@article {pmid41657896,
year = {2026},
author = {Wicaksono, WA and Thorsen, J and Stokholm, J and Berg, G},
title = {Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729707},
pmid = {41657896},
issn = {1664-302X},
abstract = {INTRODUCTION: The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.

METHODS: We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.

RESULTS: We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various Pseudomonas species, which was confirmed by analysing metagenome-assembled genomes. Pseudomonas brenneri exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.

CONCLUSION: The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma. Pseudomonadales, particularly Pseudomonas species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions' influence on asthma development.},
}

@article {pmid41657853,
year = {2026},
author = {Ayivi-Tosuh, SM and Dofuor, AK and Yamoah, JAA and Gayi, BK and Aiduenu, AF and Akomea, A and Anovunga, SA and Ekloh, W and Basing, LA},
title = {Gut-Microbiome Interactions: Characterization, Therapeutic Implications and Machine Learning.},
journal = {Sage open pathology},
volume = {19},
number = {},
pages = {30502098251415109},
pmid = {41657853},
issn = {3050-2098},
abstract = {The gut microbiome is vital in maintaining overall health, yet its complexity and dynamic interactions are still not fully understood. This diverse microbial community comprises bacteria, viruses, fungi, and archaea, contributing to metabolism, immune regulation, and disease susceptibility. However, imbalances in the gut microbiome (dysbiosis), have been linked to various diseases, underscoring the importance of understanding microbial interactions within the gut ecosystem. This review explores these interactions, focusing on biochemical and molecular mechanisms that shape microbial behavior and function. Additionally, it examines the therapeutic potential of the gut microbiome, particularly its involvement in disease progression, prevention, and treatment. The role of medicinal plants in influencing gut microbial composition is also discussed, given their potential to support microbiome health. Lastly, it highlights the integration of machine learning in microbiome research, offering new insights into microbial interactions, predictive disease modeling, and personalized medicine. By addressing these key areas, this review aims to deepen our understanding of gut-microbiome dynamics and their implications for human health and disease management.},
}

@article {pmid41657562,
year = {2025},
author = {Zhang, S and Song, X and Wen, Y and Wang, G},
title = {Chronic constipation and the brain-gut-microbiome axis: the role of 5-HT signaling and Traditional Chinese Medicine in pathophysiology and treatment.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1706411},
pmid = {41657562},
issn = {2296-858X},
abstract = {Chronic constipation (CC) is a prevalent functional gastrointestinal disorder involving complex interactions among the brain-gut-microbiome axis, with 5-hydroxytryptamine (5-HT) as a key signaling node. Aberrations in 5-HT synthesis, release, receptor expression, or reuptake disrupt gastrointestinal motility, contributing to CC pathogenesis. Traditional Chinese Medicine (TCM), including herbal compounds, monomers, acupuncture, and tuina, exerts therapeutic effects by modulating the 5-HT signaling pathway. Animal studies demonstrate that TCM interventions regulate gut microbiota, promote 5-HT production via metabolites like short-chain fatty acids (SCFAs) and bile acids, and target receptors (e.g., 5-HT3R, 5-HT4R) to enhance intestinal motility. Clinical trials validate TCM's efficacy in normalizing 5-HT levels and improving symptoms, with advantages in safety and holistic regulation. However, important gaps remain, including incomplete understanding of upstream and downstream 5-HT signaling mechanisms, paradoxical 5-HT expression, and limited investigation of comorbid emotional disorders. Future studies should explore how TCM interventions modulate the gut microbiota-5-HT axis and inflammation-related pathways to provide novel insights into CC management.},
}

@article {pmid41657545,
year = {2025},
author = {Jebril, N and Chabuk, S and Al-Sabary, A and Al-Mansouri, N and Al-Jobouri, W and Al-Saidi, S},
title = {Endospore-forming Bacillus subtilis isolated from third molar exudates and its association with cardiovascular disease: a retrospective cohort study.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1726295},
pmid = {41657545},
issn = {2673-4842},
abstract = {BACKGROUND: Various techniques have been previously modified to reduce early postoperative complications following third molar extraction. Given the influence of the oral microbiome, increasingly resistant bacteria have been linked to systemic diseases such as cardiovascular disease (CVD).

OBJECTIVE: In this study, we aimed to identify the spore-forming bacterium Bacillus subtilis isolated from third molar exudates and to investigate its potential association with CVD.

METHODS: In Iraq, dental hospitals don't keep thorough medical records for each patient. This lack of documentation makes it tough to carry out hospital-based research. Therefore, by collecting exudates from third molars, we conducted a retrospective cohort study of the population undergoing third molar exudate removal in a private dental clinic as an alternative setting to compare cardiovascular outcomes between individuals with cardiovascular disease and controls. Based on clinical assessments, body mass index, LDL cholesterol, C-reactive protein, systolic blood pressure, diastolic blood pressure, hypertension, and smoking status were measured. The study was conducted on 40 men, comprising 20 patients with diagnosed cardiovascular disease and 20 controls. Light and transmission electron microscopy were used to perform a phenotypic evaluation of the bacterial isolates (spore formation, biofilm production). Biofilm formation was assessed using Congo red agar, crystal violet staining, and scanning electron microscopy (SEM). In addition, systolic and diastolic blood pressure (SBP and DBP) values were obtained to further assess cardiovascular risk.

RESULTS: The number of B. subtilis isolates was higher in the CVD group than in the control group (non-CVD) and demonstrated significantly greater biofilm-forming ability (OD600 = 1.45 ± 0.22 vs 0.85 ± 0.19, p < 0.01). TEM confirmed dense endospore architecture from patients with CVD, while SEM revealed extensive extracellular matrix formation within CVD biofilms. Patients with oral colonization by B. subtilis showed a significantly higher prevalence of CVD (32.6%) compared to those without colonization (12.6%, p = 0.008). The presence of biofilm-positive B. subtilis strains was independently associated with CVD (OR 2.91; 95% CI, 1.23-6.83). Spore-forming B. subtilis isolates from third molars of patients with CVD demonstrated enhanced biofilm formation and sporulation phenotypes. A moderate positive correlation (r = 0.48) was also observed between B. subtilis presence and SBP and DBP. These findings suggest that these bacterial characteristics are potentially the cause of systemic inflammation and represent a potential microbial link to CVD.

CONCLUSION: In countries like Iraq, researchers run into real problems when they try to study links between oral health and other diseases. There's no NHS dental system, so they can't rely on existing records for data. Therefore, this study provides a protocol for conducting investigations related to oral health through collaboration with other institutions, such as universities. With respect to the main finding of this study, spore-forming B. subtilis isolated from third molar exudates demonstrated phenotypic characteristics that may contribute to persistent oral colonization and increase systemic inflammatory risk. The observed association with cardiovascular disease warrants further investigation into oral-systemic microbial pathways.},
}

@article {pmid41657532,
year = {2026},
author = {Ashaolu, TJ and Lee, CC and Tarhan, O and Rashidinejad, A and Jafari, SM},
title = {Nexus of Whey Proteins, Gut Dysbiosis, and Colonic Health.},
journal = {Food science & nutrition},
volume = {14},
number = {2},
pages = {e71487},
pmid = {41657532},
issn = {2048-7177},
abstract = {The gut microbiota is essential for colonic health, and its imbalance (dysbiosis) is linked to conditions like inflammatory bowel disease and metabolic disorders. Whey proteins (WPs), including β-lactoglobulin, α-lactalbumin, glycomacropeptide, and lactoferrin, possess antimicrobial, immunomodulatory, and prebiotic-like properties that may help restore microbial balance. Beyond modulating the microbiome, WPs play a significant role in reinforcing intestinal barrier integrity and regulating host metabolism. This review summarizes evidence from in vitro, in vivo, and clinical studies showing WPs can enhance beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) while suppressing harmful ones. Furthermore, WP supplementation has been shown to alleviate dysbiosis-related conditions such as colitis, obesity, and allergies by improving microbial diversity, enhancing short-chain fatty acid production, strengthening the mucosal barrier, and modulating immune responses. However, the effects vary depending on WP composition, processing, and individual microbiota. Despite encouraging results, knowledge gaps remain regarding optimal dosing and long-term impacts. Overall, WPs show promise as functional food components and potential therapeutic agents for promoting colonic health, metabolic homeostasis, and gut barrier function, but more research is needed to refine their clinical application.},
}

@article {pmid41657529,
year = {2026},
author = {Wang, H and Shi, Y and Wang, W and Li, X},
title = {Association of Anti-Inflammatory Dietary Adherence With Biomarkers and Gut Microbiota Related to Colorectal Cancer Risk: A Retrospective Study.},
journal = {Food science & nutrition},
volume = {14},
number = {2},
pages = {e71497},
pmid = {41657529},
issn = {2048-7177},
abstract = {Colorectal cancer is one of the most common cancers and a primary cause of death. The increased incidence in low- and middle-income nations highlights the need for better prevention. Chronic inflammation, obesity, and gut microbial dysbiosis are major risk factors for CRC, making nutritional interventions attractive. This study aims to examine the association between adherence to an anti-inflammatory diet and anthropometric, biochemical, inflammatory, molecular, and gut microbiota parameters related to colorectal cancer risk. In this retrospective analysis, anti-inflammatory diet adherents (n = 515) and non-adherents (n = 435) were compared. Hematological, hepatic, inflammatory, tumor, genetic/molecular, and gut microbiota tests were performed, and chi-square tests were used for categorical outcomes. Multiple regression was used to examine the association between adherence to an anti-inflammatory diet and the development of colorectal cancer. Multiple logistic regression analysis indicated that anti-inflammatory diets were associated with improved clinical, biochemical, and microbiome outcomes in patients with CRC. Diet adherence was associated with a lower risk of obesity, central obesity, dyslipidemia, anemia, and leukocytosis after adjusting for age, sex, BMI, smoking, and caloric intake (β = -1.90, SE = 0.26, OR = 0.15, 95% CI: 0.09-0.25). Several inflammatory markers, including CRP, IL-6, CEA, and MMP-9, decreased markedly (p < 0.001). Molecular alterations associated with CRC, including p53 mutation, Ki-67 overexpression, microsatellite instability, APC mutation, and β-catenin nuclear expression, were significantly decreased (p < 0.001). Bifidobacterium, Lactobacillus, Faecalibacterium prausnitzii, and Akkermansia muciniphila were increased, and pathogenic species decreased in the gut (ORs 2.10-2.30; Fusobacterium nucleatum, Clostridium difficile, pathogenic Escherichia coli; ORs 0.16-0.18). Anti-inflammatory diets significantly improve metabolic, inflammatory, tumor-related, and microbiome profiles in patients with CRC. Adherence to an anti-inflammatory dietary pattern is significantly associated with improved metabolic, inflammatory, molecular, and gut microbiota profiles, all of which are linked to colorectal cancer risk. These findings support anti-inflammatory dietary strategies as cost-effective and non-invasive approaches for colorectal cancer prevention and adjunctive management.},
}

@article {pmid41657399,
year = {2026},
author = {Abbondio, M and Tanca, A and Sau, R and Pira, G and Errigo, A and Manetti, R and Pes, GM and Bibbò, S and Dore, MP and Uzzau, S},
title = {A human fecal metaproteomic dataset from celiac disease patients on gluten-free diet with or without poly-autoimmunity.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112501},
pmid = {41657399},
issn = {2352-3409},
abstract = {This dataset provides the fecal metaproteome profiles of 28 celiac disease patients on a gluten-free diet, distinguished by the presence or absence of co-occurring autoimmune conditions. The resource includes raw liquid chromatography-tandem mass spectrometry (LC-MS/MS) files, database search results, protein/peptide identification outputs, and taxonomic/functional annotation outputs, along with comprehensive anthropometric, clinical, and dietary metadata for each patient. The identified proteins originate from microbial, human, and plant sources, consistent with the multi-database search strategy used. This collection is designed for reuse in meta-analyses and integrative studies exploring functional changes in the gut microbiome related to auto-immune status and dietary variables. The complete dataset is available via the ProteomeXchange Consortium with the identifier PXD069517.},
}

@article {pmid41657369,
year = {2026},
author = {Patil, LR and Shetty, VV and Patil, SG and Aithal, KR and Oli, AM and Kaulgud, R and Yenagi, VA and Dharne, M and Dastager, SG and Chandrasekran, AM and Prabhakaran, D},
title = {Influence of Yoga-based cardiac rehabilitation on gut-microbiome diversity and Gut-Heart-Brain axis (YoGH-Biome) in heart failure: a study protocol.},
journal = {BMJ open sport & exercise medicine},
volume = {12},
number = {1},
pages = {e003147},
pmid = {41657369},
issn = {2055-7647},
abstract = {Heart failure (HF) is a chronic and progressive cardiovascular condition associated with significant morbidity, mortality and healthcare burden. Increasing evidence points to a critical role of gut dysbiosis and the gut-heart-brain axis in HF pathophysiology. Altered gut microbiota may influence systemic inflammation, neurohormonal activity and cardiac function through gut-derived metabolites such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs). Yoga-based cardiac rehabilitation (Yoga-CaRe) is a cost-effective intervention that has been shown to improve quality of life, exercise capacity and cardiovascular outcomes in cardiac patients. However, the mechanism underlying its benefits remains unclear. Furthermore, its effect on gut microbiota diversity and the downstream impact on the gut-heart-brain axis in HF remains largely unexplored. This study outlines a prospective, randomised, open-label, blinded-endpoint trial investigating the effects of a 12-week Yoga-CaRe intervention versus enhanced standard care in 60 HF patients with reduced ejection fraction. Participants will be randomly assigned in a 1:1 ratio to either the Yoga-CaRe or the control group. The Yoga-CaRe group will participate in 20 supervised yoga sessions, complemented by guided daily home practice, while the control group will receive enhanced standard care. The trial will assess changes in gut microbiota composition, levels of gut-derived metabolites (TMAO and SCFAs), inflammatory biomarkers (TNF-α and high-sensitivity C reactive protein), heart rate variability, 6 min walk test (6MWT) and echocardiography. Biological samples and clinical data will be analysed using integrated bioinformatics and statistical approaches to evaluate intervention efficacy and identify potential mechanistic pathways. The YoGH-Biome study has received ethical clearance from the Institutional Ethics Committee of the SDM College of Medical Sciences and Hospital, India (SDMIEC/2025/1073). It is registered with the Clinical Trials Registry of India. Study results will be disseminated via scientific publications, conferences and stakeholder forums to inform integrative strategies for HF management. Trial registration number: CTRI/2023/12/060757.},
}

@article {pmid41657363,
year = {2026},
author = {Bujaldón, R and Montero, E and Chamorro, C and Marín, MJ and Iniesta, M and Sanz, M and Herrera, D},
title = {Subgingival microbiome and adjunctive use of probiotics in the treatment of periodontitis in patients with diabetes: a secondary analysis of a randomized clinical trial.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2624894},
pmid = {41657363},
issn = {2000-2297},
abstract = {BACKGROUND: Adjunctive therapies have been proposed to enhance periodontal outcomes by modulating the subgingival microbiome. However, the microbiological effects of probiotic supplementation in diabetic patients with periodontitis remain unclear, particularly when assessed using high-resolution sequencing methods.

AIM: To evaluate the effect of a Limosilactobacillus reuteri as an adjunct to subgingival instrumentation on the subgingival microbiome in the treatment of periodontitis in patients with diabetes.

METHODS: This was a secondary analysis of a randomized, triple-blind, placebo-controlled clinical trial. Forty patients with stage II-III periodontitis and diabetes received subgingival instrumentation and either L. reuteri lozenges (n = 19) or placebo (n = 21) for 3 months. Subgingival samples were collected at baseline, 3, and 6 months. The V3-V4 region of the 16S rRNA gene was sequenced and analyzed using QIIME2. Alpha diversity was analyzed with mixed-effects models, beta diversity with PERMANOVA, and differential abundance with linear models.

RESULTS: A total of 116 high-quality samples were included. Alpha and beta diversity metrics did not show significant differences between groups or across time points. L. reuteri was detected inconsistently in the subgingival microbiome, with low relative abundances and no sustained presence over time. No bacterial species exhibited significant changes in differential abundance between the probiotic and placebo groups over time.

CONCLUSIONS: Adjunctive L. reuteri supplementation did not significantly alter subgingival microbiome diversity or composition over 6 months.},
}

@article {pmid41656827,
year = {2026},
author = {Upadhyay, SK},
title = {Strigolactones Targeting Plant-Microbe Dialogues From Roots to Soil: Unlocking Pathways for Sustainable Agriculture.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70787},
doi = {10.1111/ppl.70787},
pmid = {41656827},
issn = {1399-3054},
mesh = {*Lactones/metabolism/pharmacology ; *Plant Roots/microbiology/metabolism ; *Plant Growth Regulators/metabolism ; *Agriculture/methods ; *Soil Microbiology ; Mycorrhizae/physiology ; Soil/chemistry ; Signal Transduction ; Plant Development ; },
abstract = {Strigolactones (SLs) are phytohormones derived from carotenoids that influence various aspects of plant growth, development, and the ability of plants to respond to environmental changes and microbial interactions. Initially categorized as shoot branching inhibitors, SLs are now recognized as crucial rhizospheric signaling molecules that govern nutrient availability, hormonal control, and microbial interactions. Despite significant progress in SL biology, a cohesive synthesis connecting SL molecular signaling, rhizosphere communication, and stress tolerance remains fragmented, hindering their practical use in sustainable agriculture. A more comprehensive understanding of their synthesis process (D27-CCD7/8-MAX1-CLA cascade), their perception (D14-MAX2-SMXL module), and the impact of SMXL7 on chromatin has revealed significant implications on physiology. To enhance plant development under stress conditions, SLs drive auxin transport, regulate ABA-dependent stress signaling, influence the antagonistic effects of cytokinins, and coordinate gibberellin activity with the circadian rhythm. SLs augment arbuscular mycorrhizal colonization, stimulate nodulation, and attract plant growth-promoting rhizobacteria through chemotactic and metabolic interactions. Using GR24 and SL-conjugated nanomaterials enhances plant resistance to drought, salt, and metal stress. Modifying SL-transporters with CRISPR improves SL signaling and fosters beneficial symbiotic associations. The study is crucial because it underscores the importance of SLs in recruiting beneficial microorganisms and facilitating microbial-hormonal interactions. This review proposes a cohesive conceptual framework that integrates receptor specificity, rhizospheric sensing, and microbial response, beyond mere descriptive synthesis. It sets distinct research targets, such as receptor-specific SL-analogues, in situ sensing techniques, and tailored SL-responsive microbial consortia, to make biostimulation more precise and assist crops in withstanding climatic stress more effectively.},
}

*Lactones/metabolism/pharmacology
*Plant Roots/microbiology/metabolism
*Plant Growth Regulators/metabolism
*Agriculture/methods
*Soil Microbiology
Mycorrhizae/physiology
Soil/chemistry
Signal Transduction
Plant Development

@article {pmid41656717,
year = {2026},
author = {Cho, G and Kim, DH and Kim, JS and Song, J and Kim, SJ},
title = {Bayesian Pairwise Compositional Lotka-Volterra Modeling Infers Potential Rhizosphere Microbial Suppressors of Ralstonia pseudosolanacearum.},
journal = {The plant pathology journal},
volume = {42},
number = {1},
pages = {50-60},
doi = {10.5423/PPJ.OA.10.2025.0143},
pmid = {41656717},
issn = {1598-2254},
support = {PJ01727501//Rural Development Administration/ ; },
abstract = {The Ralstonia solanacearum species complex (RSSC) is a major soil-borne pathogen of solanaceous crops. During a field experiment originally designed to monitor rhizosphere and episphere microbiomes in two pepper cultivars, a naturally emerging and asymptomatic Ralstonia dominance event was detected in the rhizosphere without visible wilt symptoms. This unexpected occurrence provided an opportunity to characterize asymptomatic RSSC dynamics and their microbial interactions under field conditions. Full-length 16S rRNA amplicon sequencing showed that one ASV (Sq_1) was nearly absent from the episphere but increased sharply in the rhizosphere from week 3 onward, dominating 20-80% of samples during weeks 7-10. Phylogenetic comparison with 93 historical Korean RSSC isolates placed Sq_1 within a 16S-defined lineage corresponding to pepper-associated R. pseudosolanacearum biovars 3 and 4. Sq_1 abundance accounted for a large portion of β-diversity turnover in the rhizosphere. After within-plot correlations were meta-analyzed, selected taxa were evaluated using a Bayesian pairwise compositional Lotka-Volterra (pcLV) model, which identified three taxa (Sq_272, TRA3-20; Sq_178, Bradyrhizobium; and Sq_124, Bryobacter) that consistently exerted inhibitory effects on Sq_1 per-interval growth. Supported by the longitudinal design and the high accuracy of PacBio full-length 16S sequencing, these findings highlight potential microbial suppressors of RSSC and demonstrate the utility of pcLV modeling for resolving directional interactions at the ASV level.},
}

@article {pmid41656565,
year = {2026},
author = {Akber, MA and Fang, X},
title = {Soil type and growth stage-dependent rhizosphere bacteriome of alfalfa under challenge by the fungal pathogen Rhizoctonia solani.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70620},
pmid = {41656565},
issn = {1526-4998},
support = {32171678//National Natural Science Foundation of China/ ; 23ZDNA009//Gansu Provincial Science and Technology Major Projects/ ; },
abstract = {BACKGROUND: Alfalfa (Medicago sativa) is the most important forage legume crop in China, but its productivity is severely threatened by root rot caused by Rhizoctonia solani. The use of resistant varieties is regarded as the most effective and sustainable strategy for disease management. However, the interaction between the host genotypes of alfalfa and R. solani in shaping the rhizosphere microbiome, and the role of these microbial assemblages in host resistance, remains poorly understood. This study investigated the rhizosphere bacteriome of alfalfa varieties with contrasting resistance to R. solani across different soil types and growth stages. Disease severity, plant biomass, and antioxidant enzyme activities were also evaluated.

RESULTS: Significant changes were observed in the composition and diversity of the bacterial community under infection by R. solani. The resistant variety exhibited higher activities of superoxide dismutase, peroxidase, and catalase. Pathogen inoculation was associated with a more complex and positively interconnected microbial network, indicating shifts in potential microbial associations. Notable shifts in α-diversity, Bray-Curtis β-diversity, and growth-stage-specific bacterial genera were observed between 8 and 16 weeks. In contrast, differences between soil types were less pronounced, which shows that the growth stage strongly influenced rhizosphere bacteriome structure.

CONCLUSION: These findings advance understanding of host-microbiome-pathogen interactions and provide a basis for microbiome-assisted strategies in sustainable management of root rot in alfalfa cultivation. © 2026 Society of Chemical Industry.},
}

@article {pmid41656437,
year = {2026},
author = {Pan, L and Cai, B},
title = {The core microbiome of the AMF hyphosphere: mineralization mechanisms of key soil mineral elements.},
journal = {Mycorrhiza},
volume = {36},
number = {1},
pages = {6},
pmid = {41656437},
issn = {1432-1890},
support = {No. 31972502//National Natural Science Foundation of China/ ; },
mesh = {*Mycorrhizae/metabolism/physiology ; *Microbiota ; *Soil Microbiology ; *Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; Sulfur/metabolism ; Carbon/metabolism ; *Minerals/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) lack the enzymatic capacity to directly mineralize many essential soil elements and therefore rely on their hyphosphere core microbiome, a microbial consortium increasingly recognized as the "second genome" of AMF. However, the definition, functional mechanisms, and ecological relevance of this core microbiome remain poorly resolved. This review addresses how hyphosphere core microorganisms regulate the mineralization of soil carbon, nitrogen, phosphorus, and sulfur. We first outline the conceptual development of the core microbiome and then, for the first time, propose a five-dimensional screening framework integrating abundance stability and universality, functional stability, dynamic responsiveness, ecological niche specificity, and community supportiveness to identify authentic core members. Using this framework, we synthesize evidence on the mechanisms by which the hyphosphere core microbiome mediates biomineralization, highlighting its role in converting organically bound nutrients into plant-available forms. By integrating the functions of hyphosphere core microorganisms across carbon, nitrogen, phosphorus, and sulfur cycles, this review provides a unified ecological perspective on how the AMF hyphosphere core microbiome drives soil nutrient turnover (Fig. 1). Overall, this framework advances understanding of hyphosphere ecology and offers practical implications for soil ecosystem restoration and sustainable agricultural management.},
}

*Mycorrhizae/metabolism/physiology
*Microbiota
*Soil Microbiology
*Soil/chemistry
Phosphorus/metabolism
Nitrogen/metabolism
Sulfur/metabolism
Carbon/metabolism
*Minerals/metabolism

@article {pmid41656241,
year = {2026},
author = {Liu, X and Qiao, Y and He, W and Chen, X and Zhou, Q and Xu, Y and Yang, Y and Li, C and Yu, J and Luo, P},
title = {Integrated multi-omics profiling reveals effects of exogenous plant growth regulators on tobacco rhizosphere under Vulpia myuros rotation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08312-4},
pmid = {41656241},
issn = {1471-2229},
support = {110202101009 (XJ-01)//Key Science and Technology Project of China National Tobacco Corporation/ ; 110202201040 (XJ-11)//Key Science and Technology Project of China National Tobacco Corporation/ ; },
}

@article {pmid41655925,
year = {2026},
author = {Ren, J and Zhang, B and Luo, K and Zhao, Y},
title = {Exploring the role of type 3 resistant starch crystalline polymorphs in modulating gut health and alleviating inflammation in colitis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150805},
doi = {10.1016/j.ijbiomac.2026.150805},
pmid = {41655925},
issn = {1879-0003},
abstract = {Type 3 Resistant starch (RS3) has garnered increasing attention for its potential therapeutic effects in inflammatory bowel diseases (IBD), such as colitis. However, the impact of different crystalline forms of RS3 on the alleviation of colitis remains unclear. This study examined A-type and B-type crystalline RS3 microparticles (ARS and BRS) derived from debranched waxy maize starch. BRS exhibited higher crystallinity and RS content than ARS by around 8% and 11%, respectively. Treatment with ARS and BRS led to a 12.5-31.1% reduction in cytokine levels (TNF-α, IL-1β, IL-6) compared to NS, while improving colon morphology. Notably, BRS more effectively promoted Lactobacillus growth, suppressed harmful Patescibacteria, and increased SCFA levels (by 5.1 μmol/g) compared to ARS. The findings underscore the significance of RS3's crystalline structure in its anti-inflammatory potential, suggesting it as a promising strategy for colitis management and offering insights into RS's benefits for gut health.},
}

@article {pmid41655800,
year = {2026},
author = {Zhu, J and Yang, L and Fang, Z and Chen, J and Fu, R and Liu, S and Chen, M},
title = {Xin-Jia-Tong-Xie-Yao-Fang restores the intestinal barrier to alleviate irritable bowel syndrome via microbial butyrate mediated PI3K/Akt pathway suppression.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108344},
doi = {10.1016/j.micpath.2026.108344},
pmid = {41655800},
issn = {1096-1208},
abstract = {BACKGROUND: Xin-Jia-Tong-Xie-Yao-Fang (XJTXYF) is a proven prescription for managing diarrhea-predominant irritable bowel syndrome (IBS-D), which is a prevalent functional gastrointestinal disorder. However, the underlying mechanism of XJTXYF remains unclear. This study aims to explore the material basis and potential mechanisms of XJTXYF against IBS-D.

METHODS: The constituents of XJTXYF were identified by UPLC-Q-TOF-MS/MS, and potential targets and pathways were screened by network pharmacology. Changes in the intestinal microbiome and fecal butyric acid levels after XJTXYF administration were analyzed through 16S rRNA sequencing and HPLC respectively. The abdominal withdrawal reflex score, serum levels of FITC-D and the expression of intestinal epithelial tight junction proteins, as well as the activity of the PI3K/Akt pathway were assessed. In-vitro experiments involved silencing GPR109A using small interfering RNA and inducing barrier damage with LPS pre-treatment in the Caco-2 cell line. Barrier function was evaluated by FITC-D permeability and tight junction protein expressions. The activity of the PI3K/Akt pathway was determined through Western blotting analysis.

RESULTS: The major active compounds of XJTXYF identified by UPLC-Q-TOF-MS/MS include Saikosaponin C, Hesperetin, Neohesperidin, Albiflorin, Quercetin and so on. The PI3K/Akt signaling pathway was predicted by network pharmacology as a potential target of XJTXYF in treating IBS-D. Animal experiments demonstrated that XJTXYF could increase body weight, improve visceral hypersensitivity, rebalance gut flora dysbiosis and upregulate fecal butyric acid content in IBS mice. The XJTXYF also showed the abilities of intestinal barrier repairment and PI3K/Akt pathway suppression. Fecal microbiota transplantation and the positive controls (NaB and Clostridium Butyricum) verified that a causal relationship existed between gut microbiome changes and IBS-D improvement after XJTXYF treatment. In-vitro experiments revealed the role of butyrate in barrier protection via PI3K/Akt inhibition.

CONCLUSION: Overall, in this study, we revealed that XJTXYF could restore intestinal barrier function through microbial butyrate mediated PI3K/Akt inhibition and improve IBS-D symptoms.},
}

@article {pmid41655731,
year = {2026},
author = {Teng, J and Li, W and Wei, Y and Wang, C and Yun, X and Lu, Y and Chen, J and Ma, X and Zhao, Y},
title = {Gut microbiome diversity and functional profiles of Culicoides across Sanya, Ruili, and Linyi, China.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108013},
doi = {10.1016/j.actatropica.2026.108013},
pmid = {41655731},
issn = {1873-6254},
abstract = {BACKGROUND: Biting midges (Culicoides spp.) are vectors of diverse microbes such as viruses, bacteria, protozoa, and nematodes that cause diseases in both wild and domestic animals. Despite their ecological significance and role in disease transmission, the composition and underlying mechanisms shaping the gut microbiota of Culicoides remain poorly characterized.

OBJECTIVES: This study aimed to investigate the composition and functional profiles of the gut microbiota of adult Culicoides collected from three representative cities spanning tropical, subtropical, and temperate climate zones in China.

METHODS: 16S high-throughput sequencing was used to study the microbial composition and function of Culicoides in the three regions. This study further incorporated six environmental factors and seven genetic diversity indices to explore their relationships with the microbial community.

RESULTS: The findings revealed significant variations in the gut microbial composition, dominant species, and diversity of Culicoides across different climate zones. NoTable differences were observed in microbial functions related to insect growth, development, and oxidative stress, with Culicoides from the Sanya zone exhibiting a greater abundance of functions and participating in more signaling processes. Environmental factors and host genetic diversity across different habitats collectively shape the composition of the gut microbiota of Culicoides. Structural equation modeling (SEM) revealed that environmental factors exert predominantly direct selective effects on microbial community assembly, whereas host genetic diversity plays a critical indirect regulatory role. These environment-host-microbiota interactions exhibit significant spatial heterogeneity. In low-latitude regions (Sanya), environmental factors mainly manifest direct filtering effects, whereas in ecotone areas (Ruili), environmental pressures indirectly modulate microbial composition by altering host genetic adaptation.

CONCLUSIONS: Our findings revealed that Culicoides gut microbiomes exhibit distinct biogeographical divergence, characterized by environment-driven variations in microbial community structure and functional potential. Host genetic adaptation serves as a key mediator and synergistic modulator of these patterns. This tripartite environment-host-microbiome interaction demonstrates clear dependence on geographic gradient.},
}

@article {pmid41655688,
year = {2026},
author = {Jin, M and Xu, F and Liu, Y and Jiang, Z},
title = {Limosilactobacillus fermentum LF61: A Multidimensional Study on Safety and Functionality from Genomics to Clinical Application.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116002},
doi = {10.1016/j.fct.2026.116002},
pmid = {41655688},
issn = {1873-6351},
abstract = {This study presents a comprehensive multidimensional assessment of the safety and functional efficacy of Limosilactobacillus fermentum LF61, a strain isolated from human milk. Genomic analysis revealed no virulence factors (VFDB), drug resistance genes (CARD), or toxin synthesis gene cluster (antiSMASH) within its chromosome (2.04 Mb) and plasmid (15.5 kb), meeting EFSA's QPS safety criteria. In vitro studies demonstrated that LF61 exhibited a 2-hour survival rate of > 98% in gastric acid (pH 2.0) and a survival rate of 99.66% in intestinal fluid (pH 8.0). LF61 was also nontoxic to Caco-2 cells (metabolic activity at 20% concentration: 100.3 ± 2.1%). An acute oral toxicity test (in ICR mice) demonstrated an LD50 >2 × 10[10] CFU/kg. In a randomized, double-blind clinical trial (n = 49), daily intake of 3×10[10] CFU of LF61 for 8 weeks increased serum levels of the antimicrobial peptide LL-37 by 12.3% (p < 0.05), and IgA, IgG, and IgM by 18.7%, 15.2%, and 9.8%, respectively (p < 0.05). Metagenomic analysis revealed that LF61 promoted colonization by short-chain fatty acid-producing bacteria, such as Mitsuokella and Turicibacter (LDA > 3), activated the carbohydrate metabolism pathway (p = 0.002), and maintained stable α-diversity in the microbiome (Shannon index p > 0.05).Collectively, our findings indicate that LF61 exerts beneficial effects via a gut-immune axis bidirectional regulatory mechanism, offering a theoretical basis and clinical evidence for the development of novel immunomodulatory probiotics targeting the gut-immune axis.},
}

@article {pmid41655417,
year = {2026},
author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P},
title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.},
journal = {Water research},
volume = {294},
number = {},
pages = {125493},
doi = {10.1016/j.watres.2026.125493},
pmid = {41655417},
issn = {1879-2448},
abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.},
}

@article {pmid41655382,
year = {2026},
author = {Gupta, N and Biswas, R and Koley, A and Mukherjee, R and Das, N and Balachandran, S and Hoque, RR},
title = {Degradation of chrysene by Rhodococcus pyridinivorans C7 isolated from earthworm gut - Deciphering microbial community dynamics of the earthworm gut.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141328},
doi = {10.1016/j.jhazmat.2026.141328},
pmid = {41655382},
issn = {1873-3336},
abstract = {This study investigates the degradation of chrysene (a priority polycyclic aromatic hydrocarbon) by Rhodococcus pyridinivorans C7, isolated from the gut of Perionyx excavatus after 60 days acclimatization in petroleum-contaminated soil. After six days of incubation, strain C7 exhibited notable enzymatic activities, with catechol 1,2-dioxygenase (1.72 ± 0.14 U/mL) and catechol 2,3-dioxygenase (2.26 ± 0.19 U/mL). The strain achieved up to 75 % degradation of chrysene (40 mg/L) within this period. Gas chromatography-mass spectrometry analysis identified dibutyl phthalate as an intermediate product on day 2 and phenol 2,6-di-tert-butyl on days 4 and 6. Cytotoxicity assays revealed that the initial byproduct was highly toxic (IC50 = 0.19 µg/mL), whereas the final metabolite exhibited markedly reduced toxicity (IC50 = 19 µg/mL), indicating detoxification. Comparative genomics using Mauve software revealed strong genomic synteny between strain C7 and other PAH-degrading Rhodococcus species. Metagenomic analysis of earthworm gut microbiomes under different treatment - control (EG-C), petroleum contaminated (EG-P) and fly ash (EG-F) identified Proteobacteria as the predominant phylum with relative abundance of 21.17 %, 33.3 %, and 34.53 % respectively. Notably, the Rhodococcus genus exhibited a 1.46-fold and 1.42-fold increase in EG-P and EG-F, respectively compared to EG-C. R. pyridinivorans was detected in both EG-P and EG-F gut samples confirming its isolation through the earthworm gut. These results demonstrate that environmental perturbations can drive distinct shifts in gut microbial composition, enriching for hydrocarbon-degrading taxa. Understanding such adaptive microbial communities provides valuable insights for developing sustainable bioremediation strategies and identifying novel microbes for environmental cleanup.},
}

@article {pmid41655373,
year = {2026},
author = {Sharma, S and Hassan, H and Abdelaziz, K},
title = {Comparative efficacy of oral and cloacal administration of Lactobacillus probiotics and postbiotics against Campylobacter jejuni colonization in broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106576},
doi = {10.1016/j.psj.2026.106576},
pmid = {41655373},
issn = {1525-3171},
abstract = {Campylobacter jejuni remains a major cause of foodborne illness worldwide, with poultry serving as the primary reservoir. In the absence of commercial vaccines or effective feed additives, probiotics and their byproducts (postbiotics) represent a promising and sustainable approach to reducing Campylobacter colonization in poultry. This study compared the efficacy of oral and cloacal administration of probiotic lactobacilli and their postbiotics in reducing Campylobacter colonization and modulating the cecal microbiome in broiler chickens. Day-old chicks were assigned to seven treatment groups that received either probiotics (live cells of four poultry-derived Lactobacillus strains: L. reuteri P43, L. acidophilus P42, L. animalis P38, and L. crispatus C25) or postbiotics (Lactobacillus supernatants) or their combination (whole cultures) orally or intracloacally, with a non-treated group serving as a control. Chickens were challenged with C. jejuni strain 81-176 at the second week of age, and cecal contents were collected at the fifth week for Campylobacter enumeration and microbiome profiling. The results revealed that both oral and cloacal administration of Lactobacillus cells significantly reduced Campylobacter cecal loads by 0.34 and 0.78 log10, respectively, compared to the control. Significant differences in microbial richness and evenness were observed among treatment groups, with groups administered orally with probiotics, postbiotics, or their combination consistently showing higher alpha diversity indices than controls. NMDS ordination confirmed distinct community clustering among the treatment groups. Differential abundance analysis (MaAsLin2) further revealed that Ruminococcus was significantly enriched in the group receiving intracloacal postbiotic treatment, whereas the genus unclassified Firmicutes was more abundant in the group that received the combined probiotic-postbiotic treatment orally. Opportunistic genera, such as Escherichia-Shigella and Faecalicoccus, were significantly higher in the control group compared to all treated groups. Overall, while probiotics and postbiotics, whether given alone or together, modulated the gut microbial composition in Campylobacter-infected broilers, the administration of probiotic cells offered additional benefits by reducing Campylobacter colonization.},
}

@article {pmid41655211,
year = {2026},
author = {Su, XJ and Ma, L and Xiong, X and Meng, JH and Wu, Q and Zhang, Y and Dong, SG and Wang, YF and Wu, JH and Zeng, QY and Zhang, HF and Li, LL and Meng, L and Peng, M and Huang, XD and Wu, LQ and Wang, X},
title = {DRD2 Deficiency Underlies Pituitary Adenoma Dependent on Escherichia coli Translocation from the Gut.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04247},
doi = {10.1002/advs.202504247},
pmid = {41655211},
issn = {2198-3844},
support = {2020]74//Hubei Provincial Engineering Research Center for Inflammation Repair/ ; 2020ZYYD026//Special Funds for Local Science and Technology Development guided by the Central Government/ ; 2023AFA079//Hubei Science Foundation for Distinguished Young Scholars/ ; WX23Z27//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ22A01//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; WZ24B86//Scientific Research Project Funds for Wuhan Health and Family Planning Commission/ ; },
abstract = {Pituitary adenoma (PA) are common intracranial tumor types that have harmful effects on human health. However, the pathogenesis of PA remains unclear yet. The intratumoral microbiome has been reported playing an important impact on the occurrence, metastasis, immune monitoring, and drug resistance of various tumors. While normal dopamine receptor D2 (DRD2) expression is enriched in the apical junction of pituitary epithelium and colonic enterocytes, various factors-induced drd2 loss dampened its expression at both sites. DRD2 deficiencies are characterized by chronic hyperprolactinemia, pituitary lactotroph hyperplasia, and prolactinomas in mice, but the role of intratumoral microbiome in prolactinomas is not known. We employed specific pathogen-free (SPF) and germ-free (GF) mice models and patient samples of pituitary adenoma. In the mice pituitary tumor model, we used mice that developed prolactinomas following estradiol treatment or DRD2 deficiencies. Pituitary tumor samples from patients with nonfunctional pituitary adenoma or prolactinomas were obtained after surgical excision. Various molecular, cellular, and sequencing techniques were used to determine the role of intratumoral microbiome in pituitary adenoma. We demonstrate that human patients or murine bearing estradiol-induction or DRD2 loss are all characterized by the presence of live intratumor bacteria in the pituitary adenoma. Using metagenomic next-generation sequencing and mass spectrometry techniques, we confirm that the bacterial species of pituitary tumor tissues is Escherichia coli. In vitro tracing and immunofluorescence assay results showed that the pathobiont Escherichia coli translocates from the gut into the pituitary gland along with DRD2 loss while the blood pituitary barrier were both destroyed in mice. The Escherichia coli are phagocytosed by the microglial cells in the pituitary gland, then activate GSDMD protein releasing HMGB1, and promote the tumorigenesis of pituitary adenoma by activating the MAPK pathway. The depletion of bacteria systemically, microglial depletion or HMGB1 inhibitor ethyl pyruvate rescued prolactinomas. Our findings suggest that DRD2 deficiency underlies pituitary adenoma dependent on Escherichia coli translocation from the gut and activating microglia GSDMD/ HMGB1/MAPK pathway, and provide a novel preclinical rationale for antimicrobial agents, microglial depletion, or HMGB1 inhibitor ethyl pyruvate for the treatment of pituitary adenoma.},
}

@article {pmid41655160,
year = {2026},
author = {Rathod, H and Jain, P and Dharme, KK and Ajazuddin, },
title = {cGAS-STING Pathway in Gastrointestinal Malignancies: Mechanistic Insights and Translational Therapeutic Opportunities.},
journal = {Journal of gastrointestinal cancer},
volume = {57},
number = {1},
pages = {38},
pmid = {41655160},
issn = {1941-6636},
mesh = {Humans ; *Nucleotidyltransferases/metabolism ; *Membrane Proteins/metabolism/agonists ; *Gastrointestinal Neoplasms/immunology/therapy/drug therapy/metabolism/pathology ; Signal Transduction/drug effects ; Tumor Microenvironment/immunology/drug effects ; Animals ; STING Protein ; Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase ; },
abstract = {BACKGROUND: An important regulator of tumor immunosurveillance and innate immune activation in gastrointestinal (GI) malignancies is the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. The release of type I interferons, dendritic cell (DC) maturation, and cytotoxic T lymphocyte recruitment are the final steps of a pathway that is typically set in motion by aberrant DNA damage, microbiome-derived DNA, or mitochondrial stress.

METHODS: Tumour has it that immunologically "cold" gastrointestinalcancers can be made more sensitive to immune-checkpoint blockade (ICB), radiation, and chemotherapy by therapeutically activating the cGAS-STING pathway, which turns them into inflamed, T-cell-permissive niches.

RESULTS: Progress in nanomedicine, small-molecule STING agonists, and tumour-microenvironment-responsive drug delivery systems has broadened the translational scope of this pathway across colorectal, gastric, and pancreatic malignancies. However, tumour-intrinsic heterogeneity, the dual immunostimulatory and immunosuppressive functions of chronic STING signalling, and delivery-related toxicities continue to pose substantial challenges.

CONCLUSION: This review consolidates current mechanistic insights, preclinical evidence, and emergent clinical data regarding the cGAS-STING pathway in gastrointestinal cancers, while emphasising biomarker-guided patient stratification and AI-powered predictive tools that could facilitate the precise application of STING-targeted therapies.},
}

Humans
*Nucleotidyltransferases/metabolism
*Membrane Proteins/metabolism/agonists
*Gastrointestinal Neoplasms/immunology/therapy/drug therapy/metabolism/pathology
Signal Transduction/drug effects
Tumor Microenvironment/immunology/drug effects
Animals
STING Protein
Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase

@article {pmid41654986,
year = {2026},
author = {Finck, J and Chowdhury, S and Griffiths, RI and Malik, AA and Eisenhauer, N and Lange, M and Mendes, LW and Gleixner, G},
title = {Plant diversity induces shifts from microbial generalists to specialist by enhancing niche differentiation, microbiome connectivity, and network stability in a temperate grassland.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00857-z},
pmid = {41654986},
issn = {2524-6372},
abstract = {BACKGROUND: Soil microbiota are key players of terrestrial ecosystem functioning, including decomposition, soil organic matter formation, and nutrient cycling, and interact strongly with plants in the rhizosphere. Several studies have demonstrated the potential of plants to alter soil microbiome assembly and functioning (i.e., through manipulation of soil organic matter pools via root exudation), which can be critical for sustaining soil ecosystem functioning. Using soil from a long-term biodiversity experiment in Germany, we investigated how soil microbial communities responded to variations in plant species richness (1-16 species), functional group richness (1-4 groups), and plant identity (grasses, legumes, small herbs, and tall herbs) using 16S rRNA gene and ITS amplicon sequencing. We examined bacterial and fungal community structure, metabolic potential, and microbial network architecture to better understand the role of the soil microbiome and its net positive relationship between biodiversity and ecosystem functioning.

RESULTS: Plant diversity induced gradual shifts in microbial community composition, while increasing soil organic carbon and nitrogen stocks. Microbial networks exhibited increased connectivity, particularly between bacteria and fungi. Meanwhile, mutualistic and antagonistic functional guild representation increased, that is the sum total of plant-beneficial (i.e., endophytes) and plant- or fungi-detrimental (i.e., pathogens and parasites) fungal guilds, respectively. Key nodes shifted from generalist taxa at low plant diversity to more specialized communities at high plant diversity. Notably, fungi responded more strongly than bacteria, and their functional potential was driven by plant functional identity rather than species richness.

CONCLUSION: At low plant diversity, generalist taxa likely exploit less complex and diverse organic carbon inputs, allowing them to dominate available niches. In contrast, higher plant diversity promotes a broader array of specialist taxa that likely benefit from the greater diversity of organic carbon compounds, and thus greater niche availability. As network complexity grows, ecosystem functions are being distributed across more taxa, leading to greater microbiome stability, and ultimately more efficient soil carbon and nutrient cycling. Our findings suggest that higher plant diversity strengthens microbial functioning and enhances microbiome resilience, that is the capacity of the microbial community to maintain soil functioning despite environmental disturbances.},
}

@article {pmid41654956,
year = {2026},
author = {Renchinsengee, N and Batsaikhan, S and Khangai, A and Boldbaatar, G and Luvsandagva, B and Lazatkhan, A and Duger, D and Khasag, O and Matsumoto, T and Yamaoka, Y},
title = {Species-level dynamics of gastric microbiome after Helicobacter pylori eradication in high-risk Mongolian population.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00805-9},
pmid = {41654956},
issn = {1757-4749},
support = {2021B13; K.O//Research Center for Global and Local Infectious Diseases, Oita University/ ; 23836904//Japan Agency for Medical Research and Development (AMED) [Adopting Sustainable Partnerships for Innovative Research Ecosystem (ASPIRE),/ ; 21357105//Science and Technology Research Partnership for Sustainable Development (SATREPS)/ ; },
abstract = {BACKGROUND: Species-level resolution is essential to understand gastric microbiome recovery after Helicobacter pylori eradication, yet short-read 16 S rRNA approaches often obscure clinically relevant changes.

METHODS: Gastric biopsies from 121 adults in Bayan-Ölgii, Mongolia (71 H. pylori-positive, 50 H. pylori-negative) were analyzed, including nine paired pre- and post-eradication gastric biopsy samples collected six months apart, enabling exploratory longitudinal analysis. Full-length 16 S rRNA (V1-V9) sequencing was performed using the Oxford Nanopore platform with EMU taxonomic assignment (SILVA v138.1/NCBI RefSeq). Ecological changes were evaluated using diversity indices, principal coordinates analysis (PCoA) with PERMANOVA, and differential abundance testing (DESeq2, FDR < 0.05). Eradication therapy (esomeprazole-bismuth-doxycycline-levofloxacin) achieved success in 54 of 57 H. pylori-positive patients (94.7%).

RESULTS: H. pylori-positive microbiomes were dominated by H. pylori (91.8% ± 3.9%) and exhibited markedly reduced diversity (Shannon = 0.44 ± 0.11) compared with H. pylori-negative samples (2.08 ± 0.25; p < 0.001). Six months after eradication, diversity increased significantly (2.17 ± 0.20; p = 0.0001), with enrichment of oral commensals including Streptococcus mitis (↑ 11.9×), Neisseria elongata (↑ 13.7×), and Prevotella melaninogenica (↑ 13.0×). However, post-eradication profiles at six months remained distinct from H. pylori-negative communities (PERMANOVA R² = 0.12; p = 0.02). In total, 174 amplicon sequence variants changed significantly, including persistence of Fusobacterium nucleatum.

CONCLUSIONS: Nanopore full-length 16 S sequencing reveals fine-scale, clinically relevant shifts that are masked by partial-gene assays. Eradication rapidly restores microbial diversity, but at six months, is associated with a novel ecological equilibrium rather than complete normalization. This species-resolved approach offers a practical framework for post-eradication microbiome monitoring and may inform strategies to reduce residual gastric cancer risk in high-burden populations.},
}

@article {pmid41654735,
year = {2026},
author = {Ma, Y and Jia, T and Zhu, W and Fan, L},
title = {Characteristics comparative of gut microbiota in four small mammal species co-occurring in the Hengduan Mountains: differences in environmental adaptation strategies between alien and endemic species.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04820-3},
pmid = {41654735},
issn = {1471-2180},
support = {32560262//National Natural Scientific Foundation of China/ ; 202401AS070039//Yunnan Fundamental Research Projects/ ; },
abstract = {The composition of gut microbiota is jointly determined by the host's food habit, ecological niche, and genetic background, serving as a direct reflection of the host's adaptation to its environment and evolutionary pressures. To investigate the distinct adaptation mechanisms of four sympatric small mammal species in the Hengduan Mountains region, this study compared the environmental adaptation strategies of endemic and alien species. This study collected ten wild specimens each of the Eothenomys miletus, Eothenomys oliter, Tupaia belangeri, and Apodemus chevrieri from Yunlong County, Yunnan Province. Using 16SrRNA gene sequencing technology, we analyzed the gut microbial composition, abundance, and community structure across species, investigating the distinct gut microbial community characteristics between the endemic species (E. miletus and E. oliter) and the alien species (T. belangeri and A. chevrieri.). Results indicate: E. miletus and E. oliter possess complex and diverse gut microbial communities with plant-degrading functions. These communities with sparse interactions are capable of utilizing multiple plant sources for nutrition and exhibit strong resilience against environmental disturbances. In contrast, T. belangeri and A.chevrieri exhibit simple, specialized, yet tightly cooperative omnivorous gut microbial communities. While capable of utilizing diverse food resources within specific adaptive environments, they demonstrate extreme specificity in adaptation to particular habitats or survival strategies and are relatively sensitive to external disturbances. Furthermore, the E. miletus, widely distributed across the Hengduan Mountains, its gut bacterial community is dominated by stochastic processes. In contrast, the T. belangeri shows a positive correlation with various gut bacteria associated with omnivorous characteristics. The distinction between these two distinct environmental adaptation strategies is particularly pronounced. In summary, Among these four sympatric small mammal species in the Hengduan Mountains, the gut microbiota of endemic and alien species showed high similarity respectively and exhibited convergence.},
}

@article {pmid41654729,
year = {2026},
author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J},
title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04500-8},
pmid = {41654729},
issn = {1471-2180},
abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.

METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.

RESULTS: Our study confirmed a statistically significant difference in the β-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.

CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.},
}

@article {pmid41654532,
year = {2026},
author = {Mohidin, AF and Ng, TCA and Santillan, E and Yang, L and Cokro, A and Wuertz, S},
title = {Enhanced resistance and resilience of anaerobic digestion microbiome after single and dual short-term disturbances.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5391},
pmid = {41654532},
issn = {2045-2322},
}

@article {pmid41654531,
year = {2026},
author = {Fernandes, AC and Reverter, A and Conteville, LC and Afonso, J and Cardoso, TF and Palhares, JCP and Mourão, GB and Regitano, LCA and Coutinho, LL},
title = {Microbiome by transcriptome interactions triggered by a switch to an alternative diet in Nellore cattle.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5371},
pmid = {41654531},
issn = {2045-2322},
support = {88887.620015/2021-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2021/14321-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/11953-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/04089-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
}

@article {pmid41654247,
year = {2026},
author = {van Vugt, WLJ and Boogaard, EVD and Tuuk, KV and Spinnewijn, L and Kreukels, BPC and Both, S and Huirne, JAF and van Mello, NM},
title = {Gynecologic function and dysfunction in transmasculine and gender diverse individuals using testosterone therapy: a systematic review.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2026.01.036},
pmid = {41654247},
issn = {1097-6868},
abstract = {OBJECTIVE: To systematically review the current literature on gynecologic function and dysfunction in transmasculine and gender diverse individuals in the context of testosterone therapy, with a focus on menstrual suppression, contraceptive needs, pelvic pain, vulvovaginal changes, and sexual health.

DATA SOURCES: PubMed, Embase and Web of Science databases were searched through September 2025 using search terms related to transmasculine individuals, assigned female at birth, reproductive organs, and testosterone and gender-affirming hormone therapy. No restrictions on publication year were applied.

STUDY ELIGIBILITY CRITERIA: Studies were included if they reported on the impact of exogenous testosterone on gynecologic or sexual (dys)function, as well as contraceptive use and choices, in transmasculine and gender diverse individuals. Only original human research studies were eligible. Studies focusing on fertility, reproductive outcomes, malignancy, histology, animal models, or individuals with differences of sex development were excluded.

All included studies were critically appraised using Joanna Briggs Institute (JBI) quality assessment tools, and findings were synthesized narratively.

RESULTS: Fifty-seven studies were included. Testosterone was generally effective in achieving menstrual suppression, though breakthrough bleeding and ovulatory activity occurred in a substantial proportion of individuals. Contraceptive needs were frequently unmet, partly due to misinformation and provider-related barriers. Pelvic pain was commonly reported, with varied etiologies. While testosterone often increased sexual desire, dyspareunia and genital discomfort were frequently described. Vaginal microbiome alterations and epithelial changes were observed, though their clinical implications remain unclear.

CONCLUSION: Testosterone-based gender-affirming hormone therapy has diverse effects on gynecologic function in transmasculine and gender diverse individuals, including both physiologically expected as well as underexplored effects. Clinicians should adopt an individualized and affirming approach to care, while further research is needed to understand long-term outcomes, improve assessment tools, and close gaps in inclusive gynecologic healthcare.},
}

@article {pmid41654223,
year = {2026},
author = {Fondevila, MF and Kreimeyer, H and Hsu, CL and Tamargo-Azpilicueta, J and Day, LZ and Gritsenko, M and Attah, K and Cabré, N and Harberts, A and Tonetti, FR and Yang, Y and Yamazaki, T and Schöler, D and Eguileor, A and Blasio, C and Meijnikman, AS and Zhang, X and Garcia-Carbonell, R and Hook, V and Zhou, E and Sun, Z and Jacobs, JM and Turner, JR and Llorente, C and , and Glass, CK and Stärkel, P and Reinheckel, T and Diaz-Moreno, I and Gonzalez, DJ and Schnabl, B},
title = {Macrophage-derived cathepsin B disrupts intestinal tight junctions through occludin degradation and promotes alcohol-associated liver disease.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.01.013},
pmid = {41654223},
issn = {1600-0641},
abstract = {BACKGROUND & AIMS: Disruption of the intestinal barrier facilitates microbial translocation to the liver and contributes to chronic liver disease. We aimed to study the role of the fecal proteome for disease progression in patients with alcohol-associated hepatitis.

METHODS: We used fecal proteomics data from a multicenter cohort of patients with alcohol-associated hepatitis (n=80), alcohol use disorder (n=20), and controls (n=19) (InTeam), and a cathepsin B activity assay in an independent multicenter cohort of patients with alcohol-associated hepatitis (n=80), alcohol use disorder (n=20), and controls (n=18) (AlcHepNet). Mice lacking cathepsin B in myeloid cells and transgenic mice overexpressing occludin in intestinal epithelial cells, were subjected to the chronic-plus-binge ethanol feeding model (NIAAA).

RESULTS: Fecal proteomics and activity analysis revealed that the protease cathepsin B progressively increased with alcohol use disorder and alcohol-associated hepatitis compared to controls, and is associated with higher short-term mortality in patients with alcohol-associated hepatitis. Cathepsin B is predominantly expressed in intestinal macrophages and is upregulated by ethanol. Cathepsin B deficiency in myeloid cells or oral treatment with the gut-restricted cathepsin B inhibitor CA074 stabilized gut barrier by preserving the tight junction protein occludin, lowered serum LPS levels, and attenuated ethanol-induced steatohepatitis. Transgenic overexpression of occludin in intestinal epithelial cells sufficed to reduce steatohepatitis and blunted the effects of CA074 in ethanol-fed mice. Cathepsin B proteolytically cleaves occludin in enzymatic assays, and its inhibition prevented occludin degradation and barrier disruption in intestinal organoids and epithelial monolayers. Molecular modeling and peptide profiling reveal specific cathepsin B-induced cleavage sites in the extracellular region of occludin.

CONCLUSIONS: Intestinal cathepsin B is an essential mediator of gut barrier dysfunction and therapeutic target in alcohol-associated liver disease.

IMPACT AND IMPLICATIONS: Intestinal barrier disruption facilitates the microbial translocation to the liver, contributing to the progression of alcohol-associated hepatitis, however the molecular mechanisms driving barrier dysfunction remain incompletely understood. Our study identified the protease cathepsin B as a key contributor to the progression of alcohol-associated liver disease by degrading the extracellular region of tight junction protein occludin in the intestine, which in turn leads to barrier disruption. This work advances the field by addressing causality, uncovering the molecular target, and proposing cathepsin B as a promising therapeutic target in alcohol-associated hepatitis, a condition for which liver transplantation remains the only effective treatment in a limited subset of patients.},
}

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household Environmental Characteristics Influence House Dust Metagenome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

@article {pmid41653954,
year = {2026},
author = {Egea, LG and Jiménez-Ramos, R and Rodríguez-Arias, L and Infantes, E},
title = {Microplastics reduce eelgrass tolerance to heat stress with implications for restoration and blue carbon.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123980},
doi = {10.1016/j.envres.2026.123980},
pmid = {41653954},
issn = {1096-0953},
abstract = {Seagrass beds are key blue-carbon ecosystems, yet their resilience is increasingly challenged by microplastic (MP) pollution and marine heatwaves (MHWs). We experimentally tested how these stressors, alone and combined, affect the seagrass Zostera marina (eelgrass) using a controlled mesocosm experiment grounded in multiple-stressor and trait-based ecological theory. Plants were grown for 43 days in sediments with or without polyethylene/polypropylene MPs and a simulated MHW, (+5°C for 15 days) was imposed in the final phase. MP exposure significantly reduced rhizome elongation (-35%), total root length (-65%), and below-ground biomass, and depleted non-structural carbohydrates (NSC) in leaves and rhizomes (-35% to -40%). Warming alone stimulated leaf growth but further reduced NSC, while the MP × MHW interaction produced the lowest below-ground growth and carbohydrate reserves, consistent with synergistic stress predicted by multiple-stressor theory. MP exposure also reshaped the microbiome enriching putative sulfur-cycling taxa in the rhizosphere and indicating more reducing sediment conditions. With a carbon-balance and holobiont framework, MPs appear to constrain resource supply (oxygen and nutrients) and increase maintenance costs, whereas warming amplifies metabolic demand. The resulting carbon deficit limits below-ground growth, traits that underpin restoration success and blue-carbon function. These findings show the importance of incorporating microplastic monitoring into seagrass management to anticipate cumulative stress under a warming ocean.},
}

@article {pmid41653836,
year = {2026},
author = {Zhu, Y and Liu, SL and Lu, X and Luo, G and Xiao, ZH and Wang, YK and Zhou, J and Qiao, SC},
title = {Clinical, Immunological and Microbiological Improvements With Zinc-Coated Healing Abutments During the Healing Phase.},
journal = {International dental journal},
volume = {76},
number = {2},
pages = {109338},
doi = {10.1016/j.identj.2025.109338},
pmid = {41653836},
issn = {1875-595X},
abstract = {PURPOSE: The aim of this study was to evaluate the clinical, immunological, and microbiological effects of zinc-coated healing abutments (Zn-TiO2 abutments) on peri-implant soft tissue as compared with the commercially used ones (Ti abutments).

METHODS: The study was a prospective, non-randomised, single-centre, open-label, proof-of-concept clinical trial. The Ti and Zn-TiO2 abutments were non-randomly connected to 2 neighbouring implants in the posterior region in each eligible patient. The bleeding-on-probing proportion (BOP%), probing pocket depth (PPD), the concentration of the pro-inflammatory cytokine (TNF-α, IL-6) in the peri-implant crevicular fluid (PICF), and the early microbial communities assessed by 16S rRNA sequencing were recorded.

RESULTS: Eleven patients with 22 implants attended the 8-week examination. The BOP% was significantly lower in the Zn-TiO2 abutments than that in the Ti abutments (24.23% ± 13.67% versus 42.42% ± 29.22%, P = .019). The concentration of TNF-α in PICF was significantly lower in the Zn-TiO2 abutments than that in the Ti abutments (22.86 ± 11.21 versus 32.05 ± 16.28, P = .022). No significant differences in PPD and IL-6 were found between the two groups. Based on the microbiome assessments, higher microbial richness and lower presence of Lancefieldella were also observed in the Zn-TiO2 abutments as compared with the Ti abutments.

CONCLUSION: Within the limitations of the study, the zinc-coated healing abutments improved early peri-implant soft tissue health clinically and immunologically. However, further studies are still needed to exclude the interference of soft tissue phenotype and confirm the relationship between microbial and clinical findings.},
}

@article {pmid41653708,
year = {2026},
author = {Pearson, M and Engen, PA and Green, SJ and Emerson, J and Naqib, A and Gattuso, P and Keshavarzian, A and Coogan, C},
title = {Microbial profiling of urothelial carcinoma and benign bladder tissue from formalin-fixed specimens.},
journal = {Urologic oncology},
volume = {44},
number = {4},
pages = {110997},
doi = {10.1016/j.urolonc.2026.110997},
pmid = {41653708},
issn = {1873-2496},
abstract = {PURPOSE: Host-associated microbiota can influence host immunity and tumor responses. Emerging evidence suggests the bladder microbiome contributes to urothelial cell carcinoma (UCC), though most data come from urine samples. Urinary microbiomes are different in UCC compared to inflamed bladder, though their impact on host immune responses is understudied. Similarly, the effect of Bacillus Calmette-Guérin (BCG) treatment on bladder microbiome remains unexplored.

MATERIALS AND METHODS: Formalin-fixed paraffin-embedded (FFPE) transurethral resection of bladder tumor (TURBT) specimens from UCC tumor stages (T1 = 42), (T2 = 5), and 16 benign pathologies were examined. Six patients who underwent BCG vaccine with post-treatment TURBT specimens were examined. Microbial communities were characterized using RNA extraction, reverse transcription, and 16S rRNA amplicon sequencing.

RESULTS: UCC patients exhibited greater microbial diversity and distinct bladder microbiome compositions compared to those with benign pathology. Several genera in the bladder including Streptococcus, Staphylococcus, Actinomyces, and Cutibacterium were more abundant in the benign group. Conversely, T1-UCC patients showed higher relative abundances of putative proinflammatory genera including Escherichia-Shigella and unclassified Yersiniaceae, plus commonly reported skin-associated dysbiotic genera Enhydrobacter and Micrococcus. Five of 6 BCG-treated patients showed marked reduction in microbial diversity along with significant alteration in their microbiome composition, including decreased relative abundance of bacteria from genera Streptococcus and Rothia.

CONCLUSIONS: This proof-of-concept study suggests that: (1) microbiome sequencing from FFPE TURBT specimens can be used for microbiota assessment and can effectively distinguish UCC from benign pathology. (2) bladder microbiomes are heavily depleted following BCG treatment, indicating therapy-induced microbiome alterations.},
}

@article {pmid41653553,
year = {2026},
author = {Ghosh, A and Bhakta, S and Kapse, N and Dhakephalkar, PK and Patra, C and Gorain, B},
title = {Micro/nanoplastic-mediated gut dysbiosis and its impact on cardiac and neuroimmune function in zebrafish model: A multi-omics approach.},
journal = {The Science of the total environment},
volume = {1017},
number = {},
pages = {181443},
doi = {10.1016/j.scitotenv.2026.181443},
pmid = {41653553},
issn = {1879-1026},
abstract = {The pervasive distribution of micro- and nanoplastics (M/NPs) across ecosystems necessitates a mechanistic investigation into their toxicological consequences. Chronic exposure to M/NPs through combined intestinal uptake and branchial contact in aquatic animals disrupts epithelial barrier integrity, alters gastric secretions and luminal pH, and induces microbial dysbiosis, evidenced by the depletion of commensal taxa and expansion of pathogenic strains. These local perturbations trigger systemic sequelae, including neurotoxicity and cardiotoxicity. Consequences on cross-species analyses demonstrate translational concordance, as human studies similarly link M/NP bioaccumulation with inflammatory bowel disease, cognitive decline, and cardiovascular dysfunction. Integrative multi-omics approaches, encompassing transcriptomic, metabolomic, and microbiome analyses, have begun to elucidate the molecular cascades underpinning M/NP toxicity, providing high-resolution insights into host-microbe-environment interactions. Notwithstanding these advances, critical gaps remain in chronic exposure modelling, capturing particle heterogeneity, and ensuring ecological realism. In this context, zebrafish (Danio rerio) provide a uniquely tractable system for gnotobiotic rearing, microbial transplantation, and live imaging, thereby enabling causal inference and functional validation in real-time. Collectively, this review establishes zebrafish as a pivotal model for elucidating M/NP-induced gut dysbiosis, neurotoxicity, and cardiotoxicity. Multi-omics analyses and translational evidence reveal systemic inflammation, immune-metabolic disruptions, and mechanistic links to human health, providing a foundation for targeted research, regulatory frameworks, and interventions to mitigate environmental M/NP exposure.},
}

@article {pmid41653320,
year = {2026},
author = {Kashyap, S and Bhattacharyya, PN and Agarwala, N},
title = {Developing Effective Bioinoculant and Engineering Plant Microbiome for Climate Resilient Agriculture: Lessons Learned and Future Roadmap.},
journal = {Current microbiology},
volume = {83},
number = {3},
pages = {161},
pmid = {41653320},
issn = {1432-0991},
support = {CRG/2023/002423//Anusandhan National Research Foundation,India/ ; },
mesh = {*Microbiota ; *Agriculture/methods ; Climate Change ; *Plants/microbiology ; *Crops, Agricultural/microbiology ; },
abstract = {Ensuring plant resilience is crucial for maintaining global food security amidst a changing climate. Leveraging the multitude of microorganisms in different environmental conditions appears to be a promising and sustainable approach to boosting agricultural productivity. However, understanding the legacy of microbial bioinoculants in agroecosystems remains a challenging issue, thereby hampering their widespread applicability and acceptance. This review offers an in-depth insight into the intricacies of designing effective bioinoculants, orchestrated by an understanding of the ecological contexts that drive their success. Furthermore, this article emphasizes the importance of adopting a holistic approach to designing effective bioinoculants, thereby enhancing their application in agriculture.},
}

*Microbiota
*Agriculture/methods
Climate Change
*Plants/microbiology
*Crops, Agricultural/microbiology

@article {pmid41652998,
year = {2026},
author = {Desorcy-Scherer, K and McNamara, K and Luellwitz, R and Stanton, E and Zuniga-Chaves, I},
title = {Early Insights Into Maternal Antidepressant Use and the Human Infant Gut Microbiome.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {10998004261423546},
doi = {10.1177/10998004261423546},
pmid = {41652998},
issn = {1552-4175},
abstract = {Maternal selective serotonin reuptake inhibitor (SSRI) use is common during pregnancy and lactation. Changes in serotonin signaling may affect diversity and composition of microbes in the gut. Although research suggests SSRI drives microbial change, the extent to which the infant gut microbiome is affected is unknown. The infant gut microbiome is critical in early life for support of developmental health including early training of the immune system and metabolic programming. A total of N = 20 (10 SSRI, 10 control) maternal/infant dyads were enrolled in a pilot study. Thirty-six infant stool samples were collected at 1-2 and 4-6 weeks of life and sequenced using 16S rRNA sequencing. Investigative models included SSRI exposure as the primary variable of interest with infant feeding pattern and mode of delivery included as covariates. Maternal antidepressant use was not associated with infant alpha (within-sample) diversity. The SSRI use may shape beta (between-sample) diversity, particularly at weeks 4-6 of life (p = .072). Increases in the genera Gemella, Staphylococcus and Corynebacterium were observed with SSRI exposure. Additionally, results reveal a SSRI-associated decrease in Lactobacillus. While this pilot study is not intended to provide conclusive evidence, it is an important step in informing future research directions. Results suggest a modest influence of maternal SSRI exposure on the infant gut microbiome. Future studies should seek to use techniques like metagenomics, providing functional information to assess for local or systemic health impact and ultimately, clinical relevance.},
}

@article {pmid41652967,
year = {2026},
author = {Rose, AM and O'Brien, AM},
title = {Observing weak adaptation of duckweeds to their local microbiome depends on local pondwater.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70165},
doi = {10.1002/ajb2.70165},
pmid = {41652967},
issn = {1537-2197},
support = {2300059//Division of Molecular and Cellular Biosciences/ ; Hatch NH00724//National Institute of Food and Agriculture/ ; },
abstract = {PREMISE: Populations can locally adapt to the biotic and abiotic factors of environments. However, detecting adaptation to biotic factors can depend on the abiotic conditions in which the adaptation is tested, and vice versa. The microbiome is one important aspect of the biotic environment: Interactions between microbiomes and their hosts are critical for host fitness and trait expression. If hosts adapt to local microbiomes, they may therefore depend on interactions with local microbes to express trait values adapted to the local abiotic environment.

METHODS: Using Lemna minor (duckweed) as a model host, we examined differences in host fitness when grown in local and nonlocal microbiomes and in local and nonlocal water. We experimentally recombined duckweeds, microbes, and water from four ponds around Durham, New Hampshire (United States) in well-plate microcosms in a growth chamber.

RESULTS: The source of duckweeds, microbes, and water all affected microbial growth, duckweed growth, and duckweed traits. However, weak, marginally significant local adaptation resulted in higher frond area only when duckweeds were paired with their local water and local microbes. Microbial growth was also marginally reduced when duckweeds were paired with microbes and water from their local site.

CONCLUSIONS: While microbiome impacts on duckweed growth and traits varied across abiotic contexts, local microbiomes provided only limited growth benefits. Harnessing the effects of plant microbiomes is an exciting area of applied research. Despite our findings, bioprospecting in local microbiomes could still be fruitful: It may be ecologically safer, and other plants may locally adapt to microbiomes.},
}

@article {pmid41652869,
year = {2026},
author = {Neil, RC and Barton, JA and Heyward, A and Francis, DS and Nankervis, L and Mock, TS and Humphrey, C and Bourne, DG},
title = {Nutritional and Microbial Responses of Pocillopora verrucosa to Co-Culture With Chromis viridis Damselfish.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70291},
pmid = {41652869},
issn = {1758-2229},
support = {//Great Barrier Reef Foundation/ ; },
mesh = {Animals ; *Anthozoa/microbiology/growth & development/physiology/chemistry ; Bacteria/classification/genetics/isolation & purification ; Coculture Techniques ; Symbiosis ; Aquaculture ; Animal Feed/analysis ; Fatty Acids/analysis ; *Perciformes ; Microbiota ; },
abstract = {Associations with fish can benefit corals by increasing growth and stress tolerance. To investigate microbial and nutritional responses of corals to fish associations in the context of enhancing coral aquaculture outcomes, Pocillopora verrucosa were cultured for 3 months with different combinations of live feeds and schools of juvenile Chromis viridis damselfish. The combined live feeds and fish treatment resulted in a bacterial community most similar to wild P. verrucosa, dominated by Endozoicomonas-affiliated taxa. Protein content was enhanced in corals with access to live feeds and/or dissolved fish wastes compared to unfed controls. Total lipid concentrations were elevated in captive corals with access to dissolved fish wastes and at moderate levels in those supplied live feeds, likely due to the activity of corals' symbionts and deposition of derived lipids from live feeds, respectively. However, all captive corals demonstrated a significant reduction in storage lipid concentration compared to samples from the wild. Fatty acid analysis indicated these shifts were likely the result of higher light levels in the field supporting Symbiodiniaceae photosynthesis and potentially feeding on wild zooplankton. Co-culturing captive corals with fish and providing appropriate live feeds may therefore offer an effective approach to improve coral nutrition, health and microbiome stability.},
}

Animals
*Anthozoa/microbiology/growth & development/physiology/chemistry
Bacteria/classification/genetics/isolation & purification
Coculture Techniques
Symbiosis
Aquaculture
Animal Feed/analysis
Fatty Acids/analysis
*Perciformes
Microbiota

@article {pmid41652766,
year = {2026},
author = {Ovai, B and Onuh, J and Aryee, ANA},
title = {The role of plant-food derived bioactives in modulating the gut microbiome, inflammation and metabolic syndrome: Regulatory and market dynamics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {227},
number = {},
pages = {118243},
doi = {10.1016/j.foodres.2025.118243},
pmid = {41652766},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metabolic Syndrome/prevention & control/microbiology ; *Inflammation/prevention & control ; *Phytochemicals/pharmacology ; Anti-Inflammatory Agents ; Antioxidants ; },
abstract = {The global increase in metabolic disorders including obesity, type 2 diabetes (T2DM), and cardiovascular disease (CVD) highlights the need for adjunctive strategies beyond conventional pharmacotherapy. Bioactive compounds (BACs) derived from plant-based foods, such as carotenoids, glucosinolates (GSLs), and bioactive peptides (BAPs), have garnered considerable interest for their capacity to modulate the gut microbiome, attenuate systemic inflammation, and mitigate key features of metabolic syndrome (MetS). Carotenoids have been associated with antioxidant and anti-inflammatory activities including inhibition of lipid peroxidation; GSLs contribute to phase II detoxification and glycemic control; while BAPs demonstrate antihypertensive activity and support probiotic growth. Despite promising mechanistic data, clinical translation remains limited. Human trials are few, generally short in duration, and often rely on surrogate biomarkers such as heme oxygenase-1, superoxide dismutase 1, C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α). Effective dosing varies by compound and formulation, with lipid and inflammatory outcomes typically assessed over 8-12 weeks, and hepatic or structural endpoints requiring ≥24 weeks. Efficacy is further influenced by interindividual variability in gut microbiota composition, dietary matrix, food processing methods, and BAC bioavailability. To advance clinical relevance, long-term, adequately powered trials in diverse populations are essential. Furthermore, regulatory challenges, commercialization constraints, and the need for standardized formulations must be addressed to expand the development of functional foods and nutraceuticals, particularly given their favorable safety profiles and potential for preventive health applications.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Metabolic Syndrome/prevention & control/microbiology
*Inflammation/prevention & control
*Phytochemicals/pharmacology
Anti-Inflammatory Agents
Antioxidants

@article {pmid41652742,
year = {2026},
author = {Van Meulebroek, L and Ghyselinck, J and Van Elst, D and Duysburgh, C and Gessner, A and Thas, O and Marzorati, M},
title = {The impact of Symprove™ multi-strain probiotic on enterotoxigenic Escherichia coli- or antibiotic-induced gut microbiome dysbiosis using high-throughput in vitro screening.},
journal = {Food research international (Ottawa, Ont.)},
volume = {227},
number = {},
pages = {118172},
doi = {10.1016/j.foodres.2025.118172},
pmid = {41652742},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; *Dysbiosis/microbiology/chemically induced ; *Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Enterotoxigenic Escherichia coli/drug effects ; Fatty Acids, Volatile/metabolism ; Adult ; Male ; High-Throughput Screening Assays ; Female ; Escherichia coli Infections/microbiology ; Fermentation ; Young Adult ; },
abstract = {The gut microbiome plays a significant role in host physiology, both in health and disease. Assessment of changes in microbial metabolites beyond short-chain fatty acids (SCFAs) following probiotic supplementation may identify additional metabolic pathways that are activated or suppressed in response to probiotics. This study assessed changes in microbial metabolites in healthy and dysbiosed microbiomes following supplementation with Symprove™, a multistrain probiotic, using the Colon-on-a-plate® miniaturized short-term batch fermentation system with a fractional factorial design. The fecal microbiome from 10 healthy human donors was evaluated under healthy and dysbiosed (enterotoxigenic Escherichia coli infection and/or low-, medium-, or high-dose antibiotics) conditions. Samples were supplemented with Symprove™ or water (control) and evaluated for microbial metabolites at 24 h and 48 h using untargeted metabolic fingerprinting, capillary gas chromatography, and targeted metabolic profiling. Favorable impacts were observed with Symprove™ supplementation across the different antibiotic doses. SCFA levels (acetate, propionate, butyrate) were significantly increased and levels of branched SCFAs were significantly decreased with Symprove™ supplementation versus control in both the healthy and dysbiosed populations. Significant increases and decreases in several other microbial metabolites were also observed with Symprove™, many of which could be considered to have beneficial effects on intestinal inflammation, intestinal barrier health, and the gut-brain axis. Symprove™ supplementation significantly affected microbial metabolism, with many of the observed changes being considered positive for human health. Importantly, these benefits were shown not only in healthy fecal microbiomes, but also in fecal microbiomes with in vitro antibiotic-induced dysbiosis, showing therapeutic potential.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Probiotics/pharmacology
*Dysbiosis/microbiology/chemically induced
*Anti-Bacterial Agents/adverse effects
Feces/microbiology
*Enterotoxigenic Escherichia coli/drug effects
Fatty Acids, Volatile/metabolism
Adult
Male
High-Throughput Screening Assays
Female
Escherichia coli Infections/microbiology
Fermentation
Young Adult

@article {pmid41652641,
year = {2026},
author = {Lu, J and Satten, GA and Meyer, KA and Launer, LJ and Ling, W and Zhao, N},
title = {Identifying unmeasured heterogeneity in microbiome data via quantile thresholding (QuanT).},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02282-9},
pmid = {41652641},
issn = {2049-2618},
support = {R01GM147162/NH/NIH HHS/United States ; 75N92023D00002/NH/NIH HHS/United States ; R01HL155417/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Microbiome data, like other high-throughput data, suffer from technical heterogeneity stemming from differential experimental designs and processing. In addition to measured artifacts such as batch effects, there is heterogeneity due to unknown or unmeasured factors, which lead to spurious conclusions if unaccounted for. With the advent of large-scale multi-center microbiome studies and the increasing availability of public datasets, this issue becomes more pronounced. Current approaches for addressing unmeasured heterogeneity in high-throughput data were developed for microarray and/or RNA sequencing data. They cannot accommodate the unique characteristics of microbiome data such as sparsity and over-dispersion.

RESULTS: Here, we introduce quantile thresholding (QuanT), a novel non-parametric approach for identifying unmeasured heterogeneity tailored to microbiome data. QuanT applies quantile regression across multiple quantile levels to threshold the microbiome abundance data and uncovers latent heterogeneity using thresholded binary residual matrices. We validated QuanT using both synthetic and real microbiome datasets, demonstrating its superiority in capturing and mitigating heterogeneity and improving the accuracy of downstream analyses, such as prediction analysis, differential abundance tests, and community-level diversity evaluations.

CONCLUSIONS: We present QuanT, a novel tool for comprehensive identification of unmeasured heterogeneity in microbiome data. QuanT's distinct non-parametric method markedly enhances downstream analyses, serving as a valuable tool for data integration and comprehensive analysis in microbiome research. Video Abstract.},
}

@article {pmid41652512,
year = {2026},
author = {Limijadi, EKS and Nishani, F and Daliu, P and Qorri, E and Hadinata, E and Santini, A and Nurkolis, F},
title = {Marine nutraceuticals and their role in modulating diabetes-induced carcinogenesis.},
journal = {Diabetology & metabolic syndrome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13098-026-02113-3},
pmid = {41652512},
issn = {1758-5996},
}

@article {pmid41652405,
year = {2026},
author = {Chen, KL and Liao, IC and Chen, CA and Kuo, CY and Jiang, YY and Lin, YC and Yuan, K and Lung, J},
title = {Distinct bacteria profiles in primary and secondary/persistent endodontic infections: a 16S rRNA gene sequencing study.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-07821-w},
pmid = {41652405},
issn = {1472-6831},
support = {CMFHR10889//Chi Mei Medical Center/ ; CORPG6N0311//Chiayi Chang Gung Memorial Hospital/ ; 109-2314-B-182A-146-MY2//Ministry of Science and Technology, Taiwan/ ; 113-2314-B-182A-057//National Science and Technology Council/ ; },
}

@article {pmid41652394,
year = {2026},
author = {Xiao, Z and Shi, Y and Zhao, D and Wang, Y and Gu, Y},
title = {Triggering mechanisms of acute thunderstorm asthma: epithelial barrier disruption and immune dysregulation.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03532-6},
pmid = {41652394},
issn = {1465-993X},
support = {No. 2023NYFYPY005//the National Natural Cultivation Project of China/ ; No. YSXH2024KYF028//the Clinical Medical Research and Clinical New Technology Promotion Project of the Inner Mongolia Physicians Association/ ; No. 2024GLLH0314//the Public Hospital Research Joint Fund Project of the Inner Mongolia Academy of Medical Sciences/ ; },
abstract = {Thunderstorm asthma (TA) refers to a phenomenon characterized by sudden onset, large-scale outbreaks, and potentially fatal acute exacerbations of asthma. Despite accumulating epidemiological evidence, its cellular and molecular mechanisms remain unclear. Recent studies have proposed a core framework involving "environmental triggers-epithelial barrier damage-immune dysregulation." During thunderstorms, high humidity and strong convection can cause pollen to hydrate and rupture into sub-pollen particles (SPPs) smaller than 2.5 μm, which may further combine with other pollutants such as particulate matter ≤ 2.5 μm(PM2.5) and ozone (O3) to form bioaerosols capable of penetrating small airways. These factors can lead to damage of the airway epithelial barrier, with sequential cellular and molecular pathophysiological changes including downregulation of various tight junction proteins in the epithelial barrier, imbalance of mucociliary clearance function, and upregulated secretion of epithelial alarmins such as interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP). This results in increased disease severity through activation of innate and adaptive immunity (e.g., type 2 innate lymphoid cells (ILC2)/T helper 2(Th2) axis activation leading to immunoglobulin E(IgE) upregulation, eosinophil activation, and mast cell degranulation; Th17-mediated neutrophilic inflammation; and toll-like receptor(TLR)-mediated innate immune processes and mucosal inflammation) and enhancement of intrinsic susceptibility factors (e.g., TLR gene polymorphisms and abnormal expression, DNA methylation and histone modifications, as well as microbiome-host interactions). According to research in meteorology, exposomics, and molecular immunology, we believe that airway epithelial barrier dysfunction and immune dysregulation play significant roles in TA. Future translational directions primarily involve establishing a population stratification and early warning system through combinations of meteorological factors with allergens/pollutants, thereby enhancing public protection and health management efforts to improve the early warning, prevention, and clinical management of TA.},
}

@article {pmid41652368,
year = {2026},
author = {Wang, L and Fang, X and Shi, L and Wang, P and Chen, W and Yang, J and Ding, Y and Cao, Z and Xie, D and Meng, K},
title = {Identification and optimized detection of two type 2 diabetes-associated enteric pathogens: Klebsiella and EPEC.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12786-w},
pmid = {41652368},
issn = {1471-2334},
}

@article {pmid41652328,
year = {2026},
author = {Patin, C and Monot, C and Marchand-Martin, L and Ancel, PY and Butel, MJ and Rozé, JC and Lepage, P},
title = {Intestinal microbiome in very-preterm infants at one month of age and association with neurodevelopmental outcome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04789-z},
pmid = {41652328},
issn = {1471-2180},
abstract = {BACKGROUND: Preterm birth is the leading cause of death in children under five years of age worldwide. The association between preterm birth and long-term outcomes is vaguely known. In very preterm infants, the gut microbiome is highly variable and impacted by the neonatal intensive care unit environment. Our objective was to better understand the crosstalk between the gut microbiome and the host at one month of age in very preterm infants and its impact on neurological outcomes at two years of age. We performed a multi-omics analysis of fecal samples collected in 2011 from 73 very preterm French infants at one month of age, grouped according to their neurodevelopment assessed at two years of age using the Ages & Stages questionnaire. Multi-omics profiling and integrative analyses were performed between 2022 and 2023, including fecal microbiome, metabolome, and host transcriptome characterization using 16 S rRNA gene sequencing, LC-MS, and mRNA sequencing, respectively.

RESULTS: The gut microbiome of very preterm infants at one month is mostly driven by either Escherichia or Staphylococcus, which are differentially associated with host immune markers (CAMP), metabolomic pathways, notably the energy pathway due to the presence of various nicotinamide adenine dinucleotides (NAD+) and two-year neurodevelopmental outcomes.

CONCLUSION: The gut microbiome at one month of age could be a noninvasive biomarker of gut immaturity and metabolic defects. Escherichia and Staphylococcus proportions were found to be the best indicators of physiological maturity and immaturity, respectively. Escherichia may help the process of intestinal maturation in preterm infants through specific metabolites production and is associated with a better neurodevelopment.},
}

@article {pmid41652299,
year = {2026},
author = {He, J and Chen, J and Liao, Y and Zhang, K and Yang, C and Huang, H and Dou, X},
title = {Facial Skin Mycobiome in Atopic Dermatitis With and Without Facial Involvement and Healthy Controls: A Case-Control Study.},
journal = {Experimental dermatology},
volume = {35},
number = {2},
pages = {e70221},
doi = {10.1111/exd.70221},
pmid = {41652299},
issn = {1600-0625},
support = {81972930//National Natural Science Foundation of China/ ; JCYJ20210324105411030//Natural Science Foundation of Shenzhen Municipality/ ; KYQD2024401//Scientific Research Foundation of Peking University Shenzhen Hospital/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Mycobiome ; Case-Control Studies ; Adult ; Female ; Male ; *Skin/microbiology ; Malassezia/isolation & purification ; Middle Aged ; Young Adult ; Face/microbiology ; Adolescent ; },
abstract = {With the growing interest in the skin microbiome in atopic dermatitis (AD), alterations in cutaneous fungal communities have garnered increasing attention. However, their role in AD pathogenesis and their association with clinical parameters remain unclear. This study characterised the facial skin mycobiome in AD patients with and without facial involvement, compared to healthy controls. Fungal composition was analysed across multiple taxonomic levels, along with assessments of alpha and beta diversity and predicted functional pathways. Basidiomycota and Ascomycota were the predominant phyla across all groups, with Malassezia as the dominant genus. At the species level, Malassezia_globosa and Malassezia_japonica were enriched in AD patients with facial involvement, whereas Malassezia_restricta was reduced compared with the other groups. In the full cohort, no significant differences in overall fungal diversity were observed; however, richness-based alpha diversity indices differed between facial AD and healthy controls in an adult-only sensitivity analysis, while Shannon and Simpson indices remained comparable. Notably, distinct differences in predicted metabolic pathways were identified among groups. Correlation analyses showed that Malassezia_restricta abundance was positively associated with body mass index (BMI), whereas Malassezia_globosa was negatively associated with disease severity. Collectively, these findings indicate that facial AD is associated with distinct mycobiome alterations, with potential age-related effects on specific taxa and diversity metrics. Further longitudinal and mechanistic studies are warranted to elucidate causal relationships and explore therapeutic implications.},
}

Humans
*Dermatitis, Atopic/microbiology
*Mycobiome
Case-Control Studies
Adult
Female
Male
*Skin/microbiology
Malassezia/isolation & purification
Middle Aged
Young Adult
Face/microbiology
Adolescent

@article {pmid41651994,
year = {2026},
author = {Huang, S and Yu, S and Zhang, W and Qi, D and Pei, X and Lu, D and Ba, M and Xuan, S and Huang, D and Yang, J and Li, Z},
title = {Sleep deprivation disrupts lacrimal gland homeostasis via hypothalamic-pituitary-adrenal axis and gut dysbiosis in mice.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09657-0},
pmid = {41651994},
issn = {2399-3642},
support = {82101089//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Sleep deprivation (SD) disrupts systemic homeostasis, but how it drives ocular surface disease remains unclear. Using a male mouse SD model, we show that chronic SD activates the hypothalamic-pituitary-adrenal (HPA) axis, elevates corticosterone, alters gut microbiota, and depletes short-chain fatty acids (SCFAs). These alterations coincide with lacrimal gland atrophy, reduced tear secretion, and increased CD4[+]/CD8[+] T cell infiltration, accompanied by activation of IL-17-associated inflammatory pathways. Pharmacological inhibition of glucocorticoid synthesis with metyrapone preserves lacrimal gland structure and function while attenuating immune activation. Microbiome-directed interventions, including SCFA supplementation and fecal microbiota transplantation, rebalance gut communities, suppress pro-inflammatory T cell responses, and maintain lacrimal gland homeostasis. Transcriptomic and immunohistochemical analyses further reveal that all three interventions converge on the downregulation of IL-17 signaling. Collectively, these findings establish an HPA-gut microbiome-lacrimal gland axis that links neuroendocrine stress to microbial dysbiosis and ocular inflammation, and they suggest therapeutic strategies for SD-associated lacrimal gland dysfunction.},
}

@article {pmid41651947,
year = {2026},
author = {Sadeghi, S and Faramarzi, MA and Siroosi, M},
title = {Enhanced meropenem activity by a microbiome derived peptide targeting oxacillinase 48 carbapenemase in carbapenem resistant Klebsiella pneumoniae isolates.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37644-2},
pmid = {41651947},
issn = {2045-2322},
support = {1402-3-101-68180//Tehran University of Medical Sciences and Health Services/ ; },
}

@article {pmid41651883,
year = {2026},
author = {Pantiukh, K and Org, E},
title = {Human gut archaea collection from Estonian population.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06742-1},
pmid = {41651883},
issn = {2052-4463},
support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; },
abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.},
}

@article {pmid41651877,
year = {2026},
author = {Zhang, E and Claesson, MJ and Cotter, PD},
title = {Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00740-8},
pmid = {41651877},
issn = {2396-8370},
support = {23/FFP-A/11857//Research Ireland/ ; 23/FFP-A/11857//Research Ireland/ ; 101060218//European Commission/ ; },
abstract = {The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.},
}

@article {pmid41651593,
year = {2026},
author = {Adame, MD and Stringer, KA and Dickson, RP},
title = {The Gut Microbiome and Short-Chain Fatty Acid Metabolites in Sepsis.},
journal = {Clinics in chest medicine},
volume = {47},
number = {1},
pages = {119-128},
doi = {10.1016/j.ccm.2025.11.006},
pmid = {41651593},
issn = {1557-8216},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Sepsis/metabolism/microbiology/physiopathology ; *Fatty Acids, Volatile/metabolism ; },
abstract = {Sepsis profoundly perturbs the intestinal microbiome and its metabolite output, yet the mechanisms by which these changes influence organ injury remain incompletely defined. In this review, we focus on short-chain fatty acids (SCFAs) as key mediators linking gut microbes to sepsis pathophysiology. We first summarize how sepsis and its treatments reshape gut communities, depleting SCFA-producing anaerobes and altering the gut metabolome. We then examine determinants of SCFA concentrations in the intestinal lumen and describe how gut-blood trafficking of these charged metabolites depends on epithelial transporters and tight-junction-regulated paracellular pathways. We highlight emerging data on how leak and pore pathways, including claudin-2-dependent pores, are upregulated in sepsis and may misdirect microbial products into the portal and systemic circulation. Finally, we synthesize experimental and human evidence for organ-specific effects of individual SCFAs: butyrate as a colonocyte fuel and barrier stabilizer, propionate as a modulator of lung immune tone, and acetate as a systemic immunometabolite that shapes inflammatory responses and sepsis outcomes. Across these sections, we outline therapeutic strategies that aim to preserve or restore SCFA-producing microbes, modify diet, target transport and permeability pathways, or deliver microbial metabolites directly. Together, these data position SCFAs and their trafficking as central to the gut-sepsis axis and as promising targets for future precision therapies.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Sepsis/metabolism/microbiology/physiopathology
*Fatty Acids, Volatile/metabolism

@article {pmid41651581,
year = {2026},
author = {Mondal, R and Yano, Y},
title = {Reply to: "Considerations on statistical analysis of NHANES data in oral microbiome diversity and mortality study".},
journal = {Atherosclerosis},
volume = {413},
number = {},
pages = {120630},
doi = {10.1016/j.atherosclerosis.2025.120630},
pmid = {41651581},
issn = {1879-1484},
}

@article {pmid41651580,
year = {2026},
author = {Shen, Y and Hu, W},
title = {Considerations on statistical analysis of NHANES data in oral microbiome diversity and mortality study.},
journal = {Atherosclerosis},
volume = {413},
number = {},
pages = {120629},
doi = {10.1016/j.atherosclerosis.2025.120629},
pmid = {41651580},
issn = {1879-1484},
}

@article {pmid41651403,
year = {2026},
author = {Suss, NR and Barat, B and Ravari, MR and Shogan, BD},
title = {The impact of the microbiome on colorectal cancer recurrence.},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {102360},
doi = {10.1016/j.gassur.2026.102360},
pmid = {41651403},
issn = {1873-4626},
abstract = {Surgical resection of a colorectal adenocarcinoma remains a cornerstone in its treatment. Yet, despite proper patient selection and neoadjuvant and/or adjuvant chemotherapy/radiation, up to 30% of patients thought to be cured will develop a postoperative recurrence. Unfortunately, the outcomes in patients who develop a postoperative recurrence are poor and are associated with high morbidity and mortality. The gut microbiome has emerged to play a role in virtually all aspects of human health. In this manuscript, we critically examine the current literature implicating the gut microbiome's role in the pathogenesis of postoperative recurrence following attempted curative resection. We discuss how microbes can drive a more advanced stage and explore how surgery itself can precipitate a gut microenvironment with tumorigenic bacteria and bacterial derived metabolites that can drive postoperative tumor formation. Finally, we review evidence as to how the gut microbiome can be manipulated to improve oncological outcomes.},
}

@article {pmid41651389,
year = {2026},
author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M},
title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.},
journal = {Developmental and comparative immunology},
volume = {176},
number = {},
pages = {105565},
doi = {10.1016/j.dci.2026.105565},
pmid = {41651389},
issn = {1879-0089},
abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.},
}

@article {pmid41651372,
year = {2026},
author = {Muhffel, MM and Aly, SS and Lucey, PM and Lean, IJ and Rossow, HA},
title = {Feeding preweaning Holstein calves a synbiotic supplement increases their energy-corrected milk yield as lactating cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27567},
pmid = {41651372},
issn = {1525-3198},
abstract = {Prebiotics and probiotics are feed additives that can benefit the host by modulating the gut microbiome, which is crucial in digestion, immunity, and overall animal health. This study aims to evaluate the effects of supplementing prebiotics, probiotics, or synbiotics to preweaning Holstein calves on their future milk yield. This study is a retrospective analysis of milk yield records from dairy cows that were randomized at birth to 1 of 4 twice-daily treatments administered during the preweaning period: (1) control, no additive (CON), (2) prebiotic (PRE; 7 mL of Saccharomyces cerevisiae yeast culture), (3) probiotic (PRO; Bacillus subtilis and Lactobacillus plantarum, delivering ∼1 billion and 250 million cfu per head per day, respectively), or (4) synbiotic (SYN; combination of both PRE and PRO at the same dosages as the PRE and PRO treatments). The study was conducted on a dairy farm in Fresno County, California, between 2019 and 2023, involving 1,296 Holstein cows over their first 3 lactations for a total of 2,735 lactations. Monthly test day records for milk yield, fat, and protein were used to calculate ECM, standardized to 4% fat and 3.3% protein, totaling 26,464 monthly test day milk records. A 2-piece splines mixed-effect regression model evaluated the effect of treatments on ECM yield. For the first lactation, ECM yield was estimated at 28.66 kg on the first DIM, peaked at 42.1 kg, and declined to 21.34 kg by 305 DIM. For parity ≥2, ECM yield was 41.06 kg at 1 DIM, peaked at 54.2 kg, and 33.74 kg at 305 DIM. The SYN treatment increased ECM yield by 1.00 kg/d compared with CON. This increase was primarily due to an increase in milk fat yield, with 0.048 kg/d more fat produced compared with the control group. No differences in ECM yield between PRE, PRO, or CON were observed. These findings suggest that supplementing SYN during the preweaning period increased milk, milk fat, and ECM yield across lactations 1, 2, and 3.},
}

@article {pmid41651364,
year = {2026},
author = {Hu, G and Gao, J and Padmakumar, V and Joshi, N and Zhu, W and Cheng, Y},
title = {The impact of methane inhibitors on ruminants: A systematic review and meta-analysis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27479},
pmid = {41651364},
issn = {1525-3198},
abstract = {The impact of methane inhibitors on ruminant performance and rumen microbial community composition is unclear. The aim of this study was to summarize the effects of methane inhibitors on the performance of ruminants and the structure of rumen microbial communities. A total of 13,043 studies were retrieved from the Web of Science database. Ultimately, 256 studies containing the variables we needed were included. The data were further extracted and processed. The study revealed the negative effects of methane inhibitors on ruminants, which were reflected in the reduction of feed intake and digestibility in ruminants. Adding methane inhibitors reduced the acetate concentration in the rumen and increased the propionate content in the rumen. There was no significant change in the α-diversity of the rumen microbiome, whereas the β-diversity of rumen microbes was enhanced. The effects of methane inhibitor supplementation showed dose-dependent significant differences, particularly in modulating rumen fermentation parameters and the structure of the microbial community. Furthermore, when the total VFA in the rumen were below 96.98 mmol/L, or the acetate concentration was below 61.26 mmol/L, or the acetate-to-propionate ratio was below 3.86, the suppression of methane production was most effective. The addition of methane inhibitors has a positive effect on the performance of ruminants, particularly by improving the structure of the rumen microbiota. Additionally, VFA have a certain threshold effect on methane production. This provides a reference for the application and selection of methane inhibitors.},
}

@article {pmid41651362,
year = {2026},
author = {Cahyo, HN and Niu, P and Pope, PB and Gimsa, U and Kuhla, B and Schwarm, A},
title = {Methane category, immune response, feed efficiency, and rumen microbial community in lactating dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26925},
pmid = {41651362},
issn = {1525-3198},
abstract = {This study aimed to assess relationships of enteric methane (CH4) yield (g/kg of DMI) with immune response, feed efficiency (ECM/DMI), and rumen microbiome in dairy cows, both in early and in late lactation. The DMI, BW, ECM yield, and CH4 emission were measured in respiration chambers in early (n = 20, 32 ± 7 DIM) and nonpregnant late lactating (n = 14, 359 ± 90 DIM) multiparous Holstein cows. The in vitro immune response was studied in response to (1) LPS using whole blood, and (2) phytohemagglutinin and concanavalin A using peripheral blood mononuclear cells. The DNA was extracted from rumen content samples (esophageal tubing) for 16S rRNA microbial analysis. Cows were divided retrospectively into an equal number of cows with low (LMY) and high (HMY) CH4 yield within each lactation group. In early lactation, CH4 yields in LMY (n = 10) and HMY cows (n = 10) were on average (±SD) 18.8 ± 1.4 and 23.5 ± 2.8 g/kg of DMI, respectively. In late lactation, CH4 yields in LMY (n = 7) and HMY cows (n = 7) were 20.8 ± 2.0 and 23.6 ± 1.7 g/kg of DMI, respectively. Statistical analysis was performed separately for each lactation group. In early lactation, we found that whole blood and isolated peripheral blood mononuclear cells from LMY compared with HMY animals were less responsive to stimulants in vitro. In addition, feed conversion efficiency was lower in LMY than HMY cows, and the relative abundance of the archaeal genus Methanospaera and the bacterial genus Marvinbryantia were higher. In late lactation, we observed no differences in immune response and feed conversion efficiency between LMY and HMY cows. Still, in LMY cows several bacterial genera including Prevotella 7, Ruminococcus gauvreauii group, and Shuttleworthia were enriched, whereas in HMY cows Methanobrevibacter, Veillonellaceae UCG-001, Succinivibrionaceae UCG-002, Rikenellaceae RC9, and CAG-352 were enriched. The results indicate that in early lactation the animals with low CH4 yield reach energy balance faster, at the expense of an inadequate immune response. Meanwhile, increased CH4 yield in early lactation may reflect higher rumen fermentation activity, fostering feed efficiency and energy availability for supporting immune function.},
}

@article {pmid41651359,
year = {2026},
author = {Xie, L and Rashid, MH and Dong, Q and Ricci, A and Opsomer, G and Pascottini, OB},
title = {Transcriptomic landscapes of the endometrium of dairy cows with clinical or subclinical endometritis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27374},
pmid = {41651359},
issn = {1525-3198},
abstract = {Subclinical (SCE) and clinical endometritis (CE) are distinct manifestations of reproductive tract inflammatory disease in dairy cows. The development of both conditions stems from postpartum dysregulation of the inflammatory response or a shift in the composition of the uterine microbiome. To gain further insight into the host responses associated with these distinct conditions, we aimed to identify changes in the endometrial transcriptomic landscape in healthy postpartum dairy cows compared with those diagnosed with SCE or CE. Twenty-four multiparous Holstein cows were evaluated for uterine health status at 35 or 36 d postpartum using vaginal discharge scoring (Metricheck) and endometrial cytology (cytobrush). Based on these evaluations, cows were classified into 3 groups: healthy (n = 12; clear or no vaginal discharge and ≤5% endometrial PMN), SCE (n = 6; clear or no vaginal discharge and >5% PMN), and CE (n = 6; mucopurulent or worse discharge and >5% PMN). Endometrial samples collected via cytobrush were stored at -80°C and total RNA was isolated; RNA sequencing was performed using an Illumina NextSeq 500 platform, generating 75 bp single-end reads. Differentially expressed genes (DEG) were identified using DESeq2 with a significance threshold of P < 0.05 and |fold change| > 2. Pathway enrichment analyses were performed using the OmicShare platform to identify enriched biological pathways among the DEG. A total of 250 DEG were identified between healthy and SCE cows, 1,291 between healthy and CE cows, and 829 between SCE and CE cows. In SCE (as compared with healthy) cows, TNF, IL-17, NOD-like receptor signaling, and cytokine-cytokine receptor interaction pathways were upregulated, whereas the FoxO signaling pathway was downregulated. In CE compared with healthy cows, upregulated DEG were enriched in IL-17, TNF, chemokine, NOD-like receptor, NF-kappa B, and toll-like receptor signaling pathways, whereas downregulated DEG were enriched in PI3K-AKT, MAPK, AMPK, Wnt, PPAR, and metabolic pathways. In CE compared with SCE, upregulated DEG were enriched in NOD-like receptor, IL-17, chemokine, B cell receptor, and cytokine-cytokine receptor interaction pathways, and downregulated DEG were enriched in the metabolic pathways, fatty acid metabolism, insulin signaling pathway, and adipocytokine signaling pathway. These findings underscore that CE and SCE conditions involve an inflammatory event but likely arise from different mechanisms. The enrichment of immune signaling pathways in CE reflects a classic infectious response, whereas the metabolic and regulatory pathway alterations in SCE suggest a dysregulated inflammatory state linked to impaired resolution mechanisms. These results highlight the need for tailored prevention and treatment strategies, such as modulating immune regulation in SCE and targeting bacterial dysbiosis and tissue damage in CE cases.},
}

@article {pmid41651219,
year = {2026},
author = {Remmani, NB and Harous, ZS and Alzaidy, RQ and Ahmednour, SA and Egusa, H and Soliman, SSM},
title = {The role of Fusobacterium nucleatum in the pathogenesis of endometriosis: A microbial and microenvironmental perspective.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103030},
doi = {10.1016/j.anaerobe.2026.103030},
pmid = {41651219},
issn = {1095-8274},
abstract = {Endometriosis is a chronic, inflammatory gynecological condition characterized by the ectopic growth of endometrial-like tissue, with an unclear etiology and limited treatment efficacy. Recent studies implicate the oral and gut commensal bacterium Fusobacterium nucleatum in the pathogenesis of endometriosis, with uterine colonization reported in up to 64% of affected women. This review highlights the potential role of F. nucleatum in disease progression, particularly through its metabolic activation within the endometrial microenvironment. We explore the contribution of key bacterial metabolites (formate, lactate, and hydrogen sulfide), proteins (FadA and Fap2), and lipids (oxidized LDL, lysophosphatidylcholines, and saturated fatty acids) to inflammation, immune evasion, and epithelial-mesenchymal transition (EMT), features that overlap with tumor biology. The review also investigates the preferential triggers of F. nucleatum translocation into the endometrium. Host factors such as hypoxia, estrogen dominance, and retrograde menstruation appear to create a permissive microenvironment that potentially facilitates F. nucleatum colonization and virulence. While current therapeutic strategies largely neglect microbial involvement, emerging approaches including targeted antimicrobials, probiotics, immunomodulators, and microenvironmental modulation offer promising avenues for microbiome-informed endometriosis management. This narrative review also underscores the urgent need for longitudinal, in vivo studies to characterize the relationship between the oral, gut, and endometrial microbiomes and their impact on disease onset and progression.},
}

@article {pmid41651145,
year = {2026},
author = {Wang, Y and Sun, T and Li, L and Wang, M and Hu, B and Chen, Z and Hu, S},
title = {Synergistic effects of carbon dots and arbuscular mycorrhizal fungi on mitigating PFAS stress and reinforcing the purification performance of constructed wetlands.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123952},
doi = {10.1016/j.envres.2026.123952},
pmid = {41651145},
issn = {1096-0953},
abstract = {Per- and polyfluoroalkyl substances (PFASs) are highly persistent pollutants that disrupt plant-microbe interactions and compromise the performance of constructed wetlands (CWs). Here, we demonstrate a synergistic strategy combining carbon dots (CDs) and arbuscular mycorrhizal fungi (AMF) to alleviate PFAS-induced stress and enhance CW remediation efficiency. CD amendment markedly improved plant physiological performance under PFAS exposure, increasing photosynthetic efficiency and antioxidant enzyme activities, while simultaneously facilitating AMF colonization. Under high PFAS concentrations, the AMF-CDs treatment increased AMF colonization density by 33.3-100% relative to AMF alone, indicating substantial protection of symbiotic functionality. Metagenomic and community analyses revealed that the AMF- CDs combination reshaped the rhizosphere microbiome, enriching taxa such as Chloroflexi, Planctomycetes, and Campylobacterota that are functionally linked to nitrogen cycling, PFAS transformation, and metabolic resilience. These microbial shifts enhanced nutrient turnover and strengthened redox coupling processes critical for pollutant degradation. Consequently, the AMF-CDs system achieved pronounced improvements in water quality, with total phosphorus (TP), chemical oxygen demand (COD), total nitrogen (TN), and NH4[+]-N removal efficiencies elevated by 34.3-158.3% compared with untreated controls. This study provides the first evidence that CDs function as nano-bridging agents that stabilize the root-microbe interface, reinforce AMF-plant symbiosis, and drive microbial community specialization toward pollutant degradation. The AMF-CDs synergistic mechanism offers a sustainable and scalable nano-bio strategy for restoring PFAS-contaminated ecosystems and advancing next generation constructed wetland technologies.},
}

@article {pmid41651131,
year = {2026},
author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C},
title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.},
journal = {Brain, behavior, and immunity},
volume = {134},
number = {},
pages = {106479},
doi = {10.1016/j.bbi.2026.106479},
pmid = {41651131},
issn = {1090-2139},
abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.

METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI < 25) or obese (BMI ≥ 30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q < 0.1 was considered statistically significant.

RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q = 0.02) and positively associated with Bacteroides thetaiotaomicron (q = 0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.

DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.},
}

@article {pmid41651126,
year = {2026},
author = {Tandon, D and Batgire, JS and Bharmal, Z and Karandikar, K and Patil, AD and Munne, K and Aranha, C and Bhor, VM},
title = {Mapping Cervical Microbiome Diversity and Inflammatory Milieu and Its Perturbation in Asymptomatic Bacterial Vaginosis and Candida Infections: Insights from a Community Clinic in Mumbai.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101067},
doi = {10.1016/j.ijmmb.2026.101067},
pmid = {41651126},
issn = {1998-3646},
abstract = {PURPOSE: The interplay between the local microbiome and inflammatory environment is crucial in modulating the immune response. This research addresses the paucity of studies in the Indian context by mapping the cervical microbiome and associated inflammatory milieu in 43 apparently healthy women and evaluating its perturbations with various asymptomatic vaginal infections.

METHODS: Cervical microbiome was mapped for forty three participants, aged 18-45, who were enrolled from a community clinic as a part of longitudinal contraceptive study from October 2021 to September 2023. Sociodemographic data, clinical history, and cervical and cervicovaginal lavage specimens were collected. Microbiome analysis involved nanopore sequencing of the entire 16S rRNA region amplicon, while cytokine assessment in cervicovaginal lavage specimens utilized multiplex immunoassays.

RESULTS: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Fusobacteria appeared as dominant phyla with 32.55% having asymptomatic bacterial vaginosis (BV),16.27% asymptomatic Candida, and 13.95% coinfections. The cervical microbiome was dominated by Lactobacillus iners (45.69%), followed by Lactobacillus helveticus (6.53%) and Lactobacillus reuteri (5.86%). Women with BV exhibited an increased abundance of Prevotella and Streptococcus, while Candida infections were associated with elevated Atopobium and Collinsella species. Pro-inflammatory cytokines (IL-1β, IL-6, TNF-α, IL-8) showed variable levels, with Lactobacillus positively correlating with the regulatory cytokine TNF-α in in Candida infections. In BV Lactobacillus species such as L. agilus, L.iners and L. salivarius showed positive correlation with TNF-α. Additionally, Lactobacillus manihotivoranswas negatively associated with IL-1β, while Lactobacillus brevis and Lactobacilluszeae showed negative correlations with IL-8 .

CONCLUSION: This study maps the cervical microbiome and cytokine profile of healthy Indian women and demonstrates that asymptomatic bacterial vaginosis and Candida infections induces variations, highlighting the complex host-microbe interactions that govern vaginal health.},
}

@article {pmid41651116,
year = {2026},
author = {Graber, LC and Moreau, CS},
title = {Insect-microbiome interactions in a changing world.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101495},
doi = {10.1016/j.cois.2026.101495},
pmid = {41651116},
issn = {2214-5753},
abstract = {Humans have greatly altered the Earth and its environments through activities such as agriculture, industry, and urbanization. In recent years, the impact of anthropogenic global change on insect populations has become a topic of increased interest, with much written for both scientists and the public on how insect populations are in decline due to climate change, land use change, and exposure to chemical pollution. Additionally, many insects host microbial symbionts, which some insect species rely on for a wide range of physiological needs such as nutrient acquisition, detoxifying diet substrate, or reproduction. This review summarizes recent experimental and observational studies on the effects of anthropogenic global change on insect microbial symbioses from multiple ecosystems and continents, with a focus on the impacts of climate change and habitat loss and degradation. Each of these modes of change has been demonstrated to affect the composition of insect microbial communities, with reduction of species diversity within microbial communities (alpha diversity) as the most common result. Results of experimental study on heat stress response in bacterial symbionts suggest that warming temperatures often associated with climate change may have direct impacts on symbiont mortality, as symbionts tend to be more sensitive to thermal stress than free-living bacteria. Habitat loss and degradation impact insect microbial symbionts via the changed microbiomes of host food and environmental substrate. Chemical pollution associated with habitat degradation has altered the microbiomes of insects, though some insects may be able to detoxify chemical pollutants with symbiotic microbial taxa. While early research has shown that human-induced climate change can have negative impacts on insect symbionts, there is still much to learn about how the changing world will impact insect microbiomes and how this in turn will impact entire ecosystems at a global scale.},
}

@article {pmid41615476,
year = {2026},
author = {Long, J and Liao, X and Han, K and Chen, J and Tang, Z and Wang, W and Wang, X and Chi, Q and Zhang, X and Zhang, H},
title = {Microbiota-gut-brain axis and neuroendocrine pathways underlie divergent mechanisms of intermittent and continuous theta-burst stimulation in autism spectrum disorder.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {98},
pmid = {41615476},
issn = {1420-9071},
support = {CDPF2023KF00001//China Disabled Persons' Federation/ ; },
abstract = {OBJECTIVE: Theta-burst stimulation, including intermittent (iTBS) and continuous (cTBS) protocols, is a promising neuromodulatory intervention for autism spectrum disorder (ASD). This study aims to elucidate the therapeutic mechanisms of iTBS and cTBS for ASD.

METHODS: Prenatal valproic acid-induced ASD rats were established and were randomized into VPA, VPA + iTBS, and VPA + cTBS groups, with a saline group as control. Core and comorbid ASD behaviors in rats were assessed. Multi-omics analyses included 16 S rRNA sequencing of cecal contents, non-targeted fecal metabolomics, and prefrontal cortex transcriptomics. Key pathways were validated via Western blot, ELISA, and immunofluorescence. Integrative analyses correlated multi-omics data with neuroendocrine findings.

RESULTS: Behavioral assessments demonstrated that both iTBS and cTBS significantly ameliorated social deficits and repetitive behaviors in VPA-exposed rats. However, protocol-specific effects on comorbidities were observed: cTBS, but not iTBS, effectively alleviated anxiety-like behaviors, whereas iTBS, but not cTBS, significantly improved learning and memory. The multi-omics approach demonstrated that iTBS primarily modulated inflammatory immune responses and energy metabolism, while cTBS predominantly regulated oxidative stress, lipid metabolism, and nucleotide metabolism. Both interventions suppressed the hyperactivated PI3K/AKT/mTOR signaling pathway, an effect potentially linked to the normalization of hypothalamic-pituitary axis function. Furthermore, we identified a potential interplay between the GH/IGF-1 axis and the gut microbiome in ASD, which was differentially modulated by iTBS and cTBS.

CONCLUSION: iTBS modulated inflammatory-immune responses and energy metabolism, while cTBS regulated oxidative stress, lipid metabolism, and nucleotide metabolism. The inhibition of the central GH/PI3K/AKT/mTOR pathway by both protocols may involve their specific regulation of distinct gut microbiota communities.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06096-2.},
}

@article {pmid41652781,
year = {2023},
author = {Wang, L and Fang, H and Xue, Z and De, J and Guo, X},
title = {Agrochemical exposure-induced seed microbiome response in barley.},
journal = {Crop health},
volume = {1},
number = {1},
pages = {16},
pmid = {41652781},
issn = {2948-1945},
support = {2021YFE0113700//Key Technologies Research and Development Program/ ; },
abstract = {The seed microbiota has great potential for enhancing agricultural practices and promoting sustainable plant growth. However, excessive and improper application of agrochemicals may have unforeseen effects on the seed microbiota, posing potential risks to crop health and even ecological integrity. Despite this, the impact of agrochemicals on seed microbiota in domesticated crops remains largely unexplored. Here, we aimed to analyze the effects of four common agrochemicals on the seed microbiome of highland barley in Tibet using high-throughput sequencing. Community diversity analysis suggests that the differences in seed microbial groups under different agrochemical treatments are not significant. Interestingly, we found that the key microbial taxa in barley seeds responded distinctly to specific agrochemicals. Lactobacillus spp. were identified as positive biomarkers in response to tebuconazole and lambda-cyhalothrin due to an increase in relative abundance as a probiotic. Conversely, Leuconostoc and Helicobacter were recognized as positive biomarkers upon exposure to pydiflumetofen, attributed to a notable reduction in the abundance of pathogens. Collectively, our findings have revealed the unique responsiveness of seed microbial taxa to agrochemical exposure. Further mechanistic insights into the responsiveness of these microbial biomarkers to agrochemicals may establish a foundational framework for microbiome-targeted verification of agrochemical application, ensuring food safety throughout the cultivation of Tibetan barley.},
}

@article {pmid41651111,
year = {2026},
author = {Fujii, T and Harada, N and Katami, H and Tanaka, A and Shimono, R},
title = {Oral Antibiotic Exposure and the Risk of Overweight and Obesity in Children with Vesicoureteral Reflux.},
journal = {Journal of pediatric surgery},
volume = {},
number = {},
pages = {163003},
doi = {10.1016/j.jpedsurg.2026.163003},
pmid = {41651111},
issn = {1531-5037},
abstract = {BACKGROUND: Continuous antibiotic prophylaxis (CAP) is widely used in children with vesicoureteral reflux (VUR) to prevent recurrent urinary tract infections, but its long-term metabolic effects are uncertain. We evaluated whether oral antibiotic exposure is associated with overweight and obesity in young children with VUR.

METHODS: Using the TriNetX Research Network, we conducted a retrospective cohort study of children aged <5 years diagnosed with VUR between 2005 and 2025. Patients were classified as antibiotic-exposed or unexposed based on prescription patterns, and propensity score matching balanced baseline covariates. Overweight and obesity were defined using body mass index (BMI) percentiles and diagnosis codes. We performed U.S.-only sensitivity and age-stratified analyses (<1 year; 1-4 years) and calculated the number needed to harm (NNH).

RESULTS: After matching, 2,665 patients were included per group. In the primary cohort aged <5 years, BMI percentile-defined overweight and obesity occurred in 60 (2.3%) of antibiotic-exposed patients and 21 (0.8%) of unexposed patients (hazard ratio [HR], 3.25; 95% confidence interval [CI], 1.97-5.34; log-rank p < 0.001). Results were similar using diagnosis code-based definitions (1.3% vs. 0.6%; HR, 2.30; 95% CI, 1.27-4.17; log-rank p = 0.005). Associations persisted in U.S.-only analyses and were stronger in children aged <1 year. The NNH for BMI-defined overweight/obesity was 69.

CONCLUSIONS: Early oral antibiotic exposure in children with VUR was significantly associated with increased risk of overweight and obesity. However, given the low absolute number of events, these findings should be interpreted cautiously and weighed against the potential benefits of CAP.},
}

@article {pmid41651105,
year = {2026},
author = {Muro, BBD and Carnevale, RF and Monteiro, MS and Leal, DF and Poor, AP and Pereira, FA and de Azevedo Ruiz, VL and Garbossa, CAP},
title = {Soluble and insoluble fiber blend improves farrowing performance and colostral immunoglobulin concentration in sows without altering fecal microbiota.},
journal = {Veterinary journal (London, England : 1997)},
volume = {316},
number = {},
pages = {106574},
doi = {10.1016/j.tvjl.2026.106574},
pmid = {41651105},
issn = {1532-2971},
abstract = {The aim of this trial was to provide a fibrous supplement in the transition diet of sows to decrease sows' constipation, improve farrowing kinetics, increase colostrum antibodies, and modulate sows' and piglets' microbiota. At day 90 of pregnancy sows were fed a standard gestation diet until farrowing (CON, n = 101) or a standard gestation diet added of 400 g of a fibrous supplement (40 % wheat bran, 25 % lignocellulose, 25 % citrus pulp, and 10 % guar gum) (FIB, n = 101). After farrowing, sows were fed a standard lactation diet, and FIB sows were fed 400 g of the fibrous supplement on top of the feed for five days. Sows from FIB had a lower (p < 0.01) incidence of constipation pre-farrowing and on the day of farrowing. Sows from FIB had a 23 min shorter (p = 0.01) farrowing duration compared to CON-sows. Sows from CON had a higher (p < 0.01) feed intake on days two and three post-farrowing. Both IgG and IgA concentrations were higher in the FIB-supplemented sows (p = 0.01). The fecal microbiome of sows and piglets was similar (p > 0.43) between groups. During the first week of life, piglets born from FIB-sows had decreased (p = 0.04) diarrhea incidence. In conclusion, the benefits of the fibrous supplement were evident in peripartal sows by decreasing farrowing duration and constipation and by increasing the concentration of immunoglobulins in the colostrum. For newborn piglets, the fibrous supplement fed to the sows did not significantly alter the fecal microbiome of sows and their litters. Nevertheless, benefits were observed in their resistance to neonatal diarrhea. Thus, using a fiber supplement in transition diets in farms may ease the management in the farrowing room and improve early-life robustness in piglets, which may decrease medication demands during the first week, contributing to more efficient neonatal care and better overall litter performance.},
}

@article {pmid41650974,
year = {2026},
author = {Ghaddar, B and Blaser, MJ and De, S},
title = {Reliable detection of Host-Microbe Signatures in cancer using PRISM.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2026.01.007},
pmid = {41650974},
issn = {1878-3686},
abstract = {Recent controversy in the cancer microbiome field highlights the need for more reliable microbial detection from human genomic data. Here, we develop PRISM, an efficient computational framework for precise microorganism identification and decontamination from low-biomass sequencing data. PRISM achieves robust performance when benchmarked on 230 independent datasets with known true-positive and contaminant taxa. We then use PRISM to profile 25 cancer types from The Cancer Genome Atlas and Clinical Proteomic Tumor Analysis Consortium. We identify consistent microbial signatures in gastrointestinal tract, head-and-neck, and urogenital tract tumors, and sparse signal elsewhere. In pancreatic cancer, we associate microbial detection with altered host protein glycosylation pathways and greater smoking exposure. Lastly, we consider the impact of sequencing approaches on positive and negative data interpretation. Overall, PRISM improves the reliability of microbial profiling and allows leveraging of existing human genomic data for the concurrent detection of host-microbial signatures with potential molecular and clinical significance.},
}

@article {pmid41650849,
year = {2026},
author = {Seto-Tetsuo, F and Katase, N and Sasaki, Y and Yukitake, H and Naito, M},
title = {Supernatants from DNase-deficient Prevotella intermedia strains enhance oral squamous cell carcinoma cell migration and invasion by activating inflammatory and epithelial-mesenchymal transition pathways.},
journal = {Biochemical and biophysical research communications},
volume = {805},
number = {},
pages = {153304},
doi = {10.1016/j.bbrc.2026.153304},
pmid = {41650849},
issn = {1090-2104},
abstract = {INTRODUCTIONS: Oral squamous cell carcinoma (OSCC) has been increasingly associated with dysbiosis of the oral microbiome. Among oral pathogens, Prevotella intermedia (P. intermedia) is frequently enriched in patients with OSCC; however, the role of its virulence factors-particularly its deoxyribonuclease (DNase) activity-remains poorly understood.

METHODS: We compared the effects of culture supernatants from wild-type P. intermedia OMA14 and DNase-deficient mutant strains (nucA, nucD and nucA nucD) on the migration and invasion of the OSCC cell line SAS, using wound healing and Matrigel invasion assays. Transcriptomic profiling of SAS cells exposed to bacterial supernatants was performed using RNA sequencing (RNA-seq), followed by differential gene expression and pathway enrichment analyses.

RESULTS: Supernatants from the nucA nucD mutant strain significantly enhanced SAS cells migration and invasion compared with those from the OMA14 strain. RNA-seq revealed marked transcriptomic reprogramming, including upregulation of genes related to extracellular matrix degradation, epithelial-mesenchymal transition (EMT), and inflammatory signaling. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses confirmed the enrichment of EMT, cytokine signaling, and tumor-promoting pathways.

CONCLUSIONS: Our findings demonstrate a dual role of bacterial DNase activity in SAS cell. Although DNases contribute to immune evasion via neutrophil extracellular trap degradation, their absence enhances tumor invasion by promoting proinflammatory and EMT-related transcriptional programs. These results highlight the complex interplay between microbial nucleases, extracellular DNA, and host signaling, providing novel insights into the contribution of the oral microbiome to OSCC pathogenesis.},
}

@article {pmid41650638,
year = {2026},
author = {Caputi, V},
title = {Functional role of the enteric nervous system in poultry intestinal health and production.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106563},
doi = {10.1016/j.psj.2026.106563},
pmid = {41650638},
issn = {1525-3171},
abstract = {Like mammals, the avian intestinal epithelium is innervated by three neuronal pathways: vagal and sympathetic terminals, which originate from ganglia outside the gut wall and send information to the brain to modulate visceral sensitivity, appetite, and gut homeostasis; and the enteric nervous system (ENS), a complex network embedded within the gut wall that functions independently from the brain. The ENS coordinates essential GI physiological functions, such as intestinal motility, peristalsis, digestion, and absorption of nutrients and water. Recent studies conducted in mammals have shown that enteric neurons can orchestrate the intestinal immune response and reduce Salmonella colonization in the GI tract. However, such neuronal-mediates defense mechanisms have not yet been explored in the poultry gut. This review will provide a comprehensive overview of the avian ENS, highlighting similarities and differences with the well-known mammalian ENS. Additionally, particular focus will be given on ENS-dependent neuroimmune interactions that could reveal novel biomolecular mechanisms to mediate health, disease susceptibility, behavior, and other aspects as affected by the chicken GI tract.},
}

@article {pmid41650276,
year = {2026},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb6265},
pmid = {41650276},
issn = {2375-2548},
mesh = {*Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology ; Animals ; Humans ; Metagenome ; Phylogeny ; Genome, Viral ; Bacteroides/virology ; },
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

*Gastrointestinal Microbiome
*Bacteriophages/genetics/physiology
Animals
Humans
Metagenome
Phylogeny
Genome, Viral
Bacteroides/virology

@article {pmid41650184,
year = {2026},
author = {Hamidabad, NM and Manzato, M and Toya, T and Lerman, LO and Lerman, A},
title = {Gut microbiome compositional clusters in association with cardiovascular risk: An observational cohort study.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0341111},
pmid = {41650184},
issn = {1932-6203},
mesh = {Humans ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Aged ; Prospective Studies ; *Cardiovascular Diseases/microbiology/epidemiology ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Cluster Analysis ; },
abstract = {AIMS: The gut microbiome (GM) is increasingly recognized for its role in atherosclerosis development. However, its potential as a biomarker for risk-stratification in patients with atherosclerotic cardiovascular (CV) comorbidities remains under-explored. This study aimed to identify distinct GM clusters associated with elevated CV risk.

METHODS: In this prospective observational cohort, patients with coronary artery disease, hypertension, hyperlipidemia, or diabetes mellitus referring to Mayo Clinic from 2013 to 2018 were enrolled. Bacterial DNA was analyzed in the V3-V5 region of 16S rDNA. Beta-diversity was plotted using Principal Coordinates Analysis. Unsupervised hierarchical clustering of the GM classified participants into two clusters. Cox regression evaluated the association between clusters and Major Adverse Cardiac Events (MACE), defined as a composite of cardiac events, heart failure, and all-cause mortality. Permutational Multivariate Analysis of Variance identified clinical factors contributing to cluster assignment. Linear Discriminant analysis identified GM taxa with differential abundance among clusters and their effect sizes.

RESULTS: Among 211 participants (median age 60 [IQR: 50-70] years; 57.3% male), two distinct GM profiles emerged (Cluster H: N = 104; Cluster L: N = 107, P < 0.001). Cluster L participants were younger (P < 0.001), more likely female (P = 0.009), and had healthier CV profiles, including lower BMI (P = 0.007), hypertension (P = 0.010), hyperlipidemia (P = 0.005), and lower coronary artery disease prevalence (P = 0.003). Over a median follow-up of 7.4 years, Cluster L had a significantly lower incidence of MACE compared to Cluster H (HR = 0.48, 95% CI: 0.26-0.91, P = 0.024). Cluster L had higher operational taxonomic units (P < 0.001) and lower Bacillota-to-Bacteroidetes ratio (P < 0.001) compared to Cluster H. The predominant taxa in Cluster L included Bacteroides, Alistipes, and Parabacteroides, whereas Blautia, Agathobacter, and Clostridium sensu stricto-1 were more abundant in Cluster H.

CONCLUSION: Distinct GM profiles are associated with varying CV risk, highlighting the potential of unsupervised GM profiling as a novel tool for risk stratification and individualized therapy.},
}

Humans
Female
Male
Middle Aged
*Gastrointestinal Microbiome/genetics
Aged
Prospective Studies
*Cardiovascular Diseases/microbiology/epidemiology
RNA, Ribosomal, 16S/genetics
Risk Factors
Cluster Analysis

@article {pmid41649942,
year = {2026},
author = {Haines, RR and Basuki, A and Tenaglia, VP and Zar, HJ and Nicol, MP and Kar Bahal, R},
title = {Corynebacterium drakensteinense sp. nov., isolated from the nasopharynx of a healthy South African infant.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {2},
pages = {},
pmid = {41649942},
issn = {1466-5034},
mesh = {*Corynebacterium/classification/isolation & purification/genetics ; *Nasopharynx/microbiology ; Humans ; *Phylogeny ; South Africa ; RNA, Ribosomal, 16S/genetics ; Infant ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Genome, Bacterial ; Whole Genome Sequencing ; Sequence Analysis, DNA ; Base Composition ; Nucleic Acid Hybridization ; },
abstract = {Emerging evidence supports the role of the nasopharyngeal microbiome in respiratory health, including association with conditions such as asthma and respiratory tract infections. One dominant commensal genus is Corynebacterium, members of which are commonly present in the nasopharynx of infants. These commensal Corynebacterium spp. have been reported to correlate with respiratory health. In this paper, we present isolate MNWGS58[T] isolated from the nasopharynx of a South African infant. Genomic analysis of the whole-genome sequence of MNWGS58[T] revealed that it is phylogenetically closely related to other Corynebacterium spp. found in the nasopharynx, Corynebacterium propinquum [85% average nucleotide identity (ANI)] and Corynebacterium pseudodiphtheriticum (84% ANI). Bacterial identification using matrix-assisted laser desorption/ionization time-of-flight MS identified MNWGS58[T] as C. pseudodiphtheriticum. The API Coryne assay identified the novel isolate as C. propinquum, and the VITEK 2 ANC assay identified the novel isolate as Corynebacterium otitidis. Both genomic analyses and phenotypic analyses show striking similarities to C. propinquum and C. pseudodiphtheriticum. The cell wall is consistent with closely related Corynebacterium spp., albeit with a higher C17:0 content. The genome is 2.48Mbp with a G+C content of 56.9 mol%. Digital DNA-DNA hybridization values for MNWGS58[T] were low when compared to C. pseudodiphtheriticum MNWGS56 and C. propinquum MNWGS51 (27.4 and 28.4%, respectively). Although there are phenotypic similarities, 85% ANI with the closest Corynebacterium spp. strongly supports the classification of a novel species of Corynebacterium, for which we propose the name Corynebacterium drakensteinense sp. nov., with the type strain MNWGS58[T] (=TSD-445[T]=NCTC 15058[T]). It will be important to elucidate the role of this novel species of Corynebacterium in the human nasopharynx and identify additional niches for this species in future studies.},
}

*Corynebacterium/classification/isolation & purification/genetics
*Nasopharynx/microbiology
Humans
*Phylogeny
South Africa
RNA, Ribosomal, 16S/genetics
Infant
DNA, Bacterial/genetics
Bacterial Typing Techniques
Genome, Bacterial
Whole Genome Sequencing
Sequence Analysis, DNA
Base Composition
Nucleic Acid Hybridization

@article {pmid41649710,
year = {2025},
author = {Cheng, R and Ke, T and Gui, F and Li, J and Zhang, X and Vílchez, JI and Matsumoto, H},
title = {drSMALL: Database for disease resistance-shaping small molecules derived from the plant microbiome.},
journal = {Crop health},
volume = {3},
number = {1},
pages = {2},
pmid = {41649710},
issn = {2948-1945},
support = {32122074//National Natural Science Foundation of China/ ; 32302291//National Natural Science Foundation of China/ ; U21A20219//National Natural Science Foundation of China/ ; 2024SZRZDC130001//Natural Science Foundation of Hangzhou/ ; 2023YFD1400901//National Key R&D Program of China/ ; 226-2024-00070//the Fundamental Research Funds for the Central Universities/ ; 2020ZL008//Strategic Research on 'Plant Microbiome and Agroecosystem Health'(Cao Guangbiao High Science and Technology Foundation)/ ; },
abstract = {Recent evidence highlights the potential of the plant microbiota to increase host plant disease resistance through the production of bioactive small molecules. However, the absence of comprehensive platforms for rapid access to this information hampers progress in the field. To address this gap, we developed the Disease Resistance-Shaping Small Molecules Database (drSMALL), a freely accessible and continuously updated resource that compiles profiles of microbial small molecules, which were experimentally evidenced to be associated with host disease resistance. drSMALL interlinks detailed information on microbial species, the small molecules they produce, host plants, and targeted pathogens, facilitating streamlined access to essential data. This initiative aims to advance the understanding of small molecules in disease resistance, filling a critical gap in data accessibility while fostering deeper exploration of sustainable agricultural practices. By leveraging the natural capabilities of plant microbiomes, drSMALL seeks to support innovative strategies for enhancing crop health and resilience against diseases.},
}

@article {pmid41649672,
year = {2025},
author = {Wang, Z and Yin, J and Tsuda, K},
title = {Harnessing Aspergillus and host M genes for sustainable phyllosphere microbiome engineering.},
journal = {Crop health},
volume = {3},
number = {1},
pages = {6},
pmid = {41649672},
issn = {2948-1945},
support = {2022YFA1304400//National Key R&D Program of China/ ; 32250710139//National Natural Science Foundation of China/ ; 32170298//National Natural Science Foundation of China/ ; GZC20230915//Postdoctoral Fellowship Program of CPSF/ ; 590323043//Hubei postdoctoral fund project/ ; },
}

@article {pmid41649661,
year = {2025},
author = {Romão, IR and do Carmo Gomes, J and Silva, D and Vilchez, JI},
title = {The seed microbiota from an application perspective: an underexplored frontier in plant-microbe interactions.},
journal = {Crop health},
volume = {3},
number = {1},
pages = {12},
pmid = {41649661},
issn = {2948-1945},
support = {UIDB/04551/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04551/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0087/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Seed-associated microbiota represent a critical yet underexplored frontier in plant-microbe interactions, offering unique insights into plant health, resilience, and development. Unlike the soil or rhizosphere microbiome, the seed microbiota is closely tied to plant reproduction, facilitating both vertical and horizontal transmission of microbes. These microbial communities influence key plant processes, including germination, stress tolerance, nutrient acquisition, and pathogen resistance, providing plants with a pre-assembled microbial consortium tailored to their needs. Despite recent advances, significant gaps remain in understanding how seed-associated microbes are acquired, their ecological dynamics, and their functional roles. High-throughput sequencing, metagenomics, and spatial imaging techniques have revealed the diversity and complexity of the seed microbiota, emphasizing their potential for agricultural innovation. This research highlights the importance of these communities in shaping plant resilience and productivity, yet questions about their ecological and evolutionary significance persist. The present review synthesizes current knowledge on the composition, inheritance mechanisms, and functional roles of the seed microbiota. It also explores strategies to harness these microbes for sustainable agriculture, including microbiome engineering and breeding for microbial compatibility. By addressing these gaps, seed microbiota research could revolutionize sustainable agriculture, enhancing crop resilience and reducing reliance on chemical inputs.},
}

@article {pmid41519703,
year = {2026},
author = {Lin, J and Ling, Z and Fan, W and Cai, Q and Yang, J and Tao, M and Guo, H and Wang, Y and Yan, X and Yang, C},
title = {Establishment of a microbial abundance prognostic model for colorectal cancer.},
journal = {BMC cancer},
volume = {26},
number = {1},
pages = {197},
pmid = {41519703},
issn = {1471-2407},
support = {(No. 2024M762749)//China Postdoctoral Science Foundation/ ; (No. SBK2023022610)//Natural Science Foundation of Jiangsu Province/ ; (No. MS2024140)//program of Jiangsu Traditional Chinese Medicine Science and Technology Development/ ; (No. 2023-2-01, 2024-2-08 and 2025-2-08)//Yangzhou City Basic Research Program (Joint Special Project) - Health and Wellness Category/ ; (No.81902422 82303937)//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Previous studies have demonstrated a close association between gut microbiota and the onset and progression of colorectal cancer (CRC). However, the prognostic and therapeutic value of microbiota in CRC remains controversial. This study integrates multiomics approaches to investigate the prognostic and therapeutic implications of microbiota in CRC.

METHODS: A CRC microbial abundance prognostic model (MAPM) was constructed utilizing bioinformatics approaches to evaluate its prognostic value. The relationship between MAPM and the clinical characteristics of CRC, as well as the immune microenvironment, was analyzed. Furthermore, key prognostic genes associated with the MAPM were identified and validated in vitro and in vivo assays.

RESULTS: The MAPM comprised 12 microbes and effectively stratified the prognosis of CRC patients. The risk score of this model exhibits a close association with the immune infiltration of CRC. Remarkably, HSF4, identified as a key gene from the MAPM, is found to be overexpressed in the tumor tissues, and its high expression independently predicts poor prognosis in CRC patients. Knockdown of HSF4 significantly inhibits the proliferation, colony formation, migration, and invasion of CRC cells in vitro, as well as the growth of xenografts in nude mice.

CONCLUSION: A MAPM is established to predict the prognosis of CRC patients, further highlighting the potential of detecting the microbiome in clinical practice. Moreover, HSF4, as a prognostic gene from the MAPM, is a promising drug target for CRC treatment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12885-025-15524-8.},
}

@article {pmid41501621,
year = {2026},
author = {Ferriol-González, C and Hernanz-Grimalt, A and Valdivia, C and García-Cobos, S and Heredia, A and García-Hernández, J and Andrés, A and Domingo-Calap, P},
title = {Effects of phage-based treatments against an OXA-48-producing Klebsiella pneumoniae isolate in simulated human gut microbiomes.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {102},
pmid = {41501621},
issn = {1471-2180},
support = {UV-INV_PREDOC-1913324//Universitat de València/ ; PREP2023-001677//Ministerio de Ciencia, Innovación y Universidades/ ; PID2023-150309OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CIACIF/2023/126//Generalitat Valenciana/ ; },
abstract = {BACKGROUND: Carbapenem-resistant K. pneumoniae (CRKP) is one of the most prevalent antimicrobial-resistant pathogens, primarily causing nosocomial infections. These bacteria often colonize the gut microbiota, and their carriage is an important risk factor for later infection. Phages are an emerging alternative against antimicrobial-resistant bacteria causing infections, but their effect on the microbiota is still poorly understood.

RESULTS: Here, we simulated the colonization of the gut microbiota of three healthy adults by an OXA-48-producing CRKP isolate in a dynamic in vitro colonic simulator (SHIME®) and evaluated the effect of phage treatments in reducing CRKP load. Phage growth dynamics in the system seemed to be dependent on phage host range, rather than the donor’s microbiota composition. Additionally, phage treatment significantly reduced K. pneumoniae load and blaOXA-48 copy number, highlighting its potential for controlling the CRKP population. Importantly, phage treatment did not affect the microbiota diversity of any of the three donors, suggesting it has a minimal impact on the microbiome.

CONCLUSIONS: Our results support the potential of phage-based strategies for the biocontrol of CRKP in the gut microbiota, reducing the abundance of this pathogen in its main reservoirs and preventing nosocomial CRKP infections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04653-6.},
}

@article {pmid41649413,
year = {2026},
author = {Jo, S and Lee, HG and Nam, DH and Park, C},
title = {Use of metabarcoding detects the rapid onset of cultivation bias in the culture-based profiling of marine sediment bacterial communities.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovag020},
pmid = {41649413},
issn = {1472-765X},
abstract = {When cultivation-based microbiology is used to isolate strains from environmental samples, the cultured populations may not represent ecologically relevant taxa in the source community. To address this, we employed pre-cultivation metabarcoding to establish a baseline community profile and detect cultivation bias. Using time-resolved cultivation of marine sediment bacteria, we demonstrated the need for initial community characterization. Sediment-derived microbiomes were cultured in Marine Broth 2216 and analyzed using 16S rRNA gene metabarcoding at 0, 6, 12, 18, and 24 h. A rapid 10-fold reduction in alpha diversity was observed within the 6 h (from 1029 amplicon sequence variants to 34-106), with the genus Vibrio reaching near-complete dominance (>95%) from 18 to 24 h, while environmentally dominant taxa such as Acinetobacter were quickly excluded. This dramatic shift illustrates that, without baseline characterization, cultivation-induced artifacts cannot be clearly distinguished from ecologically meaningful patterns. Fast-growing generalists can quickly outcompete ecologically significant taxa, distorting isolation outcomes and hindering the recovery of functionally important microorganisms. We show that metabarcoding at 0 h can identify cultivation biases, help interpret isolation results, and suggest targeted strategies for recovering ecologically relevant taxa. This integrated approach facilitates more accurate recovery and analysis of functionally significant microbial diversity.},
}

@article {pmid41649278,
year = {2026},
author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA},
title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117325},
doi = {10.1128/msystems.01173-25},
pmid = {41649278},
issn = {2379-5077},
abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.

IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.},
}

@article {pmid41649265,
year = {2026},
author = {Gu, C and Han, M and Chen, X and Liu, Y and Jian, G and Qin, Q and Yin, H and Zhou, L and Cai, D and Zhang, L and Wang, D and Li, P},
title = {Gut microbiota and metabolomic changes across preterm stages: potential associations with bronchopulmonary dysplasia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0274025},
doi = {10.1128/spectrum.02740-25},
pmid = {41649265},
issn = {2165-0497},
abstract = {UNLABELLED: The coordinated post-natal development of the gut microbiome and metabolome is essential for preterm infant health, yet its disruption is increasingly linked to adverse outcomes such as bronchopulmonary dysplasia (BPD). In this study, we performed an integrated multiomics analysis of fecal samples collected from preterm infants to characterize temporal changes in gut microbial and metabolic profiles and explore their potential associations with BPD development. This study observed a distinct trajectory of the phylum Bacteroidota as a hallmark of normal gut maturation, with its abundance progressively declining across non-BPD infants. In contrast, infants who later developed BPD exhibited early depletion followed by irregular enrichment of Bacteroidota. Correlation analysis revealed that Streptococcus abundance was positively associated with elevated cysteic acid, a metabolite linked to oxidative stress. Together, these findings suggest that altered Bacteroidota succession and Streptococcus-associated oxidative imbalance may reflect early microbial-metabolic perturbations in infants at risk of BPD. This work provides preliminary, hypothesis-generating insights into gut-associated signatures potentially relevant to BPD pathogenesis.

IMPORTANCE: Bronchopulmonary dysplasia (BPD) remains a leading cause of morbidity in preterm infants, yet early biomarkers and targeted preventive strategies are limited. By integrating microbiome and metabolome data from a pilot cohort, this study identified patterns of disrupted Bacteroidota succession and Streptococcus-associated oxidative stress that are associated with BPD risk. These findings highlight the gut as a potential extrapulmonary contributor to disease susceptibility and support early risk assessment and guide future microbiome-targeted interventions in preterm infants.},
}

@article {pmid41648806,
year = {2026},
author = {Lebeuf-Taylor, E and Cottenie, K},
title = {Marginal link between sociality and gut microbiome in disparate mammalian hosts.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag004},
pmid = {41648806},
issn = {2633-6685},
abstract = {Studies in model organisms and wild populations have uncovered manifold links between the gut microbiome and sociality, which, considering the adaptiveness of social behaviour, suggest a potentially generalized coevolution between microbiomes and social behaviour. Here, we leverage phylogenetically and ecologically diverse data from the Earth Microbiome Project to test the generality of the links between sociality and the gut microbiome in wild animals. We find evidence of a small but significant link between sociality and microbiome beta diversity, but not alpha diversity, in mammalian taxa, potentially due to socially mediated microbial transmission. Our work highlights the value of leveraging large-scale multi-study datasets to test fundamental questions about the role of sociality in host-microbiome coevolution.},
}

@article {pmid41648774,
year = {2025},
author = {Freidl, J and Huber, D and Bischof, M and Zechner, R and Pichler, C and Fickel, L and Fischer, V and Weingartner, H and Hausmann, B and Pjevac, P and Kiefel, M and Prinz, T and Gruber, G and Hartl, A},
title = {From urban to alpine: environmental microbial transfer in urban adults - the ALM Study.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1747693},
pmid = {41648774},
issn = {2296-2565},
mesh = {Humans ; Adult ; Male ; Female ; Prospective Studies ; *Microbiota ; Austria ; Feasibility Studies ; *Urban Population/statistics & numerical data ; *Agriculture ; },
abstract = {BACKGROUND: Urbanization is linked to reduced microbial exposure, increased prevalence of lifestyle-related diseases, and diminished psychological resilience. In contrast, traditional alpine farming environments offer high biodiversity and low pollution, potentially promoting restorative health effects. The ALM Study (ALpine Farming and Human Nasal Microbiome Diversity) explored the feasibility and physiological impact of a 7-day immersion in such an environment among previously unexposed ("Alm-naive") individuals.

METHODS: This prospective, single-arm feasibility study was conducted in the Riedingtal Valley, Austria. Twenty-two healthy adults (median age: 30.5 years), with no prior agricultural exposure, participated in a 7-day immersive intervention involving daily alpine farming activities. Biological (nasal swabs, venous blood), physiological (VO₂max), and psychological (WHO-5 psychological wellbeing index, EQ-5D VAS, NR-6) data were collected immediately before and after the intervention. The primary outcome was the change in nasal microbiome diversity (16S rRNA gene amplicon sequencing); secondary outcomes included hematological markers, lipid metabolism, inflammatory parameters, and wellbeing scores. Pre-post changes were analyzed using Wilcoxon signed-rank tests.

RESULTS: Nasal microbiome analysis revealed significant increases in species richness and evenness (p < 0.001). In addition, descriptive analyses indicated changes in relative phylum-level composition, with reduced Proteobacteria dominance and variable increases in Firmicutes and Actinobacteriota. Hematocrit (+3.1%, p = 0.01), reticulocyte count (+0.39%, p < 0.001), and platelet count (+27 G/L, p = 0.02) increased significantly, suggesting erythropoietic and immunological activation. Additionally, activation of the immune system became evident, as reflected by a slight but significant rise in CRP (+0.04 mg/dL, p = 0.01), in the absence of concurrent changes in IL-6 or leukocyte counts. Total cholesterol (-8.08 mg/dL, p = 0.02) and non-HDL cholesterol (-2.00 mg/dL, p = 0.01) decreased, VO₂max showed a positive trend (+3.43 mL· kg[-1]·min[-1], p = 0.07). WHO-5 psychological wellbeing scores improved markedly (+12%, p < 0.001), while other psychometric scales remained unchanged.

CONCLUSION: A 1-week immersion in a biodiverse alpine environment was associated with measurable changes in the nasal microbiome, hematological and metabolic profiles, and psychological wellbeing. These findings support both the feasibility and the potential health relevance of short-term, nature-based interventions for urban populations.},
}

Humans
Adult
Male
Female
Prospective Studies
*Microbiota
Austria
Feasibility Studies
*Urban Population/statistics & numerical data
*Agriculture

@article {pmid41648756,
year = {2025},
author = {Grønbæk, IMB and Halkjær, SI and Hansen, EH and Mollerup, S and Paulsen, SJ and Konrad, CV and Engel, S and Bulinska-Balas, M and Wellejus, A and Haaber, AB and Christensen, AH and Engsbro, AL and Petersen, AM},
title = {Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome: results from a randomised, clinical trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1701341},
pmid = {41648756},
issn = {2296-861X},
abstract = {UNLABELLED: Patients with irritable bowel syndrome experience abdominal pain and stool habit disturbances, and often also extraintestinal symptoms, such as fatigue. The disorder is linked to gut dysbiosis, and manipulation of the microbiota is considered a possible treatment strategy. This randomised, double-blinded, placebo-controlled study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (DSM 33360) (Bif195), on symptoms and gut microbiome composition in patients with diarrhoea-predominant irritable bowel syndrome. Sixty-one patients with moderate-severe disease activity were allocated to 8 weeks of treatment with either Bif195 or placebo (1:1), followed by 8 weeks of follow-up. The primary outcome was a change in symptom scores measured by the validated questionnaire, IBS-symptom severity scale. Secondary and explorative outcomes were the effects of Bif195 on intestinal symptoms, quality of life, fatigue, and the gut microbiota. Modulation of the transepithelial electrical resistance (TEER) of Caco-2 cells by Bif195 was investigated in vitro as a model of barrier integrity. The results showed no effect of Bif195 on primary or secondary outcomes; however, Bif195 lowered fatigue scores compared to placebo. Significantly increased TEER readings in vitro indicated enhanced barrier integrity, suggesting GI permeability as a mechanism for further clinical exploration.

CLINICAL TRIAL REGISTRATION: clinicaltrials.gov, identifier NCT04808271.},
}

@article {pmid41648417,
year = {2026},
author = {Arasti, S and Şapcı, AOB and Rachtman, E and El-Kebir, M and Mirarab, S},
title = {Deconvolving Phylogenetic Distance Mixtures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.18.700179},
pmid = {41648417},
issn = {2692-8205},
abstract = {Mixtures of multiple constituent organisms are sequenced in several widely used applications, including metagenomics and metabarcoding. Characterizing the elements of the sequence mixture and their abundance with respect to a reference set of known organisms has been the subject of intense research across several domains, including microbiome analyses, and methods must overcome two key challenges. First, the mixture constituents are related to each other through an evolutionary history, and hence, should not be considered independent entities. Second, sequence data is noisy, with each short read providing a limited signal. While existing approaches attempt to address these challenges, addressing both challenges simultaneously has proved challenging. For evolutionary dependencies, methods either define hierarchical clusters (e.g., taxonomies or operational taxonomic/genomic units) or use phylogenetic trees. For the second challenge, they either assemble reads into contigs, use statistical priors to summarize read placements, or attempt to analyze all reads jointly using k-mers. Despite this rich literature, a natural approach to simultaneously address both challenges has been underexplored: compute a distance from the mixture to all references, deconvolve those distances, and place the sample on multiple branches of a reference phylogeny with associated abundances. This multi-placement approach is a natural extension of the single-read phylogenetic placement used in practice. We argue that by placing the entire sample on multiple branches instead of placing reads individually, we can obtain a less noisy profile of the mixture. We formalize this approach as the phylogenetic distance deconvolution (PDD) problem, show some limits on the identifiability of PDDs, propose a slow exact algorithm, and an efficient heuristic greedy algorithm with local refinements. Benchmarking shows that these heuristics are effective and that our implementation of the PDD approach (called DecoDiPhy) can accurately deconvolve phylogenetic mixture distances while scaling quadratically. Applied to metagenomics, DecoDiPhy consolidates reads mapped to a large number of branches on a reference tree to a much smaller number of placements. The consolidated placements improve the accuracy of downstream tasks, such as sample differentiation and detection of differentially abundant taxa.},
}

@article {pmid41648390,
year = {2026},
author = {Riedmuller, KC and Dyer, JE and Ottesen, EA},
title = {Large temperature excursions have modest impacts on community composition in the high diversity gut microbiome of omnivorous American cockroaches (Periplaneta americana).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.21.700893},
pmid = {41648390},
issn = {2692-8205},
abstract = {UNLABELLED: Microbial residents of ectothermic hosts are exposed to variations in temperature that have the potential to impact their physiology and the host-microbe symbiotic relationship. In this experimental warming study, laboratory populations of American cockroaches (Periplaneta americana) were kept at a baseline low room temperature of 20-22°C or a high temperature of 30°C for two weeks. We quantified bacterial load and performed high-throughput 16S rRNA gene sequencing to assess the hindgut microbiome's response to a near 10°C shift in environmental temperature. We report modest impacts of temperature on cockroach gut microbiome composition. The high temperature treatment induced increases in the relative abundance of Proteobacteria and Euryarchaeota phyla as well as the Lactobacillaceae and Enterococcaceae families. We also observed increased interindividual variability. There were no significant differences in the dominant Bacteroidota or Firmicutes phyla and no significant losses or reductions in taxa or bacterial load, respectively. This suggests that the gut community of American cockroaches is largely resilient to prolonged increases in temperature and has implications for the cockroach to withstand the impacts of climate change.

IMPORTANCE: Insects, as with most animals, often harbor microbial symbionts that play an essential role in host health and nutrition. As insects are ectotherms, these microbial symbionts are subject to the same temperature fluctuations as their hosts, potentially impacting host temperature responses. Here, we demonstrate that the American cockroach (Periplaneta americana) gut microbiome exhibits only modest changes following an ∼10°C increase in environmental temperature. This contrasts with studies in other insects, whose microbiota were highly responsive to temperature variation. This work illustrates that the microbiota of insects may vary in their sensitivity to long-term temperature shifts, providing a more comprehensive understanding of potential variability in insect responses to climate change.},
}

@article {pmid41648363,
year = {2026},
author = {Da Silva, AC and Flantzer, L and Weinberg, J and Kyu, S and Daley-Bauer, L and Santana, AC and Talla, A and Rittgers, AL and Welbourn, S and Gordon, DE and Tomalka, JA and Marconi, VC and Jones, DP and Younes, SA},
title = {Microbiome-Derived Metabolites Shape CD4[+] T-Cell Differentiation and Immune Aging in Chronic HIV-1 Infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.13.699280},
pmid = {41648363},
issn = {2692-8205},
abstract = {The role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4[+] T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4[+] T-cell metabolic and functional states. Among these metabolites, p-cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4[+] T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4[+] T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4[+] T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4[+] T-cell metabolism and fate and promotes immune aging-associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4[+] T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo.},
}

@article {pmid41648328,
year = {2026},
author = {Baker, JL and Tang, J and Guo, M and Farias-da-Silva, FF and Barbisan, M and Burnside, M and Crofton, K and Williams, S and Rao, S and Lee, M and Drucker, SG and Higashi, D and Merritt, J and Hirose, Y and Veening, JW and Nizet, V},
title = {Monounsaturated fatty acid biosynthesis is critical for streptococcal envelope homeostasis and stress tolerance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.14.699484},
pmid = {41648328},
issn = {2692-8205},
abstract = {The genus Streptococcus contains some of the most important commensals and pathogens of the human microbiome. To obtain the fatty acids required for cell membranes, Streptococcus either produce fatty acids de novo through the fatty acid biosynthesis (fab) pathway or uptake host fatty acids through the fatty acid kinase (fak) pathway. Although both the fab and fak pathways represent potential therapeutic targets to prevent or treat infection, progress is limited because of an incomplete understanding of taxon-to-taxon variability in streptococcal lipid metabolism. Here, we examined the role of de novo monounsaturated fatty acid (MUFA) synthesis in physiology and virulence-associated traits in Streptococcus mutans, Streptococcus pyogenes, and Streptococcus pneumoniae, three major pathogens that cause disease at distinct body sites. In all three species, deletion of fabM abolished MUFA production and caused severe growth defects, decreased stress tolerance, increased antibiotic susceptibility, and defects in cell viability, morphology, and division. In S. mutans, loss of fabM also markedly reduced competence signaling and production of the mutacin IV bacteriocin. Deletion of fabM increased susceptibility to killing by human neutrophils in S. mutans and S. pneumoniae, but not S. pyogenes . Together, these findings illustrate that MUFA synthesis is broadly important for streptococcal physiology and cell membrane homeostasis, while its contribution to pathogenesis is strongly species- and context-dependent, providing leads to guide development of novel therapeutic and/or preventative strategies.},
}

@article {pmid41648281,
year = {2026},
author = {Ramachandran, SL and Pasupuleti, N and Abdill, RJ and Adikari, G and Ahlawat, B and Blekhman, R and Burgo, V and Davenport, ER and Dwivedi, A and Gupta, S and Ijinu, TP and Jamir, T and Karu, R and Kaushik, A and Komarabathini, JM and Laithangpuii, and Lalzarliana, J and Norbu, T and Pautu, T and Pawar, K and Raman, AS and Ramaswamy, R and Ranasinghe, R and Rashmi, and Sasidharan, SP and Satheesh, T and Shaji, S and Shapiro, JW and Singh, E and Singson, V and Sundararajan, A and Tennekoon, KH and Tetso, D and Urban Aragon, JA and Welikala, AHJ and Yhome, RR and Rai, N and Raghavan, M},
title = {Distinct trajectories of urbanization shape the human gut microbiome across South Asia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.22.701183},
pmid = {41648281},
issn = {2692-8205},
abstract = {Human gut microbiomes respond to lifestyle transitions, yet the extent to which these responses are conserved across spatio-cultural contexts remains undercharacterized. We present the South Asian MicroBiome ARray (SAMBAR), a population-scale 16S gut microbiome study of 575 adults from ten geographically and socio-culturally diverse South Asian communities. Each community was sampled in ancestral villages and urban centers, enabling controlled comparisons of geography and lifestyle. Relative to global cohorts, SAMBAR microbiomes occupy a distinct compositional space with stronger correlation to geography and community membership than lifestyle. Although urbanization is consistently associated with increased abundance of disease-linked taxa, microbiome responses to lifestyle transitions are largely community-driven, including the acquisition of wheat- and dairying-associated microbial modules in some communities that may facilitate non-genetic adaptation to lactase non-persistence. Microbiome responses to urbanization are heterogeneous even at regional scales, reflecting local culture and geography and underscoring the need for community-specific investigations of health impacts.},
}

@article {pmid41648232,
year = {2026},
author = {Palayyan, SR and Siddiqui, AH and Sukumaran, SK},
title = {Expression of Calca gene-derived peptides in the murine taste system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.16.700005},
pmid = {41648232},
issn = {2692-8205},
abstract = {The Calcitonin Related Polypeptide Alpha (Calca) gene is a source of four biologically active peptides with varied physiological roles. Alternative splicing of the Calca messenger RNA generates either prepro calcitonin gene related peptide (CGRP) or preprocalcitonin encoding transcripts. Proteolytic processing of preprocalcitonin generates procalcitonin, calcitonin and katacalcin. Calcitonin is a ligand for the G-protein coupled receptor calcitonin receptor (CALCR) while CGRP is a ligand for the CGRP receptor (CGRP1R) formed by the calcitonin receptor like receptor (CALCRL)receptor activity modifying protein 1 (RAMP1) complex. Interestingly, procalcitonin too, is a ligand for the CGRP1R where it can antagonize CGRP. CGRP expression in taste neurons has been documented and is posited to regulate taste signaling. Single cell and bulk RNASeq of taste papillae revealed that the preprocalcitonin but not the CGRP transcript is expressed in Tas1r3 - expressing type II taste cells, while Calcrl (but not Calcr) and Ramp1 are expressed in stem/progenitor and type I cells in the circumvallate papillae. The CGRP1R is also expressed by fibroblasts in the lingual mesenchyme. We confirmed this expression pattern using quantitative polymerase chain reaction (qPCR), RNAScope and immunohistochemistry. qPCR of geniculate and nodose-petrosal ganglia revealed that both express Cgrp and CGRP1R subunit mRNAs, but not procalcitonin and Calcr . This interesting expression patterns suggests that procalcitonin and CGRP might reciprocally regulate the CGRP1R in taste cells and lingual fibroblasts and thereby influence taste signaling, taste cell regeneration and the taste microbiome.},
}

@article {pmid41648228,
year = {2026},
author = {Dockman, RL and Ottesen, EA},
title = {Niche specialization and cross-feeding interactions shaping gut microbial fiber degradation in a model omnivore.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.22.701066},
pmid = {41648228},
issn = {2692-8205},
abstract = {The gut microbiome plays an active role in host health, producing gut metabolites that influence host digestive and immune function while also mediating microbial crosstalk. Dietary fiber is a major source of important fermentation byproducts that are generally implicated in gut community stability and host wellbeing, but dissecting microbe-specific contributions to polysaccharide metabolism in the context of a complex gut community is challenging with conventional model organisms. Using the American cockroach (Periplaneta americana) as a model omnivore, we use chemically-defined synthetic diets to identify how complex gut microbial communities respond to two of the most abundant plant polysaccharides, xylan and cellulose. To do so, we fed cockroaches synthetic diets containing one of these fibers or a mix of both in differing ratios. Through both 16S rRNA gene profiling and RNA-seq, we show that mixed fibers enrich for organisms characteristic of the source fibers as well as additional organisms only enriched in mixed-fiber diets. Through an organism-centric pangenome approach, we identify the impact of these fibers on gut microbiome activity. We found that gut communities responded strongly to xylan, with Bacteroidota belonging to Bacteroides, Dysgonomonas, and Parabacteroides producing xylan-active CAZymes at high levels. Multiple groups of Bacillota also responded strongly to a xylan diet, but appeared to act as cross-feeding secondary degraders, producing primarily xylosidases and transcripts associated with xylose utilization. In contrast, cellulose diets were associated with higher transcriptional activity among Fibrobacterota, which are typically a minor component of the cockroach gut microbiome but were the primary producers of CAZymes associated with cellulose and cellobiose degradation. These experiments provide new insight into gut microbial metabolism of these complex plant polysaccharides. Further, they highlight the utility of the cockroach model and synthetic diets to answer fundamental questions about gut microbial responses to different polysaccharides alone and in combination.},
}

@article {pmid41648142,
year = {2026},
author = {Mastrorilli, E and Herd, P and Rey, FE and Goodman, AL and Zimmermann, M},
title = {Linking interpersonal differences in gut microbiota composition and drug biotransformation activity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.21.700809},
pmid = {41648142},
issn = {2692-8205},
abstract = {Individuals vary widely in their responses to drugs, and growing evidence implicates the gut microbiome as a contributor to this variability. While prior studies show that gut bacteria can metabolize drugs, how differences in microbial community composition influence drug metabolism remains poorly understood. Here, we characterize the biotransformation of 271 drugs by 89 gut microbial communities derived from human donors and preclinical animal models. Over 90% of tested drugs were metabolized by at least one microbiome. We identified 66 drugs exhibiting highly variable metabolism across human-derived microbiomes and several drugs whose biotransformation differed markedly between human and animal microbiomes. To enable prediction of microbiota-mediated drug metabolism, we developed and compared multiple modeling approaches based on metagenomic data. These results, together with the provided data and analytical resources contribute to a better understanding of microbiome-drug interactions and support their future integration into drug discovery, personalized prescription, and therapeutic drug monitoring.},
}

@article {pmid41648012,
year = {2025},
author = {Cortez, F and Nanetti, E and Chaves, G and Pereira, AC and Mendes, MC and Oliveira, I and Leuzzi, D and Abreu, H and Martins, M and Leite, RB and Keller-Costa, T and Costa, R},
title = {Prokaryotic community structure and auxin biosynthesis in early developmental stages of farmed Atlantic Nori (Porphyra spp.).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1750184},
pmid = {41648012},
issn = {1664-302X},
abstract = {INTRODUCTION: Algal-microbiome interactions are considered pivotal for host health and development. Current understanding of the diversity and function of algal-associated microorganisms in aquaculture settings remains limited, preventing the development of microbiome-based solutions for sustainable algal growth.

METHODS: We employed cultivation-dependent and -independent approaches to determine the structure of bacterial communities associated with farmed Atlantic Nori (Porphyra dioica and Porphyra umbilicalis) at early developmental stages. 16S rRNA gene amplicon sequencing and cultivation of bacterial symbionts were performed for algal and culturing water samples harvested from indoor photobioreactors at stages S1 (conchocelis cultures growing vegetatively), S2 (conchosporangia), and S3 (young blades).

RESULTS: The phyla Pseudomonadota (Alpha- and Gammaproteobacteria classes) and Bacteroidota were dominant in algal samples, followed by Planctomycetota, Actinobacteriota, and Verrucomicrobiota. At the phylotype level, these communities were highly structured throughout the host's life cycle. Uncultivated lineages Sva0996 (Actinomycetota), OM190 (Planctomycetota), Pir4 (Planctomycetota), and the genera Blastopirellula, Algoriphagus, Hyphomonas, and Marinobacter, among others, were enriched in algal samples and presented significantly different abundances across developmental stages. In some cases (e.g., genera Aquimarina, Sulfitobacter, Maribacter, and Nonlabens), those changes were also observed in culturing water. Moreover, the genera Ensifer (Rhizobiaceae), Paraglaciecola (Alteromonadaceae), and the uncultivated lineages DEV007 (Verrucomicrobiota) and Pir4 (Planctomycetota) were consistently present in P. dioica and P. umbilicalis samples at multiple developmental stages. Several Porphyra-associated bacterial genera and putative novel species, mostly belonging to the families Roseobacteraceae, Flavobacteriaceae, and Alteromonadaceae were identified via cultivation. Many cultured members of the Porphyra microbiome produced the growth-promoting hormone auxin, particularly those belonging to the genera Alteromonas, Marinobacter, Sulfitobacter, Leucothrix, and Roseovarius.

DISCUSSION: This study unveils complex, phylogenetically distinct, and temporally structured bacterial communities possessing algal morphogenesis-inducing capacities during early developmental stages of Porphyra spp., highlighting the potential of microbiome-based interventions for sustainable growth of marine algae in aquaculture.},
}

@article {pmid41648004,
year = {2025},
author = {Goncalves, AR and Ranganathan, H and Valdes, C and Zhu, H and Zhang, B and Kok, CR and Martí, JM and Mulakken, NJ and Thissen, JB and Jaing, C and Be, NA},
title = {Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695501},
pmid = {41648004},
issn = {1664-302X},
abstract = {Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.},
}

@article {pmid41648003,
year = {2025},
author = {Wei, X and Wang, L and Zhang, H and Tan, L and Yang, S and Li, J and Liu, Z and Zhong, Q and Sun, X},
title = {Cold-resistant lactic acid bacteria in Jerusalem artichoke silage: quality, microbiome and metabolome dynamics during aerobic exposure on the Qinghai-Tibet Plateau.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699658},
pmid = {41648003},
issn = {1664-302X},
abstract = {Forage scarcity during the cold season poses a major challenge to livestock farming on the Qinghai-Tibet Plateau. Jerusalem artichoke (Helianthus tuberosus) offers a promising alternative, but aerobic exposure of its silage leads to nutrient loss and microbial spoilage under low temperatures. This study aimed to evaluate the effects of inoculating cold-resistant lactic acid bacteria (LAB)-Lactiplantibacillus plantarum GN02 (homofermentative) and Levilactobacillus brevis XN25 (heterofermentative)-on silage quality, microbiome, and metabolome dynamics during aerobic exposure. Silage was prepared from Jerusalem artichoke stems and leaves, treated with sterile water (CK), Lpl. plantarum (YZ), Lv. brevis (YD), or their mixture (YZD), and ensiled for 60 days at -5 to 8 °C. Samples were analyzed at 0, 7, and 14 days of aerobic exposure (-10 to 5 °C) for fermentation parameters (pH, organic acids, dry matter, water-soluble carbohydrates, crude protein, fibers), microbial communities via 16S rRNA and ITS sequencing, and metabolites using LC-MS-based untargeted metabolomics. Inoculation with Lpl. plantarum maintained lower pH (<5), higher lactic acid, dry matter, and water-soluble carbohydrates, while suppressing spoilage bacteria (e.g., Carnobacterium, Citrobacter) and enriching Lactobacillus. Metabolomics revealed upregulated flavonoids and octadecanoids, enhancing antioxidant defenses and downregulating carbohydrate degradation pathways. Lv. brevis accelerated spoilage with elevated pH and nutrient loss, whereas the mixture showed intermediate effects. These findings demonstrate Lpl. plantarum's efficacy in mitigating aerobic deterioration, providing a theoretical basis for optimizing silage preservation and supporting sustainable livestock production in high-altitude regions.},
}

@article {pmid41648002,
year = {2025},
author = {Zhang, H and Chen, K and Chen, R and Jia, E},
title = {Feeding patterns reprogram a gut microbial virulence-iron-quorum sensing functional axis linked to atherosclerotic risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1751844},
pmid = {41648002},
issn = {1664-302X},
abstract = {The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe[-]/[-] mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.},
}