129493},
pmid = {41916240},
issn = {1095-8630},
abstract = {Microplastics (MPs), widely distributed in marine environments, pose urgent ecological risks as emerging contaminants. However, current ecological risk assessments are largely based on the commercially produced MPs, which poorly represent in natural settings. Here, we simulated the natural aging of polyethylene MPs (PE-MPs) using ultraviolet radiation (UV) and Fenton reactions, characterized the resultant physicochemical changes, and assessed their ecological toxicity in marine medaka larvae over a 30-day exposure experiment. Short-term aging via UV and Fenton reactions primarily altered the physical properties of PE, including surface morphology, hydrophobicity, and Zeta potential. Both original and aged PE induced intestinal damage and oxidative stress in the larvae, indicating that aged PE retains its toxicity. In contrast, aged PE significantly altered the microbial community structure in the fish intestines: Roseibacillus was significantly enriched in the UV-aged polyethylene (UVPE) exposure group, while Ruegeria and Pseudomonas were enriched in the Fenton-aged polyethylene (FPE) exposure group. Functional predictions of the intestinal microbial communities indicated that exposure to FPE resulted in the upregulation of metabolism-related functions, whereas exposure to UVPE significantly downregulated similar functions. Such upregulation likely reflects microbiome reprogramming under stress rather than improved health. Overall, our study demonstrated that aged PE exhibited pronounced toxicity to marine fish and their larvae by altering gut microbiota, and thus significantly impacting energy metabolism and nutrient absorption, leading to detrimental effects on their growth and development. These findings further underscore the enhanced ecological toxicity effects of aged MPs on marine organisms, highlighting the need for better assessments of the adverse impacts of MPs in marine environments.},
}

@article {pmid41916289,
year = {2026},
author = {Chen, S and Wang, Y and Chen, B and Hou, X and Liu, S and He, S and Qi, J and Peng, Z and Pan, H and Liang, C and Wei, G and Jiao, S},
title = {Diversity-triggered 2-naphthoic acid exudation recruits keystone microbial taxa to promote soybean drought tolerance.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.002},
pmid = {41916289},
issn = {1934-6069},
abstract = {Rhizosphere microbiomes are essential for plant growth and stress tolerance, yet how microbial diversity shapes drought resilience in soybean remains unclear. Here, we demonstrate that high rhizosphere microbial diversity, generated via dilution-to-extinction manipulation of soil microbiome diversity, improves soybean performance under drought. Integrated metabolomic and transcriptomic analyses identify 2-naphthoic acid as a diversity-induced root exudate that accumulates exclusively under drought. This metabolite selectively recruits Sinorhizobium CS204 via chemotaxis and ATP-binding cassette (ABC) transporter-mediated uptake, as confirmed by in vitro substrate utilization assays and targeted mutant construction. Molecular docking and microscale thermophoresis reveal direct interactions between this metabolite and nitrogen-cycling proteins, enhancing denitrification and nitrogen fixation of S.CS204. Co-application of 2-naphthoic acid and S.CS204 significantly improves plant nutrient acquisition and photosynthesis under drought. Collectively, our study underscores the pivotal role of rhizosphere microbial diversity in triggering the exudation of root metabolites to recruit keystone taxa, establishing microbe-plant synergies that bolster drought tolerance.},
}

@article {pmid41916309,
year = {2026},
author = {Cichy, A and Dewan, A and He, Z and Fitzgerald, C and Ratkowski, M and Krasewicz, J and Ozarkar, V and Kaye, S and Teng, T and Zhang, J and Feinstein, P and Bozza, T},
title = {A microbiome-derived olfactory signal regulates inter-male aggression and social dominance in mice.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.03.009},
pmid = {41916309},
issn = {1879-0445},
abstract = {Many species use microbiome-derived metabolites as chemosensory cues, yet the chemicals involved and the sensory pathways that detect and process them remain poorly understood. Trimethylamine (TMA) is a volatile metabolite that is produced by the gut microbiome and selectively accumulated in the urine of sexually mature male mice. Here, we show that TMA regulates inter-male aggression and social dominance by activating trace amine-associated receptor 5 (TAAR5) in the main olfactory system. In wild-type mice, early aggressive behavior during male-male encounters strongly predicts eventual social status: dominant males initiate more attacks, whereas subordinate males display more defensive behaviors. Deletion of TAAR5 eliminated this asymmetry, with dominant and subordinate mice showing similar levels of aggressive and defensive behaviors. Strikingly, restoring TAAR5 expression in olfactory sensory neurons (OSNs) rescued the behavioral asymmetry, indicating that this effect is mediated by the main olfactory system and arguing against contributions from proposed TAAR5 expression in the brain. Finally, pharmacological suppression of microbial TMA production reduced inter-male aggression, and this effect was reversed by painting treated males with TMA, showing that microbiome-derived TMA is the key volatile ligand for TAAR5 in this context. Taken together, our findings identify TMA as a critical olfactory cue that signals the presence of sexually mature males and facilitates social hierarchy formation. More broadly, our results demonstrate that a microbiome-derived metabolite can shape mammalian social interactions through the main olfactory system and uncover a previously unrecognized role for the TAAR family in regulating social behavior.},
}

@article {pmid41916434,
year = {2026},
author = {Iachizzi, M and Zajac, N and Ruiz, JL and Güller, T and Rabin, R and Schalbetter, S and de Cillis, F and Moccia, MD and Cattaneo, A and Cryan, JF and Richetto, J},
title = {Probiotic treatment rescues behavioral deficits and gut microbial abnormalities induced by preconceptional stress in mothers and offspring.},
journal = {Brain, behavior, and immunity},
volume = {136},
number = {},
pages = {106571},
doi = {10.1016/j.bbi.2026.106571},
pmid = {41916434},
issn = {1090-2139},
abstract = {Depression and anxiety during pregnancy are major public health concerns with lasting consequences for mother and child. Although the gut microbiome contributes to stress and mood regulation, its role in preconceptional stress and transgenerational outcomes remains unclear. Here, we examined behavioral, microbial, and thalamic transcriptional effects of preconceptional social isolation rearing (SIR) in female mice and tested whether maternal probiotic supplementation mitigates these alterations. SIR females displayed increased anxiety-like and social-avoidant behavior, reduced gut microbial diversity, depletion of Odoribacter, Tuzzerella, and Alloprevotella, and enrichment of Bacteroides and Lachnospiraceae. A multispecies probiotic (Lactobacillus rhamnosus HN001, L. acidophilus La-14, Bifidobacterium lactis HN019) reversed these behavioral and microbial changes. Adult offspring of SIR dams showed sex-dependent behavioral deficits and microbial alterations partly reflecting maternal patterns. Prenatal SIR was associated with reduced thalamic Bdnf expression in offspring and altered Grin2a/2b selectively in males. In contrast, prenatal probiotic exposure exerted broader transcriptional effects and restored Bdnf levels in SIR offspring. SIR-induced increases in Lachnospiraceae were transmitted to offspring, whereas reductions in Ruminococcaceae were normalized by maternal probiotic treatment. Predicted functional profiling indicated sex-dependent modulation of microbial pathways related to tryptophan and central carbon metabolism. These findings demonstrate enduring transgenerational effects of preconceptional stress on the gut-brain axis and support maternal probiotic supplementation as a potential strategy to mitigate stress-induced dysregulation.},
}

@article {pmid41916460,
year = {2026},
author = {Asiri, F and Kishk, M and Karam, H and Al-Muhanna, K and Al-Najdi, F and Al-Enezi, A and Al-Khalifah, N and Hejji, AB and Al-Salameen, F and Al-Salem, SM},
title = {Innovative soil seeding with waste-derived microbial inoculums: Enhancing plastic biodegradation and Revealing microbiome shifts.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134523},
doi = {10.1016/j.biortech.2026.134523},
pmid = {41916460},
issn = {1873-2976},
abstract = {Plastic waste accumulation in terrestrial ecosystems poses a global environmental challenge, demanding sustainable alternatives to conventional disposal. Aerobic biodegradation is promising, yet most studies rely on composting systems, often overlooking different polymer types and how seeding soil with waste-derived inoculums affect polymer breakdown. This study developed an innovative soil-seeding approach using microbe-rich inoculums derived from real waste streams: compost (Comp.), activated sludge (AS), plastic-contaminated soil (PCS), and oil-contaminated soil (OCS) to enhance biodegradation of starch, compostable bioplastic (CBP), and the mineralization of linear low-density polyethylene (LLDPE). Biodegradation was evaluated under controlled soil conditions, and microbial community responses were characterized through metataxonomic profiling. Starch exhibited the highest biodegradation (71-100%), followed by CBP (31-56%) and LLDPE mineralization (12-22%). OCS and PCS significantly enhanced CBP and LLDPE degradation, respectively, corresponding to differences in organic content and carbon-to-nitrogen ratios. Shifts in microbial composition revealed polymer-specific microbial drivers, including Bacilli (Bacillaceae, Paenibacillus) and Chaetomium for starch, and Actinobacteriota, Acidimicrobiia, Mycobacterium, and Nocardioides for CBP, particularly in OCS. LLDPE degradation remained low but was modestly improved in Comp- and PCS-amended soils. Overall, this study demonstrates that targeted soil-seeding with waste-derived inoculums can substantially influence polymer degradation and microbial succession, providing a practical strategy to accelerate biodegradation in natural soils and informing future sustainable plastic-management approaches.},
}

@article {pmid41916675,
year = {2026},
author = {Boven, A and Vranken, H and Vlieghe, E and Boleij, A and Fall, K and Engstrand, L and Brusselaers, N},
title = {Commonly prescribed drugs as risk factors for Clostridioides difficile infections: a Swedish population-based case-control study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337629},
pmid = {41916675},
issn = {1468-3288},
abstract = {BACKGROUND: Clostridioides difficile infections (CDIs) are associated with antibiotic use, although the link with other drugs remains underexplored.

OBJECTIVES: To investigate the association between antibiotic and non-antibiotic drugs with microbiome-modulating activity on new occurrences of CDI.

DESIGN: We conducted a Swedish population-based case-control study from 2006 to 2019 including 42 921 cases matched with 355 159 population controls on age and sex, obtained from multiple linked Swedish registries. The effect of antibiotic and non-antibiotic use within 30 days from the index date on CDI occurrence was estimated using multivariable conditional logistic regression additionally with a lasso penalty. Models were adjusted for age and sex by design and for Charlson Comorbidity Index and concomitant drug use, providing adjusted ORs (aORs) with 95% CIs.

RESULTS: Antibiotics with the greatest CDI risk were lincosamides (aOR=31.4, 95% CI 27.9 to 35.3), combinations of penicillins (aOR=19.8, 95% CI 15.9 to 24.5), sulfonamides and trimethoprim, and cephalosporins, though no association for tetracyclines. Among non-antibiotic drugs, we found decreased risks of CDI for lipid-modifiers (aOR=0.8, 95% CI 0.8 to 0.8) and aspirin (aOR=0.8, 95% CI 0.7 to 0.8) and increased risks for antidiarrhoeals (aOR=7.3, 95% CI 6.8 to 7.8), corticosteroids (aOR=2.4, 95% CI 2.3 to 2.5), proton-pump inhibitors (PPIs) (aOR=1.8, 95% CI 1.7 to 1.8), nervous system drugs, constipation drugs, histamine H2-receptor antagonists, antidepressants, and beta blockers, but no significant risk for non-steroidal anti-inflammatory drugs.

CONCLUSIONS: We found varying effects of antibiotics on CDI, providing evidence for ongoing efforts in prudent prescribing decisions and antimicrobial stewardship. We confirmed PPI as a main risk factor for CDI and provided new evidence for other non-antibiotic drugs as potentially important risk factors considering their high prescription prevalence.},
}

@article {pmid41916943,
year = {2026},
author = {Sailesh, SS},
title = {Association between soft drink consumption and depression mediated by gut microbiome: a perspective.},
journal = {East Asian archives of psychiatry : official journal of the Hong Kong College of Psychiatrists = Dong Ya jing shen ke xue zhi : Xianggang jing shen ke yi xue yuan qi kan},
volume = {36},
number = {1},
pages = {56-59},
doi = {10.12809/eaap25136},
pmid = {41916943},
issn = {2224-7041},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Carbonated Beverages/adverse effects ; *Depression/etiology/epidemiology/microbiology ; *Sugar-Sweetened Beverages/adverse effects ; Female ; },
abstract = {This perspective synthesises current evidence on the association between soft drink consumption and depression, with emphasis on the gut microbiome as a potential mediating mechanism. PubMed, Scopus, and Google Scholar were searched using the following terms: 'soft drinks', 'sugar-sweetened beverages', 'carbonated beverages', 'soda', 'depression', 'depressive symptoms', 'mental health', 'gut microbiome', 'microbiota', and 'gut-brain axis'. Peer-reviewed original articles published in English between January 2000 and October 2025 were included if they involved human participants of any age (sample size ≥50 for observational studies), assessed soft drink or sugar-sweetened beverage consumption, and measured depression diagnosis, depressive symptoms, or depression severity. Associations between soft drink consumption and increased depression risk were consistently shown across multiple study designs and populations. Evidence for artificially sweetened beverages was less consistent and suggested potentially distinct, non-sugar-related pathways. A multicentre cohort study of 932 participants revealed that soft drink consumption predicted the major depressive disorder diagnosis (odds ratio = 1.081), with stronger effects in women (odds ratio = 1.167). Eggerthella partially mediated the soft drink-depression association, explaining approximately 4% of the association. Soft drink consumption is associated with increased depression risk through multiple biological pathways involving inflammation, metabolic dysregulation, and gut microbiome alterations. Modest effect sizes suggest the involvement of multiple interconnected mechanisms. Public health interventions to limit sugar-sweetened beverage consumption are recommended to improve physical and mental health. Healthcare providers should consider dietary assessment and counselling as part of depression prevention and treatment strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Carbonated Beverages/adverse effects
*Depression/etiology/epidemiology/microbiology
*Sugar-Sweetened Beverages/adverse effects
Female

@article {pmid41917102,
year = {2026},
author = {Roy, M and Han, D and Lee, D and Kang, B and Choi, K},
title = {Cultivation system and plant health influence root-associated bacterial community structure and interaction networks in strawberry.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45642-7},
pmid = {41917102},
issn = {2045-2322},
support = {(RS-2023-00251252 and 2020R1A6A1A03047729)//National Research Foundation of Korea/ ; (RS-2025-02613089)//Rural Development Administration/ ; },
abstract = {Strawberry is cultivated in both soil-based field and substrate-based soilless hydroponic systems, yet how cultivation context shapes root-associated bacterial communities and their interaction architecture remains unclear. We compared root-associated bacterial communities from field root-associated soil and hydroponic root-adhering substrate under asymptomatic and symptomatic conditions using 16S rRNA gene amplicon sequencing. Cultivation system was the primary driver of community structure, clearly separating field and hydroponic samples. Field communities were enriched in Firmicutes and Actinobacteria, such as Bacillaceae and Nocardioidaceae, whereas hydroponic communities showed higher relative abundances of Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia, including Chitinophagaceae and Sphingomonadaceae. Differential abundance and Random Forest analyses revealed consistent enrichment of Bacillus-associated ASVs in field samples, whereas asymptomatic and symptomatic communities showed greater compositional differentiation in hydroponic than in field samples.. Co-occurrence network analysis further demonstrated that hydroponic communities contained more taxa and interactions but exhibited lower density and clustering compared to field communities, indicating reduced structural cohesion. These findings demonstrate that cultivation system strongly influences both the composition and structural organization of strawberry root-associated bacterial communities, with implications for microbiome-informed disease management in intensive production systems.},
}

@article {pmid41917200,
year = {2026},
author = {Lee, YH and Lin, WJ and Tsai, MT and Lan, B and Chu, YL and Yang, JI and Sun, SJ},
title = {Context-dependent indirect effects mediate ecological transitions between parasitism and mutualism.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09945-9},
pmid = {41917200},
issn = {2399-3642},
support = {Academic Research-Career Development Project (Sprout Research Projects; 114L7869)//National Taiwan University (NTU)/ ; },
abstract = {Symbiotic interactions frequently shift along a mutualism-parasitism continuum, altering host fitness, population dynamics, and microbial community structure with ecological context. Here, we integrate field surveys, reciprocal breeding experiments, feeding assays, and microbiome profiling to dissect interactions between phoretic mite (Poecilochirus carabi), nematode (Rhomborhabditis regina), and their burying beetle host (Nicrophorus nepalensis) during reproduction. We show that high nematode densities reduce beetle offspring survival during metamorphosis, but co-occurring mites mitigate these costs by preying on nematodes and suppressing vertical transmission, thereby enhancing beetle fitness. Both mites and nematodes are equally effective at suppressing bacterial loads on carrion, but mites drive greater shifts in carcass microbiome composition. Carcasses exposed to both symbionts display the most pronounced shifts in bacterial communities, suggesting that inter-symbiont interactions have cascading effects on host-associated microbiota. Intriguingly, in the absence of nematodes, mites impose fitness costs on their beetle hosts. These results demonstrate that the net effects of mites on beetle fitness emerge largely through indirect, density-dependent interactions with nematodes and microbial competitors. By integrating macro-symbiont and microbiome perspectives, our study highlights how phoresy extends beyond passive dispersal to actively restructure host-symbiont networks, highlighting the overlooked potential of indirect effects in driving context-dependent mutualism within multisymbiotic systems.},
}

@article {pmid41917642,
year = {2026},
author = {Gao, J and Ren, X and Hu, Y and Li, G and Yang, T and Xiao, J},
title = {New Trends and Challenges in Academic Research on Adolescent Growth and Development.},
journal = {Advances in experimental medicine and biology},
volume = {1505},
number = {},
pages = {411-420},
pmid = {41917642},
issn = {0065-2598},
mesh = {Humans ; Adolescent ; *Adolescent Development/physiology ; *Adolescent Health/trends ; Gastrointestinal Microbiome/physiology ; Epigenesis, Genetic ; *Biomedical Research/trends ; },
abstract = {Adolescence is a critical period for physical and psychological growth and development when individuals undergo a burst growth in physical size, hormonal re-adjustment, and brain development. In recent years, research studies have changed from descriptive growth charts toward focusing on the roles of multiple factors that affect adolescent health, including epigenetic regulators, genetic traits, social stressors, and gut microbiota. Compared to traditional factors like nutrition and hormones, environmental factors, personalized genomics, social media exposure, and gut-microbiome, etc. are increasing recognized as novel critical regulators of adolescent health. Currently, the goal of academic research in adolescence is to understand the interactions and underlying mechanisms of these factors and to develop targeted interventions for addressing adolescent health issues. Therefore, this chapter mainly discusses the new trends, key challenges, and translational research potential in these rapidly advancing field of adolescent growth and development.},
}

Humans
Adolescent
*Adolescent Development/physiology
*Adolescent Health/trends
Gastrointestinal Microbiome/physiology
Epigenesis, Genetic
*Biomedical Research/trends

@article {pmid41917750,
year = {2026},
author = {Yeh, GY and Wayne, PM and Mehta, D},
title = {Inside the Gut-Mind Connection: Mind-Body Medicine Meets the Microbiome Revolution.},
journal = {Journal of integrative and complementary medicine},
volume = {},
number = {},
pages = {27683605261438880},
doi = {10.1177/27683605261438880},
pmid = {41917750},
issn = {2768-3613},
}

@article {pmid41917988,
year = {2026},
author = {Liu, M and Li, S and Cui, Y and Zhu, X and Wang, Z and Sun, H and Li, D and Liu, B and Shi, Y},
title = {Tryptophan metabolism mediated by the gut microbiota inhibits pyroptosis via the AhR signaling pathway to maintain intestinal epithelial homeostasis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02408-7},
pmid = {41917988},
issn = {2049-2618},
support = {CARS-34//Modern Agro-industry Technology Research System of China/ ; No. 244200510010//Science and Technology Innovation Leading Talent in Central Plains/ ; },
abstract = {BACKGROUND: The intestinal epithelial barrier protects the gut from pathogen invasion as well as exposure to food antigens and toxins. Increasing evidence has linked the gut microbiota to the function of the intestinal epithelial barrier. Fecal microbiota transplantation (FMT) can treat various intestinal diseases by reshaping the gut microbiota. However, the mechanisms by which FMT exerts its effects across different gastrointestinal conditions remain unclear. Moreover, its limitations are significant, including issues related to donor selection, the complexity of the microbiome, potential infection risks, inconsistent clinical responses, and ethical and legal considerations. Therefore, exploring the microbes and metabolites that mediate the effects of FMT as a replacement for traditional FMT is of great importance. In this study, we aim to investigate the gut microbiota and its metabolites to support the therapeutic role of FMT in intestinal barrier damage and elucidate its potential molecular mechanisms.

RESULTS: Our findings indicate that FMT prevents Lipopolysaccharide (LPS)-induced pyroptosis and damage to the colonic epithelial barrier. Mechanistically, FMT treatment reprograms the composition of gut microbiota, increasing the relative abundance of Lactobacillus reuteri and the levels of tryptophan metabolites (ILA, IAld, and IAA) in the colon, thereby inhibiting pyroptosis and protecting the intestinal epithelial barrier. Importantly, the AhR/NLRP3 axis is essential for the pyroptosis-inhibitory effects of Lactobacillus reuteri and its tryptophan metabolites.

CONCLUSIONS: Our results provide the first evidence that targeting the regulation of Lactobacillus reuteri and tryptophan metabolism is a promising strategy for inhibiting pyroptosis and improving intestinal epithelial homeostasis.},
}

@article {pmid41918066,
year = {2026},
author = {Singh, N and DuBrock, HM and Prisco, SZ and Dai, Z and Zheng, Q and Fallon, MB and Thenappan, T and Ventetuolo, CE and Jose, A},
title = {The Importance of Liver-Lung Communication in Pulmonary Vascular Diseases.},
journal = {Comprehensive Physiology},
volume = {16},
number = {2},
pages = {e70140},
pmid = {41918066},
issn = {2040-4603},
support = {HL134625/HL/NHLBI NIH HHS/United States ; HL141268/HL/NHLBI NIH HHS/United States ; HL174007/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; HL158596/HL/NHLBI NIH HHS/United States ; HL162794/HL/NHLBI NIH HHS/United States ; HL170096/HL/NHLBI NIH HHS/United States ; HL169509/HL/NHLBI NIH HHS/United States ; HL16497/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; },
mesh = {Humans ; *Lung/physiology/physiopathology ; *Liver/physiology/physiopathology ; Animals ; Hepatopulmonary Syndrome/physiopathology ; *Lung Diseases/physiopathology ; Gastrointestinal Microbiome/physiology ; Hypertension, Pulmonary/physiopathology ; },
abstract = {In normal health, the liver and lungs enjoy a close anatomic, physiologic, and functional relationship. In the context of pulmonary vascular disease, however, there is accumulating evidence that the interplay between the gut microbiome, hepatic system, and pulmonary vasculature (so-called "gut-liver-lung" axis) plays an important role in driving disease pathogenesis and determining clinical outcomes. Despite recognizing the importance of the gut-liver-lung axis in pulmonary vascular disease however, little is known about the clinical characteristics, circulating factors, and physiologic pathways that mediate this important axis of communication. In this clinical and translationally focused review, we provide an overview of liver-lung communication in normal physiology, and contrast this with gut-liver-lung derangements in pulmonary arterial hypertension, portopulmonary hypertension, and hepatopulmonary syndrome. We conclude with identifying key gaps in knowledge that will need to be addressed in order to manipulate the gut-liver-lung axis to prevent worsening pulmonary vascular disease, develop novel therapeutics, and improve patient outcomes.},
}

Humans
*Lung/physiology/physiopathology
*Liver/physiology/physiopathology
Animals
Hepatopulmonary Syndrome/physiopathology
*Lung Diseases/physiopathology
Gastrointestinal Microbiome/physiology
Hypertension, Pulmonary/physiopathology

@article {pmid41918094,
year = {2026},
author = {Liu, Y and Liu, W and Pu, J and Wang, Y and Kang, Z and Zheng, H and Chang, W and Zheng, X and Yang, Q and Xu, H and Feng, Z and Dong, K and Li, J},
title = {Compositional disparities and potential pathogenic mechanisms of the ocular microbiome in cataract patients: insights from high-throughput sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05009-4},
pmid = {41918094},
issn = {1471-2180},
support = {2023L118//Science and Technology Innovation Program for Higher Education Institutions of Shanxi Province/ ; 2024149//Laboratory Special Project of the Health Commission of Shanxi Province/ ; B202201//Doctoral Fund Project of Shanxi Eye Hospital/ ; 2024NITFID303//Independent Research Program of the National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases/ ; },
}

@article {pmid41918359,
year = {2026},
author = {Fairfield, H and Reagan, MR},
title = {Fiber: A New Myeloma Prevention Approach with Abundant Positive Effects.},
journal = {Cancer discovery},
volume = {16},
number = {4},
pages = {623-625},
doi = {10.1158/2159-8290.CD-26-0152},
pmid = {41918359},
issn = {2159-8290},
mesh = {Humans ; *Multiple Myeloma/prevention & control/diet therapy ; *Dietary Fiber/administration & dosage/therapeutic use ; Quality of Life ; Obesity/diet therapy/complications ; },
abstract = {In a recent study by Shah, Cogrossi, and colleagues, patients with overweight/obesity and pre-myeloma diseases (monoclonal gammopathy of undetermined significance or smoldering myeloma) were mailed 12 weeks of high-fiber meals, provided with nutritional counseling, and required to track their food intake and weight. The intervention was well tolerated and improved quality of life, metabolic health, gut microbiome composition, and immune system function while supporting stable or improved multiple myeloma disease trajectories. See related article by Shah et al., p. 697.},
}

Humans
*Multiple Myeloma/prevention & control/diet therapy
*Dietary Fiber/administration & dosage/therapeutic use
Quality of Life
Obesity/diet therapy/complications

@article {pmid41918498,
year = {2026},
author = {Belhedi, M and Sghaier-Hammami, B and Hammami, SBM and Ben Slema, S and De Bellis, P and Somma, S and Nafati, H and Hibar, K and Abi Saad, C and Moretti, A and Masiello, M},
title = {Microbial biodiversity in Tunisian olive grove soils: a reservoir of phytopathogenic fungi and potential beneficial microorganisms.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1770745},
pmid = {41918498},
issn = {2673-6128},
abstract = {INTRODUCTION: Intercropping in olive orchards increases the risk of soil-borne fungal infections, particularly when associated crops are susceptible to the same pathogens. This study aimed to identify soil-borne microorganisms colonizing the roots and rhizosphere of olive trees in Tunisia intercropped with Solanaceae plants and to evaluate co-occurring bacterial communities for their potential to mitigate wilt disease and promote plant health.

MATERIAL AND METHODS: Endophytic fungi and bacteria were isolated from olive soils and roots collected from three olive orchards subjected to different intercropping systems. Fungal strains were molecularly identified at the species level using Internal Transcribed Spacer (ITS) and translation elongation factor 1-α (TEF1) gene sequencing, while bacterial strains were characterized by rep-PCR profiling and 16S rDNA sequencing. The pathogenicity of selected Fusarium strains was assessed by in vitro inoculation of detached olive leaves, olive twigs, and tomato seedlings. Antagonistic activity of bacterial strains against selected Fusarium species was evaluated using dual-culture assays, and bacteria-fungi interactions were further investigated by scanning electron microscopy (SEM).

RESULTS AND DISCUSSION: A total of 83 fungal and 40 bacterial strains were isolated. The fungal community was dominated by Fusarium species (62%), followed by Phoma (13%) and Alternaria (10%) species, while Verticillium dahliae was not detected at any site. The prevalence and virulence of Fusarium varied among olive groves, with the highest incidence observed at Sidi Bou Ali, where olive trees were intercropped with tomato, and the lowest at Kairouan, where potato intercropping was less frequent. Pathogenicity assays showed that 12 out of 15 of the tested Fusarium strains caused symptoms on both olive tissues and tomato seedlings. Bacterial communities were dominated by Bacillus species and Priestia megaterium. Bacillus species were particularly abundant at the site with the highest Fusarium pressure. The in vitro assay showed that several bacteria exhibited antagonistic activity against pathogenic fungi, with growth inhibition ranging from 8% to 68%, including volatile organic compound-mediated effects. SEM analyses revealed that Bacillus amyloliquefaciens inhibited fungal growth through biofilm formation and hyphal alteration.},
}

@article {pmid41918618,
year = {2026},
author = {Her, TK and Pszczolkowski, VL and Chung, G and Woollett, LA and Alejandro, EU},
title = {Multiparity as a Key Variable in Metabolism and Pregnancy Research.},
journal = {Current opinion in physiology},
volume = {47},
number = {},
pages = {},
pmid = {41918618},
issn = {2468-8673},
support = {R01 DK136237/DK/NIDDK NIH HHS/United States ; },
abstract = {Parity is defined as the total number of pregnancies reaching ≥20 weeks of gestation. It is an important variable to consider in any metabolic studies involving maternal or offspring health, as multiparity has been identified as a potential driver of numerous aspects of reproduction, maternal-fetal programming, and the health of both maternal and offspring. Currently, it is understood that multiparity may increase the risk of maternal pregnancy complications, such as preeclampsia and gestational diabetes mellitus (GDM), which can have subsequent long-term effects on both the maternal and offspring. Although there are some differences in data between rodents and humans, multiparity has been shown to disrupt glucose homeostasis, decrease pancreatic beta-cell proliferation, alter cardiac hemodynamics, and change the composition of the gut microbiome. In this review, we discuss what is known in the current literature about the impact of multiparity on pregnancy outcomes, maternal health, and offspring health.},
}

@article {pmid41918694,
year = {2026},
author = {Zheng, W and Liang, Y and Li, J},
title = {The neonatal lung microbiome: a dynamic determinant of respiratory health, disease, and novel therapeutics.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1770578},
pmid = {41918694},
issn = {2296-2360},
abstract = {The neonatal lung, once considered sterile, is now recognized to harbor a dynamic and complex microbiome that plays a critical role in respiratory health and disease. This review synthesizes current evidence on the composition, development, and functional impact of the lung microbiome in neonates, with a focus on its involvement in key respiratory disorders such as bronchopulmonary dysplasia, respiratory syncytial virus infection, neonatal acute respiratory distress syndrome, cystic fibrosis, and asthma predisposition. We place particular emphasis on the bidirectional communication along the gut-lung axis as a central mechanism, wherein intestinal microbiota and their metabolites modulate pulmonary immunity and inflammation. Emerging multi-omics studies that integrate microbial data with host metabolomic and immune profiles are highlighted for their role in deciphering disease-specific dysbiotic signatures and mechanistic pathways. Critically, this review advances the discussion beyond association by evaluating the translational potential of the microbiome as both a diagnostic biomarker and a therapeutic target. We provide a critical appraisal of innovative microbiome-targeted strategies-including probiotics, postbiotics, phage therapy, and bacterial lysates-and discuss the unique challenges and future directions for translating these approaches into safe, effective clinical interventions for vulnerable neonates. By bridging foundational science with clinical implications, this work aims to inform the development of novel, ecology-informed therapeutics to prevent and mitigate neonatal respiratory diseases.},
}

@article {pmid41918737,
year = {2026},
author = {Edwards, JS and De Paris, K},
title = {Inflammation at the maternal-fetal interface: a perspective on interacting risk factors for preterm birth in sub-Saharan African women living with HIV.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1741921},
pmid = {41918737},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *HIV Infections/immunology/drug therapy/complications/epidemiology/virology ; *Premature Birth/immunology/epidemiology/etiology ; Risk Factors ; Africa South of the Sahara/epidemiology ; *Inflammation/immunology ; Vagina/microbiology/immunology ; *Pregnancy Complications, Infectious/immunology/virology ; Microbiota/immunology ; Macrophages/immunology ; Infant, Newborn ; *Maternal-Fetal Exchange/immunology ; },
abstract = {Globally, approximately 10% of all babies are born prematurely. The vast majority of preterm births, defined as birth <37 weeks of gestation, occur in low- and middle-income countries (LMICs) in Asia and Africa. Furthermore, premature birth has become the leading cause of death in infants under the age of 5 years. Thus, to improve maternal and infant health outcomes, better diagnostics and intervention strategies are urgently needed. However, the multifactorial etiology of preterm birth provides a major obstacle in achieving this goal. A common factor to many adverse birth outcomes, including preterm birth, is aberrant immune activation at the maternal-fetal interface. The specific cause of immune activation, however, remains unknown. Both HIV and an anaerobe-rich vaginal microbiota have been independently identified as risk factors for preterm birth, and both factors also promote inflammation and immune activation at mucosal sites. The interplay of HIV and microbiota is widely acknowledged, although mostly in the context of the intestinal microbiome. This review will highlight how the regulatory function of macrophages at the maternal-fetal interface can be altered in response to HIV and antiretroviral therapy and to changes in vaginal microbiota. We proceed to discuss interactions between the various factors and propose a dual-hit model in which macrophages act as mediators of inflammation at the maternal-fetal interface in response to specific vaginal commensals and HIV infection in sub-Saharan African women with preterm birth outcomes.},
}

Humans
Female
Pregnancy
*HIV Infections/immunology/drug therapy/complications/epidemiology/virology
*Premature Birth/immunology/epidemiology/etiology
Risk Factors
Africa South of the Sahara/epidemiology
*Inflammation/immunology
Vagina/microbiology/immunology
*Pregnancy Complications, Infectious/immunology/virology
Microbiota/immunology
Macrophages/immunology
Infant, Newborn
*Maternal-Fetal Exchange/immunology

@article {pmid41918738,
year = {2026},
author = {Lee, AR and Yang, SW and Lee, SY and Jeon, SB and Kang, HY and Choi, JW and Park, JH and Park, JH and Son, SB and Jeong, Y and Lee, JH and Kim, W and Cho, ML},
title = {Mitochondrial transplantation ameliorates experimental autoimmune encephalomyelitis by modulating the Th17/Treg balance and restoring metabolic homeostasis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1698136},
pmid = {41918738},
issn = {1664-3224},
mesh = {*Encephalomyelitis, Autoimmune, Experimental/therapy/immunology/metabolism/pathology ; Animals ; *Th17 Cells/immunology/metabolism ; *Mitochondria/transplantation/metabolism ; *T-Lymphocytes, Regulatory/immunology/metabolism ; Mice ; Humans ; Female ; Homeostasis ; Multiple Sclerosis/immunology/therapy/metabolism ; Oxidative Stress ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Spinal Cord/pathology/immunology/metabolism ; Disease Models, Animal ; Reactive Oxygen Species/metabolism ; },
abstract = {INTRODUCTION: Mitochondrial dysfunction has been increasingly implicated in the pathogenesis of multiple sclerosis (MS), contributing to oxidative stress, immune dysregulation, and neurodegeneration. Current therapies primarily target inflammation but do not adequately address mitochondrial impairment or progressive tissue damage. This study aimed to evaluate the therapeutic potential of mitochondrial transplantation in experimental autoimmune encephalomyelitis (EAE), a murine model of MS, by investigating its effects on immune modulation, mitochondrial function, and tissue integrity.

METHODS: EAE was induced in mice using myelin oligodendrocyte glycoprotein. Isolated mitochondria were administered intravenously, and clinical progression, spinal cord histology, immune cell populations, mitochondrial activity, fibrosis, and gut microbiota composition were assessed. Additionally, human peripheral blood mononuclear cells (PBMCs) from MS patients were co-cultured with mitochondria to examine ATP production, reactive oxygen species levels, and T cell differentiation.

RESULTS: Mitochondrial transplantation significantly reduced EAE severity, spinal cord inflammation, demyelination, and fibrosis. Treated mice showed increased regulatory T (Treg) cells, reduced T helper 17 (Th17) cells, improved mitochondrial biogenesis, and decreased oxidative stress. Gut microbiome analysis revealed beneficial compositional changes. In human PBMCs, mitochondrial transfer enhanced ATP synthesis, suppressed mitochondrial ROS, and promoted Treg differentiation while inhibiting pro-inflammatory cytokines.

DISCUSSION: Our findings suggest that mitochondrial transplantation restores mitochondrial function, rebalances immune responses, and mitigates neuroinflammation and fibrosis in EAE. This approach offers a novel therapeutic strategy for MS by addressing both metabolic and immunological drivers of disease progression.},
}

*Encephalomyelitis, Autoimmune, Experimental/therapy/immunology/metabolism/pathology
Animals
*Th17 Cells/immunology/metabolism
*Mitochondria/transplantation/metabolism
*T-Lymphocytes, Regulatory/immunology/metabolism
Mice
Humans
Female
Homeostasis
Multiple Sclerosis/immunology/therapy/metabolism
Oxidative Stress
Mice, Inbred C57BL
Gastrointestinal Microbiome
Spinal Cord/pathology/immunology/metabolism
Disease Models, Animal
Reactive Oxygen Species/metabolism

@article {pmid41918743,
year = {2026},
author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F},
title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1745166},
pmid = {41918743},
issn = {1664-3224},
mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; },
abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.

METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.

RESULTS AND DISCUSSION: On average, 23.29% ± 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% ± 17.88%), pyelonephritis (22.75% ± 12.91%), asymptomatic bacteriuria (18.17% ± 17.14%)] and 30.63% ± 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% ± 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.},
}

Humans
*Extracellular Traps/immunology/metabolism
Female
Pilot Projects
Male
*Urinary Tract Infections/immunology/microbiology/urine
Middle Aged
Adult
*Neutrophils/immunology/metabolism
Aged
Biomarkers
Pyelonephritis/immunology/urine
Bacteriuria/immunology

@article {pmid41918843,
year = {2026},
author = {Huang, Q and Liang, Z and Cui, Y and Diao, J and Zhou, T and Shi, L and Deng, Z and Wang, R and Yuan, H and Chen, K and Du, Y and Chen, A and Chen, J and Xiao, W},
title = {Uremic Clearance Granules Regulate Immune Equilibrium via Gut Microbiome to Alleviate Chronic Renal Failure.},
journal = {Biomaterials research},
volume = {30},
number = {},
pages = {0342},
pmid = {41918843},
issn = {1226-4601},
abstract = {Chronic renal failure (CRF) is the common end point of various chronic kidney diseases, and there is currently no specific drug for CRF. Effectively halting its progression remains a clinical challenge. Gut microbiota disorders are a key factor influencing immune dysfunction in chronic kidney disease patients. Intervening in gut microbiota to improve immune regulatory function in patients could serve as a new strategy for treating CRF with Traditional Chinese Medicine. Uremic Clearance Granules (UCG), a Traditional Chinese Medicine formulation, effectively attenuate CRF progression, but their active components and mechanisms remain undefined. This study investigates how UCG mitigate CRF via coordinated regulation of gut microbiota, metabolites, and the T helper 17 cells / regulatory T cell axis. Using an adenine-induced CRF mouse model, we combined gut microbiota depletion, fecal microbiota transplantation, 16S rRNA sequencing, and metabolomics to delineate the gut-kidney interactions underlying UCG efficacy. Flow cytometry quantified immune cell profiles in blood, and microbial intervention experiments verified the therapeutic role of Bifidobacterium animalis (B. animalis). In this study, we found that UCG treatment alleviated renal injury, reduced intestinal permeability, and up-regulated intestinal barrier markers. Microbiota depletion and fecal microbiota transplantation demonstrated that UCG's renoprotective effects depend on gut microbial modulation. Specifically, UCG ameliorates CRF through gut-kidney axis remodeling by enhancing B. animalis abundance and sophocarpine, thereby rebalancing T helper 17/regulatory T immunity and preserving renal function. These findings identify a microbiota-dependent immunometabolic mechanism for UCG and highlight a potential therapeutic strategy for CRF via the drug-microbiota axis.},
}

@article {pmid41918857,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M},
title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20990},
pmid = {41918857},
issn = {2167-8359},
mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; },
abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.

METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.

RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.},
}

*Peptides/genetics/pharmacology
*Antineoplastic Agents/pharmacology
*Metagenome
Humans
*Genome, Microbial
*Software
High-Throughput Nucleotide Sequencing
Algorithms
Computational Biology/methods

@article {pmid41918873,
year = {2026},
author = {Duan, Y and Yang, M and Li, M and Sun, Y and Liu, S},
title = {Microbiome and metabolite signatures for cirrhosis to HCC risk stratification: progress, controversies, and gaps.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1793213},
pmid = {41918873},
issn = {2235-2988},
mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/metabolism/pathology/etiology ; *Liver Cirrhosis/microbiology/metabolism/complications/pathology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/microbiology/metabolism/pathology/etiology ; Fatty Acids, Volatile/metabolism ; Risk Assessment ; Disease Progression ; Dysbiosis ; Bile Acids and Salts/metabolism ; },
abstract = {The progression from cirrhosis to hepatocellular carcinoma (HCC) is a key outcome in the management of chronic liver disease. This process has a long incubation period and significant individual differences, making early warning still difficult. Clinical follow-up mainly relies on imaging examinations and alpha fetoprotein, but the ability to identify high risk precancerous states is limited. The imbalance of gut microbiota and its metabolites may occur earlier than the visible stage of tumors. They can affect barrier integrity, chronic inflammation, immune surveillance, and metabolic homeostasis through the gut liver axis, and participate in the formation of a pro tumor microenvironment. Therefore, such changes may provide more upstream risk stratification clues for the population with cirrhosis. This article summarizes previous research evidence and summarizes the common microbiome and metabolite characteristics of cirrhosis and high-risk populations, including a decrease in short chain fatty acid (SCFA) related symbiotic bacteria, an increase in inflammation related bacteria, bile acid spectrum shift, and other intestinal derived metabolite abnormalities. This article also outlines the key mechanisms that these features may correspond to, such as barrier damage and microbial translocation, immune suppression, etc. There are still significant uncertainties at present. The effect of SCFA is context dependent. Different etiologies, diets, medications, and complications can lead to significant confounding and affect cross cohort consistency. Subsequent research requires longitudinal cohort validation and the promotion of multi omics integration and the construction of interpretable predictive models to support clinical translation.},
}

Humans
*Carcinoma, Hepatocellular/microbiology/metabolism/pathology/etiology
*Liver Cirrhosis/microbiology/metabolism/complications/pathology
*Gastrointestinal Microbiome
*Liver Neoplasms/microbiology/metabolism/pathology/etiology
Fatty Acids, Volatile/metabolism
Risk Assessment
Disease Progression
Dysbiosis
Bile Acids and Salts/metabolism

@article {pmid41918874,
year = {2026},
author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D},
title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1782744},
pmid = {41918874},
issn = {2235-2988},
mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; },
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.

METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.

RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-α and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.

DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.},
}

Humans
Female
*Probiotics/administration & dosage
*Diabetes, Gestational/microbiology
Pregnancy
*Gastrointestinal Microbiome/drug effects
Adult
Metabolomics/methods
Metagenomics
Multiomics

@article {pmid41918946,
year = {2026},
author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG},
title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.},
journal = {ERJ open research},
volume = {12},
number = {2},
pages = {},
pmid = {41918946},
issn = {2312-0541},
abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.

METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32 weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and α-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).

CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.},
}

@article {pmid41918963,
year = {2026},
author = {Athithan, P and Ishaq, SL and Allen-Vercoe, E and O'Doherty, KC},
title = {Microbes first into the life rafts: preserving microbiomes to secure health in degrading ecosystems.},
journal = {Sustainable microbiology},
volume = {},
number = {},
pages = {},
pmid = {41918963},
issn = {2755-1970},
support = {R15 DK133826/DK/NIDDK NIH HHS/United States ; },
abstract = {All organisms on the planet intrinsically rely on microbial ecosystems, and there are increasing calls from research communities to consider microbiota when administering personal or public health, ecosystem health, and the use of microbiota in personal or environmental health remediation, such as reducing the impacts of climate change, or protecting at-risk habitats which host rare microbiota. Through our collective work on the integral nature of microbiomes to host and environmental health, on health policy, and on the development of research and policy agendas, we have previously developed the concept of 'microbiome stewardship' and guidelines to promote consideration of microbial communities broadly or in specific scenarios. The practicality of stewarding one versus many microbiota is highly contextual, and will require different strategies for different scales of conservation. Here, we provide scientific arguments for the need for microbial stewardship, examples of possible solutions scaled to different ecological challenges or conservation goals, discourse on the logistical challenges which have been cited by research communities, and opportunities to use cutting-edge microbiome concepts and technology to implement large-scale interventions.},
}

@article {pmid41918966,
year = {2026},
author = {Jiang, W and Liu, J and Chen, A and Zhao, T and Xu, Z and Xu, L and Du, Y and Guan, X and Ding, J and Liu, Y and Sun, D},
title = {Antimicrobial Peptides as Novel Ecological Approaches to Caries Prevention.},
journal = {Drug design, development and therapy},
volume = {20},
number = {},
pages = {592732},
pmid = {41918966},
issn = {1177-8881},
mesh = {*Dental Caries/prevention & control/microbiology ; Humans ; *Antimicrobial Peptides/pharmacology/chemistry ; Biofilms/drug effects ; Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {Antimicrobial strategies have consistently been a central theme in caries prevention research. Due to their potent antibacterial properties and the potential for multifunctionality through sequence modification, antimicrobial peptides (AMPs) are emerging as promising candidates for anticaries therapeutics. Traditional investigations primarily focused on the broad-spectrum bactericidal efficacy of AMPs to eradicate cariogenic bacteria; however, this approach may inadvertently harm the beneficial oral microbiome. With advancing knowledge of oral microecology, the focus has progressively shifted towards ecological approaches. These strategies aim to selectively modulate cariogenic populations or the disease-associated microbiota while preserving microbial diversity and maintaining ecological balance, as demonstrated in multispecies biofilm models and sequencing-based microbiome analyses. Current innovations include targeting specific pathogens, regulating virulence factors, utilizing bio-responsive mechanisms within the cariogenic microenvironment, and disrupting dental plaque biofilms. This article reviews the current progress and limitations of antimicrobial peptide-based ecological approaches to caries control and offers valuable insights for the future design and optimization of antimicrobial peptides with microecology regulating effects or other promising functions aiding caries prevention.},
}

*Dental Caries/prevention & control/microbiology
Humans
*Antimicrobial Peptides/pharmacology/chemistry
Biofilms/drug effects
Microbiota/drug effects
*Anti-Bacterial Agents/pharmacology/chemistry

@article {pmid41918983,
year = {2026},
author = {Weingarden, AR},
title = {Strengths and limitations of in vitro and animal models to advance understanding of human diet‒microbiome interactions.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2636336},
pmid = {41918983},
issn = {2993-3935},
abstract = {The gut microbiome is a critical mediator of human health. As the intestinal microbiota is far more metabolically diverse than humans, it plays a significant role in the digestion of food, particularly food components that are nutritionally inaccessible to the human host. While no system can fully recapitulate the in vivo interactions of food, the host, and the gut microbiome in the human body, in vitro and animal model tools are critical for studying these complex relationships. Here, we review many of the common in vitro and animal models used to manipulate and study how the gut microbiome affects and is affected by diet. We focus on colonic fermentation systems, with or without small intestinal contribution, bioreactors with both microbial and host epithelial cell components, and animal models that have been developed to study these relationships. We will review the limitations of these systems while also discussing new innovations that seek to address these limitations.},
}

@article {pmid41918985,
year = {2026},
author = {Keskey, R and Meltzer, R and Toni, T and Hyoju, S and Cohn, E and Cao, J and Benjamin, A and Lam, A and Zaborin, A and Zaborina, O and Alverdy, J},
title = {Microbiota-accessible carbohydrates enhance gut microbiota stability and antibiotic resilience through production of quorum sensing molecule AI-2.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2646055},
pmid = {41918985},
issn = {2993-3935},
abstract = {Dietary fiber and fat shape the gut microbiota and human health, yet their role in modulating the response of the microbiota to antibiotics remains underexplored. We hypothesized that dietary fiber, independent of fat content, mitigates antibiotic-induced weight loss and diarrhea in a microbiota-dependent manner. Mice were fed refined diets varying in fat and fiber contents for 6 weeks, compared to a standard plant-based chow diet. Following antibiotic administration, fiber consumption independent of fat reduced diarrhea and weight loss. High-fiber diets increased Bacteroidetes and decreased Firmicutes and Proteobacteria prior to antibiotic exposure, all of which correlated with elevated cecal short-chain fatty acids (SCFAs). Fermentable fiber increased AI-2 quorum-sensing pathway activity and improved Firmicutes resiliency to antibiotics. Supplementation with AI-2 reduced antibiotic-induced weight loss in mice fed high-fat, low-fiber diets. These findings suggest that fermentable fiber alters the gut microbiota composition and function, enhancing microbial resiliency and host tolerance to antibiotics. Dietary supplementation with microbiota-accessible fiber increased AI-2 production, stabilized Firmicutes populations, and attenuated antibiotic-associated weight loss, independent of dietary fat content.},
}

@article {pmid41919041,
year = {2026},
author = {Bizzarri, E and Proietti, S and Falconieri, GS and Caruso, C and Bertini, L},
title = {Exploring the molecular landscape of environmental responses in the Antarctic plant Colobanthus quitensis: insights from metatranscriptomic analysis.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1774223},
pmid = {41919041},
issn = {1664-462X},
abstract = {INTRODUCTION: The harsh environmental conditions of Antarctica significantly influence plant responses, impacting both defence mechanisms and developmental processes. Moreover, plant-associated microbial communities further modulate physiological functions, creating a complex network of interactions. This study aimed to investigate how local environmental conditions and plant-associated microbiota shape the transcriptomic landscape of the Antarctic plant Colobanthus quitensis.

MATERIALS AND METHODS: A comparative metatranscriptomic analysis was conducted on plants collected from three sites spanning a coastal-to-inland gradient of increasing climatic severity to investigate both the functional roles of differentially expressed plant genes and taxonomic profiling of the associated microbial community. In addition, the content of photosynthetic and protective pigments was quantified biochemically to assess whether environmental conditions influence the photosynthetic pathway.

RESULTS AND DISCUSSION: The results suggested that Site 2 (Puchalski Station) represents a particularly favourable microenvironment that optimises the physiological performance of C. quitensis, supporting enhanced homeostasis and the activation of multiple stress-response strategies. Furthermore, distinct variations in microbial community composition were observed across the sites, underscoring the interplay between local environment and plant-associated microbiota.

CONCLUSIONS: These findings highlight the sensitivity of C. quitensis to minor environmental changes and suggest that its associated microbiome could serve as an early-warning system for ecological change in Antarctica.},
}

@article {pmid41919346,
year = {2025},
author = {Berretta, A and Schwab, C},
title = {Fermentation-driven interactions of gut microbes with their environment.},
journal = {Essays in biochemistry},
volume = {69},
number = {6},
pages = {},
doi = {10.1042/EBC20253057},
pmid = {41919346},
issn = {1744-1358},
mesh = {*Fermentation ; *Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Butyrates/metabolism ; },
abstract = {The gut microbiome has gained a lot of attention in recent decades due to the multitude of interactions it has with the host. One of the main ways the microbiota communicates with the host is through the fermentation of dietary or host-derived nutrients. Fermentation of carbohydrates and amino acids yields structurally and compositionally different metabolites that have distinct functionality within the gut microbial community but also in the interaction with the host. The most abundant fermentation metabolites are the short-chain carboxylic acids acetate, butyrate, and propionate. While important contributions to host health have been attributed to these three, there are other compounds formed by fermentation whose relevance in the gut becomes increasingly recognized. In this essay, we will present how gut physiological properties relate to microbial fermentation capacity. We will introduce the diversity of fermentation pathways and relate functionality to the intrinsic properties of fermentation-derived metabolites. Finally, we will present strategies to restore disrupted fermentation activity.},
}

*Fermentation
*Gastrointestinal Microbiome/physiology
Humans
Animals
Butyrates/metabolism

@article {pmid41919524,
year = {2026},
author = {Jain, A},
title = {Advances in New Approach Methodologies for Assessing ADME Properties of Nano-formulations.},
journal = {Xenobiotica; the fate of foreign compounds in biological systems},
volume = {},
number = {},
pages = {1-36},
doi = {10.1080/00498254.2026.2653145},
pmid = {41919524},
issn = {1366-5928},
abstract = {Conventional animal models face ethical concerns and scientific limitations, as interspecies differences often fail to capture the unique pharmacokinetics of nanomaterials.This review highlights advances in Non-Animal Models, including organoid-based systems that replicate human tissue structure, microfluidic organ-on-chip platforms that mimic dynamic physiology, and computational approaches such as physiologically based pharmacokinetic (PBPK) modelling, molecular dynamics, and machine learning.Innovations such as vascularized organoids, multi-organ chip networks, and artificial intelligence-driven refinement are evaluated for their potential to improve predictive accuracy.Remaining challenges, including scalability, standardisation, and incorporation of immune and microbiome components, are critically discussed.By integrating technological advances with regulatory perspectives, this review underscores New Approach Methodologies as a transformative pathway toward more ethical, human-relevant, and predictive nanomedicine development.},
}

@article {pmid41919539,
year = {2026},
author = {Liu, J and Sun, Y and Wu, J and Tang, S and Ding, G},
title = {[Comparative analysis of microbial communities in different oral ecological niches of preschool children].},
journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology},
volume = {44},
number = {2},
pages = {197-205},
doi = {10.7518/hxkq.2025.2025285},
pmid = {41919539},
issn = {2618-0456},
mesh = {Humans ; Child, Preschool ; *Microbiota ; Child ; *Mouth Mucosa/microbiology ; RNA, Ribosomal, 16S/genetics ; *Tongue/microbiology ; *Bacteria/classification/genetics ; *Tooth/microbiology ; *Dental Plaque/microbiology ; Male ; Mouth/microbiology ; },
abstract = {OBJECTIVES: This study aims to investigate the structural differences, dominant bacterial genera, and potential functions of microbial communities in different oral ecological niches (dorsal tongue, tooth surface, and buccal mucosa) of preschool children to clarify the influence of local microenvironments on microbial colonization and provide a theoretical basis for the microbiota-targeted regulation of pediatric oral diseases.

METHODS: A total of 105 plaque samples were collected from the dorsal tongue, tooth surface, and buccal mucosa of 35 healthy preschool children (aged 4-6 years). High-throughput sequencing of the 16S rRNA gene was performed to analyze the microbial community structure and alpha/beta diversity. Principal coordinate analysis, UPGMA clustering, and LEfSe analysis were used to identify niche-specific dominant genera. PICRUSt2 was applied to predict the potential metabolic functional profiles across niches.

RESULTS: Spatial hete-rogeneity in microbial composition and structure was observed across the three oral niches. Species richness was significantly higher on the tooth surface and buccal mucosa than on the dorsal tongue. The dominant phyla included Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Fusobacteria, and Patescibacteria. At the genus level, Actinomyces and Corynebacterium were enriched on the tooth surface, Veillonella was enriched on the dorsal tongue, and Streptococcus was predominant on the buccal mucosa. Beta diversity and clustering analyses confirmed distinct microbial community structures among the niches. LEfSe analysis identified several niche-specific genera. PICRUSt2 functional prediction revealed significant differences in amino acid metabolism, carbohydrate metabolism, cell motility, translation, signal transduction, immune system, infectious disea-ses, and membrane transport (P<0.05).

CONCLUSIONS: The dorsal tongue, tooth surface, and buccal mucosa in preschool children harbor distinct microbial communities with different taxonomic composition, diversity, and functional potential. The findings suggest that local microenvironmental factors shape oral microbiota and may contribute to the early onset of oral diseases. This study provides foundational data and theoretical insights for early microbiome-based risk assessment and personalized oral health interventions in children.},
}

Humans
Child, Preschool
*Microbiota
Child
*Mouth Mucosa/microbiology
RNA, Ribosomal, 16S/genetics
*Tongue/microbiology
*Bacteria/classification/genetics
*Tooth/microbiology
*Dental Plaque/microbiology
Male
Mouth/microbiology

@article {pmid41919541,
year = {2026},
author = {Xu, Y and Wang, S and Zhou, J},
title = {[Oral homeostasis imbalance under hypoxia].},
journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology},
volume = {44},
number = {2},
pages = {215-223},
doi = {10.7518/hxkq.2026.2025427},
pmid = {41919541},
issn = {2618-0456},
mesh = {*Homeostasis ; Humans ; *Hypoxia/physiopathology ; Mouth Mucosa/physiopathology ; Microbiota ; Salivary Glands/physiopathology ; Bone Remodeling ; },
abstract = {Hypoxia disrupts oral homeostasis through multiple interconnected pathways, including interference with tooth germ development, impairment of salivary gland function and salivary buffering capacity, compromise of the oral mucosal barrier, imbalance in jawbone and alveolar bone remodeling, and alterations in the diversity and functionality of the oral microbiome. These disturbances collectively contribute to the onset and progression of oral diseases. Moreover, disruption of oral homeostasis may, in turn, affect systemic homeostasis, increasing the risk of disorders in other organ systems through mechanisms involving inflammatory mediator release and microbial translocation. Here, we systematically review the effects and underlying mechanisms of hypoxia exposure on oral homeostasis, and further explore the interconnections between hypoxia-induced oral dysregulation and systemic homeostatic imbalance. This review aims to provide a comprehensive understanding of the regulatory networks linking oral and systemic homeostasis under hypoxia, thereby offering potential insights for maintaining homeostatic balance.},
}

*Homeostasis
Humans
*Hypoxia/physiopathology
Mouth Mucosa/physiopathology
Microbiota
Salivary Glands/physiopathology
Bone Remodeling

@article {pmid41919563,
year = {2026},
author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W},
title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70091},
pmid = {41919563},
issn = {1522-7278},
abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.},
}

@article {pmid41919917,
year = {2026},
author = {Mall, A and Rode, KJ and Marx, CJ},
title = {Evolution uncovers a general tradeoff between recovery after heat shock and growth at elevated temperatures.},
journal = {mBio},
volume = {},
number = {},
pages = {e0330525},
doi = {10.1128/mbio.03305-25},
pmid = {41919917},
issn = {2150-7511},
abstract = {Fitness tradeoffs between different environments enable the maintenance of microbial diversity. While the importance of tradeoffs is clear, it has been surprisingly difficult to predict which traits they will occur between and at how granular a level. For example, it is unclear whether performance between a constant versus pulsed exposure of the same stress tends to be positively correlated, independent of each other, or negatively correlated. Empirically, it has been shown that a critical feature structuring microbial communities is temperature. However, the compatibility between strategies to deal with different forms of heat stress is unclear. For instance, are strains that grow well at higher temperatures also stronger at withstanding heat shock? To understand how environmental microbes can adapt to better deal with heat stress, we performed an evolution experiment using a dominant phyllosphere microbe Methylobacterium extorquens in a regime of intermittent heat shock. We identified the genetic basis of adaptation, discovering a large number of loci capable of mediating adaptation to heat shock, many of which had not been previously linked to heat stress. Despite the genetic divergence among evolved isolates, we discovered a general tradeoff between heat shock resistance and growth at consistently elevated temperatures. We found this tradeoff was not limited to evolved isolates, but also represented across a sample of environmentally isolated Methylobacterium strains. These findings indicate a generic conflict between strategies to deal with heat shock recovery and growth at elevated temperatures, suggesting even variation in intensities of a stressor can drive diversity in microbial strategies.IMPORTANCEOne of the key forces shaping the microbial diversity in nature is temperature. However, temperature in ecological settings is variable, and it is unknown if strategies to deal with different intensities of high temperature are compatible or not. Using evolution experiments, we identify the genetic basis of adaptation to heat shock in Methylobacterium extorquens, a dominant member of the phyllosphere microbiome. We discover a number of genetic targets where beneficial mutations improve heat shock resistance, most of which have not been implicated with heat stress before. For both the evolved isolates and a set of environmentally isolated Methylobacterium strains, we discover a general tradeoff between recovery after heat shock and growth at elevated temperatures. While the strategies to deal with increasing temperatures have garnered significant interest, our results suggest that even different intensities of heat stress can select for distinct and incompatible strategies and can drive microbial diversification in ecological settings.},
}

@article {pmid41919968,
year = {2026},
author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C},
title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0039226},
doi = {10.1128/aem.00392-26},
pmid = {41919968},
issn = {1098-5336},
abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.},
}

@article {pmid41920102,
year = {2026},
author = {Bruyere, D and Delahaye, T and Nikkels, A and Herfs, M},
title = {Pathophysiology of cutaneous commensal human papillomaviruses.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.02.011},
pmid = {41920102},
issn = {1523-1747},
abstract = {Cutaneous human papillomaviruses (HPVs), particularly those of the β-genus, have traditionally been viewed as harmless constituents of the skin microbiome. However, a debate has emerged over the past few years regarding their possible contribution to cancer development. In immunocompetent hosts, commensal β-HPVs may contribute to immune education and cutaneous homeostasis. In contrast, under immunosuppression, their increased viral load (combined with UV-induced DNA damage) can promote early oncogenic events and facilitate cancer initiation, through a "hit-and-run" mechanism. This context-dependent behavior defines β-HPVs as dynamic modulators of skin health, capable of exerting protective or pathogenic effects within the cutaneous ecosystem depending on host and environmental factors.},
}

@article {pmid41731377,
year = {2026},
author = {Diouf, AM and Mbaye, AL and Deh, M and Lahlali, R and Elhoumaizi, MA and Rchiad, Z and Barakate, M},
title = {Comparative metagenomic analysis of bacterial and fungal communities associated with bayoud-resistant and susceptible date palm cultivars in the Zagora oasis-Morocco.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41731377},
issn = {1471-2180},
abstract = {BACKGROUND: Fusarium oxysporum f. sp. albedinis (Foa) is a destructive soil-borne fungal pathogen responsible for bayoud disease, which threatens date palm cultivation in North Africa. This disease has caused significant agricultural losses, particularly in Morocco, where the Zagora oasis is a key region for date palm production. Within this oasis, two cultivars—Black Bousthammi and Jihel—are mainly cultivated and exhibit complete resistance and high susceptibility to Foa, respectively. Thus, this study aimed to identify and compare the bacterial and fungal communities associated with the two cultivars and understand their assemblage regarding the disease resistance or susceptibility. Moreover, we explored the influence of each cultivar on the composition and structure of its root-associated microbiome and examined its relationship with the microbial populations present in the surrounding bulk soil, to better understand the recruitment dynamics that shape the microbiome in the roots.

RESULTS: The results revealed significant differences in microbiome composition between the bulk soil and roots of the two date palm cultivars, and between the microbiome of the resistant and susceptible cultivars as well. Moreover, we observed that date palm cultivars had a greater effect on bacterial community composition than on fungal population. Interestingly, the susceptible cultivar exhibited a higher enrichment of several beneficial genera, such as Pseudomonas, Lysinibacillus, Actinomadura, Halomonas, Kocuria, Serratia, Phyllobacterium, Bacillus, Streptomyces, and Trichoderma.

CONCLUSION: The presence of these beneficial genera, known for their antagonistic activity against phytopathogens, may reflect a recruitment pattern associated with pathogen pressure in the susceptible cultivar. This study is the first to compare the microbial communities between a bayoud-resistant and susceptible cultivar and provides insights into the potential role of the root microbiome when plants are under pathogen pressure. This reinforces the need to further elucidate the genetic and biological mechanisms that trigger microbiome assembly, which could be a key step in developing effective methods to manage the bayoud disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04837-8.},
}

@article {pmid41909894,
year = {2025},
author = {Hensen, T and Ahmad, S and Kastenmüller, G and Kraaij, R and Ghanbari, M and Ikram, A and Kaddurah-Daouk, R and Thiele, I},
title = {In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2443171},
pmid = {41909894},
issn = {2993-3935},
support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; },
abstract = {The gut microbiome has become increasingly recognized for its role in the pathogenesis of Alzheimer's disease (AD) and is thought to influence AD pathogenesis via metabolic crosstalk with the host. However, mechanistic pathways connecting the gut microbiome to AD pathogenesis remain unknown. To explore potential mechanistic pathways in AD pathogenesis, we created host-microbiome whole-body metabolic models personalized with 16S rRNA microbiome data and predicted emergent metabolic contributions of gut microbiomes. We analyzed 63 metabolites in blood with previously known links with AD. These in silico predictions were then associated with major risk factors for AD in a cohort of 1,065 aging non-AD individuals and subsequently used to inform targeted analyses on serum metabolomics. Our analysis identified increased host-microbial production of L-arginine in older individuals. Lower production of deoxycholate correlated with the neuroprotective APOE E2 allele and it decreased with higher global cognition. Serum metabolomics from the same individuals of cholesterol products and bile acid metabolism corroborated the modeling predictions, suggesting a potential link between the APOE genotype and cognitive health. In conclusion, this study associated metabolic gut microbiome influences on human metabolism with risk factors for AD and identified cholesterol and bile acid metabolism to potentially link with AD pathogenesis.},
}

@article {pmid41909897,
year = {2025},
author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M},
title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2527766},
pmid = {41909897},
issn = {2993-3935},
abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.},
}

@article {pmid41909899,
year = {2025},
author = {Rozenberga, M and Saksis, R and Elbere, I and Birzniece, L and Briviba, M and Konrade, I and Klovins, J},
title = {Tracking the origin of bacterial DNA in blood: Indication of localized and sporadic transfer from other body sites.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2482771},
pmid = {41909899},
issn = {2993-3935},
abstract = {Recent studies propose the existence of a blood microbiome, but its composition, origin, and dynamics remain largely unresolved. In this pilot study, we analyzed the bacterial DNA present in the blood of 10 volunteers by comparing the taxonomic profiles of 16S rRNA gene sequences from skin, vaginal, oral, and fecal samples. After applying stringent decontamination protocols, we detected bacterial DNA in all blood samples, predominantly from the Pseudomonas genus. A key finding was the identification of 32 unique Amplicon Sequence Variants (ASVs) that were identical between blood and a single body site within individual participants, with no overlap between multiple body sites or across different participants. This participant-specific overlap suggests a true biological origin of bacterial DNA in blood, likely stemming from localized bacterial migration, such as from the skin. Additionally, 27.4% of the ASVs in blood were found in other body sites, with the highest overlap observed in skin samples. Furthermore, 25.3% of blood ASVs persisted after three months, suggesting a consistent pattern in the bacterial DNA composition detected in blood over time. These findings deepen our understanding of the blood microbiome and provide a basis for future research linking blood microbiota to health and disease phenotypes.},
}

@article {pmid41909901,
year = {2025},
author = {Teo, Y and Lavrinienko, A and Albertos Torres, D and Asare, PT and Ruder, A and Dominguez-Bello, MG and Egli, A and Bokulich, NA and Vonaesch, P},
title = {Evaluating long-term stool preservation methods for maximizing the recovery of viable human fecal microbiota.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2594958},
pmid = {41909901},
issn = {2993-3935},
abstract = {UNLABELLED: The gut microbiome plays a fundamental role in human health, prompting efforts to catalog and preserve its diversity across human populations. While DNA sequencing dominates microbiome research, cultivation remains essential for mechanistic studies and therapeutic development. However, best practices for long-term stool preservation remain limited. Here, we compared the stability of eight cryopreservation treatments for maintaining viable stool microbiota over a 1-y storage period at -80 °C (freezer) or at -196 °C (liquid nitrogen) using samples from infants, children, and adults. Combining cultivation on six media with 16S rRNA sequencing, we show that ultralow-temperature cryopreservation has a minimal impact on microbiota diversity compared to fresh cultures. Standard glycerol preservation and simple snap-freezing performed comparably to more complex and costly protocols, with all cultured samples retaining donor-specific microbiota profiles after long-term cryopreservation. The lack of strong treatment-specific effects on microbiota composition suggests a shared microbial response to freeze‒thaw stress favoring taxa with broad environmental tolerance. Our findings offer practical, low-cost strategies for stool biobanking.

IMPORTANCE: The cultivation of bacterial taxa from complex communities, such as those in fecal samples, is essential for mechanistic studies and the development of microbiota-based therapeutics, including defined consortia and individual probiotic strains. Such cultivation efforts typically rely on previously stored samples; however, systematic knowledge regarding long-term preservation strategies that ensure the viability and regrowth of constituent bacterial taxa remains limited. In this study, we systematically evaluated 16 distinct cryopreservation conditions to assess their efficacy in maintaining bacterial viability. Our results show that conventional glycerol-based preservation and simple snap-freezing are comparable in performance to more elaborate and cost-intensive protocols. Moreover, we identified the duration of sample transport prior to freezing as a critical determinant of post-thaw bacterial recovery. These findings provide valuable data on the relative effectiveness of various preservation methods and support the use of low-cost, easily implementable strategies that are particularly suitable for application in resource-limited settings.},
}

@article {pmid41909902,
year = {2025},
author = {Andalib, KMS and Rodosy, FB and Habib, A},
title = {The living medicine inside us: in vitro therapeutic prospects of human gut bacteria.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2480093},
pmid = {41909902},
issn = {2993-3935},
abstract = {Gut microbial metabolism is intimately coupled to host health and disease. Recent knowledge on potential health benefits of gut microbiome lays the groundwork for development of novel therapeutic strategies. But how microbiota-derived metabolites impact on host-microbiome crosstalk remains untapped from therapeutic perspectives. In this study, six gut bacteria sourced from a fecal pool of forty healthy donors were cultured in three distinct growth media. Subsequently, the bacteria were identified through 16S rRNA gene sequencing and subjected to metabolite extraction to evaluate their anti-microbial, anti-oxidant and anti-thrombotic potential. Findings reveal strong anti-oxidant activities in the metabolic-extracts from all the isolates. Metabolites derived from Lactobacillus rhamnosus, Priestia flexa and Bacillus subtiilis inhibited the growth of clinically pathogenic strains Escherichia coli ATCC-8739, Salmonella typhi ATCC-1408 and Staphylococcus aureus ATCC-6538. Escherichia fergusonii originated metabolites demonstrated the highest efficacy in lysing blood clots compared to streptokinase. Additionally, extracts from all the isolates exhibited significant ability to delay coagulation time, competing with standard warfarin. Thus, the findings of our early-stage study provide novel insights into metabolomic functions of gut microbiota. This study underscores the significance of exploring these active metabolites for prospective therapeutic and clinical exploration at the intersection of drug discovery and live bio-therapeutics.},
}

@article {pmid41909904,
year = {2025},
author = {Ramakrishnan, M and Cross, TL and Organski, AC and Saiprasad, SM and Simpson, AMR and Tancredi, DJ and Van Haute, MJ and Christensen, CM and Lewis, ZT and Auchtung, TA and Walter, J and Hutkins, R and Savaiano, DA},
title = {Two-week supplementation of Bifidobacterium adolescentis iVS-1 reduces symptoms associated with lactose intolerance in lactose maldigesters.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2508199},
pmid = {41909904},
issn = {2993-3935},
abstract = {Probiotic supplements containing high β-galactosidase-producing bacteria may aid in the management of lactose intolerance. We previously isolated a strain of Bifidobacterium adolescentis, iVS-1, from the fecal sample of a human donor after consumption of galactooligosaccharides (GOS), a prebiotic derived from lactose. Therefore, it was hypothesized that iVS-1 might reduce symptoms associated with lactose maldigestion. Compared to other probiotic strains, iVS-1 had high β-galactosidase activity and reduced gas formation by fecal communities during in vitro fermentations of lactose or milk. A randomized placebo-controlled clinical trial was then conducted with 21 lactose maldigesters, randomized to receive either B. adolescentis iVS-1 (n = 11) or placebo (n = 10) daily for 2 weeks. Compared to the two-week run-in period, iVS-1 abundance was higher both at the end of the treatment period (p = 0.0005) and after the 2-week post-treatment period (p = 0.045). The iVS-1 group reported less overall daily symptoms during the treatment period when compared to placebo (p = 0.032) and had significant improvement for fecal urgency (p = 0.033) and diarrhea (p = 0.006). The metabolism of lactose, reduction of gas, and improvement of multiple gastrointestinal symptoms suggest that B. adolescentis iVS-1 may be an effective treatment for lactose intolerance. Trial Registration: The trial is registered at ClinicalTrials.gov (https://clinicaltrials.gov/study/NCT05668468).},
}

@article {pmid41909905,
year = {2025},
author = {Chakraborty, J and Lanchenba Singh, N and Kumar Das, B},
title = {Gut microbiome and lung cancer: mechanisms, interactions, and dietary interventions.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2501313},
pmid = {41909905},
issn = {2993-3935},
abstract = {Lung cancer continues to claim countless lives globally. Several studies have shown that the gut microbiome is vital in maintaining healthy lung function through the gut-lung axis. A comparison between the gut microflora of healthy volunteers and lung cancer patients revealed that changes in the composition of gut microflora occur in lung cancer patients. The gut microflora may contribute to lung cancer by influencing immune reactions, inflammatory pathways, bacterial metabolites modulating host metabolism, microbiome dysbiosis, genotoxicity, virulence, and bacteria-induced epigenetic alterations. Thus, it may be assumed that maintaining a healthy gut microflora could help prevent lung cancer. Nutraceuticals are specialized products designed to support health and address specific nutritional needs. They contain ingredients like vitamins, minerals, probiotics, polyphenols, and herbs to reduce the risk or impact of certain illnesses. Nutraceuticals, including probiotics and polyphenols, play a role in preventing and treating various cancers, including lung cancer, by modulating the gut microbiome. This review examines the link between the gut microbiome and lung cancer, how it contributes to cancer development, and the impact of dietary interventions - particularly probiotics, polyphenols, and dietary fibers - on lung cancer prevention and treatment.},
}

@article {pmid41909906,
year = {2025},
author = {Shibi Anilkumar, A and Thomas, SM and Veerabathiran, R},
title = {Gut microbial metabolites as a convergence point between autoimmunity and solid tumors.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2470805},
pmid = {41909906},
issn = {2993-3935},
abstract = {The human gut microbiome, a diverse community of trillions of microorganisms, is essential for controlling numerous bodily functions, such as metabolism, immune response, and epithelial barrier integrity. The gut microbiota comprises bacteria, viruses, fungi, and other microorganisms that affect human health, metabolic pathways, and immune responses. Dysbiosis, or the imbalance of gut microbial composition, has been linked to the pathogenesis of several ailments, including cardiovascular conditions, gastrointestinal conditions, allergies, obesity, autoimmune disorders, and tumors. The interaction between gut microbes and immune responses, mainly through Tregs cells and Th17 cells, underscores the microbiome's function in immune regulation. Furthermore, gut microbial metabolites act as signaling molecules and substrates for metabolic processes, impacting autoimmune disorders and cancer development. Recent research highlights the microbiome's potential role in cancer immunoediting, where gut microbial metabolites may either promote or suppress cancer progression by modulating inflammation and immunosuppression. This review delves into the critical functions of the gut microbiome, its influence on autoimmune disorders, and the emerging connection between gut microbial metabolites and cancer immunoediting, offering new insights into their impact on human health and disease.},
}

@article {pmid41909907,
year = {2025},
author = {Ishii, C and Suzuki, M and Murakami, S and Song, I and Soejima, Y and Kato, M and Fukuda, S},
title = {Ecologically robust gut environment associated with personalized metabolic responses in a Japanese cohort.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2574930},
pmid = {41909907},
issn = {2993-3935},
abstract = {The gut microbiota produces numerous metabolites that affect host physiology. However, the effects of daily diet on human fecal metabolome profiles and their robustness are not well understood, and examinations of intra-individual stability over multiple time points are limited. Here, we investigated the robustness of the human intestinal environment through fecal metabolome and microbiome profiling in response to daily dietary fluctuations. We analyzed 176 fecal samples from 25 healthy Japanese individuals subjected to three dietary regimens, including heterogeneous and homogeneous diets. Fecal metabolome and microbiome profiles were unique to each individual. Further in-depth analyses of seven of these individuals showed that these profiles were stable despite daily dietary fluctuations in six individuals. In addition, random forest classification successfully predicted each subject's identity based on their metabolome profile. The correlation analysis also revealed that the food-metabolite and food-microbiome relationships were highly personalized. The findings from this study suggest that individual diet prior to sample collection is unlikely to influence the fecal metabolome and microbiome data to an extent that is not representative of the individual's "normal" condition, which may lower barriers to future research on the gut environment and its implications for host health.},
}

@article {pmid41909910,
year = {2025},
author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J},
title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2570502},
pmid = {41909910},
issn = {2993-3935},
abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.},
}

@article {pmid41909911,
year = {2025},
author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO},
title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {2589861},
pmid = {41909911},
issn = {2993-3935},
abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.},
}

@article {pmid41910033,
year = {2026},
author = {Jinato, T and Sikaroodia, M and Gilleveta, PM and Dissayabutra, T and Tangkijvanich, P and Bajaj, JS and Chuaypen, N},
title = {Gut Microbiome Signatures Differ in Cirrhosis With and Without Hepatocellular Carcinoma in a Southeast Asian Cohort.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70358},
pmid = {41910033},
issn = {1440-1746},
support = {C2F//Second Century Fund/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; HEA_FF_68_159_3000_028//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF68//Fundamental Fund 2025/ ; B36G660004//Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {BACKGROUND: Gut microbiota, microbial metabolites, and inflammatory cytokines play key roles in the pathogenesis of cirrhosis and hepatocellular carcinoma (HCC); however, data from Southeast Asia are limited. This study examined microbial composition, intestinal permeability, butyrate-related gene expression, and cytokine profiles in Thai patients with cirrhosis, with and without HCC.

METHODS: This cross-sectional study included 30 healthy controls, 33 patients with cirrhosis without HCC, and 44 patients with HCC (HCC-cirr). Fecal samples were analyzed using 16S rRNA sequencing. Microbial functional profiles were predicted using KEGG Orthology-based pathway inference. Gut permeability markers (intestinal fatty acid-binding protein [I-FABP] and lipopolysaccharide-binding protein [LBP]), butyrate-associated gene (BCoAT) expression, and cytokine profiles were assessed.

RESULTS: Alpha diversity (Chao1) was significantly lower in HCC-cirr patients than in healthy controls (p < 0.001) and patients with cirrhosis (p = 0.008). Beta diversity also differed significantly between HCC-cirr and controls (p = 0.008). Ligilactobacillus, Catenibacterium, and Alloprevotella were enriched in the cirrhosis group, whereas HCC-cirr patients showed increased Ruminococcus gnavus and reduced butyrate producers (Coprococcus, Subdoligranulum). Functional prediction suggested pathway differences between cirrhosis and HCC-cirr, including folate, sulfur, tyrosine metabolism, and steroid biosynthesis. BCoAT expression was significantly decreased in HCC (p = 0.006). Plasma LBP and I-FABP were significantly elevated in HCC-cirr (p = 0.033, p < 0.001), with I-FABP also higher than in cirrhosis (p = 0.002). Proinflammatory cytokines (GM-CSF, IL-10, IL-18, IL-1α, IL-7, IL-8, and M-CSF) were elevated in HCC-cirr.

CONCLUSIONS: Among the Thai cohort, HCC with cirrhosis was associated with distinct gut microbial changes, reduced BCoAT expression, increased gut permeability, and cytokine alterations, highlighting the contribution of gut dysbiosis and microbial by-products to liver disease progression.},
}

@article {pmid41910132,
year = {2026},
author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A},
title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019126},
doi = {10.1128/msystems.00191-26},
pmid = {41910132},
issn = {2379-5077},
abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.

IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.},
}

@article {pmid41910137,
year = {2026},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0418725},
doi = {10.1128/spectrum.04187-25},
pmid = {41910137},
issn = {2165-0497},
abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.

IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20°C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25°C and 30°C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.},
}

@article {pmid41910192,
year = {2026},
author = {Saqib, S and Latousakis, D and Virtanen, S and Kalliala, I and Holster, T and Juge, N and Salonen, A},
title = {Exploratory analyses of cervicovaginal mucus O-glycan composition and microbiota profiles in unexplained infertility.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwag023},
pmid = {41910192},
issn = {1460-2423},
abstract = {In addition to the specific causes of infertility, two components of the vaginal ecosystem, the vaginal microbiota and the cervicovaginal mucus (CVM), may be associated to reduced fecundity and the success of infertility treatments. The aim of this study was to explore the composition of the CVM O-glycans and vaginal microbiota in women with unexplained infertility. We collected CVM and vaginal swab samples during medically induced ovulation from 19 women with unexplained infertility. Mucin O-glycosylation profiles were generated through Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight (MALDI-ToF) mass spectrometry and taxonomic profiles of the vaginal microbiota through 16S rRNA gene amplicon sequencing. Altogether 57 O-glycan structures were identified, dominated by core 1 and 2 structures. A significant proportion, nearly 85%, of the glycans were fucosylated and five structures dominated the profiles, accounting for >50% of the glycans observed in most samples. The vaginal microbiota of the patients was dominated by Lactobacillus crispatus (79%), followed by Lactobacillus jensenii (32%) and Lactobacillus iners (21%) and Gardnerella vaginalis (5%, single sample). PERMANOVA analysis indicated significant associations between the glycan structures and dominant taxa (q = 0.0011, R2 = 0.37). This exploratory study provides initial insights into the composition and variation of CVM O-glycans in unexplained fertility and in relation to the vaginal microbiota composition, laying a groundwork for future research.},
}

@article {pmid41910204,
year = {2026},
author = {Green, L and Marchesani, A and Joyner, JL},
title = {The Atlanta Urban Watershed Harbors Antibiotic Resistant Halotolerant Bacteria.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag084},
pmid = {41910204},
issn = {1365-2672},
abstract = {AIMS: Rapid urbanization of the Chattahoochee River has decreased the water quality with higher levels of anthropogenic bacteria from nonpoint source pollution. Introduced bacteria are variable across urban watersheds but only monitored by the abundance of fecal indicator bacteria. Staphylococcus aureus is a halotolerant, opportunistic pathogen associated with aquatic pollution, but impact on the microbial ecology is not well understood in freshwater systems. Describing the halotolerant subset of the aquatic microbiome, can expand upon the health risk of bacterial pollution.

METHODS & RESULTS: Surface water samples along the Chattahoochee River were collected and halotolerant bacteria were cultured using selective agar, typical for growing Staphylococcus species. Bacteria colonies were isolated then characterized by morphology, biochemical tests, and antibiotic resistance screening. Antibiotic resistance profiles showed isolates with a high percentage of resistance to penicillin (86.2%) and novobiocin (17.2%). Biofilm formation was common with 41.4% of isolates formed moderate to strong biofilms. 16S rRNA gene sequencing identified isolates to not be Staphylococcus spp. but within two predominant groups, Bacillus spp. and Priestia spp.

CONCLUSIONS: The Priestia genus is poorly known in freshwater systems; though the combination of antibiotic resistance, biofilm formation, and spore-forming traits indicate that it has key survival characteristics. Halotolerant bacteria harbor opportunistic human pathogens and a public health risk because the bacteria have a high prevalence of antibiotic resistance and biofilm capability, which contribute to environmental persistence and reservoirs for antibiotic resistance genes. This environmental resistome is a notable and developing characteristic of the urban aquatic microbiome.},
}

@article {pmid41910238,
year = {2026},
author = {Le, NNT and Xue, S and Mu, H and Wu, J and Xi, C and Marhaba, T and Zhang, W},
title = {Soil chemistry and microbiome modulation through water irrigation containing oxygen, hydrogen, and carbon dioxide nanobubbles.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0217325},
doi = {10.1128/aem.02173-25},
pmid = {41910238},
issn = {1098-5336},
abstract = {Nanobubble technology has shown considerable promise in sustainable agriculture due to its ability to enhance seed germination, plant growth, and soil quality without leaving harmful residues. While benefits are often attributed to improved soil aeration and soil texture changes (e.g., permeability), nanobubbles may also influence soil microbiome, an essential driver of plant health and nutrient cycling. This study systematically investigated how different nanobubble types-oxygen, hydrogen, and carbon dioxide-modulate soil chemistry and microbial community structure over a 4-week period. Multivariate analyses on microbiome taxonomic composition revealed distinct microbial responses to each gas type. Oxygen and hydrogen nanobubble treatments resulted in more pronounced shifts in microbial composition and functional potential compared to carbon dioxide nanobubbles. These shifts included enrichment of bacterial taxa associated with nutrient turnover, pollutant degradation, and pathogen suppression, such as Flavobacteriaceae, Comamonadaceae, Nannocystaceae, and Blastocatellaceae. Functional predictions showed that oxygen and hydrogen nanobubbles could promote metabolic pathways related to organic compound degradation and remediation of contaminated soil. Microbial network analysis further highlighted the beneficial impacts of nanobubbles on keystone taxa, such as Flavobacteriaceae, which in turn play pivotal roles in shaping soil ecosystem functions. Together, these findings demonstrate that gas-specific nanobubble irrigation can steer soil microbiome dynamics in ways that may enhance soil fertility, resilience, and crop productivity.IMPORTANCEThis study provides new insights into how nanobubble irrigation can be used to improve soil health and agricultural sustainability. By demonstrating that oxygen and hydrogen nanobubbles selectively enrich beneficial microbial taxa linked to soil nutrient turnover, pollution degradation, and pathogen suppression, this study identifies a promising approach to enhance plant growth and soil health through new nanobubble-driven processes. The detection of keystone taxa responsive to nanobubble treatments also reveals potential microbial mechanisms underlying the interactions between nanobubbles, soil, and plant health. Together, these findings highlight nanobubble irrigation as a novel and scalable strategy for microbiome engineering that could advance sustainable crop production and environmental stewardship. Furthermore, while prior studies have primarily focused on the microbial effects of air and oxygen nanobubbles, our study systematically examined and compared the impacts of less explored nanobubble types, specifically hydrogen and carbon dioxide, demonstrating the broad versatility of nanobubbles for diverse agricultural applications.},
}

@article {pmid41910252,
year = {2026},
author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y},
title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0252325},
doi = {10.1128/aem.02523-25},
pmid = {41910252},
issn = {1098-5336},
abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.},
}

@article {pmid41910273,
year = {2026},
author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P},
title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0179025},
doi = {10.1128/msystems.01790-25},
pmid = {41910273},
issn = {2379-5077},
abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.

IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.},
}

@article {pmid41910342,
year = {2026},
author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D},
title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085625},
doi = {10.1128/msphere.00856-25},
pmid = {41910342},
issn = {2379-5042},
abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.

IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.},
}

@article {pmid41910441,
year = {2026},
author = {Manti, M and Dimitriadis, K and Dri, E and Mavromoustakou, K and Vakka, A and Koutsopoulos, G and Tsioufis, P and Katsimichas, T and Siakavellas, S and Gazouli, M and Tsioufis, K},
title = {Transcatheter aortic valve implantation and gut microbiota: Rationale and design of the 'GUT-TAVI' cohort study.},
journal = {Science progress},
volume = {109},
number = {1},
pages = {368504261426427},
doi = {10.1177/00368504261426427},
pmid = {41910441},
issn = {2047-7163},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Transcatheter Aortic Valve Replacement/methods ; *Aortic Valve Stenosis/surgery/microbiology ; Prospective Studies ; Methylamines/blood ; Female ; Male ; Aged ; Cohort Studies ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Hemodynamics ; },
abstract = {ObjectiveAlterations in gut microbiota have been reported in patients with aortic valve stenosis (AVS), yet the impact of haemodynamic restoration following transcatheter aortic valve implantation (TAVI) on microbiota composition remains unclear. This study protocol describes a prospective cohort investigation designed to examine changes in gut microbiota and related metabolic markers after TAVI.Methods'GUT-TAVI' is a single-centre, prospective observational cohort study enrolling 40 adults with severe AVS undergoing TAVI. Stool samples will be collected at two timepoints (1 month to 1 day pre-TAVI and 3 months post-TAVI) for 16S-rRNA sequencing. Serum trimethylamine N-oxide (TMAO), standard biochemical markers, echocardiographic parameters, and dietary adherence scores will also be assessed. The primary endpoint is the change in gut microbiota composition following TAVI. Secondary analyses will examine associations between microbiota changes, haemodynamic parameters, and TMAO levels while accounting for potential confounders.ResultsAs a protocol, no results are yet available. Planned analyses include alpha- and beta-diversity comparisons, multi-variable modelling, sub-group analyses, and sensitivity analyses addressing antibiotic exposure and procedural variability.ConclusionsThis study may provide preliminary insights into how haemodynamic improvement after TAVI is associated with changes in gut microbiota and metabolic function. Findings may help inform future, larger-scale studies investigating the gut-heart axis in cardiovascular diseases.},
}

Humans
*Gastrointestinal Microbiome
*Transcatheter Aortic Valve Replacement/methods
*Aortic Valve Stenosis/surgery/microbiology
Prospective Studies
Methylamines/blood
Female
Male
Aged
Cohort Studies
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Hemodynamics

@article {pmid41910593,
year = {2026},
author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , },
title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002618},
pmid = {41910593},
issn = {1536-4828},
abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.

OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).

METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.

RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.

CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.},
}

@article {pmid41910796,
year = {2026},
author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D},
title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41910796},
issn = {1573-7446},
abstract = {UNLABELLED: Shrimp aquaculture is a rapidly expanding food sector; however, its sustainability is challenged by disease outbreaks often linked to imbalances in the microbiome. Here, we characterized the microbial communities in the intestines of shrimp and pond water from three Egyptian farms (A, B, and C) using Oxford Nanopore long-read sequencing. Descriptive comparisons of relative abundance and diversity trends revealed that pond water harbored significantly higher alpha diversity than shrimp guts. In contrast, beta diversity confirmed a strong separation between host-associated and environmental microbiomes. For the observed phyla, taxonomic profiling revealed that shrimp guts were dominated by Proteobacteria, Actinomycota, and Bacillota, whereas pond water contained additional constituents, including Cyanobacteria and Bacteroidota. Pathogen-associated genera, particularly Vibrio spp. and Pseudomonas spp., were more abundant in water samples, with farm-specific variations linked to management practices such as salinity and feed protein content. Venn analysis highlighted that pond water harbored the largest pool of unique taxa, reinforcing its role as a putative reservoir for pathogens. These findings provide the first integrative microbiome baseline for Egyptian shrimp farms, underscoring the need for microbiome-informed management to mitigate the risk of pathogens.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11259-026-11113-7.},
}

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
}

@article {pmid41910951,
year = {2026},
author = {Dasgupta, S},
title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261419483},
doi = {10.1177/15578100261419483},
pmid = {41910951},
issn = {1557-8100},
abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.},
}

@article {pmid41911313,
year = {2026},
author = {Odem, MA and Simbassa, SB and Alvarez, CF and Jeilu, O and Simar, SR and Bosserman, R and Dutta, S and Galdamez, W and Ayele, H and Hanson, BM and Proctor, DM and Krachler, AM},
title = {Shiga toxin increases intestinal transit to displace resident microbes and facilitate pathogen colonization.},
journal = {PLoS pathogens},
volume = {22},
number = {3},
pages = {e1014104},
doi = {10.1371/journal.ppat.1014104},
pmid = {41911313},
issn = {1553-7374},
abstract = {Shiga toxin (Stx)-producing Escherichia coli (STEC) is a major cause of food-borne illnesses, and disease severity correlates with the production of Shiga toxins. While clinical symptoms such as bloody diarrhea and haemolytic uremic syndrome have been attributed to Stx, its contribution to bacterial fitness is not well understood. Here, we demonstrate that Stx2 enhances STEC colonization of the zebrafish gut by facilitating the partial displacement of gut resident microbes. Infection with Stx2-producing STEC strains or direct exposure of fish to purified Stx2 induces alterations in the zebrafish microbiome structure, impacting several bacterial phyla and genera, notably Pseudomonads. We show that Stx2 is sufficient to facilitate these changes by accelerating intestinal transit, leading to increased expulsion of select gut microbes, including resident Pseudomonas species. Additionally, prokinetic drug treatment causes similar changes in gut transit and expulsion of Pseudomonas. Collectively, these findings detail a novel mode of action of Stx2 on the host, and shed light on its contribution to bacterial fitness within the host intestine.},
}

@article {pmid41911577,
year = {2026},
author = {Kaplunova, V and Alioui, H and Griguschies, T and Müller, L and Joisten-Rosenthal, V and Lautwein, T and Metzger, S and Durán, P and Loo, E},
title = {Artificial soil (ArtSoil): Recreating soil conditions in synthetic plant growth media.},
journal = {The Plant journal : for cell and molecular biology},
volume = {126},
number = {1},
pages = {e70833},
pmid = {41911577},
issn = {1365-313X},
support = {390686111//Cluster of Excellence on Plant Sciences/ ; Wolf Frommer//Alexander von Humboldt-Stiftung/ ; 391465903/GRK 2466//Deutsche Forschungsgemeinschaft/ ; 458090666//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Soil/chemistry ; *Arabidopsis/growth & development ; *Culture Media/chemistry ; Soil Microbiology ; Sucrose/metabolism ; Microbiota ; Plant Development ; },
abstract = {Controlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form symbiosis with microbes, and plant growth is influenced by soil edaphic factors. Thus, physiological and multi-omic analyses of plants grown on synthetic media will differ from those of soil-grown plants due to the influence of sucrose, and the absence of microbiota and soil edaphic factors on plant growth. The rapid advances in spatial omics call for accurate characterization of plants grown under conditions similar to soil. To address the issue, we developed Artificial Soil (ArtSoil), a growth medium containing essential nutrients for plant growth, and aqueous soil extract (ASE) to maintain soil microbiomes and edaphic factors, simultaneously eliminating the need for sugar supplementation in the medium. We compared Arabidopsis thaliana grown on conventional media and on ArtSoil under various growth conditions. We showed that complex soil microbiota in ArtSoil promote plant growth without physiological side effects induced by sucrose. We demonstrate an application for ArtSoil in single-cell transcriptomics and report microbiota-induced cell-type-specificity in immune and nitrogen signaling. We tested ArtSoil with six types of ASEs to demonstrate its potential to decouple nutrient effects from microbiota in plant growth. We conclude that ArtSoil offers a more physiologically relevant alternative to conventional media for studying plant growth within a soil-like context.},
}

*Soil/chemistry
*Arabidopsis/growth & development
*Culture Media/chemistry
Soil Microbiology
Sucrose/metabolism
Microbiota
Plant Development

@article {pmid41911622,
year = {2026},
author = {Naim, A and van Staaveren, N and Leishman, EM and Nicklas, AL and Tulpan, D and Forsythe, P and Harlander, A},
title = {Preference and behavioral responses to synbiotic supplementation via drinking water in laying hens under social stress.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106860},
doi = {10.1016/j.psj.2026.106860},
pmid = {41911622},
issn = {1525-3171},
abstract = {Synbiotics (SYN) have the potential to enhance animal health, but their efficacy depends on both biological impact and voluntary intake, particularly under stress, when hydration and gut support are critical. This study presents the first investigation of SYN supplementation delivered exclusively through drinking water in laying hens, evaluating both preference and behavioral responses, particularly feather pecking, during a period of social stress induced by repeated mixing of unfamiliar birds. A total of 226 White Leghorn hens (37 weeks old) were housed in enriched floor pens with simultaneous access to color-coded SYN-enriched and plain water containers. Following a 2-week associative learning phase and 1-week washout, hens entered a 6-week preference testing period encompassing pre-stress, stress, and post-stress phases. Water consumption was measured at the group level, while individual jug visits were tracked using RFID technology. Feather pecking was measured (10 min/day) and feather damage assessed according to severity. Hens showed a clear preference for SYN-enriched water, consuming significantly more than plain water (p < 0.0001). While overall intake remained stable, SYN consumption fluctuated across stress phases, with the strongest preference pre-stress and a modest decline during stress. Although hens with higher rates of severe feather pecking (SFP) visited SYN-enriched water more frequently than hens with lower rates (p = 0.0288), suggesting a potential coping mechanism, overall, SFP rates remained stable across all phases. Notably, the level of SFP observed during the pre-stress phase was already sufficient to cause progressive plumage deterioration, which continued throughout the study. The proportion of birds with severe feather damage rose from 39.4% to 53.5%, while those with intact plumage dropped from 37.6% to 19.9% over time. Thus, SYN supplementation via drinking water is feasible and preferred by laying hens, even under stress. These findings highlight the potential of nutraceuticals delivered through drinking water to influence hen behavior; however, the progressive plumage deterioration despite stable SFP rates suggests that SYN supplementation alone may be insufficient, underscoring the need for integrated management strategies.},
}

@article {pmid41912274,
year = {2026},
author = {Dutton, CL and Goeckner, A and Goldwire, T and Grupstra, CGB and Houghtaling, D and Nonnamaker, LE and Subalusky, A},
title = {Bioreactors on the Move: How Animals Contribute to Microbial Community Coalescence and Shape Ecosystem Function.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70291},
doi = {10.1111/1462-2920.70291},
pmid = {41912274},
issn = {1462-2920},
support = {//Florida Atlantic University/ ; //University of Florida/ ; //United States National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Ecosystem ; *Bioreactors/microbiology ; Fishes/microbiology ; Oligochaeta/microbiology ; Bacteria/classification ; Soil Microbiology ; },
abstract = {Microbiome community coalescence-the mixing of separate microbial communities and their environments resulting in a novel community-represents an important but understudied ecological process at the animal-environment interface. Here, we propose that animals function as "mobile bioreactors" across landscapes, ingesting environmental microbes that undergo selective filtering within the animal gut that are then deposited back into the environment alongside the animal's native microbiota. This coalescence of animal and environmental microbiomes can significantly alter ecosystem processes including nutrient cycling, organic matter decomposition, and trophic interactions. We synthesize emerging evidence from terrestrial, freshwater, and marine ecosystems demonstrating how animal-facilitated microbial coalescence influences ecosystem functioning. Through case studies of hippos in African rivers, fish on coral reefs, and earthworms in soil, we illustrate how these coalescence events create novel microbial communities with distinct functional capabilities. We identify methodological approaches for investigating these phenomena and outline key knowledge gaps, particularly regarding the persistence of animal microbiota in environmental settings and their quantitative contribution to ecosystem processes. Here we highlight the importance of studying animal-environmental coalescence events with far reaching implications for our understanding of ecosystem processes, animal health, and environmental resilience.},
}

Animals
*Microbiota
*Ecosystem
*Bioreactors/microbiology
Fishes/microbiology
Oligochaeta/microbiology
Bacteria/classification
Soil Microbiology

@article {pmid41912276,
year = {2026},
author = {Luko-Sulato, K and Sulato, ET and Osman, JR and Nolasco-Jiménez, P and Morales, D and Rezende, GS and Rodrigues, CA and Maintinguer, SI and da Cunha, AF and Rosolen, V},
title = {Soil Microbiome of Tropical Seasonal and Permanent Small Wetlands.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70306},
doi = {10.1111/1758-2229.70306},
pmid = {41912276},
issn = {1758-2229},
support = {2021/06332-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/15396-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Wetlands ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; *Microbiota ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Tropical Climate ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Characterisation of the microbial communities of two small tropical wetlands under two distinct hydrological regimes (permanent and seasonal), across a rainy and dry season was performed by 16S rRNA amplicon sequencing. We identified 48 bacterial phyla across the two wetland types, seasons and depths and 83% of the bacterial sequences consistently corresponded to six phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Proteobacteria and Verrucomicrobia. The seasonal wetland presented a predominance of Chloroflexi, Nitrospirae, Actinobacteria and Acidobacteria, whereas the permanent wetland showed higher relative abundances of Planctomycetes, Bacteroidetes, Proteobacteria and Firmicutes. Archaeal communities also differed, with Crenarchaeota predominating in the seasonal and Euryarchaeota in the permanent wetland. Microbial communities showed pronounced compositional shifts across wetland type, season and depth, while maintaining stable alpha diversity, with depth was the dominant driver. Functional inference suggested that aerobic ammonia oxidation, nitrate reduction and sulphur compound respiration were the predominant putative metabolic pathways in the seasonal wetland and methanogenesis, fermentation, dark hydrogen oxidation, nitrogen fixation, photoautotrophy, ureolysis and hydrocarbon degradation in the permanent wetland. The permanent wetland exhibited sparse correlation with environmental drivers, consistent with long-term saturation and chronic nutrient limitation, while the seasonal wetland presented influence of pH, nutrients and SOC on microbial community structure.},
}

*Wetlands
Seasons
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
*Microbiota
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
Tropical Climate
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41912342,
year = {2026},
author = {Engelen, MPKJ and van der Meij, BS},
title = {Targeting muscle, mitochondria, and microbiome: nutritional and exercise strategies across wasting diseases and conditions.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {29},
number = {3},
pages = {211-213},
doi = {10.1097/MCO.0000000000001220},
pmid = {41912342},
issn = {1473-6519},
}

@article {pmid41912530,
year = {2026},
author = {Jiang, J and Poulsen, CS and Boulund, U and Shah, S and Trivedi, U and Bhattacharyya, M and Neumann, AU and Dai, DLY and Petersen, C and Hoskinson, C and Moraes, TJ and Mandhane, PJ and Simons, E and Azad, MB and Subbarao, P and Bønnelykke, K and Chawes, B and Turvey, SE and Sørensen, SJ and Thorsen, J and Stokholm, J},
title = {Early life bacteria and sibling exposure associate with restoration of the infant gut microbiome after cesarean section.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71185-6},
pmid = {41912530},
issn = {2041-1723},
abstract = {Long-term gut microbiome perturbation following Cesarean section (CS) delivery has been associated with an increased risk of developing childhood asthma. Whether such CS-associated microbiome composition can be modulated by environmental exposures or ecological interactions, and thereby mitigate disease risk, is unclear. In the COPSAC2010 birth cohort (N = 700), we develop a restoration score quantifying the degree to which the 1-year gut microbiome resembled that of vaginally delivered infants. We identify predictors of this restoration score in the 1-week gut microbiome. In addition, having older siblings is linked to a higher restoration score, mediated by increased abundances of restoration-associated bacteria. The restoration score, including association with delivery mode, older siblings and later asthma as well as early bacterial drivers, is successfully replicated in the independent Canadian birth cohort, CHILD. These insights suggest that specific early-life bacteria and sibling exposure may support microbiome restoration and confer protective effects against asthma risk.},
}

@article {pmid41913243,
year = {2026},
author = {Mancin, E and Casto-Rebollo, C and Maltecca, C and Ibañez-Escriche, N and Mantovani, R and Sartori, C and Tiezzi, F},
title = {Insights into pig resilience: the Microbiome-genetic connection.},
journal = {Porcine health management},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40813-026-00506-4},
pmid = {41913243},
issn = {2055-5660},
}

@article {pmid41913289,
year = {2026},
author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P},
title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00828-2},
pmid = {41913289},
issn = {1757-4749},
abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.},
}

@article {pmid41913604,
year = {2026},
author = {Wang, HY and Li, C and Pan, YP},
title = {[Imbalance and reconstruction of periodontal homeostasis: new perspectives on the pathogenesis, prevention and treatment of periodontitis].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {445-451},
doi = {10.3760/cma.j.cn112144-20251209-00499},
pmid = {41913604},
issn = {1002-0098},
support = {2023YFC2506300//National Key R&D Program of China/ ; },
abstract = {Periodontal homeostasis is a dynamic equilibrium based on healthy periodontal structures, a relatively stable oral microbiome, appropriately regulated host immunity, coordinated cellular metabolism, and a functional dentition with normal occluion. This review aims to systematically elucidate the key mechanisms underlying the maintenance and disruption of periodontal homeostasis. The dysregulation of microbiota and excessive immune activation mutually reinforce each other, serving as the core driving forces for the occurrence and progression of periodontitis. On this basis, a treatment approach oriented toward "re-establishing periodontal homeostasis" is proposed. Based on microbiota remodeling and structural reconstruction, combined with host immune regulation and immunometabolic intervention, emphasizing systemic risk factor management and functional dentition reconstruction, we aim to establish a personalized, precise, and sustainable new model for periodontal prevention and treatment.},
}

@article {pmid41913620,
year = {2026},
author = {Wang, XY and Yao, YJ and Li, LL and Yan, FH},
title = {[From oral microbiome dysbiosis to renal injury: research advances in the mechanism of association between periodontitis and diabetic kidney disease].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {4},
pages = {582-588},
doi = {10.3760/cma.j.cn112144-20251112-00446},
pmid = {41913620},
issn = {1002-0098},
support = {82301100//National Natural Science Foundation of China/ ; BK20220198//Natural Science Foundation of Jiangsu Province/ ; 0224C001//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; YKK23177//Nanjing Foundation for Development of Science and Technology/ ; },
abstract = {Periodontitis, a chronic inflammatory disease driven by dysbiosis of the oral microbiome, has increasingly been recognized for its systemic impact beyond the oral cavity. Growing evidence links periodontitis to the onset and progression of diabetic kidney disease (DKD), suggesting that disturbances of oral microbial homeostasis may influence distant organs through systemic circulation or the oral-gut-kidney axis. Such interactions can trigger systemic inflammation, immune dysregulation, oxidative stress, and metabolic disturbances, thereby accelerating renal injury. This review summarizes recent advances on the potential mechanisms linking periodontitis to DKD progression and highlights the key role of oral microbial dysbiosis and related systemic effects.},
}

@article {pmid41913730,
year = {2026},
author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A},
title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {65},
pmid = {41913730},
issn = {2732-5121},
abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.},
}

@article {pmid41913906,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y},
title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {590621},
pmid = {41913906},
issn = {1178-7074},
abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.},
}

@article {pmid41913928,
year = {2026},
author = {Mulinde, T and Sousa, LGV and Castro, J and George, SD and Muzny, CA and Cerca, N},
title = {Evidence from a broad-range PNA probe links several Prevotella species to bacterial vaginosis.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20902},
pmid = {41913928},
issn = {2167-8359},
mesh = {Female ; Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Prevotella/genetics/isolation & purification ; *Peptide Nucleic Acids/genetics ; Vagina/microbiology ; Sensitivity and Specificity ; Biofilms/growth & development ; Adult ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most prevalent vaginal infection among reproductive-age women. It is associated with multiple adverse health outcomes in women including adverse pregnancy outcomes, an increased risk of pelvic inflammatory disease, infertility, and an increased risk of HIV and other sexually transmitted infections. BV is characterized by an imbalance in the vaginal microbiota, namely a decrease in protective Lactobacillus species and an overgrowth of facultative and strict anaerobic bacteria, leading to the development of a polymicrobial biofilm. Despite extensive research, the etiology of BV remains unclear, and its pathophysiology is not fully understood. It has been hypothesized that P. bivia, in combination with Gardnerella spp., plays an important role in the early development of the BV biofilm. We previously developed a peptide nucleic acid (PNA) probe specifically targeting P. bivia to investigate its role as a potential early colonizer. However, our recent findings have raised doubts about the specificity of this association, suggesting a broader involvement of other Prevotella species in incident BV (iBV).

METHODS: A new PNA probe targeting Prevotella spp. 23S rRNA was developed compared to the existing P. bivia-specific probe. This new probe was optimized in vitro through a variation of hybridization temperatures and times. Its performance was evaluated using a collection of 28 Prevotella strains representing 24 different species and 38 non-Prevotella spp. typically found in BV in order to assess its sensitivity and specificity. Both probes were tested on vaginal swab specimens from women with and without BV to assess the bacterial count and detection of Prevotella species.

RESULTS: In vitro validation demonstrated that the new Prevotella spp. probe achieved a specificity of 100% and sensitivity of 96%. As expected, its broader detection allowed identification of a wider range of Prevotella spp. compared to the P. bivia-specific probe, which was intentionally restricted to a single species. Application to clinical specimens revealed that the new probe identified a significantly higher count of Prevotella spp. in 6/9 (66.6%) BV-positive specimens compared to the P. bivia-specific probe. In 2/9 (22.2%) healthy control specimens, greater Prevotella spp. detection was also observed.

CONCLUSIONS: Our findings suggest that the involvement of Prevotella spp. in BV extends beyond P. bivia, implicating a wider range of species which could be present in the polymicrobial BV biofilm. The broader specificity of this new Prevotella spp. probe provides a valuable tool for future research on the vaginal microbiome and the pathogenesis of BV.},
}

Female
Humans
*Vaginosis, Bacterial/microbiology/diagnosis
*Prevotella/genetics/isolation & purification
*Peptide Nucleic Acids/genetics
Vagina/microbiology
Sensitivity and Specificity
Biofilms/growth & development
Adult

@article {pmid41914163,
year = {2026},
author = {Kozin, S and Kravtsov, A and Lyasota, O and Dorohova, A and Ivlev, V and Chikhirzhina, E and Moiseev, A and Nesterova, V and Babenkova, P and Popov, K and Fedulova, L and Dzhimak, S},
title = {Consumption of Water Similar to Martian Water in Terms of Deuterium Content by Mammals Leads to the Development of an Adaptation Syndrome and Activation of Protective Mechanisms Against Stress.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39086},
doi = {10.31083/FBE39086},
pmid = {41914163},
issn = {1945-0508},
support = {125011700394-5//State Task Force of the Southern Scientific Center of the Russian Academy of Sciences for 2025/ ; },
mesh = {Animals ; *Deuterium/analysis ; Rats, Wistar ; Rats ; *Adaptation, Physiological ; Male ; *Stress, Physiological ; Brain/metabolism ; *Water/chemistry ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Deuterium is unevenly distributed in natural waters, while the same applies to the content of deuterium in ice on Mars. Moreover, changes in the deuterium content of drinking water are known to affect the bodies of mammals. Thus, since plans are in place to send people to Mars in the coming years, understanding the effects of water with a Martian isotopic composition is necessary. Therefore, this study aimed to evaluate the impact of water with an increased deuterium content of 1200 ppm on the dynamics of indicators in the body of mammals.

METHODS: The study was conducted on Wistar rats. The metabolic profile of blood and the content of deuterium in it were studied in dynamics by days using nuclear magnetic resonance (NMR) spectroscopy. Additionally, the isotopic composition of brain tissue was studied in dynamics by days using isotope mass spectrometry. A further study was conducted on the functioning of the antioxidant system in blood plasma and brain tissue using PCR analysis, chemiluminescence, and biochemical analysis methods; the intestinal microbiome was also studied. The durations of the animal experiments were 31 (blood and brain study) and 38 (stress-protective activity study) days.

RESULTS: On day 23, the deuterium content in the blood plasma increased to 856 parts per million (ppm), and to 260 ppm in the brain on day 31. This increase led to an imbalance in the antioxidant/prooxidant processes. This effect was accompanied by shifts in the intensity of oxidative processes, alongside changes in enzyme activity and the expression of genes responsible for their synthesis, shifts in amino acid composition, and changes in the concentration of metabolites and microbiome molecules in the blood plasma. By the fifth and eighth days, the number of Bacteroides in the intestines had decreased by 14% and 21.8%, respectively, compared to the values measured on day zero of the experiment. Meanwhile, the population of Firmicutes-type bacteria increased by 12% and 16% on the fifth and eighth days, respectively, compared to the indicators measured on day zero of the experiment.

CONCLUSION: An increase in the concentration of deuterium in the body promotes the development of a stress reaction and the activation of compensatory mechanisms aimed at adaptation.},
}

Animals
*Deuterium/analysis
Rats, Wistar
Rats
*Adaptation, Physiological
Male
*Stress, Physiological
Brain/metabolism
*Water/chemistry
Gastrointestinal Microbiome

@article {pmid41914171,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN},
title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39439},
doi = {10.31083/FBE39439},
pmid = {41914171},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.

METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.

RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).

CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.},
}

Animals
Female
Cattle/microbiology
*Endometrium/microbiology/metabolism
*Microbiota
High-Throughput Nucleotide Sequencing
*Metagenomics

@article {pmid41914284,
year = {2026},
author = {Wang, P and Ding, L and Lang, Z and Zhang, Y and Yu, Y},
title = {Therapeutic Modulation of the Gut Microbiome in Coronary Artery Disease: Current Evidence and Future Directions.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {3},
pages = {45081},
doi = {10.31083/FBL45081},
pmid = {41914284},
issn = {2768-6698},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Coronary Artery Disease/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Synbiotics/administration & dosage ; Methylamines/metabolism ; Diet ; },
abstract = {The gut microbiome is increasingly recognized as a modifiable contributor to coronary artery disease (CAD). This narrative review integrates mechanistic and clinical evidence regarding short-chain fatty acids (SCFAs), trimethylamine-N-oxide (TMAO), and bile acids, and appraises therapeutic modulation via diet; probiotics, prebiotics, and synbiotics; fecal microbiota transplantation (FMT); and drug-microbiome interactions. SCFAs generally confer anti-inflammatory and lipid-regulatory effects, whereas bile acid signaling exhibits context-dependent metabolic actions. Findings regarding TMAO are inconsistent; in several cohorts, associations with cardiovascular risk become null or attenuated after adjustment for renal function (estimated glomerular filtration rate [eGFR]) and dietary patterns. Most interventional studies are small, use surrogate endpoints, and vary in strains and dosing, limiting certainty. Microbiome profiles differ across geographic regions, racial and ethnic groups, and dietary patterns, underscoring the need for stratified approaches. Routine FMT in CAD remains constrained by safety, feasibility, and ethical and logistical considerations. Overall, the microbiome represents a promising yet unproven therapeutic target in CAD. Future trials should standardize interventions, rigorously control for confounders, evaluate drug-microbiome interactions, and be adequately powered to detect clinical events to enable precision medicine.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Coronary Artery Disease/therapy/microbiology/metabolism
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
Fatty Acids, Volatile/metabolism
Bile Acids and Salts/metabolism
Synbiotics/administration & dosage
Methylamines/metabolism
Diet

@article {pmid41914628,
year = {2026},
author = {Fu, Y and Long, N and Sourn, P and Li, W and He, Z and Tan, W and Yuan, J and Chen, Y and Wu, J and Wang, S and Feng, L and Wang, Z and Ding, W},
title = {Distinct vaginal microbial signatures in pregnancies complicated by antiphospholipid syndrome: depletion of Lactobacillus johnsonii and enrichment of Bifidobacterium dentium.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0388225},
doi = {10.1128/spectrum.03882-25},
pmid = {41914628},
issn = {2165-0497},
abstract = {UNLABELLED: Antiphospholipid syndrome (APS) is a systemic autoimmune disease that contributes substantially to recurrent pregnancy loss, fetal death, intrauterine growth restriction, and preeclampsia, posing major threats to maternal and fetal health. These obstetric complications exhibit clinical similarities to those resulting from vaginal dysbiosis, yet the vaginal microbiota in APS pregnancies has not been systematically investigated. In this study, we characterized the vaginal microbiome in 33 pregnant women with APS and 90 healthy controls using 16S rRNA gene sequencing. We identified a unique microbial signature in APS pregnancies that differed from the commonly observed pattern of increased microbial diversity and Lactobacillus depletion seen in classical vaginal dysbiosis. Specifically, while overall alpha diversity and Lactobacillus dominance were preserved, we observed distinct compositional restructuring characterized by selective depletion of Lactobacillus johnsonii and marked enrichment of Bifidobacterium dentium. A logistic regression model integrating the relative abundances of these microbial biomarkers demonstrated robust diagnostic performance in differentiating pregnancies with APS from healthy pregnancies, with risk scores significantly correlating with clinical parameters and pregnancy outcomes. This study demonstrates that pregnant women with APS display a distinct vaginal microbiome pattern defined by species-specific compositional restructuring rather than global dysbiosis. These microbial alterations may contribute to APS-related pregnancy morbidity, highlighting vaginal microbial signatures as promising noninvasive biomarkers for risk stratification and potential therapeutic targets in obstetric APS management.

IMPORTANCE: Antiphospholipid syndrome (APS) is an autoimmune disease that causes recurrent miscarriage, fetal death, and pregnancy complications in women of reproductive age. While coagulation dysfunction is a known contributing factor, whether APS is accompanied by vaginal microbiota alterations and their role in adverse outcomes remains unclear. We discovered that pregnant women with antiphospholipid syndrome harbor a unique vaginal microbial community: they exhibit depletion of the protective species Lactobacillus johnsonii while showing enrichment of Bifidobacterium dentium, a bacterium typically found in the gut. Unlike typical vaginal infections that display widespread microbial dysbiosis, antiphospholipid syndrome induces only selective alterations in specific bacterial species. These microbial signatures correlated with hematological parameters and adverse pregnancy histories, including prior miscarriages. Our findings suggest that monitoring vaginal microbiota could provide a simple, noninvasive approach to identify high-risk pregnancies in women with antiphospholipid syndrome and may guide novel screening strategies for pregnancy-related disorders targeting the vaginal microbiome.},
}

@article {pmid41914631,
year = {2026},
author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS},
title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219825},
doi = {10.1128/spectrum.02198-25},
pmid = {41914631},
issn = {2165-0497},
abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.},
}

@article {pmid41914733,
year = {2026},
author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D},
title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0235725},
doi = {10.1128/aem.02357-25},
pmid = {41914733},
issn = {1098-5336},
abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.},
}

@article {pmid41914747,
year = {2026},
author = {Franklin, S and Sahasrabhojane, P and Hayase, T and Hayase, E and Chang, C-C and Senapati, J and Desikan, SP and Kadia, T and Lorenzi, PL and Jenq, RR and Shelburne, SA and Galloway-Peña, J},
title = {Short-chain fatty acid-producing microbes differentiate non-infectious and infectious neutropenic fever in leukemia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0134325},
doi = {10.1128/msystems.01343-25},
pmid = {41914747},
issn = {2379-5077},
abstract = {UNLABELLED: Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruptions to treatment-related infections, it typically examines NF as the outcome, leaving a gap in understanding how the microbiome and metabolic factors distinguish infectious from non-infectious cases. Stool samples from acute myeloid leukemia patients were analyzed to characterize gut microbiome composition and fecal metabolites at baseline and at fever onset. Machine learning models, network analyses, and functional profiling were used to differentiate infectious NF vs non-infectious NF at baseline and at fever onset. The baseline model (area under the receiver operating characteristic [AUROC] = 0.769) identified higher levels of Akkermansia, Enterobacter, Escherichia-Shigella, and Flavonifractor as predictors of infectious NF, while Collinsella, Lachnospiraceae, Coprococcus, and acetic acid were linked to non-infectious cases. At fever onset, Enterococcus was enriched in infectious NF, whereas Gemella, Butyrate, Lachnospiraceae, Ruminococcaceae, and Eisenbergiella abundances favored non-infectious NF outcomes (AUROC = 0.752). Network analyses also revealed greater functional diversity and microbiome-metabolome connectivity in non-infectious cases at fever onset. This study suggests that gut microbiota and metabolites may serve as biomarkers for distinguishing infectious from non-infectious neutropenic fever, warranting further validation in larger cohorts.

IMPORTANCE: Our study tackles the challenge of managing neutropenic fever (NF) in immunocompromised patients whose numbers have increased due to various immunodeficiencies and treatments that suppress immune function. Fever is often the only sign of a serious infection in these patients, yet there are neither clear patterns linking risk factors to infection nor biomarkers reliable for ruling out non-infectious causes. As a result, febrile patients are typically empirically treated for major pathogens, even in the absence of confirmed infections, which propagates antimicrobial resistance and gut dysbiosis. Our research utilizes gut microbiome and targeted metabolomic profiling from two cohorts of patients with acute myeloid leukemia undergoing chemotherapy and employs a machine learning framework to distinguish between infectious and non-infectious NFs at baseline and upon fever onset.},
}

@article {pmid41914795,
year = {2026},
author = {},
title = {Corrigenda to 'Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos'.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432716},
doi = {10.1177/13872877261432716},
pmid = {41914795},
issn = {1875-8908},
}

@article {pmid41914849,
year = {2026},
author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y},
title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0035926},
doi = {10.1128/aem.00359-26},
pmid = {41914849},
issn = {1098-5336},
abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.},
}

@article {pmid41914961,
year = {2026},
author = {Maigoro, AY and Lee, JH and Heo, D-R and Yun, B-R and Lee, HI and Kwon, H-W},
title = {Spatiotemporal variation in the microbiome of Aedes vexans from Korea reveals regional markers linked to environmental risk factors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258725},
doi = {10.1128/spectrum.02587-25},
pmid = {41914961},
issn = {2165-0497},
abstract = {Aedes vexans is a widespread mosquito species known to carry West Nile virus (WNV); however, our understanding of how its microbiome changes across different regions and seasons, particularly in temperate areas such as South Korea, remains limited. In this study, we examined the microbiome of Aedes vexans collected from 16 locations over 3 consecutive summer months. Using 16S rRNA sequencing, we found that the microbiome was largely made up of Proteobacteria, but the specific genera present, like Dickeya, Spiroplasma, and members of Enterobacterales, varied depending on the location and time of collection. Dickeya, in particular, was more common in inland areas and stayed relatively stable over time, which suggests it could serve as a useful microbial marker. We also observed a significant absence of Wolbachia, a common endosymbiont in mosquitoes, which hypothesizes potential increased risk of WNV transmission. Diversity analyses showed clear differences in microbial communities by region, and we found seasonal patterns in genera like Asaia and Pseudomonas, which were correlated to mosquito abundance and local environmental conditions. These patterns held up when we looked at co-occurrence networks between microbes. Altogether, this is the first study to track Aedes vexans microbiome across both space and time in Korea, and our findings offer new insights into mosquito ecology and the potential use of bacteria in disease control strategies.IMPORTANCEUnderstanding the dynamics of the mosquito microbiome is essential for predicting disease risk and developing targeted vector control strategies. Aedes vexans, a globally distributed species and potential vector for West Nile virus (WNV), has seen a notable population increase in South Korea, yet its microbial ecology remains poorly characterized. This study provides the first comprehensive spatiotemporal analysis of Aedes vexans microbiota across Korea, identifying key microbial taxa that vary by region and season. The absence of Wolbachia, a known antiviral symbiont, and the dominance of Dickeya, a plant-associated genus with potential ecological implications, underscore the need for microbiome-informed surveillance tools. By highlighting native microbial signatures and their environmental drivers, this work lays the groundwork for microbiota-based monitoring of vector populations and opens new avenues for symbiont-based interventions in arbovirus control.},
}

@article {pmid41915085,
year = {2026},
author = {Liang, J and Zang, S and Wang, Z and Zhang, R},
title = {Cancer and aging: complex associations and therapeutic targets.},
journal = {Molecular biomedicine},
volume = {7},
number = {1},
pages = {},
pmid = {41915085},
issn = {2662-8651},
support = {No. 202303021221201//Shanxi Provincial Basic Research Program/ ; },
mesh = {Humans ; *Aging/genetics/pathology ; *Neoplasms/therapy/pathology/genetics/metabolism/etiology ; Animals ; Cellular Senescence ; Genomic Instability ; Autophagy ; Epigenesis, Genetic ; Molecular Targeted Therapy ; },
abstract = {The incidence of cancer increases markedly with aging, and the two processes share underlying molecular mechanisms. In the context of global population aging and rising cancer incidence, nine convergent hallmark axes have been identified: genomic instability, epigenetic drift, inflammation-immunity imbalance, microbiome dysbiosis, metabolic reprogramming, telomere attrition, stem cell exhaustion, cellular senescence, and autophagy dysfunction. These hallmarks constitute an integrated regulatory network that operates synergistically, antagonistically, or through bidirectional feedback across molecular, cellular, and microenvironmental levels. Genomic instability, epigenetic remodeling, chronic inflammation, microbiome dysbiosis, and metabolic reprogramming in aging often act synergistically to promote tumorigenesis, whereas telomere attrition and stem cell exhaustion primarily exert antagonistic, tumor-suppressive effects. Cellular senescence and autophagy dysfunction display context-dependent dual roles. Importantly, this network framework has direct relevance to cancer therapeutics. Although chemotherapy, radiotherapy, and immunotherapy effectively suppress tumor progression, they frequently induce therapy-induced senescence, characterized by cell-cycle arrest and a senescence-associated secretory phenotype, thereby accelerating functional decline and increasing long-term toxicities in older patients. The proposed "synergistic-antagonistic-dual" framework linking aging and cancer not only helps explain the disproportionate cancer burden in older adults but also supports a "one drug, two targets" therapeutic paradigm. Targeting these shared pathways has delayed aging phenotypes and suppressed tumorigenesis in preclinical studies and early clinical trials, highlighting the potential of integrated interventions that concurrently address aging and cancer.},
}

Humans
*Aging/genetics/pathology
*Neoplasms/therapy/pathology/genetics/metabolism/etiology
Animals
Cellular Senescence
Genomic Instability
Autophagy
Epigenesis, Genetic
Molecular Targeted Therapy